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1. Metagenomic Next-Generation Sequencing Reveals Individual Composition and Dynamics of Anelloviruses during Autologous Stem Cell Transplant Recipient Management

Author: Valérie Cheynet, Bruno Lina, François Mallet, Frédéric Reynier, Alexandre Pachot, Jérémie Becker, Clémentine Sarkozy, Antonin Bal, Karen Brengel-Pesce, Florence Morfin, Sophie Trouillet-Assant, Gilles Salles, Laurence Josset, Pierre Sesques, Gaelle Vilchez, Guy Oriol, Laboratoire de Biologie et de Pharmacologie Appliquée (LBPA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), Electronique Quantique, Laboratoire Pierre Aigrain (LPA), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Laboratory of Virology East, Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Lyon (CRCL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), BIOASTER, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Département de Recherche Fondamentale sur la Matière Condensée (DRFMC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre Hospitalier Universitaire de Nice (CHU Nice), Système macromoléculaires et mmunovirologie humaine, IFR128-bioMérieux SA-Centre National de la Recherche Scientifique (CNRS), Systèmes Macromoléculaires et Physiopathologie Humaine (SMPH), BIOMERIEUX-Centre National de la Recherche Scientifique (CNRS), and Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS)
Subjects: 0301 basic medicine, Torque teno virus, Viral metagenomics, torque teno virus, lcsh:QR1-502, Antineoplastic Agents, Pilot Projects, [SDV.CAN]Life Sciences [q-bio]/Cancer, Disease, Bioinformatics, Transplantation, Autologous, Anelloviridae, lcsh:Microbiology, DNA sequencing, 03 medical and health sciences, stem cell transplant recipients, Drug Therapy, Virology, Humans, Human virome, Prospective Studies, biology, Communication, Genetic Variation, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, biology.organism_classification, DNA Virus Infections, Transplant Recipients, Blood, 030104 developmental biology, Infectious Diseases, Metagenomics, DNA, Viral, immunocompromised patients, next-generation sequencing, viral metagenomics, Stem cell, Multiple Myeloma, Stem Cell Transplantation
Abstract: International audience; Over recent years, there has been increasing interest in the use of the anelloviruses, the major component of the human virome, for the prediction of post-transplant complications such as severe infections. Due to an important diversity, the comprehensive characterization of this viral family over time has been poorly studied. To overcome this challenge, we used a metagenomic next-generation sequencing (mNGS) approach with the aim of determining the individual anellovirus profile of autologous stem cell transplant (ASCT) patients. We conducted a prospective pilot study on a homogeneous patient cohort regarding the chemotherapy regimens that included 10 ASCT recipients. A validated viral mNGS workflow was used on 108 plasma samples collected at 11 time points from diagnosis to 90 days post-transplantation. A complex interindividual variability in terms of abundance and composition was noticed. In particular, a strong sex effect was found and confirmed using quantitative PCR targeting torque teno virus, the most abundant anellovirus. Interestingly, an important turnover in the anellovirus composition was observed during the course of the disease revealing a strong intra-individual variability. Although more studies are needed to better understand anellovirus dynamics, these findings are of prime importance for their future use as biomarkers of immune competence.
Published: 2018
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2. Evaluation of the Accelerate Pheno\texttrademark system for rapid identification and antimicrobial susceptibility testing of Gram-negative bacteria in bloodstream infections

Author: Laurent Desmurs, Waël Salka, Marine Ibranosyan, Christine Fuhrmann, Ghislaine Descours, François Vandenesch, Olivier Dauwalder, Thi Lam Thuy Hoang, Anne-Gaëlle Ranc, Maud Baume, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Pathogenèse des légionelles- Legionella pathogenesis (LegioPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Time Factors, Ceftazidime, Bacteremia, medicine.disease_cause, law.invention, 0302 clinical medicine, Medical microbiology, law, polycyclic compounds, Medicine, Antimicrobial susceptibility testing, 030212 general & internal medicine, Child, Aged, 80 and over, Accelerate Pheno\texttrademark system, biology, General Medicine, Middle Aged, 3. Good health, Anti-Bacterial Agents, Bacterial Typing Techniques, Infectious Diseases, Gram staining, Child, Preschool, Gram-negative bacteria, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, medicine.drug, Microbiology (medical), Enterobacteriales, Adult, medicine.medical_specialty, Adolescent, Cefepime, 030106 microbiology, Microbial Sensitivity Tests, 03 medical and health sciences, Young Adult, Internal medicine, Sepsis, Humans, Aged, business.industry, Pseudomonas aeruginosa, Infant, Newborn, Infant, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Bloodstream infections, business, Gram-Negative Bacterial Infections
Abstract: International audience; Identification and antimicrobial susceptibility testing (AST) are critical steps in the management of bloodstream infections. Our objective was to evaluate the performance of the Accelerate Pheno\texttrademark System, CE v1.2 software, for identification and AST of Gram-negative pathogens from positive blood culture bottles. A total of 104 bottles positive for Gram-negative bacteria collected from inpatients throughout our institution were randomly selected after Gram staining. The time-to-identification and AST results, and the raw AST results obtained by the Accelerate Pheno\texttrademark system and routine techniques (MALDI-TOF MS and VITEK\textregistered2, EUCAST guidelines) were compared. Any discrepant AST result was tested by microdilution. The Pheno\texttrademark significantly improved turn-around times for identification (5.3 versus 23.7~h; p \textless 0.0001) and AST (10.7 versus 35.1~h; p \textless 0.0001). Complete agreement between the Accelerate Pheno\texttrademark system and the MALDI-TOF MS for identification was observed for 96.2% of samples; it was 99% (98/99) for monomicrobial samples versus 40% (3/5) for polymicrobial ones. The overall categorical agreement for AST was 93.7%; it was notably decreased for beta-lactams (cefepime 84.4%, piperacillin-tazobactam 86.5%, ceftazidime 87.6%) or Pseudomonas aeruginosa (71.9%; with cefepime 33.3%, piperacillin-tazobactam 77.8%, ceftazidime 0%). Analysis of discrepant results found impaired performance of the Accelerate Pheno\texttrademark system for beta-lactams (except cefepime) in Enterobacteriales (six very major errors) and poor performance in P. aeruginosa. The Accelerate Pheno\texttrademark system significantly improved the turn-around times for bloodstream infection diagnosis. Nonetheless, improvements in the analysis of polymicrobial samples and in AST algorithms, notably beta-lactam testing in both P. aeruginosa and Enterobacteriales, are required for implementation in routine workflow.
Published: 2018
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3. No relationship between late HIV diagnosis and social deprivation in newly diagnosed patients in France

Author: Maxime HENTZIEN, Isabelle Poizot-Martin, Tristan Ferry, Véronique Avettand-Fenoel, Firouzé BANI-SADR, Pierre Delobel, Anne Galinier, Cyrille Delpierre, Bruno MARCHOU, Florence ADER, André Cabié, Guillaume Martin-Blondel, Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre Régional de Soins et de Coordination en matière de VIH [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC), Service des maladies infectieuses et tropicales, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris]-Université Paris Diderot - Paris 7 (UPD7), Centre Hospitalier Tourcoing, département des maladies infectieuses [CH Tourcoing], Centre Hospitalier de Tourcoing, Centre de Recherche en Cancérologie de Lyon (CRCL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre Léon Bérard [Lyon]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département des Maladies Infectieuses [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Département des Maladies Infectieuses [CHU Nice] (Hôpital de l'Archet), Hôpital l'Archet - CHU de Nice, Service des maladies infectieuses et tropicales [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), Département des Maladies Infectieuses [CHRU Montpellier], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Université Montpellier 1 (UM1), Recherches Translationnelles sur le VIH et les maladies infectieuses (TransVIHMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 1 (UM1)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Universtié Yaoundé 1 [Cameroun]-Université de Montpellier (UM), Service d'Immuno-hématologie clinique [Hôpital Sainte Marguerite - APHM], Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud )-Assistance Publique - Hôpitaux de Marseille (APHM), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité d'Infectiologie [CHU de Reims] (Hôpital Robert Debré), Hôpital universitaire Robert Debré [Reims]-Centre Hospitalier Universitaire de Reims (CHU Reims), Laboratoire de Virologie Médicale et Moléculaire - EA 4684 (CardioVir), Université de Reims Champagne-Ardenne (URCA)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Centre Hospitalier Universitaire de Reims (CHU Reims), the Dat’AIDS Study Group : Brégigeon S, Zaegel-Faucher O, Obry-Roguet V, Orticoni M, Soavi MJ, Luquet-Besson I, Ressiot E, Carta-Padovani M, Ducassou MJ, Bertone H, Galie S, Galinier A, Monclar M, Martinet P, Ritleng AS, Ivanova A, Blanco-Betancourt C, Lions C, Alvarez M, Biezunski N, Debard A, Delobel P, Fourcade C, Marchou B, Martin-Blondel G, Porte L, Mularczyk M, Garipuy D, Saune K, Lepain I, Marcel M, Puntis E, Ceppi C, Cua E, Cottalorda J, Dellamonica P, Demonchy E, Dunais B, Durant J, Etienne C, Ferrando S, Fuzibet JG, Garraffo R, Risso K, Mondain V, Naqvi A, Oran N, Perbost I, Pillet S, Prouvost-Keller B, Pradier C, Wehrlen-Pugliese S, Rosenthal E, Sausse S, Roger PM, Bernaud C, Billaud E, Biron C, Bonnet B, Bouchez S, Boutoille D, Brunet-Cartier C, Hall N, Jovelin T, Morineau P, Raffi F, Reliquet V, Hue H, Larmet L, Pineau S, Ferré V, André-Garnier E, Rodallec A, Vivrel F, Lefebvre M, Grossi O, Biron C, Point P, Aubry O, Cheret A, Choisy P, Landman R, Duvivier C, Valantin MA, Agher R, Katlama C, Lortholary, Avettand-Fenoel V, Rouzioux C, Consigny PH, Cessot G, Touam F, Usubillaga R, Benhadj K, Cabié A, Abel S, Pierre-François S, Ouka M, Martial J, Rey D, Ebel E, Fischer P, Partisani M, Cheneau C, Priester M, Batard ML, Bernard-Henry C, E Mautort E, Chirouze C, Drobacheff-Thiébaut C, Faller JP, Faucher JF, Foltzer A, Gil H, Hustache-Mathieu L, Hoen B, Jacomet C, Laurichesse H, Lesens O, Vidal M, Mrozek N, Aumeran C, Baud O, Beytout J, Coban D, Casanova S, Rouger C, Berger JL, N'Guyen Y, Lambert D, Kmiec I, Hentzien M, Peyramond D, Chidiac C, Ader F, Biron F, Boibieux A, Ferry T, Miailhes P, Perpoint T, Degroodt S, Atoui N, Casanova ML, Le Moing V, Makinson A, Meftah N, Merle De Boever C, Montes B, Psomas C., Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Toulouse [Toulouse], Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot - Paris 7 (UPD7)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), HCL Groupement Hospitalier Nord [Lyon]-Hospices Civils de Lyon (HCL), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques er émergentes (TransVIHMI), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Assistance Publique - Hôpitaux de Marseille (APHM)-Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud ), Université de Reims Champagne-Ardenne (URCA)-Centre Hospitalier Universitaire de Reims (CHU Reims)-SFR CAP Santé (Champagne-Ardenne Picardie Santé), Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV)-Université de Reims Champagne-Ardenne (URCA)-Université de Picardie Jules Verne (UPJV), Université Montpellier 1 (UM1)-Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Centre Hospitalier Universitaire de Reims (CHU Reims)-Hôpital universitaire Robert Debré [Reims], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Service d'infectiologie [CHU Nice], Centre Hospitalier Universitaire de Nice (CHU Nice), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud ), Centre Hospitalier Universitaire de Reims (CHU Reims), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de santé sexuelle [CHU Toulouse], Pôle Santé publique et médecine publique [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Recherches Translationnelles sur le VIH et les maladies infectieuses endémiques et émergentes (TransVIHMI), Institut de Recherche pour le Développement (IRD)-Université de Yaoundé I-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), and Université de Reims Champagne-Ardenne (URCA)-Université de Reims Champagne-Ardenne (URCA)
Subjects: Adult, Male, 0301 basic medicine, Gerontology, Delayed Diagnosis, [SDV]Life Sciences [q-bio], 030106 microbiology, Population, late diagnosis, HIV Infections, Logistic regression, Men who have sex with men, deprivation, key population, 03 medical and health sciences, 0302 clinical medicine, Risk Factors, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Humans, Pharmacology (medical), Prospective Studies, 030212 general & internal medicine, Homosexuality, Male, Heterosexuality, 10. No inequality, education, education.field_of_study, business.industry, Health Policy, HIV, Health Status Disparities, Odds ratio, Middle Aged, medicine.disease, Confidence interval, 3. Good health, Logistic Models, Infectious Diseases, Social deprivation, Socioeconomic Factors, Quartile, age, Coinfection, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, business, Demography
Abstract: International audience; OBJECTIVES: The aim of the study was to determine whether there is a relationship between social deprivation and time of HIV diagnosis in France. METHODS: Prospectively collected data from a multicentre database were used in the study. Patients with a first HIV diagnosis between 1 January 2014 and 31 December 2015 were selected from the database. Deprivation was measured using the European Deprivation Index (EDI), which is an ecological index constructed from the address of residence and based on the smallest geographical census unit, in which individuals are classified so as to be comparable with national quintiles. Time of diagnosis was classified as being at an early, intermediate, late, or advanced stage of disease. Age, gender, distance from home to HIV centre, most probable route of infection, and hepatitis B or C coinfection were considered in the analysis. Because of a strong interaction between gender and most probable route of infection, we constructed a 'population' variable: men who have sex with men (MSM), heterosexual men and women. RESULTS: Of 1421 newly diagnosed patients, 44% were diagnosed either late or at an advanced stage of disease, and 46.3% were in the highest deprivation quintile. Using multivariate logistic regression, 'population' [odds ratio (OR) 0.62 (95% confidence interval (CI) 0.48-0.78) for MSM compared with women] and age [OR 1.39 (95% CI 1.07-1.80), 1.72 (1.32-2.23) and 1.86 (1.40-2.47) for the second, third and fourth quartiles, respectively, compared with the first quartile] were found to be related to late diagnosis. EDI level was not related to late HIV diagnosis. CONCLUSIONS: 'Population' seems to be more relevant than EDI to define evidence-based interventions to limit late diagnosis.
Published: 2018
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4. Association between biofilm formation phenotype and clonal lineage in Staphylococcus aureus strains from bone and joint infections

Author: Jason Tasse, Sophie Trouillet-Assant, Jérôme Josse, Patricia Martins-Simões, Florent Valour, Carole Langlois-Jacques, Stéphanie Badel-Berchoux, Christian Provot, Thierry Bernardi, Tristan Ferry, Frédéric Laurent, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), BioFilm Control, Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Male, Arthritis, Infectious, Staphylococcus aureus, Virulence Factors, lcsh:R, lcsh:Medicine, Middle Aged, Staphylococcal Infections, biochemical phenomena, metabolism, and nutrition, Bone Diseases, Infectious, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Phenotype, Bacterial Proteins, Species Specificity, Biofilms, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Surgical Wound Infection, [SDV.IMM]Life Sciences [q-bio]/Immunology, lcsh:Q, Female, Treatment Failure, lcsh:Science
Abstract: International audience; Biofilm formation is a critical virulence factor responsible for treatment failure and chronicity in orthopaedic device-related infections (ODIs) caused by Staphylococcus aureus. Clonal lineages differ in terms of their biofilm forming capacities. The aim of this study was to investigate the correlation between the clonal complex (CC) affiliation and biofilm phenotype of 30 clinical S. aureus isolates responsible of ODI based on i) early biofilm formation using BioFilm Ring Test\textregistered and mature biofilm formation using crystal violet assays, ii) biofilm composition using DNase and proteinase K activity, and iii) prevention of biofilm formation by cloxacillin, teicoplanin and vancomycin using Antibiofilmogram\textregistered (biofilm minimal inhibitory concentration-bMIC). In terms of early biofilm formation, the CC30 strains were significantly slower than the CC5, CC15 and CC45 strains. CC45 strains produced significantly more mature biofilm than other group of strains did. The formation of biofilms was highly dependent on the presence of extracellular DNA in the CC5, CC15 and CC30 strains whereas it was mostly dependent on the presence of proteins in CC45. Finally, the CC30 group highlighted higher proportion of susceptible (bMIC \textless breakpoints of EUCAST guidelines) for cloxacillin, teicoplanin and vancomycin compared to the other CCs. These results demonstrate that the biofilm phenotype of clinical S. aureus isolates from ODIs is strongly related to their respective CC affiliation.
Published: 2018
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5. Oral ofloxacin and clindamycin as an alternative to the classic rifampicin-clindamycin in hidradenitis suppurativa: retrospective analysis of 65 patients

