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1. Quantitative Polymerase Chain Reaction from Malaria Rapid Diagnostic Tests to Detect Borrelia crocidurae, the Agent of Tick-Borne Relapsing Fever, in Febrile Patients in Senegal

Author

El Hadji Ibrahima, Ndiaye, Diatta, Georges, Adama Zan, Diarra, Bassene, Hubert, Sokhna, Cheikh, Parola, Philippe, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Maladies infectieuses persistantes et émergentes en Afrique de l’Ouest [Dakar, Sénégal] (Equipe 3 - VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Parasitology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

In endemic malaria areas, Plasmodium is currently diagnosed mainly through the use of rapid diagnostic tests (RDTs). However, in Senegal, many causes of fever remain unknown. Tick-borne relapsing fever, an often-neglected public health problem, is the main cause of consultation for acute febrile illness after malaria and flu in rural areas. Our objective was to test the feasibility of extracting and amplifying DNA fragments by quantitative polymerase chain reaction (qPCR) from malaria-negative RDTs for Plasmodium falciparum (malaria Neg RDTs P.f) to detect Borrelia spp. and other bacteria. Between January and December 2019, malaria Neg RDTs P.f were collected on a quarterly basis in 12 health facilities in four regions of Senegal. The DNA extracted from the malaria Neg RDTs P.f was tested using qPCR and the results were confirmed by standard PCR and sequencing. Only Borrelia crocidurae DNA was detected in 7.22% (159/2,202) of RDTs. The prevalence of B. crocidurae DNA was higher in July (16.47%, 43/261) and August (11.21%, 50/446). The annual prevalence was 9.2% (47/512) and 5.0% (12/241) in Ngayokhem and Nema-Nding, respectively, health facilities in the Fatick region. Our study confirms that B. crocidurae infection is a frequent cause of fever in Senegal, with a high prevalence of cases in health facilities in the regions of Fatick and Kaffrine. Malaria Neg RDTs P.f are potentially a good source of pathogen sampling for the molecular identification of other causes of fever of unknown origin, even in the most remote areas.

Published
2023

2. Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis

Author

Magdy Wasfy, Reham, Zoaiter, Malak, Bilen, Melhem, Tidjani Alou, Maryam, Lo, Cheikh Ibrahima, Bellali, Sara, Caputo, Aurelia, Alibar, Stéphane, Andrieu, Claudia, Raoult, Didier, Fournier, Pierre Edouard, Million, Matthieu, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Biology, Microbiology
Abstract

International audience

Published
2023

3. In vitro maintenance of the endosymbiont Wolbachia of Dirofilaria immitis

Author

Manoj, Ranju Ravindran Santhakumari, Latrofa, Maria Stefania, Louni, Meriem, Laidoudi, Younes, Fenollar, Florence, Otranto, Domenico, Mediannikov, Oleg, Department of Veterinary Medicine, University of Bari, Valenzano, Bari, Italy, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Medicina Veterinaria, Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Polytechnic University of Bari, and Bu-Ali Sina University

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, General Veterinary, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Insect Science, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Parasitology, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience

Published
2023

4. Bartonella quintana Transmitted by Head Lice: An Outbreak of Trench Fever in Senegal

Author

Alissa Hammoud, Meriem Louni, Florence Fenollar, Hubert Bassene, Masse Sambou, Nathalie Duclos, Georges Diatta, Cheikh Sokhna, Anthony Levasseur, Didier Raoult, Oleg Mediannikov, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
Microbiology (medical), Infectious Diseases, [SDV]Life Sciences [q-bio]
Abstract

