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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. 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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4. 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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5. 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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6. 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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7. 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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8. 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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9. 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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10. 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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11. 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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12. 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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13. 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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14. 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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15. 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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16. 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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17. 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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18. 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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19. 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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20. 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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20 results on '"HCL Groupement Hospitalier Nord [Lyon]"'

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19. 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)

20. Amplification and pyrosequencing of near-full-length hepatitis C virus for typing and monitoring antiviral resistant strains

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