Author: Axel-Patrice Villani, Anne Tristan, A. Boibieux, Denis Jullien, Philippe Guillem, J. Delaunay, Service de dermatologie, consultation d'allergologie, Hôpital Edouard-Herriot, Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Clinique du Val d'Ouest, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Centre National de Reference des Staphylocoques, Université de Lyon, Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Centre interrégional de référence Rhône-Alpes - Auvergne des infections ostéo-articulaires complexes, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: Adult, Male, Ofloxacin, Adolescent, Administration, Oral, Dermatology, medicine.disease_cause, Drug Administration Schedule, Microbiology, 030207 dermatology & venereal diseases, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Pharmacotherapy, medicine, Humans, Hidradenitis suppurativa, 030212 general & internal medicine, Child, ComputingMilieux_MISCELLANEOUS, Retrospective Studies, Dose-Response Relationship, Drug, business.industry, Drug Substitution, Clindamycin, Middle Aged, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Hidradenitis Suppurativa, Treatment Outcome, Staphylococcus aureus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Drug Therapy, Combination, Female, Anaerobic bacteria, Coagulase, Rifampin, business, Rifampicin, medicine.drug
Abstract: Rifampicin/Clindamycin (RC) combination is recommended as first line therapy in moderate to severe Hidradenitis Suppurativa (HS) by European S1 guidelines (1–3), notably because a large variety of microorganisms have been isolated from HS lesions: most represented bacteria appear to be Staphylococcus aureus, Coagulase negative staphylococci (CoNS) and anaerobic bacteria from normal skin flora. It has been hypothesized that these bacteria could play a central role in the initiation and maybe in the maintenance of HS lesions, possibly by being a source of antigens in a dysregulated immune response. This article is protected by copyright. All rights reserved.
Published: 2018
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6. Microbiologic epidemiology depending on time to occurrence of prosthetic joint infection: a prospective cohort study

Author: C. Triffault-Fillit, T. Ferry, F. Laurent, P. Pradat, C. Dupieux, A. Conrad, A. Becker, S. Lustig, M.H. Fessy, C. Chidiac, F. Valour, T. Perpoint, A. Boibieux, F. Biron, P. Miailhes, F. Ader, S. Roux, F. Daoud, J. Lippman, E. Braun, Y. Gillet, L. Hees, E. Servien, Y. Herry, R. Gaillard, A. Schneider, M.-H. Fessy, A. Viste, P. Chaudier, R. Desmarchelier, T. Mouton, C. Courtin, L. Louboutin, S. Martres, F. Trouillet, C. Barrey, F. Signorelli, E. Jouanneau, T. Jacquesson, A. Mojallal, F. Boucher, H. Shipkov, J. Château, F. Aubrun, I. Bobineau, C. Macabéo, F. Vandenesch, J.-P. Rasigade, F. Craighero, L. Boussel, J.-B. Pialat, I. Morelec, M. Janier, F. Giammarile, M. Tod, M.-C. Gagnieu, S. Goutelle, S. Gerbier-Colomban, T. Benet, E. Mabrut, Centre interrégional de référence Rhône-Alpes - Auvergne des infections ostéo-articulaires complexes, Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pathogenèse des légionelles- Legionella pathogenesis (LegioPath), Service de Chirurgie Orthopédique [Centre Albert Trillat], Centre Albert Trillat [Hôpital de la Croix-Rousse - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Hôpital de la Croix-Rousse [CHU - HCL], Centre Hospitalier Lyon-Sud - Chirurgie orthopédique et Traumatologie, Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), Male, Prosthetic joint infection, medicine.medical_specialty, Prosthesis-Related Infections, Time Factors, Epidemiology, medicine.medical_treatment, Joint Prosthesis, 030106 microbiology, Context (language use), medicine.disease_cause, Bacterial Physiological Phenomena, Microbiology, Prosthesis, Antimicrobial therapy, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Humans, 030212 general & internal medicine, Prospective Studies, Prospective cohort study, Aged, Arthritis, Infectious, Bacteria, business.industry, General Medicine, Middle Aged, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Infectious Diseases, Staphylococcus aureus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Etiology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Vancomycin, Female, business, Empiric, medicine.drug
Abstract: International audience; OBJECTIVES: The high microbiologic diversity encountered in prosthetic joint infection (PJI) makes the choice of empirical antimicrobial therapies challenging, especially in cases of implant retention or one-stage exchange. Despite the risk of dysbiosis and toxicity, the combination of vancomycin with a broad-spectrum β-lactam is currently recommended in all cases, even if Gram-negative bacilli (GNB) might be less represented in late PJI. In this context, this study aimed to describe the microbiologic epidemiology of PJI according to the chronology of infection. METHODS: This prospective cohort study (2011-2016) evaluated the microbiologic aetiology of 567 PJI according to time of occurrence from prosthesis implantation-early (\textless3~months), delayed (3-12~months) and late (\textgreater12~months)-as well as mechanism of acquisition. RESULTS: Initial microbiologic documentation (n~=~511; 90.1%) disclosed 164 (28.9%) Staphylococcus aureus (including 26 (16.1%) methicillin-resistant S.~aureus), 162 (28.6%) coagulase-negative staphylococci (including 81 (59.1%) methicillin-resistant coagulase-negative staphylococci), 80 (14.1%) Enterobacteriaceae, 74 (13.1%) streptococci and 60 (10.6%) Cutibacterium acnes. Considering nonhaematogenous late PJI (n~=~182), Enterobacteriaceae (n~=~7; 3.8%) were less represented than in the first year after implantation (n~=~56; 17.2%; p \textless0.001), without difference regarding nonfermenting GNB (4.6% and 2.7%, respectively). The prevalence of anaerobes (n~=~40; 21.9%; including 32 (80.0%) C.~acnes) was higher in late PJI (p \textless0.001). Consequently, a broad-spectrum β-lactam might be useful in 12 patients (6.6%) with late PJI only compared to 66 patients (20.3%) with early/delayed PJI (p \textless0.001). CONCLUSIONS: Considering the minority amount of GNB in late postoperative PJI, the empirical use of a broad-spectrum β-lactam should be reconsidered, especially when a two-stage exchange is planned.
Published: 2017
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7. Clinical metagenomics of bone and joint infections: a proof of concept study OPEN

Author: William Mouton, Jacques Schrenzel, Vladimir Lazarevic, Frédéric Laurent, Myriam Girard, Tristan Ferry, Etienne Ruppé, Genomic Research Laboratory [Geneva, Switzerland], Geneva University Hospital (HUG), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département des Maladies Infectieuses [HCL Groupement Hospitalier Nord, Lyon], Département de Génétique et de Médecine de Laboratoire [Geneva, Switzerland], Laboratoire de Bactériologie [Geneva, Switzerland], Geneva University Hospital (HUG)-Geneva University Hospital (HUG), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), HCL Groupement Hospitalier Nord [Lyon]-Hospices Civils de Lyon (HCL), Dupuis, Christine, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, Male, Fastidious organism, 0301 basic medicine, medicine.drug_class, Science, Treatment outcome, Antibiotics, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, Joint infections, Proof of Concept Study, Article, Microbiology, 03 medical and health sciences, Antibiotic resistance, Species level, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Drug Resistance, Bacterial, medicine, Humans, Pathogen, Osteitis, Aged, Aged, 80 and over, ddc:616, Arthritis, Infectious, [SDV.GEN]Life Sciences [q-bio]/Genetics, Multidisciplinary, Computational Biology, Middle Aged, biology.organism_classification, Anti-Bacterial Agents, 3. Good health, Treatment Outcome, 030104 developmental biology, Metagenomics, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Metagenome, Medicine, Female, Bacteria
Abstract: International audience; Bone and joint infections (BJI) are severe infections that require a tailored and protracted antibiotic treatment. Yet, the diagnostic based on culturing samples lacks sensitivity, especially for hardly culturable bacteria. Metagenomic sequencing could potentially address those limitations. Here, we assessed the performances of metagenomic sequencing on 24 BJI samples for the identification of pathogens and the prediction of their antibiotic susceptibility. For monomicrobial samples in culture (n = 8), the presence of the pathogen was confirmed by metagenomics in all cases. For polymicrobial samples (n = 16), 32/55 bacteria (58.2%) were found at the species level (and 41/55 [74.5%] at the genus level). Conversely, 273 bacteria not found in culture were identified, 182 being possible pathogens and 91 contaminants. A correct antibiotic susceptibility could be inferred in 94.1% and 76.5% cases for monomicrobial and polymicrobial samples, respectively. Altogether, we found that clinical metagenomics applied to BJI samples is a potential tool to support conventional culture. Context. Bone and joint infections (BJI) are severe infections that affect a growing number of patients 1. Along with the surgical intervention, the microbiological diagnosis is a keystone of the management of BJI in (i) identifying the bacteria causing the infection and (ii) assessing their susceptibility to antibiotics. Currently, this is achieved by culturing surgical samples on various media and conditions, together with a long time of incubation to recover fastidiously-growing bacteria that can be involved in BJI. Still, some bacteria will not grow under these conditions because of extreme oxygen sensitivity, a prior antibiotic intake or metabolic issues (e.g. quiescent bacteria in chronic infections). Consequently, the antibiotic treatment may not span all the bacteria involved in the infection, which can favour the relapse and the need for a new surgery. Clinical metagenomics refers to the concept of sequencing all the DNA (i.e. all the genomes) present in a clinical sample with the purpose of identifying pathogens and inferring their antibiotic susceptibility pattern 2. This new, culture-independent method takes advantages of the thrilling development of next-generation sequenc-ing (NGS) technologies since the mid-2000s. The NGS platforms typically yield thousands to millions of reads (sequences of size ranging from 100 bp to a few kbp), which virtually enables to recover the sequences of all the genes present in the sample, yet in a disorganised fashion. Substantial bio-informatics efforts are thereby needed to reconstruct and reorder the original sequences in genomes, and are referred to as the assembly process. Hence, various information such as the taxonomic identification of the present species, antibiotic resistance determinants (ARDs), mutations (as compared to a reference genome or sequence), single nucleotide variants (SNVs, for clonality assessment) and virulence genes can be determined. Clinical metagenomics is an emerging field in medicine. So far, a few attempts to use metagenomics on clinical samples have been performed (on urines 3, 4 , cerebrospinal fluid or brain biopsy 5, 6 , blood 7 and skin granuloma 8) likely because of the high price of metagenomics and the complexity of the management of sequence data for clinical microbiologists. To the best of our knowledge, metagenomics has never been applied to BJI samples.
Published: 2017
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8. Detection of mecC-Positive Staphylococcus aureus: What To Expect from Immunological Tests Targeting PBP2a?

Author: Jean-Winoc Decousser, Céline Dupieux, Robert Hill, Sophie Trouillet-Assant, Anders Rhod Larsen, Christopher Teale, Robert Skov, Mark A. Holmes, Frédéric Laurent, Coralie Bouchiat, Bruno Pichon, Angela Kearns, Andreas Petersen, Giles Edwards, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Statens Serum Institut [Copenhagen], Public Health England [London], Department of Veterinary Medicine, University of Cambridge [UK] (CAM), Hôpital Antoine Béclère, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Sud - Paris 11 (UP11), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), Methicillin-Resistant Staphylococcus aureus, Staphylococcus aureus, 030106 microbiology, Microbial Sensitivity Tests, Biology, Immunologic Tests, medicine.disease_cause, Methicillin resistance, Homology (biology), Microbiology, 03 medical and health sciences, methicillin resistance, Bacterial Proteins, medicine, Penicillin-Binding Proteins, PBP2a detection, Humans, Animals, Letter to the Editor, ComputingMilieux_MISCELLANEOUS, rapid tests, mecC, Nucleic acid sequence, biochemical phenomena, metabolism, and nutrition, Staphylococcal Infections, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Rapid identification, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Immunological tests, [SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract: Rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) isolates is pivotal for the control of their dissemination and for accurate management of infected patients. In 2011, a new mec variant, named mecC , that shows only 70% nucleotide sequence homology with the classical mecA
Published: 2017
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9. Non-contiguous finished genome sequence of Staphylococcus capitis CR01 (pulsetype NRCS-A)

Author: P. Martins Simões, Azeddine Ibrahimi, Frédéric Laurent, S. El Kabbaj, H. Lemriss, S. Lemriss, Marine Butin, Jean-Philippe Rasigade, Laboratory of Research and Medical Analysis, Moroccan Royal Gendarmerie, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Royal Moroccan Gendarmerie, Department of Biotechnology Laboratory (Med-Biotech), Mohammed V University in Rabat, Centre National de Reference des Staphylocoques, Université de Lyon, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Mohammed V de Rabat [Agdal] (UM5)
Subjects: draft-genome, medicine.disease_cause, Genome, 03 medical and health sciences, Plasmid, methicillin resistance, Intensive care, late-onset sepsis, Genetics, medicine, Gene, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, biology, 030306 microbiology, Staphylococcus capitis (NCRS-A), Ribosomal RNA, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Staphylococcus capitis, Short Genome Reports, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Staphylococcus
Abstract: International audience; Staphylococcus capitis is a coagulase-negative staphylococcus (CoNS) commonly found in the human microflora. Recently, a clonal population of Staphylococcus capitis (denominated NRCS-A) was found to be a major cause of late-onset sepsis (LOS) in several neonatal intensive care units in France. Here, we report the complete genome sequence and annotation of the prototype Staphylococcus capitis NCRS-A strain CR01. The 2,504,472 bp long genome (1 chromosome and no plasmids) exhibits a G+C content of 32.81%, and contains 2,468 protein-coding and 59 tRNA genes and 4 rRNA genes.
Published: 2014
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10. Evaluation of a commercial immunochromatographic assay for rapid routine identification of PBP2a-positive Staphylococcus aureus and coagulase-negative staphylococci

Author: Hélène Salord, Céline Dupieux, Frédéric Laurent, Sophie Trouillet-Assant, Jason Tasse, Sylvestre Tigaud, Olivia Raulin, Chantal Roure-Sobas, A. M. Freydière, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), Transcriptional Activation, Meticillin, Time Factors, medicine.drug_class, Staphylococcus, 030106 microbiology, Cephalosporin, Antibiotics, Drug resistance, medicine.disease_cause, Sensitivity and Specificity, Chromatography, Affinity, Microbiology, 03 medical and health sciences, Cefoxitin, medicine, PBP2a detection, Penicillin-Binding Proteins, Staphylococci, Rapid test, business.industry, General Medicine, biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Penicillin, Infectious Diseases, Staphylococcus aureus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Methicillin Resistance, Coagulase, Immunochromatography, business, medicine.drug
Abstract: International audience; We evaluated the performance of an immunochromatographic assay (PBP2a Culture Colony Test - Alere\texttrademark), detecting protein-binding penicillin 2a on staphylococci primary isolates in only 6minutes. The assay is highly sensitive for the direct detection of MRSA on various culture media whereas it requires cefoxitin induction for methicillin-resistant coagulase-negative staphylococci.
Published: 2016
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11. Antibiotic Activity of Escherichia coli against Multiresistant Staphylococcus aureus

Author: Richard Bonnet, Guillaume Dalmasso, Antony Cougnoux, F. Laurent, Tiphanie Faïs, Julien Delmas, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis, Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Staphylococcus aureus, medicine.drug_class, [SDV]Life Sciences [q-bio], 030106 microbiology, Antibiotics, Biology, medicine.disease_cause, Microbiology, 03 medical and health sciences, Nonribosomal peptide, Genomic island, medicine, Escherichia coli, Pharmacology (medical), Letters to the Editor, Pharmacology, chemistry.chemical_classification, 3. Good health, Anti-Bacterial Agents, 030104 developmental biology, Infectious Diseases, chemistry, bacteria, Microbial Interactions
Abstract: The pks genomic island present in Escherichia coli encodes polyketides (PK) and nonribosomal peptide (NRP) synthases. As discussed in an elegant study published recently ([1][1]), this leads to the synthesis of numerous and still not fully purified and characterized PK-NRP compounds that confer to
Published: 2016
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12. Pathophysiological Mechanisms of Staphylococcus Non-aureus Bone and Joint Infection: Interspecies Homogeneity and Specific Behavior of S. pseudintermedius