Background Louse-borne trench fever caused by Bartonella quintana is a neglected public health concern, known to be transmitted from body louse feces via scratching. No viable B. quintana have ever been isolated from head lice before; therefore, their role as a vector is still poorly understood. Methods In Senegal, the implementation of a permanent local surveillance system in a point-of-care laboratory (POC) allows the monitoring of emerging diseases. Here we used culture as well as molecular and genomic approaches to document an outbreak of trench fever associated with head lice in the village of Ndiop. Head lice and blood samples were collected from febrile patients between November 2010 and April 2015. Genomes of 2 isolated strains of B. quintana were sequenced and analyzed. Results A total of 2289 blood samples were collected in the 2010–2015 period. From 2010–2013, B. quintana DNA was detected by polymerase chain reaction (PCR) in 0.25% (4/1580). In 2014, 228 blood samples were collected, along with 161 head lice from 5 individuals. B. quintana DNA was detected in 4.4% (10/228) of blood samples, and in lice specimens collected from febrile patients (61.7%, 50/81) and non-febrile patients (61.4%, 43/70). Two B. quintana strains were isolated from blood and head lice from 2 different patients. Genomic sequence analysis showed 99.98% overall similarity between both strains. Conclusions The presence of live B. quintana in head lice, and the genetic identity of strains from patients’ blood and head lice during a localized outbreak in Senegal, supports the evidence of head lice vectorial capacity.

Published
2022

5. Analysis of trapped mosquito excreta as a noninvasive method to reveal biodiversity and arbovirus circulation

Author

Grégory L'Ambert, Mathieu Gendrot, Sébastien Briolant, Agnès Nguyen, Sylvain Pages, Laurent Bosio, Vincent Palomo, Nicolas Gomez, Nicolas Benoit, Hélène Savini, Bruno Pradines, Guillaume André Durand, Isabelle Leparc‐Goffart, Gilda Grard, Albin Fontaine, Entente Interdépartementale pour la démoustication du littoral méditerranéen (EID), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Biofidal, Université Montpellier 1 (UM1), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Unité des Virus Emergents (UVE), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Culicidae, Flavivirus, [SDV]Life Sciences [q-bio], Genetics, Animals, Humans, Biodiversity, West Nile virus, Arboviruses, Ecology, Evolution, Behavior and Systematics, Biotechnology
Abstract

Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Some of these pathogens circulate into complex cryptic cycles involving several animal species as reservoir or amplifying hosts. Detection of cases in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or nonendemic areas. We identified West Nile virus circulation in Camargue, a wetland area in South of France, using a cost-effective xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito species community on several sampling sites, together with the vertebrate hosts on which they fed prior to being captured using amplicon-based metabarcoding on mosquito excreta without processing any mosquitoes. Mosquito excreta-based virus surveillance can complement standard surveillance methods because it is cost-effective and does not require personnel with a strong background in entomology. This strategy can also be used to noninvasively explore the ecological network underlying arbovirus circulation.

Published
2022

6. Seaweed extracts as promising biostimulants for enhancing lead tolerance and accumulation in tomato (Solanum lycopersicum)

Author

Oumaima El Khattabi, Said El Hasnaoui, Maria Toura, Fatima Henkrar, Blanche Collin, Clement Levard, Fabrice Colin, Nawal Merghoub, Abdelaziz Smouni, Mouna Fahr, Université Mohammed V de Rabat [Agdal] (UM5), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme de géochimie isotopique ASTER-CEREGE, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Aqueous extract, Phaeophyceae, Antioxidant activity, Heavy metals, Chlorophyceae, [SDE]Environmental Sciences, Plant, Plant Science, Aquatic Science, Phytoremediation
Abstract

Aqueous seaweed extracts are a biological product which have beneficial effects on plant growth as well as improving their resistance to several biotic and abiotic stresses. This work aimed to evaluate the effect of aqueous extracts of three seaweeds Fucus spiralis, Cystoseira ericoides (Phaeophyceae) and Ulva lactuca (Chlorophyceae) harvested from Atlantic coast of Rabat region in Morocco, on lead (Pb) tolerance and accumulation in tomato (Solanum lycopersicum) plants. Aqueous extracts were obtained by the combination of 2 extraction processes, ultrasonication and heating. The brown seaweeds F. spiralis and C. ericoides extracts had good antioxidant activity in the DPPH assay. The growth and physiological parameters were compared between Solanum lycopersicum seedlings grown in hydroponic conditions at 0 and 100 μmol Pb with or without 4% seaweed extract. The F. spiralis and C. ericoides extracts significantly increased the aboveground parts and roots biomass compared to control plants treated with Pb alone. In Pb stress conditions, these seaweed extracts enhanced the plant’s tolerance with a reduction of anthocyanin and proline content. F. spiralis extract treatment led to a significant Pb accumulation in aboveground parts of the plant. The effect of U. lactuca extract on tomato plants biomass, anthocyanin and proline was not significant. The study demonstrated that the aqueous extracts of F. spiralis and C. ericoides improved the plant response to heavy metals stress, highlighting the potential use of these seaweeds in phytoremediation processes.