Author: Yousef Maali, Patrica Martins-Simoes, Florent Valour, Daniel Bouvard, Michele Bes, Marisa Haenni, Tristan Ferry, Laurent Frederic, Sophie Trouillet-Assant, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Institute for Advanced Biosciences / Institut pour l'Avancée des Biosciences (Grenoble) (IAB), Centre Hospitalier Universitaire [Grenoble] (CHU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Etablissement français du sang - Auvergne-Rhône-Alpes (EFS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre National de Reference des Staphylocoques, Université de Lyon, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), Staphylococcus pseudintermedius, media_common.quotation_subject, 030106 microbiology, lcsh:QR1-502, Virulence, medicine.disease_cause, Microbiology, lcsh:Microbiology, 03 medical and health sciences, fibronectin, medicine, Internalization, Tropism, media_common, Original Research, biology, Staphylococcus non-aureus, biology.organism_classification, invasion, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, In vitro, 3. Good health, Fibronectin, Staphylococcus aureus, Immunology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, integrin α5β1, Staphylococcus, bone and joint infection (BJI)
Abstract: International audience; Implicated in more than 60% of bone and joint infections (BJIs), Staphylococci have a particular tropism for osteoarticular tissue and lead to difficult-to-treat clinical infections. To date, Staphylococcus aureus internalization in non-professional phagocytic cells (NPPCs) is a well-explored virulence mechanism involved in BJI chronicity. Conversely, the pathophysiological pathways associated with Staphylococcus non-aureus (SNA) BJIs have scarcely been studied despite their high prevalence. In this study, 15 reference strains from 15 different SNA species were compared in terms of (i) adhesion to human fibronectin based on adhesion microplate assays and (ii) internalization ability, intracellular persistence and cytotoxicity based on an in vitro infection model using human osteoblasts. Compared to S. aureus, S. pseudintermedius was the only species that significantly adhered to human fibronectin. This species was also associated with high (even superior to S. aureus) internalization ability, intracellular persistence and cytotoxicity. These findings were confirmed using a panel of 17 different S. pseudintermedius isolates. Additionally, S. pseudintermedius internalization by osteoblasts was completely abolished in β1 integrin-deficient murine osteoblasts. These results suggest the involvement of β1 integrin in the invasion process, although this mechanism was previously restricted to S. aureus. In summary, our results suggest that internalization into NPPCs is not a classical pathophysiologic mechanism of SNA BJIs. S. pseudintermedius appears to be an exception, and its ability to invade and subsequently induce cytotoxicity in NPPCs could explain its severe and necrotic forms of infection, notably in dogs, which exhibit a high prevalence of S. pseudintermedius infection.
Published: 2016
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13. Genome Sequences of Multiresistant Staphylococcus capitis Pulsotype NRCS-A and Methicillin-Susceptible S. capitis Pulsotype NRCS-C

Author: S. Lemriss, H. Lemriss, S. El Kabbaj, Azeddine Ibrahimi, Patricia Martins-Simoes, Jean-Philippe Rasigade, Marine Butin, Frédéric Laurent, L. Lahlou, Yann Dumont, Department of Biotechnology Laboratory (Med-Biotech), Mohammed V University in Rabat, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Laboratoire des Recherches d'Analyses Techniques et Scientifiques, Gendarmerie Royale, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Université Mohammed V de Rabat [Agdal] (UM5), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Strain (biology), Biology, medicine.disease_cause, biology.organism_classification, Genome, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Microbiology, Staphylococcus capitis, 03 medical and health sciences, 030104 developmental biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, medicine, [SDV.IMM]Life Sciences [q-bio]/Immunology, Prokaryotes, Molecular Biology, Staphylococcus, ComputingMilieux_MISCELLANEOUS
Abstract: Here, we report the draft genome sequences of methicillin-susceptible Staphylococcus captis pulsotype NCRS-C (CR02 strain) and multiresistant Staphylococcus captis pulsotype NCRS-A (CR07 strain).
Published: 2016
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14. Wide geographical dissemination of the multiresistant Staphylococcus capitis NRCS-A clone in neonatal intensive-care units

Author: Jean-Charles Picaud, Azeddine Ibrahimi, Marine Butin, Olivier Denis, Patricia Martins-Simoes, Jean-Philippe Rasigade, Margaret A. Deighton, Frédéric Laurent, Hélène Meugnier, Richard V. Goering, Olivier Claris, H. Lemriss, François Vandenesch, Angela Kearns, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Centre National de Reference des Staphylocoques, Université de Lyon, Department of Biotechnology Laboratory (Med-Biotech), Mohammed V University in Rabat, Creighton University, Public Health England [London], Royal Melbourne Institute of Technology University (RMIT University), Université libre de Bruxelles (ULB), Service Réanimation Néonatale, Groupement Hospitalier Est, Hospices Civils de Lyon, Hospices Civils de Lyon (HCL)-Groupement Hospitalier Est, Service de Néonatalogie [Lyon], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université Mohammed V de Rabat [Agdal] (UM5)
Subjects: 0301 basic medicine, Male, Antibiotic resistance, Staphylococcus, vancomycin, Drug Resistance, SmaI, Drug Resistance, Multiple, Bacterial, Neonatal, Child, Phylogeny, Molecular Epidemiology, Cross Infection, biology, Bacterial, General Medicine, Single Nucleotide, Staphylococcal Infections, 3. Good health, Anti-Bacterial Agents, Europe, Intensive Care Units, Infectious Diseases, Child, Preschool, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Multiple, Microbiology (medical), Adult, Adolescent, Genotype, 030106 microbiology, Staphylococcal infections, Polymorphism, Single Nucleotide, neonatology, Microbiology, 03 medical and health sciences, Intensive Care Units, Neonatal, Intensive care, Sepsis, medicine, Pulsed-field gel electrophoresis, Humans, Typing, Polymorphism, Preschool, coagulase-negative Staphylococcus, clone, Molecular epidemiology, Infant, Newborn, Australia, Infant, medicine.disease, biology.organism_classification, Newborn, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Staphylococcus capitis, Molecular Typing
Abstract: International audience; Nosocomial late-onset sepsis represents a frequent cause of morbidity and mortality in preterm neonates. The Staphylococcus capitis clone NRCS-A has been previously described as an emerging cause of nosocomial bacteraemia in French neonatal intensive-care units (NICUs). In this study, we aimed to explore the possible unrecognized dissemination of this clone on a larger geographical scale. One hundred methicillin-resistant S. capitis strains isolated from neonates (n = 86) and adult patients (n = 14) between 2000 and 2013 in four different countries (France, Belgium, the UK, and Australia) were analysed with SmaI pulsed-field gel electrophoresis (PFGE) and dru typing. The vast majority of NICU strains showed the NRCS-A pulsotype and the dt11c type (96%). We then randomly selected 14 isolates (from neonates, n = 12, three per country; from adult patients, n = 2), considered to be a subset of representative isolates, and performed further molecular typing (SacII PFGE, SCCmec typing, and multilocus sequence typing-like analysis), confirming the clonality of the S. capitis strains isolated from neonates, despite their distant geographical origin. Whole genome single-nucleotide polymorphism-based phylogenetic analysis of five NICU isolates (from the different countries) attested to high genetic relatedness within the NRCS-A clone. Finally, all of the NRCS-A strains showed multidrug resistance (e.g. methicillin and aminoglycoside resistance, and decreased vancomycin susceptibility), with potential therapeutic implications for infected neonates. In conclusion, this study represents the first report of clonal dissemination of methicillin-resistant coagulase-negative Staphylococcus clone on a large geographical scale. Questions remain regarding the origin and means of international spread, and the reasons for this clone's apparent predilection for neonates.
Published: 2016
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15. Genome Sequence of a Clinical Staphylococcus aureus Strain from a Prosthetic Joint Infection

Author: Christiane Forestier, Frédéric Laurent, Sonia Chatellier, Valérie Collin, Christine Franceschi, Claire Marquès, BioMérieux SA [La Balme Les Grottes], Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), BRICHEUX, Genevieve, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Whole genome sequencing, musculoskeletal diseases, Strain (biology), 030106 microbiology, Total knee arthroplasty, Prosthetic joint infection, Biology, medicine.disease_cause, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Microbiology, 03 medical and health sciences, 030104 developmental biology, Staphylococcus aureus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genetics, medicine, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Prokaryotes, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Biology, Sequence (medicine)
Abstract: Here, we report the genome sequence of Staphylococcus aureus LYO-S2, an isolate with sequence type (ST) 45 that was isolated in 2001 from a prosthetic joint infection.
Published: 2016
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16. Adaptive processes of Staphylococcus aureus isolates during the progression from acute to chronic bone and joint infections in patients

Author: Trouillet-Assant, Sophie, Lelievre, Lucie, Martins-Simões, Patrícia, Gonzaga, Luiz, Tasse, Jason, Valour, Florent, Rasigade, Jean-Philippe, Vandenesch, François, Muniz Guedes, Rafael Lucas, Ribeiro de Vasconcelos, Ana Tereza, Caillon, Jocelyne, Lustig, Sebastien, Ferry, Tristan, Jacqueline, Cédric, Loss de Morais, Guilherme, Laurent, Frédéric, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Bioinformatics Laboratory, Laboratorio Nacional de Computação Cientifica [Rio de Janeiro] (LNCC / MCT)-MCTI, Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Centre National de Reference des Staphylocoques, Université de Lyon, Thérapeutiques cliniques et expérimentales des infections (EA 3826) (EA 3826), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Service de Chirurgie Orthopédique [Centre Albert Trillat], Centre Albert Trillat [Hôpital de la Croix-Rousse - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Hôpital de la Croix-Rousse [CHU - HCL], Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: CELLULAR MICROBIOLOGY, CORPS HUMAIN, ARTICULATION HUMAINE, [SDV.IB]Life Sciences [q-bio]/Bioengineering, PATHOLOGIE
Abstract: Staphylococcus aureus bone and joint infection (BJI) is associated with significant rates of chronicity and relapse. In this study, we investigated how S. aureus is able to adapt to the human environment by comparing isolates from single patients with persisting or relapsing BJIs that were recovered during the initial and recurrent BJI episodes. In vitro and in vivo assays and whole-genome sequencing analyses revealed that the recurrent isolates induced a reduced inflammatory response, formed more biofilms, persisted longer in the intracellular compartments of host bone cells, were less cytotoxic and induced less mortality in a mouse infection model compared with the initial isolates despite the lack of significant changes at the genomic level. These findings suggest that S. aureus BJI chronicization is associated with an in vivo bacterial phenotypical adaptation that leads to decreased virulence and host immune escape, which is linked to increased intraosteoblastic persistence and biofilm formation.
Published: 2016
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17. Evaluation of the BD GeneOhm Methicillin-Resistant Staphylococcus aureus (MRSA) Assay as a Method for Detection of MRSA Isolates, Using a Large Collection of European and North African Isolates

Author: Sylvestre Tigaud, Sophie Trouillet-Assant, Jerome Etienne, Hélène Meugnier, Frédéric Laurent, Michèle Bes, François Vandenesch, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, This study was supported by funds from a research grant (DMNAFLKS1-264864) to F.L. from BD Diagnostics., Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Davoine, Laure-Hélène, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: DNA, Bacterial, Methicillin-Resistant Staphylococcus aureus, Microbiology (medical), [SDV.IMM] Life Sciences [q-bio]/Immunology, North africa, Biology, medicine.disease_cause, Staphylococcal infections, Microbiology, 03 medical and health sciences, 0302 clinical medicine, Africa, Northern, medicine, Humans, Molecular diagnostic techniques, Northern, 030212 general & internal medicine, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Bacteriological Techniques, 0303 health sciences, 030306 microbiology, SCCmec, Bacterial, Bacteriology, DNA, Staphylococcal Infections, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virology, Methicillin-resistant Staphylococcus aureus, 3. Good health, body regions, Europe, Molecular Diagnostic Techniques, Staphylococcus aureus, Africa, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, North african, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract: Using a large collection of European and North African methicillin-resistant Staphylococcus aureus (MRSA) isolates with a variety of genetic backgrounds and staphylococcal cassette chromosome mec (SCC mec ) types, we evaluated the reliability of the BD GeneOhm MRSA assay. Results revealed high performance of this test for detecting MRSA strains provided from Europe and North Africa (98.3%).
Published: 2014
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18. Effects of antibiotics on biofilm and unattached cells of a clinical Staphylococcus aureus isolate from bone and joint infection

Author: Valérie Collin, Frédéric Laurent, Sonia Chatellier, Anne Pracros, Jason Tasse, Christine Franceschi, Claire Marquès, Christiane Forestier, BioMérieux SA [La Balme Les Grottes], Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), Staphylococcus aureus, medicine.drug_class, Fusidic acid, Antibiotics, Microbial Sensitivity Tests, Biology, Fosfomycin, medicine.disease_cause, Microbiology, 03 medical and health sciences, medicine, Humans, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Biofilm, Osteomyelitis, General Medicine, biochemical phenomena, metabolism, and nutrition, Staphylococcal Infections, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Biofilms, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Vancomycin, [SDV.IMM]Life Sciences [q-bio]/Immunology, Gentamicin, Daptomycin, Joint Diseases, medicine.drug
Abstract: International audience; Treatment of orthopaedic infections remains challenging owing to the inability of antibiotics to eradicate biofilms and prevent their regrowth. The present study characterized the effects of 12 antibiotics on in vitro biofilm formed by a representative strain of meticillin-susceptible Staphylococcus aureus (MSSA) isolated from a bone infection. Determination of the minimum biofilm eradication concentrations indicated that in vitro eradication of 24 h-old biofilms required concentrations up to 51,200 times higher than MICs. The influence of the same panel of antibiotics was also investigated on biofilm formation at concentrations including the breakpoints, by numbering viable cells in the suspensions (individual cells) and the biofilm biomass. Except for fusidic acid, the presence of antibiotics during the initial steps of biofilm formation resulted in significant decreases in the number of sessile viable bacteria at the highest concentrations tested. Ceftarolin, daptomycin, fosfomycin, gentamicin, ofloxacin, rifampicin and vancomycin were the most effective drugs. Confocal microscopy analysis indicated that daptomycin was more efficient at bacteria lysis than gentamicin and vancomycin. However, viable individual cells were still detectable in the assays performed with ceftarolin, fosfomycin, ofloxacin, rifampicin and vancomycin at concentrations for which no sessile cells were detected. Although none of the molecules tested was effective at classical therapeutic concentrations against 24 h-old MSSA biofilms, all except fusidic acid were able to impair biofilm formation at concentrations near the breakpoints. However, presence of viable individual unattached cells could imply a significant risk of microbial dissemination and increased risk of infections.
Published: 2015
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19. Mupirocin Resistance in Isolates of Staphylococcus spp. from Nasal Swabs in a Tertiary Hospital in France

Author: Sacha Flammier, Jean-Philippe Rasigade, Sophie Trouillet-Assant, Anaïs Sapin, Frédéric Laurent, François Vandenesch, Anne Tristan, Oana Dumitrescu, Céline Dupieux, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), Genotype, Epidemiology, Staphylococcus, Drug Resistance, Mucous membrane of nose, Mupirocin, Drug resistance, medicine.disease_cause, Staphylococcal infections, Polymerase Chain Reaction, Microbiology, Tertiary Care Centers, chemistry.chemical_compound, Disk Diffusion Antimicrobial Tests, Drug Resistance, Bacterial, medicine, Prevalence, Humans, Etest, business.industry, Bacterial, Staphylococcal Infections, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Anti-Bacterial Agents, Nasal Mucosa, Phenotype, chemistry, Genes, Genes, Bacterial, Staphylococcus aureus, Nasal Swab, Carrier State, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, lipids (amino acids, peptides, and proteins), France, business
Abstract: Mupirocin is a topical antibiotic largely used to eradicate staphylococcal nasal carriage. Here, we investigated the prevalence of mupirocin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates recovered from patients in different wards in a hospital (Lyon, France), which were determined both phenotypically with an Epsilometer test (Etest) and genetically by PCR for mupA and mupB .
Published: 2015
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20. Putative invasive pulmonary aspergillosis in critically ill patients with chronic obstructive pulmonary disease: a matched cohort study

Author: Oana Dumitrescu, Rodrigue Dessein, Florent Wallet, Arnaud Friggeri, Marion Le Maréchal, Laurent Argaud, Thomas Rimmelé, Aurélie Cottereau, Anne-Lise Bienvenu, Claire Delsuc, Florence Ader, Emilie Fréalle, Sophie Jarraud, Saad Nseir, Pillet, Lauriane, Hôpital Edouard Herriot, Service Anesthésie Réanimation, Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Département Anesthésie-Réanimation, Hôpital Roger Salengro, CHRU de Lille, Hôpital Roger Salengro, CHRU de Lille, Lille, France, Laboratoire de Parasitologie et de Mycologie médicale [CHRU Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Service de parasitologie et mycologie médicale [Hôpital de la Croix Rousse, Lyon], Hôpital de la Croix-Rousse [CHU - HCL], Laboratoire de Bacteriologie [CHRU Lille], Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Maladies chroniques, santé perçue, et processus d'adaptation (APEMAC), Université de Lorraine (UL), Service d'anesthésie-réanimation [Centre Hospitalier Lyon Sud - HCL], Faculté de Médecine Henri Warembourg - Université de Lille, Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Pathogenèse des légionelles- Legionella pathogenesis (LegioPath), CHU Lille, CNRS, Inserm, Institut Pasteur de Lille, Université de Lille, Recherche translationnelle : relations hôte-pathogènes - EA 7366, Lille Inflammation Research International Center (LIRIC) - U995, Centre Hospitalier Régional Universitaire [Lille] [CHRU Lille], Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204 [CIIL], Centre National de Référence (CNR) des Enterovirus et Parechovirus [HCL Lyon] [CNR - laboratoire associé], Recherche translationelle relations hôte-pathogènes, Centre Hospitalier Lyon Sud [CHU - HCL] [CHLS], Maladies chroniques, santé perçue, et processus d'adaptation [APEMAC], Lille Inflammation Research International Center - U 995 [LIRIC], Université Lille 2 - Faculté de Médecine, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: Male, Antifungal Agents, [SDV]Life Sciences [q-bio], Mesh:Invasive Pulmonary Aspergillosis/mortality, Mesh:Prognosis, Critical Care and Intensive Care Medicine, outcomes, Cohort Studies, Pulmonary Disease, Chronic Obstructive, 0302 clinical medicine, Mesh:Critical Illness/therapy, Risk Factors, Mesh:Risk Factors, 030212 general & internal medicine, Mesh:Aged, fungal-infections, Aged, 80 and over, Invasive Pulmonary Aspergillosis, Mesh:Chronic Obstructive/mortality, 0303 health sciences, COPD, pseudomonas-aeruginosa, Mesh:Chronic Obstructive/microbiology, Middle Aged, Prognosis, Mesh:Intensive Care Units, 3. Good health, [SDV] Life Sciences [q-bio], Intensive Care Units, medicine.anatomical_structure, clinical-features, Female, Allergic bronchopulmonary aspergillosis, Cohort study, Mesh:Female, medicine.medical_specialty, Critical Illness, Mesh:Chronic Obstructive/complications, Pulmonary disease, Mesh:Male, 03 medical and health sciences, Mesh:Retrospective Studies, General & Internal Medicine, Mesh:Middle Aged, Mesh:80 and over, medicine, Humans, Mesh:Cohort Studies, Intensive care medicine, Aged, Retrospective Studies, Mesh:Invasive Pulmonary Aspergillosis/etiology, 030306 microbiology, business.industry, Critically ill, Research, Retrospective cohort study, Mesh:Antifungal Agents/therapeutic use, Mesh:Invasive Pulmonary Aspergillosis/diagnosis, fumigatus, Invasive pulmonary aspergillosis, medicine.disease, Mesh:Pulmonary Disease, Mesh:Humans, biofilms, business, Respiratory tract
Abstract: Introduction Patients with advanced chronic obstructive pulmonary disease (COPD) are at risk for developing invasive pulmonary aspergillosis. A clinical algorithm has been validated to discriminate colonization from putative invasive pulmonary aspergillosis (PIPA) in Aspergillus-positive respiratory tract cultures of critically ill patients. We focused on critically ill patients with COPD who met the criteria for PIPA. Methods This matched cohort study included critically ill patients with COPD from two university hospital intensive care units (ICUs). We studied the risk factors for PIPA as well as the impact of PIPA on short- and long-term outcomes. Whether PIPA was associated with a pattern of bacterial colonization and/or infection 6 months before and/or during ICU stay was assessed. In addition, antifungal strategies were reviewed. Results Fifty cases of PIPA in critically ill patients with COPD in the ICU were matched with one hundred control patients with COPD. The ICU short- and the long-term (at 1 year) mortality were significantly increased in the PIPA group (p p p = 0.004 and p Conclusions PIPA was a strong death predictor in critically ill patients with COPD. The use of corticosteroids and antibiotics before ICU admission was a risk factor for PIPA. PIPA was not associated with a specific bacterial pattern of colonization or infection. Prompting antifungal treatment in critically ill patients with COPD who have PIPA may not be the only factor involved in prognosis reversal.
Published: 2015
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21. Methicillin-susceptible strains responsible for postoperative orthopedic infection are not selected by the use of cefazolin in prophylaxis

Author: Tristan Ferry, Sébastien Lustig, Florent Valour, William Mouton, Frédéric Laurent, Patricia Martins-Simoes, Sophie Trouillet-Assant, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Service de Maladies Infectieuses et Tropicales [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Service de Chirurgie Orthopédique [Centre Albert Trillat], Centre Albert Trillat [Hôpital de la Croix-Rousse - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL)-Hôpital de la Croix-Rousse [CHU - HCL], Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Methicillin-Resistant Staphylococcus aureus, 0301 basic medicine, Microbiology (medical), medicine.medical_specialty, MALADIE, ARTICULATION HUMAINE, 030106 microbiology, Cefazolin, medicine.disease_cause, Methicillin resistance, PROPHYLAXIS, Microbiology, BIOMECANIQUE, 03 medical and health sciences, Postoperative Complications, polycyclic compounds, medicine, Humans, Orthopedic Procedures, Nasal colonization, Antibiotic prophylaxis, STAPHYLOCOCCUS AUREUS, Arthritis, Infectious, business.industry, OS, Bacterial Infections, General Medicine, Antibiotic Prophylaxis, biochemical phenomena, metabolism, and nutrition, Bone Diseases, Infectious, bacterial infections and mycoses, Methicillin-resistant Staphylococcus aureus, Anti-Bacterial Agents, 3. Good health, CEFAZOLIN, Infectious Diseases, Staphylococcus aureus, Orthopedic surgery, Methicillin Resistance, [SDV.IB]Life Sciences [q-bio]/Bioengineering, BONE AND JOINT INFECTION, business, medicine.drug
Abstract: Comparison of methicillin-susceptible Staphylococcus aureus (MSSA) isolates responsible for bone and joint infection (BJI, n=73) and nasal colonization (n=57) revealed similar prevalence of ²-lactamase (blaZ) type A production, associated with cefazolin hydrolysis, suggesting that blaZ type A - carrying MSSA isolates implicated in postoperative BJI are not selected by cefazolin prophylaxis.
Published: 2016
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22. HIV-1-Associated Kidney Disease in an Elite Controller

Author: Caroline Charre, Sandrine Lemoine, Vinca Icard, Rabeyrin Maud, Jean-Claude Tardy, Pierre Chiarello, Matthieu Godinot, Véronique Avettand-Fenoel, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Service de Virologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Service de Biochimie et Biologie Moléculaire Grand Est [HCL, Lyon] (Centre de Biologie et de Pathologie), Hôpital de la Croix-Rousse [CHU - HCL], and CarMeN, laboratoire
Subjects: [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Public Health, Environmental and Occupational Health, HIV Infections, Kidney Diseases/complications, CD4 Lymphocyte Count, HIV Seropositivity, Infectious Diseases, hiv-1, HIV Infections/complications, HIV-1, Humans, Kidney Diseases, Elite Controllers
Abstract: No abstract available
Published: 2022
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23. Adherence to opioid agonist therapy predicts uptake of direct-acting antivirals in people who use drugs: results from the French national healthcare database (the ANRS FANTASIO study)

Author: Benjamin Rolland, Caroline Lions, Vincent Di Beo, Patrizia Carrieri, Nicolas Authier, Tangui Barré, Jessica Delorme, Philippe Mathurin, François Bailly, Camelia Protopopescu, Fabienne Marcellin, Service Universitaire d’Addictologie de Lyon [CH Le Vinatier, Bron] (Pôle MOPHA - SUAL), Centre Hospitalier le Vinatier [Bron], Psychiatric Disorders, Neuroscience Research and Clinical Research (PSYR2), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Neuro-Dol (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Service des Maladies de l'Appareil Digestif et de la Nutrition [CHRU Lille], Hôpital Claude Huriez [Lille], CHU Lille-CHU Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Service d'hépatologie et d’addictologie [GH Nord, Lyon], HCL Groupement Hospitalier Nord [Lyon], Hôpital de la Croix-Rousse [CHU - HCL], and Hospices Civils de Lyon (HCL)
Subjects: Male, MESH: Antiviral Agents, [SDV]Life Sciences [q-bio], MESH: Delivery of Health Care, Medicine (miscellaneous), Hepacivirus, MESH: Analgesics, Opioid, Antiviral Agents, Humans, MESH: Hepacivirus, Drug use, DAA, MESH: Hepatitis C, MESH: Humans, Public Health, Environmental and Occupational Health, Hepatitis C, Chronic, Hepatitis C, MESH: Male, Buprenorphine, MESH: Hepatitis C, Chronic, Analgesics, Opioid, Psychiatry and Mental health, Female, Delivery of Health Care, MESH: Female, Methadone
Abstract: Background Opioid agonist therapy (OAT) is associated with reduced injection, reduced HCV transmission, and more opportunities to initiate hepatitis C virus (HCV) treatment in people who use drugs (PWUD). We aimed to study the extent to which adherence to OAT was predictive of increased uptake of direct-acting antivirals (DAA) in PWUD with chronic HCV infection. Methods Using the French national healthcare system database, we targeted PWUD (i.e. with a history of OAT) who had chronic HCV infection and were eligible for DAA during 2014–2016. Adherence to OAT was computed as a time-varying variable expressing the proportion of days covered by OAT receipt, over any six-month interval before DAA receipt. We used a Cox proportional hazards model to estimate the association between adherence to OAT and the rate of DAA uptake after adjustment for age, sex, alcohol use disorder, socioeconomic status, and liver disease severity. Results Among the 22,615 persons included in the ANRS FANTASIO study, 3438 (15.2%) initiated DAA during the study period. After multivariable adjustment, adherence to OAT was associated with a higher rate of DAA initiation. However, this association was not linear, and only individuals on OAT for 20% or more of the time in the previous six-month period had a higher rate of DAA initiation (adjusted hazard ratio [95% confidence interval]: 1.28 [1.18–1.38]). Other variables associated with DAA initiation were male sex, older age, cirrhosis or liver cancer, and higher socioeconomic status. Conclusions Adherence to OAT is a major predictor of DAA initiation in PWUD living with chronic HCV infection in France. Our results also suggest that even moderate adherence to OAT can facilitate DAA uptake. Adequate HCV training for OAT prescribers together with interventions to ensure adherence to OAT will help improve DAA initiation rates and reach HCV elimination goals.
Published: 2022
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24. Characterization of a novel composite staphylococcal cassette chromosome mec (SCCmec-SCCcad/ars/cop) in the neonatal sepsis-associated Staphylococcus capitis pulsotype NRCS-A

Author: Martins Simões, Patricia, Rasigade, Jean-Philippe, Lemriss, H., Butin, Marine, Ginevra, Christophe, Lemriss, S., Goering, R. V., Ibrahimi, A., Picaud, J. C., El Kabbaj, S., Vandenesch, François, Laurent, Frédéric, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Centre National de Reference des Staphylocoques, Université de Lyon, Laboratoire des Recherches d'Analyses Techniques et Scientifiques, Gendarmerie Royale, Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi, Rabat, Morocco, Pathogenèse des légionelles- Legionella pathogenesis (LegioPath), Creighton University School of Medicine, HCL Groupement Hospitalier Nord [Lyon], Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Mohammed V de Rabat [Agdal] (UM5), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: Methicillin-Resistant Staphylococcus aureus, Male, Infant, Newborn, Bacterial, Infant, Chromosomes, Bacterial, bacterial infections and mycoses, Newborn, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Chromosomes, Arsenic, Mechanisms of Resistance, Sepsis, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Copper, Cadmium
Abstract: International audience; Multiresistant Staphylococcus capitis pulsotype NRCS-A has been reported to be a major pathogen causing nosocomial bacteremia in preterm infants. We report that the NRCS-A strain CR01 harbors a novel 60.9-kb composite staphylococcal cassette chromosome mec (SCCmec) element, composed of an SCCmec with strong homologies to Staphylococcus aureus ST398 SCCmec and of an SCCcad/ars/cop harboring resistance genes for cadmium, arsenic, and copper. Whole-genome-based comparisons of published S. capitis strains suggest that strain CR01 acquired the two elements independently.
Published: 2013
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25. PSMs of hypervirulent Staphylococcus aureus act as intracellular toxins that kill infected osteoblasts

Author: Jerome Etienne, Jérémy Ranfaing, Gerard Lina, Florence Couzon, Sylvestre Tigaud, Yvonne Benito, Frédéric Laurent, Sophie Trouillet-Assant, Anaïs Sapin, Cédric Badiou, Binh An Diep, Michèle Bes, François Vandenesch, Yannick Lhoste, Tristan Ferry, Jean-Philippe Rasigade, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Département de Microbiologie Clinique [HCL Groupement Hospitalier Nord, Lyon], Hospices Civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon], Department of Medicine [San Francisco], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), University of California [San Francisco] (UCSF), University of California-University of California, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Messenger, Leukocidin, Intracellular Space, Pathogenesis, medicine.disease_cause, Pathogen, Staphylococci, 0303 health sciences, Staphylococcal infection, Multidisciplinary, Cell Death, Phenol-soluble modulin, Bacterial, Osteoblast, Osteomyelitis, 3. Good health, Bacterial Pathogens, Panton-Valentine leukocidin, Host-Pathogen Interaction, Community-Acquired Infections, medicine.anatomical_structure, Staphylococcus aureus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Medicine, Infectious diseases, [SDV.IMM]Life Sciences [q-bio]/Immunology, Intracellular, Research Article, Methicillin-Resistant Staphylococcus aureus, Science, Bacterial diseases, Bacterial Toxins, Virulence, Biology, Microbiology, 03 medical and health sciences, Species Specificity, Virology, medicine, Humans, RNA, Messenger, 030304 developmental biology, Osteoblasts, 030306 microbiology, Intracellular parasite, Gene Expression Regulation, Bacterial, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, Methicillin-resistant Staphylococcus aureus, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacterial Load, Gene Expression Regulation, Virulence Factors and Mechanisms, RNA, Delivery of Health Care
Abstract: International audience; Epidemic community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) is associated with more severe and acute forms of osteomyelitis than healthcare-associated (HA-) MRSA. Although S. aureus is now recognized as a facultative intracellular pathogen, the contribution of osteoblast invasion by CA-MRSA to the pathogenesis of osteomyelitis is unknown. Using an ex vivo model of intracellular infection of human osteoblasts, we demonstrated that CA-MRSA strains of diverse lineages share an enhanced ability to kill infected osteoblasts compared to HA-MRSA. Cytotoxicity comparisons of CA-MRSA isogenic deletion mutants revealed that phenol-soluble modulins (PSMs), a class of membrane-damaging exoproteins that are expressed at higher levels in CA-MRSA than in HA-MRSA, are involved in this osteoblast killing, whereas other major CA-MRSA virulence determinants, the Panton-Valentine leukocidin and alpha-toxin, are not involved. Similarly, functional agr and sarA regulators, which control the expression of PSMs and alpha-toxin, were required for the expression of the intracellular cytotoxic phenotype by CA-MRSA, whereas the saeRS regulator, which controls the expression of alpha-toxin but not PSMs, had no impact on cytotoxicity. Finally, PSM transcript levels determined by quantitative reverse-transcriptase PCR were significantly higher in CA-MRSA than in HA-MRSA strains and associated with cell damage in MRSA-infected osteoblasts. These findings provide new insights into the pathogenesis of severe CA-MRSA osteomyelitis and unravel a novel virulence strategy of CA-MRSA, based on the invasion and subsequent killing of osteoblasts by PSMs acting as intracellular toxins.
Published: 2013
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26. Perioperative Outcomes in Patients Who Received Spinal Chloroprocaine for Total Hip or Knee Arthroplasty-Consecutive Case Series Study

Author: Khaleifah Alhefeiti, Ana-Maria Patrascu, Sebastien Lustig, Frederic Aubrun, Mikhail Dziadzko, Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Research on Healthcare Performance (RESHAPE - Inserm U1290 - UCBL1), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), HCL Groupement Hospitalier Nord [Lyon], and Cadic, Ifsttar
Subjects: SPINAL ANAESTHESIA, CHLOROPROCAINE, [SPI.MECA.BIOM] Engineering Sciences [physics]/Mechanics [physics.med-ph]/Biomechanics [physics.med-ph], arthroplasty, chloroprocaine, perioperative outcome, spinal anaesthesia, [SPI.MECA.BIOM]Engineering Sciences [physics]/Mechanics [physics.med-ph]/Biomechanics [physics.med-ph], General Medicine, PERIOPERATIVE OUTCOME, ARTHROPLASTY
Abstract: Spinal anaesthesia is an established component of perioperative management for fast-track lower limbs arthroplasty. Short-acting local anaesthetics may present an interesting option for primary non-complicated knee (TKA) and hip (THA) arthroplasty. We describe the perioperative outcomes in patients operated under fixed 50 mg spinal chloroprocaine for total hip and knee replacement. In this retrospective case series study, 65 patients were analysed (median age 65 years, 55% females, benefit from THA (n = 31), TKA (n = 25), and unicompartmental knee arthroplasty (n = 9)). In all cases, anaesthesia duration (87 min) was sufficient for successful surgery (52 min). Up to 45% of patients (THA and less in TKA) developed postoperative pain in the post-anaesthesia care unit (PACU), requiring intravenous morphine titration (up to 7.5 mg). One patient developed severe breakthrough pain requiring advanced regional analgesia. The median PACU stay was up to 97 min (less in TKA), and the incidence of nausea and urinary retention was low. All patients were able to start physical therapy on the same day of surgery. These findings encourage the use of a short-acting agent for spinal anaesthesia in patients with primary non-complicated arthroplasty; however, the relay analgesia should be systematically implemented to avoid breakthrough pain in PACU.
Published: 2022
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27. The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example