Published
2022

7. Attitude toward a COVID-19 vaccine in France. Different factors according to age (COVID-19 vaccine: The French population’s attitude)

Author

Alleaume, Caroline, Peretti-Watel, Patrick, Verger, Pierre, Launay, Odile, Grp, Coconel, Raude, Jocelyn, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), CIC Cochin Pasteur (CIC 1417), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôtel-Dieu-Groupe hospitalier Broca-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), The COCONEL Group, École des Hautes Études en Santé Publique [EHESP] (EHESP), Centre de recherche en économie et management (CREM), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Sud - Paris 11 (UP11)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Groupe d'Etude des Méthodes de l'Analyse Sociologique de la Sorbonne (GEMASS), Fondation Maison des sciences de l'homme (FMSH)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Fondation Maison des sciences de l'homme (FMSH)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)- Southeastern Health Regional Observatory (ORS Paca)-Inserm CIC 1417, Université Paris, Faculté de Médecine Paris Descartes, AP-HP, Hôpital Cochin, and Département des sciences humaines et sociales (SHS)

Subjects
Health (social science), Vaccination, Enquête COCONEL, Covid 19, Refus, Elderly, Attitude, Enquêtes de cohorte, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, France, Population âgée, Geriatrics and Gerontology, COCONEL cohort surveys, Gerontology
Abstract

International audience; Like in many countries, the French health authorities are pinning their hopes on vaccination to stop the spread of the COVID-19 pandemic. However, this requires the public to get the vaccine. Based on six COCONEL surveys carried out during and after the lockdown among the general French adult population, which aimed to explore life conditions during this period and individual perceptions of the situation, this paper aims to investigate the acceptability of a putative vaccine against COVID-19 among the French population, and more specifically to compare attitudes among the elderly, who are more vulnerable to the disease, with those of younger people. Out of the 8,036 respondents, 27.5% declared that they would refuse the vaccine if it were available. Among the age groups of particular interest, 29.2% of people aged 18–64 said they would refuse the vaccine, compared to 12.4% of respondents aged 65 or over. For both groups, this refusal rate fluctuated depending on the date of the survey, gender, household composition, level of household income, and uptake of the last flu vaccine. In conclusion, more attention should be paid to elderly people, as they were more likely to report hostility toward vaccination in general. Finally, considering that several vaccines are now available, further studies should be done to study vaccine uptake in relation to the vaccine offered.; La campagne vaccinale contre la COVID-19 est une priorité sanitaire. Toutefois, l’adhésion de la population française à cette vaccination est un élément clé de sa réussite. À la lumière de six enquêtes COCONEL réalisées en population générale adulte pendant et après le confinement dans l’objectif de documenter les conditions de vie des Français pendant cette période ainsi que leur perception des mesures mises en place par les autorités, cet article propose d’analyser l’intention de se faire vacciner des Français à l’égard d’une vaccination contre la COVID-19, selon l’âge. Plus spécifiquement, l’intention des personnes âgées de 65 ans et plus, particulièrement vulnérables face à cette maladie, comparativement aux personnes plus jeunes. Parmi les 8 036 répondants, 27,5 % refuseraient ce vaccin s’il était disponible ; 29,2 % des 18-64 ans contre 12,4 % des 65 ans et plus. Quel que soit l’âge, ce refus de vaccination varie selon la date d’enquête, mais aussi selon le genre, la composition du foyer, le niveau de revenus, ainsi que la pratique vaccinale antérieure contre la grippe saisonnière. En conclusion, une attention particulière devra être portée aux personnes âgées de 65 ans et plus qui sont plus enclines à manifester une hostilité à la vaccination en général. Enfin, la mise sur le marché de différents vaccins devrait encourager à poursuivre les analyses de l’adhésion vaccinale au regard du vaccin proposé.