Author: Dalal Nour, Rayane Rafei, Alessandra P. Lamarca, Luiz G. P. de Almeida, Marwan Osman, Mohamad Bachar Ismail, Hassan Mallat, Atika Berry, Gwendolyne Burfin, Quentin Semanas, Laurence Josset, Hamad Hassan, Fouad Dabboussi, Bruno Lina, Philippe Colson, Ana Tereza R. Vasconcelos, Monzer Hamze, Laboratoire Microbiologie Santé et Environnement (LMSE), Faculty of Public Health, Lebanese University, Tripoli ((LMSE)), Lebanese University [Beirut] (LU), Laboratorio Nacional de Computação Cientifica [Rio de Janeiro] (LNCC / MCT), Cornell University [New York], Laboratoire Microbiologie Santé et Environnement [Tripoli, Liban] (LMSE), Université Libanaise, Ministry of Public Health [Beirut, Lebanon], Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), HCL Groupement Hospitalier Nord [Lyon], Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Medical Care Laboratory, Lebanese University, Faculty of the Public Health IV, Zahle, Lebanon, Institut des Agents Infectieux, Laboratoire Associé au Centre National de Référence des Virus des Infections Respiratoires, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Laboratoire Microbiologie Santé et Environnement - LMSE [Tripoli, Lebanon] (Faculté de Santé Publique), and Université Libanaise-Ecole Doctorale des Sciences et de Technologie [Tripoli, Lebanon]
Subjects: lineages, Infectious Diseases, SARS-CoV-2, B.1.398, Virology, [SDV]Life Sciences [q-bio], Lebanon, dispersal
Abstract: International audience; In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers crossing the Lebanese–Syrian border, and we also analyze the Lebanese genomic dataset available at GISAID. Our results show that SARS-CoV-2 infections in Lebanon during this period were shaped by the turnovers of four dominant SARS-CoV-2 lineages, with B.1.398 being the first to thoroughly dominate. Lebanon acted as a dispersal center of B.1.398 to other countries, with intercontinental transmissions being more common than within-continent. Within the country, the district of Tripoli, which was the source of 43% of the total B.1.398 sequences in our study, was identified as being an important source of dispersal in the country. In conclusion, our findings exemplify the butterfly effect, by which a lineage that emerges in a small area can be spread around the world, and highlight the potential role of developing countries in the emergence of new variants.
Published: 2022
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28. Bacterial Cross-Transmission between Inanimate Surfaces and Patients in Intensive Care Units under Real-World Conditions: A Repeated Cross-Sectional Study

Author: Elisabetta Kuczewski, Laetitia Henaff, Anne Regard, Laurent Argaud, Anne-Claire Lukaszewicz, Thomas Rimmelé, Pierre Cassier, Isabelle Fredenucci, Sophie Loeffert-Frémiot, Nagham Khanafer, Philippe Vanhems, Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Santé publique, épidémiologie et écologie évolutive des maladies infectieuses (PHE3ID), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Agents Infectieux [Lyon] (IAI), Hôpital de la Croix-Rousse [CHU - HCL], HCL Groupement Hospitalier Nord [Lyon], Laboratoires Anios-Ecolab Company [Lezennes] (LAEC), CarMeN, laboratoire, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL)
Subjects: Acinetobacter baumannii, Cross Infection, hospital-acquired infection, Bacteria, environment, hospital, ICU, high-touch surfaces, bacteria, contamination, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Public Health, Environmental and Occupational Health, [SDV] Life Sciences [q-bio], Intensive Care Units, Cross-Sectional Studies, Humans
Abstract: Background/Objectives: Contaminated surfaces play an important role in the nosocomial infection of patients in intensive care units (ICUs). This study, conducted in two ICUs at Edouard Herriot Hospital (Lyon, France), aimed to describe rooms’ microbial ecology and explore the potential link between environmental contamination and patients’ colonization and/or infection. Methods: Environmental samples were realized once monthly from January 2020 to December 2021 on surfaces close to the patient (bedrails, bedside table, and dedicated stethoscope) and healthcare workers’ high-touch surfaces, which were distant from the patient (computer, worktop/nurse cart, washbasin, and hydro-alcoholic solution/soap dispenser). Environmental bacteria were compared to the cultures of the patients hospitalized in the sampled room over a period of ± 10 days from the environmental sampling. Results: Overall, 137 samples were collected: 90.7% of the samples close to patients, and 87.9% of the distant ones were positives. Overall, 223 bacteria were isolated, mainly: Enterococcus faecalis (15.7%), Pantoea agglomerans (8.1%), Enterobacter cloacae/asburiae (6.3%), Bacillus cereus and other Bacillus spp (6.3%), Enterococcusfaecium (5.8%), Stenotrophomonas maltophilia (5.4%), and Acinetobacter baumannii (4.9%). Throughout the study, 142 patients were included, of which, n = 67 (47.2%) were infected or colonized by at least one bacterium. In fourteen cases, the same bacterial species were found both in environment and patient samples, with the suspicion of a cross-contamination between the patient–environment (n = 10) and environment–patient (n = 4). Conclusions: In this work, we found a high level of bacterial contamination on ICU rooms’ surfaces and described several cases of potential cross-contamination between environment and patients in real-world conditions.
Published: 2022
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29. Novel calixarene-based surfactant enables low dose split inactivated vaccine protection against influenza infection

Author: Marie Eve Hamelin, Elodie Desuzinges Mandon, Bruno Lina, Aurélien Traversier, Anne Champagne, Manuel Rosa-Calatrava, Andrés Pizzorno, Guy Boivin, Emmanuel Dejean, Anass Jawhari, Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), CALIXAR, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Laval [Québec] (ULaval), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), and HCL Groupement Hospitalier Nord [Lyon]
Subjects: [SDV]Life Sciences [q-bio], 030231 tropical medicine, Hemagglutinin (influenza), Mice, Surface-Active Agents, 03 medical and health sciences, Influenza A Virus, H1N1 Subtype, 0302 clinical medicine, Antigen, Pulmonary surfactant, Influenza, Human, Calixarene, Triton, Animals, Humans, 030212 general & internal medicine, Hemagglutinin, Neutralizing antibody, Antigens, Viral, Mice, Inbred BALB C, General Veterinary, General Immunology and Microbiology, biology, Chemistry, H1N1, Vaccination, Low dose, Public Health, Environmental and Occupational Health, Split inactivated influenza antigen, Antibodies, Neutralizing, Virology, 3. Good health, Infectious Diseases, Vaccines, Inactivated, Immunization, Detergent/surfactant, Influenza Vaccines, Inactivated vaccine, biology.protein, Molecular Medicine, Female, Calixarenes
Abstract: International audience; Influenza A viruses cause major morbidity and represent a severe global health problem. Current influenza vaccines are mainly egg-based products requiring the split of whole viruses using classical detergents such as Triton X-100, which implies certain limitations. Here, we report the use of the novel calixarene-based surfactant CALX133ACE as an alternative to classical detergents for influenza inactivated split vaccine preparation. We confirmed that CALX133ACE-based split HA antigens are fully functional and quantifiable by the "gold standard" method SRID. Additionally, as in the case of the Triton X-100-based split, the CALX133ACE-based split antigens are stable for at least 6 months at 4 °C. Moreover, immunization of mice with CALX133ACE-based split NYMC X-179A (H1N1) antigens harboring 10 to 30-fold less antigen than the commercialized trivalent inactivated vaccines Vaxigrip® or Fluviral® induced comparable efficient protection and neutralizing antibody responses against A(H1N1)pdm09 infection. Taken together, our results demonstrate for the first time the use of a calixarene-based detergent as an efficient splitting agent for the production of optimized influenza split antigens, paving the way for significant improvement in the vaccine manufacturing process, notably with regard to the current regulation on the prohibition of endocrine disruptors, such as Triton X-100.
Published: 2020
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30. Diagnostic accuracy of fluorescence flow-cytometry technology using Sysmex XN-31 for imported malaria in a non-endemic setting

Author: Stéphane Picot, Thomas Perpoint, Christian Chidiac, Alain Sigal, Etienne Javouhey, Yves Gillet, Laurent Jacquin, Marion Douplat, Karim Tazarourte, Laurent Argaud, Martine Wallon, Charline Miossec, Guillaume Bonnot, Anne-Lise Bienvenu, HCL Groupement Hospitalier Nord [Lyon], Institut de Chimie et Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Supérieure de Chimie Physique Électronique de Lyon (CPE)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Université de Lyon, Hôpital Edouard Herriot [CHU - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Health Service and Performance Research (HESPER), Université de Lyon-Université de Lyon, Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut de Chimie du CNRS (INC)-École Supérieure Chimie Physique Électronique de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Sciences, EDP
Subjects: Technology, Plasmodium, Microscopy, Veterinary (miscellaneous), [SDV]Life Sciences [q-bio], Flow Cytometry, Diagnostic accuracy, Malaria, Sysmex XN-31, [SDV] Life Sciences [q-bio], Infectious Diseases, PCR, Artificial Intelligence, LAMP, Insect Science, parasitic diseases, Humans, Animal Science and Zoology, Parasitology, Prospective Studies, RDT
Abstract: Malaria diagnosis based on microscopy is impaired by the gradual disappearance of experienced microscopists in non-endemic areas. Aside from the conventional diagnostic methods, fluorescence flow cytometry technology using Sysmex XN-31, an automated haematology analyser, has been registered to support malaria diagnosis. The aim of this prospective, monocentric, non-interventional study was to evaluate the diagnostic accuracy of the XN-31 for the initial diagnosis or follow-up of imported malaria cases compared to the reference malaria tests including microscopy, loop mediated isothermal amplification, and rapid diagnostic tests. Over a one-year period, 357 blood samples were analysed, including 248 negative and 109 positive malaria samples. Compared to microscopy, XN-31 showed sensitivity of 100% (95% CI: 97.13-100) and specificity of 98.39% (95% CI: 95.56-100) for the initial diagnosis of imported malaria cases. Moreover, it provided accurate species identification asfalciparumor non-falciparumand parasitaemia determination in a very short time compared to other methods. We also demonstrated that XN-31 was a reliable method for patient follow-up on days 3, 7, and 28. Malaria diagnosis can be improved in non-endemic areas by the use of dedicated haematology analysers coupled with standard microscopy or other methods in development, such as artificial intelligence for blood slide reading. Given that XN-31 provided an accurate diagnosis in 1 min, it may reduce the time interval before treatment and thus improve the outcome of patient who have malaria.Précision diagnostique de la technique de cytométrie de flux en fluorescence utilisant le Sysmex XN-31 pour le paludisme d’importation en zone non endémique.Le diagnostic du paludisme basé sur la microscopie est rendu difficile par la disparition progressive des microscopistes expérimentés en zone non-endémique. À côté des méthodes conventionnelles, la technique de cytométrie de flux en fluorescence utilisant le Sysmex XN-31, un automate d’analyse hématologique, a été enregistrée pour participer au diagnostic du paludisme. L’objectif de cette étude prospective, monocentrique et non-interventionelle était d’évaluer la précision diagnostique du XN-31 pour le diagnostic initial et le suivi des cas de paludisme d’importation en comparaison des tests de référence dont la microscopie, l’amplification isothermale en boucle, et des tests de diagnostic rapide. Durant une période d’un an, 357 échantillons de sang ont été analysés, dont 248 négatifs et 109 positifs pour le paludisme. En comparaison de la microscopie, le XN-31 a montré une sensibilité de 100 % (95 % CI : 97.13-100) et une spécificité de 98.39 % (95 % CI : 95.56-100) pour le diagnostic initial des cas de paludisme d’importation. De plus, l’identification des espècesfalciparumet non-falciparumainsi que la parasitémie ont été précises dans un temps très court en comparaison des autres méthodes. Nous avons aussi démontré que le XN-31 était une méthode fiable pour le suivi des patients à J3, J7 et J28. Le diagnostic du paludisme peut être amélioré en zone non-endémique par l’utilisation d’automates d’hématologie spécialisés, associés à la microscopie standard ou d’autres méthodes en développement telle que l’intelligence artificielle appliquée à la lecture des lames de sang. Dans la mesure où le XN-31 produit un diagnostic précis en une minute, cela peut réduire le délai avant le traitement et donc améliorer l’issue pour les patients souffrant de paludisme.
Published: 2022
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31. Nurse-to-Nurse Familiarity and Mortality in the Critically Ill. A Multicenter Observational Study

Author: Antoine Duclos, Cécile Payet, Loredana Baboi, Bernard Allaouchiche, Laurent Argaud, Frédéric Aubrun, Julien Bohé, Frédéric Dailler, Jean-Luc Fellahi, Jean-Jacques Lehot, Vincent Piriou, Thomas Rimmelé, Delphine Terragrossa, Stéphanie Polazzi, Claude Guérin, CarMeN, laboratoire, Université de Lyon, Pôle Information Médicale Evaluation Recherche (IMER), Hospices Civils de Lyon (HCL), Hôpital de la Croix-Rousse [CHU - HCL], Université Claude Bernard Lyon 1 (UCBL), Service d'anesthésie-réanimation [Centre Hospitalier Lyon Sud - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Université de Lyon-Université de Lyon-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hôpital Edouard Herriot [CHU - HCL], Hôpital neurologique et neurochirurgical Pierre Wertheimer [CHU - HCL], Health Service and Performance Research (HESPER), Université de Lyon-Université de Lyon, HCL Groupement Hospitalier Nord [Lyon], and Service de Médecine Intensive et Réanimation [Lyon] (MIR)
Subjects: Pulmonary and Respiratory Medicine, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Staffing, Working familiarity, Nurse-to-nurse familiarity, Intensive Care Unit Organization, Critical Care and Intensive Care Medicine, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Outcome
Abstract: RATIONALE: Nurse-to-nurse familiarity at work should strengthen the components of team working and enhance its efficiency. However, its impact on patient outcomes in critical care remains poorly investigated. OBJECTIVES: To explore the role of nurse-to-nurse familiarity on inpatient deaths during intensive care unit stay. METHODS: Retrospective observational study in eight adult academic intensive care units between 01/01/2011 and 31/12/2016. MEASUREMENTS AND MAIN RESULTS: Nurse-to-nurse familiarity was measured across day and night 12-hour daily shifts as the mean number of previous collaborations between each nursing team member during previous shifts within the given Intensive Care Unit (suboptimal if\textless50). Primary outcome was a shift with at least one inpatient death, excluding death of patients with a decision to forego life-sustaining therapy. A multiple modified Poisson regression was computed to identify the determinants of mortality per shift, taking into account intensive care unit, patients' characteristics, patient-to-nurse and patient-to-assistant nurse ratios, nurse experience length and workload. A total of 43,479 patients were admitted of whom 3,311 (8%) died. Adjusted model showed a lower risk of a shift with mortality when nurse-to-nurse familiarity increased in the shift (relative risk 0.90 [0.82-0.98] 95%confidence intervals per 10 shifts, p=0.012). Low nurse-to-nurse familiarity during the shift combined with suboptimal patient-to-nurse and assistant-nurse ratios (suboptimal if \textgreater2.5 and \textgreater4, respectively) were associated with increased risk of shift with mortality (1.84 [1.15-2.96], p\textless0.001). CONCLUSIONS: Shifts with low nurse-to-nurse familiarity were associated with an increased risk of patient deaths.
Published: 2022
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32. Teignes de l’enfant : algorithme de prise en charge après l’arrêt de la commercialisation de la griséofulvine en France

Author: Nicolas Dupin, M. Caseris, J. Toubiana, Sophie Brun, Bernard Guillot, A. Maruani, Olivier Chosidow, J. Menotti, Marie Beylot-Barry, S. Barbarot, L. Chouchana, J.-P. Gangneux, Françoise Botterel, C. Moreau, Physiopathologie des Adaptations Nutritionnelles (PhAN), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Tours (UT), Université de Nantes (UN), CHU Trousseau [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), MethodS in Patients-centered outcomes and HEalth ResEarch (SPHERE), Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Institut de recherche en santé, environnement et travail (Irset), Université d'Angers (UA)-Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Hôpital Robert Debré, Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Parasitologie-Mycologie, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Henri Mondor-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Hospices Civils de Lyon (HCL), HCL Groupement Hospitalier Nord [Lyon], Université Paris Cité (UPCité), CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Bordeaux Research In Translational Oncology [Bordeaux] (BaRITOn), Université de Bordeaux (UB)-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Saint-André, Université de Bordeaux (UB), Service de Dermatologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Hôpital Henri Mondor, Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université d'Angers (UA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Environnement Ville Société (EVS), École normale supérieure - Lyon (ENS Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2021
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33. Lower HCV treatment uptake in women who have received opioid agonist therapy before and during the DAA era: The ANRS FANTASIO project

Author: Philippe Mathurin, Vincent Di Beo, Camelia Protopopescu, Fabienne Marcellin, François Bailly, Tangui Barré, Jessica Delorme, Nicolas Authier, Teresa Rojas Rojas, Benjamin Rolland, Maria Patrizia Carrieri, Marion Coste, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Neuro-Dol (Neuro-Dol), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Lille Inflammation Research International Center - U 995 (LIRIC), Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Service des Maladies de l'Appareil Digestif et de la Nutrition [CHRU Lille], Hôpital Claude Huriez [Lille], CHU Lille-CHU Lille-Fédération Hospitalière de France-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Service d'hépatologie et d’addictologie [GH Nord, Lyon], HCL Groupement Hospitalier Nord [Lyon], Service Universitaire d’Addictologie de Lyon [CH Le Vinatier, Bron] (Pôle MOPHA - SUAL), Centre Hospitalier le Vinatier [Bron], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), and Dupuis, Christine
Subjects: Male, Databases, Factual, 030508 substance abuse, Medicine (miscellaneous), medicine.disease_cause, Health Services Accessibility, 0302 clinical medicine, Pegylated interferon, Interquartile range, Health care, Medicine, 030212 general & internal medicine, 10. No inequality, Reimbursement, Hepatitis C virus, Health Policy, Confounding, Middle Aged, 3. Good health, Female, France, 0305 other medical science, medicine.drug, Adult, medicine.medical_specialty, Antiviral Agents, Direct acting antivirals, 03 medical and health sciences, Sex Factors, Internal medicine, Humans, Women, Healthcare Disparities, Primary Health Care, Opioid agonist therapy, business.industry, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Hepatitis C, Chronic, Opioid-Related Disorders, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Confidence interval, Opioid, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Barrier to care, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Interferons, business, Delivery of Health Care
Abstract: Background In the era of direct-acting antivirals (DAA) for the treatment of hepatitis C virus (HCV) infection, HCV treatment uptake remains insufficiently documented in key populations such as people with opioid dependence. Access to opioid agonist therapy (OAT) is facilitated in France through delivery in primary care, and individuals with opioid dependence can be identified as those receiving OAT. Women with opioid dependence are especially vulnerable because of associated sex-related stigma, discrimination, and marginalization, all of which negatively interfere with access to HCV prevention and care. This study, based on data collected between 2012 and 2016 in France, aimed to assess whether (i) chronically HCV-infected women with opioid dependence had lower rates of HCV treatment uptake than their male counterparts during the same period (i.e., study period), and (ii) the advent of DAA resulted in increased treatment uptake rates in these women. Methods Individuals with opioid dependence were identified as those receiving OAT at least once during the study period. Analyses were based on exhaustive anonymous care delivery data from the French national healthcare reimbursement database. We used multinomial logistic regression to estimate sex-based disparities in HCV treatment uptake (DAA or pegylated-interferon (Peg-IFN)-based treatment versus no treatment) while accounting for potential confounders. Results The study sample comprised 27,127 individuals, including 5640 (20.8%) women. Median [interquartile range] age was 45 [40–49] years. Between 2012 and 2016, 70.9 (women: 77.2; men: 69.3), 17.3 (14.2; 18.2) and 11.7% (8.6%; 12.5%) of the study sample received, respectively, no HCV treatment, DAA and Peg-IFN-based treatment only. After multiple adjustment for potential confounders, women were 41% (adjusted odds-ratio (AOR) [95% confidence interval (CI]): 0.59[0.53−0.65]) and 28% (0.72[0.66−0.78]) less likely than men to have had Peg-IFN-based and DAA treatment, respectively. Conclusion Despite increased HCV treatment uptake in women with opioid dependence in the DAA era, rates remain lower than for men. In the coming years, access to DAA treatment will continue to increase in France thanks to a forthcoming simplified model of HCV care which includes primary care as an entry point. Nevertheless, a greater understanding of sex-specific barriers to HCV care and the implementation of appropriate sex-specific measures remain a priority.
Published: 2019
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34. Subcutaneous Antibiotic Therapy: The Why, How, Which Drugs and When

Author: Hernández-Ruiz, Virgilio, Forestier, Emmanuel, Gavazzi, Gaëtan, Ferry, Tristan, Grégoire, Nicolas, Breilh, Dominique, Paccalin, Marc, Goutelle, Sylvain, Roubaud-Baudron, Claire, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], CHU Bordeaux [Bordeaux], Centre Hospitalier Métropole Savoie [Chambéry], Groupe de Recherche et d'Etude du Processus Inflammatoire (GREPI), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), CHU Grenoble, Hospices Civils de Lyon (HCL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Centre hospitalier universitaire de Poitiers (CHU Poitiers), Pharmacologie des anti-infectieux et antibiorésistance (PHAR2), Université de Poitiers-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie des maladies cardiovasculaires = Biology of Cardiovascular Diseases, Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CIC - Poitiers, Université de Poitiers-Centre hospitalier universitaire de Poitiers (CHU Poitiers)-Direction Générale de l'Organisation des Soins (DGOS)-Institut National de la Santé et de la Recherche Médicale (INSERM), HCL Groupement Hospitalier Nord [Lyon], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bordeaux Research In Translational Oncology [Bordeaux] (BaRITOn), Université de Bordeaux (UB)-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM), and CCSD, Accord Elsevier
Subjects: [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Subcutaneous, subcutaneously administered, antibiotics, antimicrobials, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; To describe the rationale for subcutaneous (SC) administration of antibiotics from available published data and to make propositions to help clinicians in daily practice. Narrative review. Hospitalized patients, persons in long-term care facilities and ambulatory care. We searched the MEDLINE/PubMed electronic database for evidence supporting SC administration of antibiotics up to September 2019; the results of this primary search were supplemented by searching the references of the identified articles, as well as by searching in Google Scholar. Regarding tolerability, efficacy, and pharmacokinetic/pharmacodynamic profiles, most studies suggest that the SC route could be an alternative to the intravenous route, particularly for time-dependent antibiotics and among certain patient populations, such as patients with poor venous access, swallowing disorders, or behavioral disturbance. However, clinical evidence of the benefits and risks of SC antibiotic administration is still scarce and of low level. SC administration of antibiotics may be useful in various settings such as in hospitalized patients and among those in long-term care facilities or being cared for at home. However, further clinical studies are needed to assess the pharmacokinetic/pharmacodynamic properties, as well as the risks and benefits of SC administration of antibiotics. In this review, we highlight the potential benefits of SC administration of antibiotics and address practical recommendations for its use. This information will enable improvement of treatment strategies and present the SC route as a potential option in specific situations.
Published: 2021
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35. Prolonged-release buprenorphine formulations: Perspectives for clinical practice

Author: Mathieu Chappuy, Benoit Trojak, Philippe Nubukpo, Patrick Bendimerad, Georges Brousse, Benjamin Rolland, Jérôme Bachellier, Service Universitaire d’Addictologie de Lyon [CH Le Vinatier, Bron] (Pôle MOPHA - SUAL), Centre Hospitalier le Vinatier [Bron], Service d'addictologie, Groupement hospitalier Centre, Hospices civils de Lyon, Hospices Civils de Lyon (HCL), Centre de Soins, d'Accompagnement et de Prévention en Addictologie , Groupement hospitalier Nord, Hospices Civils de Lyon, Service de psychiatrie générale et addictologie [CHU de Dijon], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Cognition, Action, et Plasticité Sensorimotrice [Dijon - U1093] (CAPS), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM), Pôle Universitaire d’Addictologie en Limousin, CH Esquirol [Limoges] (CH Esquirol), Neuroépidémiologie Tropicale (NET), CHU Limoges-Institut d'Epidémiologie Neurologique et de Neurologie Tropicale-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), CHRU de Tours, Équipe de Liaison et de Soins en Addictologie, Tours, France, CH La Rochelle, Service de psychiatrie, groupe hospitalier de La Rochelle-Ré-Aunis, Service de Psychiatrie B et d'addictologie [Clermont-Ferrand], CHU Clermont-Ferrand, UFR de Médecine, Université d'Auvergne - Clermont-Ferrand I (UdA), Centre de recherche en neurosciences de Lyon (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CCSD, Accord Elsevier, HCL Groupement Hospitalier Nord [Lyon], Hôpital Bretonneau, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Université Clermont Auvergne (UCA), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: medicine.medical_specialty, Dose, Narcotic Antagonists, [SDV.MHEP.PSM] Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, Receptors, Opioid, mu, 030226 pharmacology & pharmacy, Partial agonist, Opioid dependence, Dependance aux opioides, 03 medical and health sciences, Subcutaneous injection, 0302 clinical medicine, Prolonged release, medicine, Humans, Prolonged-release, Pharmacology (medical), Opiacés, Action prolongee, business.industry, Opioid use disorder, Opioid-Related Disorders, medicine.disease, 3. Good health, Buprenorphine, Analgesics, Opioid, Opiates, Opioid, [SDV.MHEP.PSM]Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, Emergency medicine, business, Substitution, Methadone, medicine.drug
Abstract: International audience; Buprenorphine and methadone are the two main opioid agonist treatments approved for opioid use disorder. Buprenorphine is a partial agonist of the mu opioid receptors, which has been merely available through sublingual form until now. In practice, the use of buprenorphine is smoother than that of methadone, and it induces reduced risks of overdose. However, sublingual buprenorphine also exposes to risks (e.g., withdrawal, misuse) and constraints (e.g., daily intake). Three new galenic formulations of prolonged-release buprenorphine (PRB) are being commercialized and should allow some improvements in patients' comfort and safety. This narrative review aims to describe the main technical features and efficacy and safety data of these PRBs, as well as patients' and professionals' expectancies and concerns, using data of the scientific literature and the regulatory texts. PRBs consist of one subcutaneous implant and two subcutaneous injection depots. Sixmo(R)/Probuphine(R) is a six-month-long implant which needs to be surgically placed and removed and is approved for subjects previously treated with a maximum daily dose of 8mg of sublingual buprenorphine, and can be used only for two successive periods of six months before the subject needs to be switched back to sublingual form. Sublocade(R) is a one-month-long depot formulation that is indicated in switch from sublingual buprenorphine, and which proposes only two dose schemes, i.e., 100 and 300mg monthly. Buvidal(R)/Brixadi(R) is a one-week- or one-month-long depot formulation with multiple dosages, which can be used in initiation or in switched from sublingual formulations. While opioid users report some concerns with a risk of coercive use of long-acting forms of buprenorphine, both users and professionals deem that these new specialties could be particularly appreciated in stabilized patients bothered with the daily intake of the treatments, or specific situations at risk of treatment dropout (e.g., following hospital discharge or prison release).
Published: 2020
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36. Impact of Coexistence Phenotype Between Staphylococcus aureus and Pseudomonas aeruginosa Isolates on Clinical Outcomes Among Cystic Fibrosis Patients

Author: Briaud, Paul, Bastien, Sylvère, Camus, Laura, Boyadjian, Marie, Reix, Philippe, Mainguy, Catherine, Vandenesch, François, DOLEANS-JORDHEIM, Anne, Moreau, Karen, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), association Vaincre la mucoviscidose association Gregory Lemarchal French Ministry of Education and Research Fondation pour la Recherche MedicaleECO20170637499, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and ROSSI, Sabine
Subjects: Microbiology (medical), cystic fibrosis, Staphylococcus aureus, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Infectious Diseases, infectionPseudomonas, Immunology, clinical outcome, Microbiology, aeruginosa, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: International audience; Staphylococcus aureus (SA) is the major colonizer of the lungs of cystic fibrosis (CF) patients during childhood and adolescence. As patients age, the prevalence of SA decreases and Pseudomonas aeruginosa (PA) becomes the major pathogen infecting adult lungs. Nonetheless, SA remains significant and patients harboring both SA and PA are frequently found in the worldwide cohort. The overall impact of co-infection remains controversial. Furthermore, co-infecting isolates may compete or coexist. The aim of this study was to analyse if co-infection and the coexistence of SA and PA could lead to worse clinical outcomes. The clinical and bacteriological data of 212 Lyon CF patients were collected retrospectively, and patients were ranked into three groups, SA only (n = 112), PA only (n = 48) or SA plus PA (n = 52). In addition, SA and PA isolates from co-infected patients were tested in vitro to define their interaction profile. Sixty five percent (n = 34) of SA/PA pairs coexist. Using univariate and multivariate analysis, we confirm that SA patients have a less severe clinical condition than others, and PA induces a poor outcome independently of the presence of SA. Regarding co-infection, no significant difference in clinical outcomes was observed between patients with coexisting pairs and patients with competitive pairs. However, when compared to SA mono-infected patients, patients with coexisting pair presented higher frequency and length of hospitalizations and more exacerbations. We suggest that coexistence between SA and PA may be an important step in the natural history of lung bacterial colonization within CF patients. © Copyright © 2020 Briaud, Bastien, Camus, Boyadjian, Reix, Mainguy, Vandenesch, Doléans-Jordheim and Moreau.
Published: 2020
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37. Assessment of serological techniques for screening patients for COVID-19 (COVID-SER): a prospective, multicentric study

Author: Trouillet-Assant, Sophie, Albert Vega, Chloe, Bal, Antonin, Nazare, Julie Anne, Fascia, Pascal, Paul, Adèle, Massardier-Pilonchery, Amélie, d Aubarede, Constance, Guibert, Nicolas, Pitiot, Virginie, Lahousse, Matthieu, Boibieux, André, Makhloufi, Djamila, Simon, Chantal, Rabilloud, Muriel, Trabaud, Mary Anne, Gueyffier, François, Fassier, Jean-Baptiste, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospices Civils de Lyon (HCL), Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), HCL Groupement Hospitalier Nord [Lyon], Cardiovasculaire, métabolisme, diabétologie et nutrition (CarMeN), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hospices Civils de Lyon (HCL), Hôpital Henry Gabrielle [CHU - HCL], Unité Mixte de Recherche Epidémiologique et de Surveillance Transport Travail Environnement (UMRESTTE UMR_T9405), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Gustave Eiffel, Hôpital Edouard Herriot [CHU - HCL], Université de Lyon, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Hospices Civils de LyonFondation des Hospices Civils de Lyon, COVID-SER study group: Jérôme Adnot, Dulce Alfaiate, Antonin Bal, Alain Bergeret, André Boibieux, Florent Bonnet, Gaëlle Bourgeois, Florence Brunel-Dalmas, Eurydice Caire, Barbara Charbotel, Pierre Chiarello, Laurent Cotte, Constance d'Aubarede, François Durupt, Escuret Vanessa, Fascia Pascal, Fassier Jean-Baptiste, Fontaine Juliette, Gaillot-Durand Lucie, Gaymard Alexandre, Gillet Myriam, Godinot Matthieu, Gueyffier François, Guibert Nicolas, Josset Laurence, Lahousse Matthieu, Lina Bruno, Lozano Hélène, Makhloufi Djamila, Massardier-Pilonchéry Amélie, Milon Marie-Paule, Moll Frédéric, Morfin Florence, Narbey David, Nazare Julie-Anne, Oria Fatima, Paul Adèle, Perry Marielle, Pitiot Virginie, Prudent Mélanie, Rabilloud Muriel, Samperiz Audrey, Schlienger Isabelle, Simon Chantal, Trabaud Mary-Anne, Trouillet-Assant Sophie, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and CarMeN, laboratoire
Subjects: Male, SARS-CoV-2, public health, [SDV]Life Sciences [q-bio], COVID-19, General Medicine, Antibodies, Viral, diagnostic microbiology, [SDV] Life Sciences [q-bio], molecular diagnostics, Humans, Mass Screening, Female, Serologic Tests, Public Health, Prospective Studies, Pandemics
Abstract: International audience; INTRODUCTION: The COVID-19 pandemic caused by SARS-CoV-2 threatens global public health, and there is an urgent public health need to assess acquired immunity to SARS-CoV-2. Serological tests might provide results that can be complementary to or confirm suspected COVID-19 cases and reveal previous infection. The performance of serological assays (sensitivity and specificity) has to be evaluated before their use in the general population. The neutralisation capacity of the produced antibodies also has to be evaluated. METHODS AND ANALYSIS: We set up a prospective, multicentric clinical study to evaluate the performance of serological kits among a population of healthcare workers presenting mild symptoms suggestive of SARS-CoV-2 infection. Four hundred symptomatic healthcare workers will be included in the COVID-SER study. The values obtained from a control cohort included during the prepandemic time will be used as reference. A workflow was set up to study serological response to SARS-CoV-2 infection and to evaluate antibody neutralisation capacity in patients with a confirmed SARS-CoV-2 infection. The sensitivity and specificity of the tests will be assessed using molecular detection of the virus as a reference. The measurement of IgM and IgG antibodies will be performed once per week for 6 consecutive weeks and then at 6, 12, 18, 24 and 36 months after the diagnosis. The kinetics of IgM and IgG will determine the optimal period to perform serological testing. The proportion of false negative PCR tests in symptomatic subjects will be determined on the basis of subsequent seroconversions. ETHICS AND DISSEMINATION: Ethical approval has been obtained from the national review board for biomedical research in April 2020 (Comité de Protection des Personnes Sud Méditerranée I, Marseille, France) (ID RCB 2020-A00932-37). Results will be disseminated through presentations at scientific meetings and publications in peer-reviewed journals. TRIAL REGISTRATION NUMBER: NCT04341142.
Published: 2020
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38. J Am Med Dir Assoc