Published
2022

8. Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota

Author

Hamame, Afaf, Magdy Wasfy, Reham, Lo, Cheikh Ibrahima, Fenollar, Florence, Raoult, Didier, Fournier, Pierre-Edouard, Houhamdi, Linda, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Multidisciplinary, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Two new bacterial strains, Marseille-P2698T (CSUR P2698 = DSM 103,121) and Marseille-P2260T (CSUR P2260 = DSM 101,844 = SN18), were isolated from human stools by the culturomic method. We used the taxonogenomic approach to fully describe these two new bacterial strains. The Marseille-P2698T strain was a Gram-negative, motile, non-spore-forming, rod-shaped bacterium. The Marseille-P2260T strain was a Gram-positive, motile, spore-forming rod-shaped bacterium. Major fatty acids found in Marseille-P2698T were C15:0 iso (63%), C15:0 anteiso (11%), and C17:0 3-OH iso (8%). Those found in Marseille-P2260T strain were C16:00 (39%), C18:1n9 (16%) and C18:1n7 (14%). Strains Marseille-P2698T and Marseille-P2260T had 16S rRNA gene sequence similarities of 91.50% with Odoribacter laneusT, and of 90.98% and 95.07% with Odoribacter splanchnicusT and Eubacterium sulciT, respectively. The exhibited digital DNA-DNA Hybridization values lower than 20.7%, and Orthologous Average Nucleotide Identity values lower than 73% compared to their closest related bacterial species O. splanchnicusT and E. sulciT respectively. Phenotypic, biochemical, phylogenetic, and genomic results obtained by comparative analyses provided sufficient evidence that both of the two studied strains Marseille-P2698T and Marseille-P2260T are two new bacterial species and new bacterial genera for which the names Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. were proposed, respectively.

Published
2023

9. Influence of the healthcare pathway on the outcome of patients with infective endocarditis

Author

Florent Arregle, Nicolas Iline, Roch Giorgi, Mary Philip, Sandrine Hubert, Frederique Gouriet, Jean Paul Casalta, Frédéric Collart, Alberto Riberi, Hélène Martel, Sébastien Renard, Laurence Camoin, Anne Claire Casalta, Hubert Lepidi, Didier Raoult, Michel Drancourt, Gilbert Habib, Département de Cardiologie [Hôpital de la Timone - APHM], Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Biostatistique et technologies de l'information et de la communication (BioSTIC) - [Hôpital de la Timone - APHM] (BiosTIC ), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Département de Chirurgie Cardiaque [Hôpital de la Timone - APHM], and Hôpital de la Timone [CHU - APHM] (TIMONE)

Subjects
MESH: Endocarditis, MESH: Humans, Endocarditis, Referral centre, MESH: Delivery of Health Care, MESH: Retrospective Studies, Endocarditis, Bacterial, General Medicine, Critical Care and Intensive Care Medicine, MESH: Prospective Studies, Anti-Bacterial Agents, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Anti-Bacterial Agents, Humans, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Hospital Mortality, Prospective Studies, MESH: Endocarditis, Bacterial, MESH: Hospital Mortality, Mortality, Cardiology and Cardiovascular Medicine, Delivery of Health Care, Retrospective Studies, Healthcare pathway
Abstract