Author: Tristan Ferry, Virgilio Hernández-Ruiz, Emmanuel Forestier, Sylvain Goutelle, Gaëtan Gavazzi, Claire Roubaud-Baudron, Dominique Breilh, Marc Paccalin, Nicolas Grégoire, GInGer (Groupe Infectio-Gériatrie), Biologie des maladies cardiovasculaires = Biology of Cardiovascular Diseases, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán - National Institute of Medical Science and Nutrition Salvador Zubiran [Mexico], CHU Bordeaux [Bordeaux], Centre Hospitalier Métropole Savoie [Chambéry], Groupe de Recherche et d'Etude du Processus Inflammatoire (GREPI), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), CHU Grenoble, Hospices Civils de Lyon (HCL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Centre hospitalier universitaire de Poitiers (CHU Poitiers), Pharmacologie des anti-infectieux et antibiorésistance (PHAR2), Université de Poitiers-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bordeaux (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), CIC - Poitiers, Université de Poitiers-Centre hospitalier universitaire de Poitiers (CHU Poitiers)-Direction Générale de l'Organisation des Soins (DGOS)-Institut National de la Santé et de la Recherche Médicale (INSERM), HCL Groupement Hospitalier Nord [Lyon], Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Bordeaux Research In Translational Oncology [Bordeaux] (BaRITOn), and Université de Bordeaux (UB)-CHU Bordeaux [Bordeaux]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: medicine.medical_specialty, medicine.drug_class, Injections, Subcutaneous, Antibiotics, subcutaneously administered, MEDLINE, antibiotics, antimicrobials, 03 medical and health sciences, 0302 clinical medicine, Ambulatory care, Antibiotic therapy, medicine, Humans, 030212 general & internal medicine, Risks and benefits, Intensive care medicine, General Nursing, business.industry, Health Policy, Swallowing Disorders, Subcutaneous, General Medicine, 3. Good health, Anti-Bacterial Agents, Tolerability, Pharmaceutical Preparations, Electronic database, Geriatrics and Gerontology, business, 030217 neurology & neurosurgery, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Objectives To describe the rationale for subcutaneous (SC) administration of antibiotics from available published data and to make propositions to help clinicians in daily practice. Design Narrative review. Setting and Participants Hospitalized patients, persons in long-term care facilities and ambulatory care. Methods We searched the MEDLINE/PubMed electronic database for evidence supporting SC administration of antibiotics up to September 2019; the results of this primary search were supplemented by searching the references of the identified articles, as well as by searching in Google Scholar. Results Regarding tolerability, efficacy, and pharmacokinetic/pharmacodynamic profiles, most studies suggest that the SC route could be an alternative to the intravenous route, particularly for time-dependent antibiotics and among certain patient populations, such as patients with poor venous access, swallowing disorders, or behavioral disturbance. However, clinical evidence of the benefits and risks of SC antibiotic administration is still scarce and of low level. Conclusions and Implications SC administration of antibiotics may be useful in various settings such as in hospitalized patients and among those in long-term care facilities or being cared for at home. However, further clinical studies are needed to assess the pharmacokinetic/pharmacodynamic properties, as well as the risks and benefits of SC administration of antibiotics. In this review, we highlight the potential benefits of SC administration of antibiotics and address practical recommendations for its use. This information will enable improvement of treatment strategies and present the SC route as a potential option in specific situations.
Published: 2019
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39. Impact of Pregnancy on Intra-Host Genetic Diversity of Influenza A Viruses in Hospitalised Women: A Retrospective Cohort Study

Author: Gil Dubernard, Maxime Pichon, Vanessa Escuret, Bruno Simon, Laurence Josset, Pascal Gaucherand, Pierre-Adrien Bolze, Grégory Destras, Martine Valette, Bruno Lina, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Hospices Civils de Lyon (HCL), HCL Groupement Hospitalier Nord [Lyon], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hôpital de la Croix-Rousse [CHU - HCL], Groupement Hospitalier Est [Bron], PICHON, Maxime, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: ultra-deep sequencing, Viral pathogenesis, Virulence, Viral quasispecies, 03 medical and health sciences, Immune system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Clinical significance, 030304 developmental biology, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, Genetic diversity, Pregnancy, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 030306 microbiology, business.industry, Brief Report, Retrospective cohort study, General Medicine, quasispecies, medicine.disease, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], viral diversity, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Immunology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, pregnancy, business, influenza
Abstract: International audience; Characterising dynamics of Influenza A Viruses (IAV) within-host evolution is an active field of research which may lead to a better understanding of viral pathogenesis. Using a pregnant mouse model, a study has recently suggested that immune modulation during pregnancy could promote the emergence of IAV quasispecies with increased virulence. Herein, we assess the clinical relevance of these findings in humans. We studied IAV intra-host diversity (ihD) in pregnant (n = 36) and non-pregnant (n = 23) women hospitalized in Lyon for IAV infection (01/2015-05/2018). Whole IAV genomes present in nasopharyngeal samples were sequenced in duplicate to analyze reproducible intra-host single nucleotide variants (ihSNV). Counts, relative frequencies and locations of ihSNV were used as indicators of ihD. The median ihSNV/kb counts per segment were between 0 and 1.3. There was >81% ihSNV at relative frequencies between 1-5% for H1N1 and >51% for H3N2 IAV. No significant difference was noted between pregnant and non-pregnant women when considering all or only non-synonymous ihSNV. Seven convergent non-synonymous ihSNV were found; none were significantly associated with pregnancy. These results suggest that modulation of the immune system during pregnancy in humans does not impact IAV ihD, in contrast to mice.
Published: 2019
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40. Baseline characteristics and clinical symptoms related to respiratory viruses identified among patients presenting with influenza-like illness in primary care

Author: M. Valette, Clément Turbelin, S van der Werf, Sylvie Behillil, Bruno Lina, Lisandru Capai, Cécile Souty, Ana-Maria Vilcu, Shirley Masse, Thierry Blanchon, Alessandra Falchi, Isabelle Bonmarin, Thomas Hanslik, C. Pino, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Laboratoire de Virologie [UNIV Corse-Inserm] (EA7310), Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Service de Médecine Interne [AP-HP Hôpital Ambroise Paré], Hôpital Ambroise Paré [AP-HP], Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), This project has received funding from the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No 634446 to conduct the study in individuals aged 65 years or older and from Santé publique France, the national public health agency in France., European Project: 634446,H2020,H2020-PHC-2014-two-stage,I-MOVE-plus(2015), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pascal Paoli (UPP), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Institut Pasteur [Paris], École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Male, Rhinovirus, viruses, MESH: Respiratory Syncytial Virus, Human, medicine.disease_cause, Logistic regression, [SDV.MHEP.PSR]Life Sciences [q-bio]/Human health and pathology/Pulmonology and respiratory tract, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Nasopharynx, MESH: Metapneumovirus, MESH: Child, Influenza-like illness, 030212 general & internal medicine, Respiratory system, Child, Respiratory Tract Infections, MESH: Orthomyxoviridae, MESH: Aged, Surveillance, MESH: Middle Aged, MESH: Rhinovirus, biology, MESH: Influenza, Human, MESH: Infant, Newborn, Age Factors, virus diseases, General Medicine, Middle Aged, Orthomyxoviridae, Primary care, MESH: Infant, 3. Good health, Infectious Diseases, MESH: Young Adult, Baseline characteristics, Child, Preschool, Female, France, Seasons, Microbiology (medical), Adult, medicine.medical_specialty, Adolescent, 030106 microbiology, Virus, Article, MESH: Primary Health Care, Diagnosis, Differential, 03 medical and health sciences, Young Adult, Human metapneumovirus, MESH: Diagnosis, Differential, Internal medicine, Influenza, Human, medicine, Humans, Aged, MESH: Adolescent, MESH: Age Factors, Respiratory viruses, MESH: Humans, Primary Health Care, business.industry, MESH: Child, Preschool, Infant, Newborn, Infant, Respiratory infections, MESH: Adult, biology.organism_classification, Influenza, MESH: Male, MESH: Nasopharynx, respiratory tract diseases, MESH: France, Respiratory Syncytial Virus, Human, MESH: Respiratory Tract Infections, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Metapneumovirus, business, MESH: Seasons, MESH: Female
Abstract: International audience; Objectives: We aimed to identify patients' clinical characteristics associated with respiratory viruses identified among patients presenting with influenza-like illness (ILI).Methods: A sample of patients of all ages presenting with ILI was included by physicians of the French Sentinelles network during two seasons (2015/16 and 2016/17). Nasopharyngeal samples were tested for the presence of influenza virus (IV), respiratory syncytial virus (RSV), human rhinovirus (HRV) and human metapneumovirus (HMPV). Patients' characteristics associated with each of the four virus classes were studied using multivariate logistic regressions.Results: A total of 5859 individuals were included in the study: 48.0% tested positive for IV, 7.9% for HRV, 7.5% for RSV and 4.1% for HMPV. Cough was associated with IV (OR 2.14, 95% CI 1.81–2.52) RSV (OR 2.52, 95% CI 1.75–3.74) and HMPV detection (OR 2.15, 95% CI 1.40–3.45). Rhinorrhoea was associated mainly with HRV detection (OR 1.75, 95% CI 1.34–2.32). Headache was associated with IV detection (OR 1.75, 95% CI 1.34–2.32), whereas absence of headache was associated with RSV and HMPV detection. Dyspnoea was associated with RSV detection (OR 2.33, 95% CI 1.73–3.12) and absence of dyspnoea with IV detection. Conjunctivitis was associated with IV detection (OR 1.27, 95% CI 1.08–1.50). Some associations were observed only in children: dyspnoea and cough with RSV detection (age
Published: 2019
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41. Whole Genome Sequencing of A(H3N2) Influenza Viruses Reveals Variants Associated with Severity during the 2016–2017 Season

Author: Gwendolyne Burfin, Maxime Pichon, Martine Valette, Bruno Lina, Bruno Simon, Mathilde Richard, Laurence Josset, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), HCL Groupement Hospitalier Nord [Lyon], Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Erasmus University Medical Center [Rotterdam] (Erasmus MC), PICHON, Maxime, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Virology
Subjects: 0301 basic medicine, Male, lcsh:QR1-502, severity, Genome, Severity of Illness Index, lcsh:Microbiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Child, Genetics, Aged, 80 and over, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], High-Throughput Nucleotide Sequencing, virus diseases, Middle Aged, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Vaccination, Hospitalization, Infectious Diseases, Child, Preschool, NGS, Epidemiological Monitoring, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female, epidemiology, France, Seasons, influenza, Adult, Adolescent, 030106 microbiology, Context (language use), Viral quasispecies, Genome, Viral, Biology, DNA sequencing, Article, 03 medical and health sciences, Young Adult, SDG 3 - Good Health and Well-being, Virology, Intensive care, Influenza, Human, Humans, Disease burden, Aged, Retrospective Studies, Whole genome sequencing, Whole Genome Sequencing, Influenza A Virus, H3N2 Subtype, Infant, Newborn, Genetic Variation, Infant, quasispecies, vaccination, 030104 developmental biology, Amino Acid Substitution, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: International audience; Influenza viruses cause a remarkable disease burden and significant morbidity and mortality worldwide, and these impacts vary between seasons. To understand the mechanisms associated with these differences, a comprehensive approach is needed to characterize the impact of influenza genomic traits on the burden of disease. During 2016-2017, a year with severe A(H3N2), we sequenced 176 A(H3N2) influenza genomes using next generation sequencing (NGS) for routine surveillance of circulating influenza viruses collected via the French national influenza community-based surveillance network or from patients hospitalized in the intensive care units of the University Hospitals of Lyon, France. Taking into account confounding factors, sequencing and clinical data were used to identify genomic variants and quasispecies associated with influenza severity or vaccine failure. Several amino acid substitutions significantly associated with clinical traits were found, including NA V263I and NS1 K196E which were associated with severity and co-occurred only in viruses from the 3c.2a1 clade. Additionally, we observed that intra-host diversity as a whole and on a specific set of gene segments increased with severity. These results support the use of whole genome sequencing as a tool for the identification of genetic traits associated with severe influenza in the context of influenza surveillance.
Published: 2019
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42. Emergence of enterovirus D68 clade D1, France, August to November 2018

Author: Laurence Josset, Antonin Bal, Karen Brengel-Pesce, Thierry Wirth, Karl Stefic, F. Morfin, Marianne Coste-Burel, Bruno Lina, Mouna Lazrek, Marina Sabatier, Isabelle Schuffenecker, Centre National de Référence des Entérovirus, Hospices Civils de Lyon (HCL), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), BIOMERIEUX, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Service de virologie [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes), Service de Virologie [Lille], Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), Service de bactériologie-virologie [Tours], Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Hôpital Bretonneau, Morphogénèse et antigénicité du VIH et du virus des Hépatites (MAVIVH - U1259 Inserm - CHRU Tours ), Centre Hospitalier Régional Universitaire de Tours (CHRU Tours)-Université de Tours (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Hôpital Bretonneau-Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), and Université de Tours-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Tours (CHRU TOURS)
Subjects: 0301 basic medicine, Male, Epidemiology, Genetic analysis, Communicable Diseases, Emerging, Disease Outbreaks, respiratory infection, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genotype, Clade, Child, Respiratory Tract Infections, Phylogeny, Aged, 80 and over, Enterovirus D, Human, whole genome sequencing, Respiratory infection, Middle Aged, 3. Good health, Child, Preschool, Population Surveillance, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, France, Rapid Communication, Adult, medicine.medical_specialty, Adolescent, 030106 microbiology, Biology, 03 medical and health sciences, Young Adult, Virology, medicine, Enterovirus Infections, Humans, emergence, Aged, metagenomics, outbreak, Public Health, Environmental and Occupational Health, Outbreak, Infant, enterovirus D68, Sequence Analysis, DNA, Genetic divergence, Molecular Typing, 030104 developmental biology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Enterovirus D68
Abstract: International audience; We report a seasonal increase of enterovirus D68 (EV-D68) cases in France, with 54 cases detected between 19 August and 14 November 2018. Molecular typing revealed that 20 of 32 of the isolates belonged to clade D1, only sporadically detected before in France. Median age of D1-cases was 42 years, 10 developed severe respiratory signs and one had neurological complications. The 2018-D1 viruses showed a genetic divergence of 3.34 % with D1 viruses identified previously.
Published: 2019
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43. Which sample for the transport of mycoplasma, eSwab® or dry swab?

Author: Pichon, Maxime, Gebeile, Rémi, Lina, Bruno, Jacquet, Géraldine, Gaymard, Alexandre, PICHON, Maxime, Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Centre de Biologie et Pathologie Nord [Hôpital de la Croix-Rousse, CHU-HCL], HCL Groupement Hospitalier Nord [Lyon], and DYNABIO
Subjects: sampling, eSwab®, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, mycoplasma, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, dry swabs
Abstract: International audience; Mycoplasma hominis (MH) and Ureaplasma urealyticum (UU), belonging to mycoplasmas, are implicated in genital and urinary infections. These bacteria are extremely sensitive to environmental factors but remain detectable by culture methods. This study aimed to compare performance of detection on samples performed on eSwab® or dry swabs. Eighty-five genital samples were prospectively collected on dry- and e-Swab, at the Dynabio Croix-Rousse laboratory (Lyon, France), from January to March 2017, searching for mycoplasma infection. After incubation for 48 hours, cultures were qualitatively and quantitatively analyzed by a single qualified operator. On these samples, 23 specimens sampled on dry swabs were positive for UU and 2 for MH (versus 26 and 4 for eSwab). Quantification on eSwab® and dry swabs were statistically correlated (r=0.9118; and r=0.7155; p< 0.01 respectively) without discrepant results. No sample was double-positive during this study. With an important sensitivity (without alteration of the bacterial quantification) and regarding to the gravity of this infection on at-risk patients, as young and/or pregnant woman, the eSwab® sampling seem to improve the pre-analytic phase. However, the benefice to use these sampling methods for long-term conservations has to be evaluated.
Published: 2019
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44. Vaccin grippal quadrivalent : quels changements pour quels bénéfices ?

Author: Gaëtan Gavazzi, Claude Hannoun, Catherine Weil-Olivier, Odile Launay, Jacques Gaillat, Luc Martinez, Anne Mosnier, Laurence Josset, Pascal Crépey, Réseau des Groupes Régionaux d'Observation de la Grippe (GROG), Coordination nationale, CIC Cochin Pasteur (CIC 1417), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu-Université Paris Descartes - Paris 5 (UPD5)-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire [Grenoble] (CHU), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], École des Hautes Études en Santé Publique [EHESP] (EHESP), Recherche en Pharmaco-épidémiologie et Recours aux Soins (REPERES), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP), Université Paris Diderot - Paris 7 (UPD7), Centre Hospitalier Annecy-Genevois [Saint-Julien-en-Genevois], Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP), and Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Cochin [AP-HP]-Hôtel-Dieu-Université Paris Descartes - Paris 5 (UPD5)-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: business.industry, Lineage (evolution), General Medicine, Virus diseases, Vaccine efficacy, medicine.disease_cause, Virology, Vaccin grippal quadrivalent, Virus, 3. Good health, Vaccin anti grippal, 03 medical and health sciences, 0302 clinical medicine, Vaccine strain, Antigen, Immunization, 030225 pediatrics, Influenza A virus, Medicine, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 030212 general & internal medicine, business
Abstract: International audience; Currently, circulating viruses responsible for annual seasonal influenza epidemics belong to two influenza A subtypes, A(H1N1) and A(H3N2), and to two antigenically distinct type B lineages, B/Yamagata and B/Victoria lineages. Like diseases due to influenza A virus, influenza B virus diseases may have severe consequences and should be prevented. Until now, in France, the vaccines used to prevent seasonal influenza were trivalent, systematically targeting viruses belonging to both A subtypes and to one or other of the B lineages. The protective efficacy of trivalent vaccines is diminished during the seasons when viruses belonging to both B lineages cocirculated or when the circulating dominant type B virus belonged to a lineage different from that targeted by the vaccine strain. By targeting viruses belonging to both B lineages, quadrivalent vaccines improve the antigenic concordance between circulating and vaccine type B strains. Three inactivated quadrivalent vaccines are authorized for marketing in France and should be available for the 2018-2019 season. It is expected that, by providing enlarged protection, these quadrivalent influenza vaccines will improve vaccine efficacy, the confidence in immunization of the public, the satisfaction of health professionals, and ultimately will help to complete immunization coverage.
Published: 2018
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45. Impact of the Respiratory Microbiome on Host Responses to Respiratory Viral Infection

Author: Bruno Lina, Laurence Josset, Maxime Pichon, Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Davoine, Laure-Hélène
Subjects: 0301 basic medicine, 16S, [SDV.IMM] Life Sciences [q-bio]/Immunology, Viral pathogenesis, viral infections, Immunology, lcsh:Medicine, Disease, Review, Biology, 03 medical and health sciences, 0302 clinical medicine, Immune system, respiratory microbiome, Drug Discovery, medicine, Pharmacology (medical), Microbiome, Pathogen, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Pharmacology, whole genome sequencing, Gastrointestinal Microbiome, lcsh:R, respiratory tract, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Biomarker (cell), 030104 developmental biology, Infectious Diseases, medicine.anatomical_structure, 030228 respiratory system, NGS, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Respiratory tract
Abstract: International audience; Viruses are responsible for most of both upper and lower acute respiratory infections (ARIs). The microbiome-the ecological community of microorganisms sharing the body space, which has gained considerable interest over the last decade-is modified in health and disease states. Even if most of these disturbances have been previously described in relation to chronic disorders of the gastrointestinal microbiome, after a short reminder of microbiome characteristics and methods of characterization, this review will describe the impact of the microbiome (mainly respiratory) on host responses to viral ARIs. The microbiome has a direct environmental impact on the host cells but also an indirect impact on the immune system, by enhancing innate or adaptive immune responses. In microbial infections, especially in viral infections, these dramatic modifications could lead to a dramatic impact responsible for severe clinical outcomes. Studies focusing on the microbiome associated with transcriptomic analyses of the host response and deep characterization of the pathogen would lead to a better understanding of viral pathogenesis and open avenues for biomarker development and innovative therapeutics.
Published: 2017
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46. A European multi-centre External Quality Assessment (EQA) study on phenotypic and genotypic methods used for Herpes Simplex Virus (HSV) drug resistance testing

Author: David Boutolleau, Graciela Andrei, Natasha Ohemeng-Kumi, Renata Piorkowska, Sonia Burrel, David F. Bibby, Jean L. Mbisa, Brendan Crowley, Robert Snoeck, Baharak Afshar, Florence Morfin, Emilie Frobert, Sarah Gillemot, Public Health England [London], European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Control, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie et des Maladies Infectieuses (CIMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), St James’s Hospital [Dublin, Ireland], Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Centre d'Immunologie et de Maladies Infectieuses (CIMI)
Subjects: 0301 basic medicine, Adult, Male, Genotyping Techniques, 030106 microbiology, Population, Drug Resistance, HSL and HSV, Drug resistance, Microbial Sensitivity Tests, medicine.disease_cause, Virus genotyping, Antiviral Agents, 03 medical and health sciences, Young Adult, Phenotypic methods, Virology, External quality assessment, Genotype, Drug Resistance, Viral, medicine, Humans, Simplexvirus, Viral, education, Child, Herpes Simplex Virus (HSV), education.field_of_study, business.industry, Drug resistance testing, Assay sensitivity, Gold standard (test), [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Europe, 030104 developmental biology, Infectious Diseases, Herpes simplex virus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, External Quality Assessment, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, business
Abstract: International audience; BACKGROUND: Herpes Simplex Virus (HSV) drug resistance is a significant public health concern among immunocompromised individuals. Phenotypic assays are considered the gold standard method for detecting HSV drug resistance. However, plaque reduction assays (PRAs) are technically demanding, often with long turnaround times of up to four weeks. In contrast, genotypic tests can be performed within a few days. OBJECTIVES: The development and coordination of the first European External Quality Assessment (EQA) study to evaluate phenotypic and genotypic methods used for HSV drug resistance testing in specialised reference laboratories. STUDY DESIGN: Four HSV-1 or HSV-2 strains with different antiviral susceptibility profiles were isolated from clinical samples. Isolates were quantified by qPCR, and aliquoted in culture medium. One isolate was distributed at two dilutions to help assess assay sensitivity. The panel was distributed to five European centres with a six-week deadline for the return of phenotypic and genotypic results, together with clinical reports. RESULTS: Four out of five participating labs returned results by the deadline. Limited results were later available from the fifth lab. Phenotypic and genotypic data were largely, but not completely, concordant. An unusual resistance profile shown by one of the samples was explained by the detection of a mixed virus population after extensive further investigation by one of the centres. CONCLUSIONS: Discordant clinical outputs reflecting the diversity of phenotypic methodologies demonstrated the utility of this exercise. With emerging genotypic technologies looking to supplant phenotyping, there is a need for curated public databases, accessible interpretation tools and standardised control materials for quality management. By establishing a network of testing laboratories, we hope that this EQA scheme will facilitate ongoing progress in this area.
Published: 2017
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47. Decontamination of Intravaginal Probes Infected by Human Papillomavirus (HPV) Using UV-C Decontamination System

Author: Yahia Mekki, Bruno Lina, K Lebail-Carval, Maxime Pichon, Geneviève Billaud, Pascal Gaucherand, Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), HCL Groupement Hospitalier Nord [Lyon], and PICHON, Maxime
Subjects: HPV, Human dna, Genital cancer, lcsh:Medicine, 030501 epidemiology, Hpv detection, Article, 03 medical and health sciences, ultraviolet disinfection, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, genital cancer, Medicine, 030212 general & internal medicine, Human papillomavirus, disinfection, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Chromatography, business.industry, lcsh:R, General Medicine, Human decontamination, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Transvaginal ultrasound, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, intravaginal ultrasound, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, 0305 other medical science, business
Abstract: Background: This three-step study evaluated ultraviolet-C (UV-C) efficacy against human papillomavirus (HPV) found on vaginal ultrasound probes. Methods: The first two steps evaluated UV-C disinfection of vaginal ultrasound probes in routine condition. During the first phase, the probe (n = 100) was sampled after a complete cleaning and disinfection protocol, i.e., cleaning with chemically impregnated wipes, followed by UV-C. During the second phase, the probe (n = 47) was sampled after cleaning and UV-C. The final step consisted of applying mixes of HPV on a dedicated, covered probe (n = 15) then sampling the cover, the probe after removal of the cover, after cleaning, and after UV-C. HPV detection was performed using CLART&reg, HPV2 PCR (Genomica, Madrid, Spain). Results: In the first phase, no probes were found to be positive for both DNA after UV-C. In the second phase, eight probes were found to be positive after cleaning (seven with human DNA and one with HPV) and negative after UV-C. In the final phase, one probe was found to be positive for HPV for each sample except after UV-C. Conclusions: Covers followed by a chemically impregnated wipe are not sufficient to ensure patient safety during vaginal ultrasound examinations. UV-C is effective in routine conditions against contaminations found on vaginal ultrasound probes, especially HPV.
Published: 2019
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48. Impact on antiviral resistance of E119V, I222L and R292K substitutions in influenza A viruses bearing a group 2 neuraminidase (N2, N3, N6, N7 and N9)

Author: Jean-Sébastien Casalegno, Manuel Rosa-Calatrava, Bruno Lina, Alexandre Gaymard, Olivier Ferraris, Caroline Picard, M. Valette, Aymeric Charles-Dufant, M. Sabatier, Vanessa Escuret, Jean-Claude Cortay, Michèle Ottmann, Emilie Frobert, Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), Oseltamivir, viruses, 030106 microbiology, Mutation, Missense, Drug Resistance, Neuraminidase, medicine.disease_cause, Antiviral Agents, Virus, 03 medical and health sciences, chemistry.chemical_compound, Zanamivir, Reassortant Viruses, Drug Resistance, Viral, Influenza A virus, medicine, Humans, Pharmacology (medical), Viral, Pharmacology, biology, Laninamivir, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Reverse genetics, Reverse Genetics, 3. Good health, Infectious Diseases, chemistry, Mutation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, [SDV.IMM]Life Sciences [q-bio]/Immunology, Missense, medicine.drug
Abstract: International audience; OBJECTIVES: While subtype-specific substitutions linked to neuraminidase (NA) inhibitor resistance are well described in human N1 and N2 influenza NAs, little is known about other NA subtypes. The aim of this study was to determine whether the R292K and E119V?\textpm?I222L substitutions could be associated with oseltamivir resistance in all group 2 NAs and had an impact on virus fitness. METHODS: Reassortant viruses with WT NA or variant N2, N3, N6, N7 or N9 NAs, bearing R292K or E119V?\textpm?I222L substitutions, were produced by reverse genetics. The antiviral susceptibility, activity, Km of the NA, mutation stability and in vitro virus fitness in MDCK cells were determined. RESULTS: NA activities could be ranked as follows regardless of the substitution: N3?>=?N6?\textgreater?N2?>=?N9?\textgreater?N7. Using NA inhibitor resistance interpretation criteria used for human N1 or N2, the NA-R292K substitution conferred highly reduced inhibition by oseltamivir and the N6- or N9-R292K substitution conferred reduced inhibition by zanamivir and laninamivir. Viruses with the N3- or N6-E119V substitution showed normal inhibition by oseltamivir, while those with the N2-, N7- or N9-E119V substitution showed reduced inhibition by oseltamivir. Viruses with NA-E119V?+?I222L substitutions showed reduced inhibition (N3 and N6) or highly reduced inhibition (N2, N7 and N9) by oseltamivir. Viruses bearing the NA-R292K substitution had lower affinity and viruses bearing the NA-E119V substitution had higher affinity for the MUNANA substrate than viruses with corresponding WT NA. CONCLUSIONS: NA-R292K and E119V?+?I222L substitutions conferred reduced inhibition by oseltamivir for all group 2 NAs. Surveillance of NA inhibitor resistance for zoonotic and human influenza viruses and the development of novel antiviral agents with different targets should be continued.
Published: 2016
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49. Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains

Author: Patrice Morand, Alban Caporossi, P. Trémeaux, Patrice Andre, E. Santoni, M.-A. Thélu, Sylvie Larrat, Katia Fusillier, Wim P. Burmeister, Nicolas Tarbouriech, Olivier François, C. Ramière, Vincent Leroy, L. Geneletti, Institut de Biologie et Pathologie [CHU Grenoble] (IBP), CHU Grenoble-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie Computationnelle et Mathématique (TIMC-IMAG-BCM), Techniques de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble - UMR 5525 (TIMC-IMAG), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre d'Investigation Clinique [Grenoble] (CIC Grenoble ), CHU Grenoble-Hôpital Michallon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Virologie [HCL, Lyon] (Institut des Agents Infectieux), Hospices civils de Lyon (HCL)-HCL Groupement Hospitalier Nord [Lyon]-Centre National de Reference des virus des Infections Respiratoires France Sud [HCL, Lyon], Service d'hépato-gastroentérologie, CHU Grenoble, Laboratoire de Virologie, Hospices Civils de Lyon (HCL), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-CHU Grenoble
Subjects: 0301 basic medicine, Microbiology (medical), Daclatasvir, Pyrrolidines, Sofosbuvir, Genotype, Genotyping Techniques, Hepatitis C virus, 030106 microbiology, Mutation, Missense, Hepacivirus, Biology, medicine.disease_cause, Recombinant virus, Antiviral Agents, 03 medical and health sciences, chemistry.chemical_compound, Drug Resistance, Viral, medicine, Humans, NS5A, Genotyping, NS5B, Genetics, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Imidazoles, Valine, General Medicine, Sequence Analysis, DNA, Hepatitis C, Chronic, Virology, 3. Good health, 030104 developmental biology, Infectious Diseases, chemistry, RNA, Viral, Carbamates, Nucleic Acid Amplification Techniques, medicine.drug
Abstract: International audience; Directly acting antivirals have contributed considerable progress to hepatitis C treatment, but they show variable activity depending on viral genotypes and subtypes. Therefore, accurate genotyping including recombinant form detection is still of major importance, as is the detection of resistance-associated mutations in case of therapeutic failure. To meet these goals, an approach to amplify the hepatitis C virus (HCV) near-complete genome with a single long-range PCR and sequence it with Roche GS Junior was developed. After optimization, the overall amplification success rate was 73% for usual genotypes (i.e. HCV1a, 1b, 3a and 4a, n = 16 of 22) and 45% for recombinant forms RF_2k/1b (n = 5 of 11). After pyrosequencing and subsequent de novo assembly, a near-full-length genomic consensus sequence was obtained for 19 of 21 samples. The genotype and subtype were confirmed by phylogenetic analysis for every sample, including the suspected recombinant forms. Resistance-associated mutations were detected in 7 of 13 samples at baseline, in the NS3 (n = 3) or NS5A region (n = 4). Of these samples, the treatment of one patient included daclatasvir and that patient experienced a relapse. Viral sequences from pre- and post-treatment samples of four patients who relapsed after sofosbuvir-based therapy were compared: the selected variants seem too far from the NS5B catalytic site to be held responsible. Although tested on a limited set of samples and with technical improvements still necessary, this assay has proved to be successful for both genotyping and resistance-associated variant detection on several HCV types.
Published: 2015
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50. Invasive aspergillosis in patients with hematological malignancies: incidence and description of 127 cases enrolled in a single institution prospective survey from 2004 to 2009

Author: Frank-Emmanuel Nicolini, Mauricette Michallet, Philippe Vanhems, Anne-Lise Bienvenu, Frédérique de Monbrison, Anne C. M. Thiébaut, Marie-Christine Nicolle, Mohamad Sobh, Stéphane Picot, Antoine Duclos, Marie-Antoinette Piens, Xavier Thomas, Giovanna Cannas, Nicolas Voirin, Thomas Bénet, Hôpital Edouard Herriot [CHU - HCL], Hospices Civils de Lyon (HCL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), HCL Groupement Hospitalier Nord [Lyon], Service d'Hygiène, Epidémiologie et Prévention [Hôpital Edouard Herriot - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Santé Individu Société (SIS), Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Hospices Civils de Lyon (HCL)-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Evaluation et modélisation des effets thérapeutiques, Département biostatistiques et modélisation pour la santé et l'environnement [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Delmotte, Stéphane, and Santé Individu Société - SIS (SIS)
Subjects: [SDV.MHEP.HEM] Life Sciences [q-bio]/Human health and pathology/Hematology, Adult, Male, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], medicine.medical_specialty, Antigens, Fungal, hematologic disease, Aspergillosis, Severity of Illness Index, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Internal medicine, Severity of illness, medicine, Humans, Prospective Studies, hospital, Prospective cohort study, Original Research, invasive aspergillosis, business.industry, Incidence (epidemiology), Data Collection, Cancer, [SDV.MHEP.HEM]Life Sciences [q-bio]/Human health and pathology/Hematology, Hematology, Middle Aged, medicine.disease, Confidence interval, Surgery, Clinical trial, Radiography, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Hematologic Neoplasms, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, surveillance, incidence, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Infection Control Practitioners
Abstract: Background: The study objectives were: 1) to report on invasive aspergillosis patients in a hematology department; and 2) to estimate its incidence according to the hematologic diagnosis.Design and methods: A prospective survey of invasive aspergillosis cases was undertaken between January 2004 and December 2009 in the hematology department of a university hospital. Meetings with clinicians, mycologists and infection control practitioners were organized monthly to confirm suspected aspergillosis cases. Demographic characteristics, clinical and complementary examination results were recorded prospectively. Information on hospitalization was extracted from administrative databases. Invasive aspergillosis diagnosis followed the European Organization for Research and Treatment of Cancer criteria, and proven and probable IA cases were retained. A descriptive analysis was conducted with temporal trends of invasive aspergillosis incidence assessed by adjusted Poisson regression.Results: Overall, 4,073 hospitalized patients (78,360 patient-days) were included in the study. In total, 127 (3.1%) patients presented invasive aspergillosis. The overall incidence was 1.6 per 1,000 patient-days (95% confidence interval: 1.4, 1.9) with a decrease of 16% per year (-1%, -28%). The incidence was 1.9 per 1,000 patient-days (1.5, 2.3) in acute myeloid leukemia patients with a decrease of 20% per year (-6%, -36%). Serum Aspergillus antigen was detected in 89 (71%) patients; 29 (23%) had positive cultures, and 118 (93%), abnormal lung CT scans. One-month mortality was 13%; 3-month mortality was 42%. Mortality tended to decrease between 2004 and 2009.Conclusions: Invasive aspergillosis incidence and mortality declined between 2004 and 2009. Knowledge of invasive aspergillosis characteristics and its clinical course should help to improve the management of these patients with severe disease.
Published: 2011
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