Aims To determine the prognosis of patients treated for infective endocarditis (IE) according to their healthcare pathway. To assess how the ESC guidelines are implemented concerning the performance of transoesophageal echocardiography, the use of antibiotic therapy, and the performance of valve surgery; and to compare the epidemiological profile of IE according to the type of centres in which the patients are hospitalized. Methods and results In a prospective multicentric study including 22 hospitals in the South-East of France, 342 patients were classified into three groups according to their healthcare pathway: 119 patients diagnosed and taken care entirely in a reference centre or hospital with cardiac surgery [Referral Center (RC) group], 111 patients diagnosed and initially taken care in a non-RC (NRC), then referred in a centre including cardiac surgery [transferred to the Referral Center (TRC) group] and 112 patients totally taken care in the NRC (NRC group). One-year mortality was 26% (88 deaths) and was not significantly different between Groups 1 and 2 (20 vs. 21%, P = 0.83). Patients in the NRC group had a higher mortality (37%) compared with patients in the RC and TRC groups (P Conclusion Prognosis of patients with IE is influenced by their healthcare pathway. Patients treated exclusively in NRC have a worse prognosis than patients treated in referral or surgical centres.

Published
2022

10. Confirmatory Virucidal Activity of Ionised Active Water S-100® on the SARS-CoV-2 Virus

Author

Nathalie Wurtz, Issam Hasni, Audrey Bancod, Bernard La Scola, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
body regions, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Article Subject, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience; Ionised active water S-100® has been proposed as an original solution for use in dermocosmetics and for the treatment of wounds such as burns and atopic dermatitis. Among the mechanisms of action that are not completely understood, an antimicrobial activity would appear to be important. In the context of the COVID-19 pandemic, we assessed the inactivating efficacy of this solution on SARS-CoV-2 based on the recommendations of the NF-EN-14476+A2 standard. The tests carried out demonstrated that ionised active water S-100® 40% has a virucidal activity on SARS-CoV-2 which is at least 3.1 log after a contact time of 30 seconds and 3.5 log after two minutes at 20°C under clean conditions. Assays were also performed at 4°C and 37°C, and the results obtained are identical to those obtained at 20°C. This demonstration of the virucidal effect of ionised water against SARS-CoV-2 paves the way for the development of usage as an alternative disinfectant in SARS-CoV-2 control.

Published
2022

11. Culture and identification of a 'Deltamicron' SARS‐CoV‐2 in a three cases cluster in southern France

Author

Philippe Colson, Pierre‐Edouard Fournier, Jeremy Delerce, Matthieu Million, Marielle Bedotto, Linda Houhamdi, Nouara Yahi, Jeremy Bayette, Anthony Levasseur, Jacques Fantini, Didier Raoult, Bernard La Scola, COMBE, Isabelle, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Unité de Neurobiologie des canaux Ioniques et de la Synapse (UNIS - Inserm U1072), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Base Sequence, SARS-CoV-2, COVID-19, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Phylogeny
Abstract

Multiple SARS-CoV-2 variants have successively, or concommitantly spread worldwide since summer 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J/AY.4-Omicron 21K/BA.1 “Deltamicron” recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1,163-1,421 reads and mean nucleotide diversity of 0.1-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening qPCR, we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.

Published
2022

12. Habitat mosaic as a driver of the resilience of native species: The case of the assemblage of small mammals from the city of Franceville, Gabon

Author

J. B. Mangombi‐Pambou, O. Fossati‐Gaschignard, N. N'Dilimabaka, O. Banga Mve‐Ella, N. M. Longo Pendy, S. E. Dibakou, O. Mediannikov, F. Fenollar, E. Leroy, M. Bourgarel, Centre International de Recherches Médicales de Franceville (CIRMF), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Université des Sciences et Techniques de Masuku (USTM), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
urban rodents, [SDV]Life Sciences [q-bio], habitat gradient, central African city, Animal Science and Zoology, community composition, landscape heterogeneity, Ecology, Evolution, Behavior and Systematics, introduced rodents
Abstract

International audience; Rodents (Rodentia) are the most abundant and diverse order of mammals, present in all habitats, including urban areas. The traffic linked to globalisation has favoured their involvement in biological invasions that have an impact on local biodiversity, the economy and human health. In Franceville, Gabon, little is known about the rodent community. We therefore studied the composition and distribution of rodents along a gradient highlighting the heterogeneity of the city's landscape. The three habitat types studied showed no difference in small mammal abundance, while the diversity index was higher in the vegetated habitat (SDI = 0.73) compared to the outdoor (SDI = 0.71) and indoor (SDI = 0.45) habitats. Our work shows the importance of vegetal remnants in the city for the maintenance of native species. It also highlights the impact of introduced species on small mammal assemblages and the need for management to reduce the factors of their proliferation.

Published
2023

13. Prognostic value of cardiovascular magnetic resonance T1 mapping and extracellular volume fraction in nonischemic dilated cardiomyopathy

Author

Farah Cadour, Morgane Quemeneur, Loic Biere, Erwan Donal, Zakarya Bentatou, Jean-Christophe Eicher, François Roubille, Alain Lalande, Roch Giorgi, Stanislas Rapacchi, Sébastien Cortaredona, Farouk Tradi, Axel Bartoli, Serge Willoteaux, François Delahaye, Stephanie M. Biene, Lionel Mangin, Nadine Ferrier, Jean-Nicolas Dacher, Fabrice Bauer, Guillaume Leurent, Pierre-Axel Lentz, Hélène Kovacsik, Pierre Croisille, Franck Thuny, Monique Bernard, Maxime Guye, Alain Furber, Gilbert Habib, Alexis Jacquier, Centre de résonance magnétique biologique et médicale (CRMBM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Exploration Métabolique par Résonance Magnétique [Hôpital de la Timone - APHM] (CEMEREM), Hôpital de la Timone [CHU - APHM] (TIMONE)-Centre de résonance magnétique biologique et médicale (CRMBM), Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Centre National de la Recherche Scientifique (CNRS), MitoVasc - Physiopathologie Cardiovasculaire et Mitochondriale (MITOVASC), Université d'Angers (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM), Laboratoire Traitement du Signal et de l'Image (LTSI), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pontchaillou [Rennes], Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Physiologie & médecine expérimentale du Cœur et des Muscles [U 1046] (PhyMedExp), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Imagerie et Vision Artificielle [Dijon] (ImViA), Université de Bourgogne (UB), CHU Dijon, Institut des sciences de la santé publique [Marseille] (ISSPAM), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital de la Timone [CHU - APHM] (TIMONE), Biostatistique et technologies de l'information et de la communication (BioSTIC) - [Hôpital de la Timone - APHM] (BiosTIC ), Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Hospices Civils de Lyon (HCL), Centre Hospitalier Annecy-Genevois [Saint-Julien-en-Genevois], Centre Hospitalier de Vichy (CH Vichy), Endothélium, valvulopathies et insuffisance cardiaque (EnVI), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Rouen, Normandie Université (NU), CHU Montpellier, Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-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 Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne] (CHU ST-E), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hôpital Nord [CHU - APHM], Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Native T1, Cardiac magnetic resonance, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Radiological and Ultrasound Technology, Myocardial fibrosis, [SDV]Life Sciences [q-bio], Extracellular volume (ECV), Radiology, Nuclear Medicine and imaging, Cardiology and Cardiovascular Medicine, Late gadolinium enhancement, Prognostic value, Nonischemic dilated cardiomyopathy
Abstract

Background Heart failure- (HF) and arrhythmia-related complications are the main causes of morbidity and mortality in patients with nonischemic dilated cardiomyopathy (NIDCM). Cardiovascular magnetic resonance (CMR) imaging is a noninvasive tool for risk stratification based on fibrosis assessment. Diffuse interstitial fibrosis in NIDCM may be a limitation for fibrosis assessment through late gadolinium enhancement (LGE), which might be overcome through quantitative T1 and extracellular volume (ECV) assessment. T1 and ECV prognostic value for arrhythmia-related events remain poorly investigated. We asked whether T1 and ECV have a prognostic value in NIDCM patients. Methods This prospective multicenter study analyzed 225 patients with NIDCM confirmed by CMR who were followed up for 2 years. CMR evaluation included LGE, native T1 mapping and ECV values. The primary endpoint was the occurrence of a major adverse cardiovascular event (MACE) which was divided in two groups: HF-related events and arrhythmia-related events. Optimal cutoffs for prediction of MACE occurrence were calculated for all CMR quantitative values. Results Fifty-eight patients (26%) developed a MACE during follow-up, 42 patients (19%) with HF-related events and 16 patients (7%) arrhythmia-related events. T1 Z-score (p = 0.008) and global ECV (p = 0.001) were associated with HF-related events occurrence, in addition to left ventricular ejection fraction (p 32.1% (optimal cutoff) remained the only CMR independent predictor of HF-related events occurrence (HR 2.15 [1.14–4.07], p = 0.018). In the arrhythmia-related events group, patients had increased native T1 Z-score and ECV values, with both T1 Z-score > 4.2 and ECV > 30.5% (optimal cutoffs) being independent predictors of arrhythmia-related events occurrence (respectively, HR 2.86 [1.06–7.68], p = 0.037 and HR 2.72 [1.01–7.36], p = 0.049). Conclusions ECV was the sole independent predictive factor for both HF- and arrhythmia-related events in NIDCM patients. Native T1 was also an independent predictor in arrhythmia-related events occurrence. The addition of ECV and more importantly native T1 in the decision-making algorithm may improve arrhythmia risk stratification in NIDCM patients. Trial registration NCT02352129. Registered 2nd February 2015—Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT02352129

Published
2023

14. Who Were Hospitalized Deceased Patients from COVID-19 During the First Year of Pandemic? Retrospective Analysis of 1104 Deceased Patients in South of France

Author

Sylvie Arlotto, Kevin Legueult, Alice Blin, Sebastien Cortaredona, Audrey Giraud-Gatineau, Laurent Bailly, Marie-Thérèse Jimeno, Léa Delorme, Philippe Brouqui, Jean-Christophe Lagier, Matthieu Million, Jean Dellamonica, Philippe Colson, Michel Carles, Didier Raoult, Christian Pradier, Stéphanie Gentile, Aix-Marseille Université - École de médecine (AMU SMPM MED), Aix-Marseille Université - Faculté des sciences médicales et paramédicales (AMU SMPM), Aix Marseille Université (AMU)-Aix Marseille Université (AMU), Hôpital l'Archet, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Centre Hospitalier Universitaire de Nice (CHU Nice), Service de l'Information Médicale [Marseille], Hôpital de la Timone [CHU - APHM] (TIMONE), Hôpital Nord [CHU - APHM], Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), CHU Nice [Cimiez], Hôpital Cimiez [Nice] (CHU), Centre d'Information et de Soin de l'Immuno-déficience Humaine Nice, and CISIH Nice

Subjects
Aged, 80 and over, Hospitalization, Frailty, SARS-CoV-2, [SDV]Life Sciences [q-bio], Humans, COVID-19, Comorbidity, Mortality, Pandemics, Aged, Retrospective Studies, premature
Abstract

Introduction Following the first year of the COVID-19 pandemic, a complete analysis of the characteristics of the deceased hospitalized patients was performed, to identify factors related to premature mortality and to compare patient profiles according to the epidemic periods. Methods Retrospective analysis of 1104 deceased patients in two University Hospitals in South-eastern France, between March 1, 2020 and March 12, 2021 from Hospital’s electronic medical records was performed. Results Mean age was 80 years (± 11.1) and 10% of the deceased were younger than 65 years with specific comorbidities, e.g., genetic conditions, metastatic cancer, or massive obesity. Among the three clusters identified, two clusters (75% of deceased patients) include very elderly patients with numerous comorbidities, and differ by their proportion of dependent institutionalized patients. The third cluster is made up of younger patients with fewer but severe comorbidities. Deceased patients’ profiles varied according to the epidemic periods: during the first period (March–June 2020), more patients were institutionalized. The second period (September–December2020) coincided with a higher mortality rate. Conclusions This study confirmed that most patients hospitalized and dying from COVID-19 were frail, i.e., elderly and/or highly comorbid and that the small proportion of young patients had severe comorbidities.

Published
2022

15. An instrument to measure psychosocial determinants of health care professionals’ vaccination behavior: Validation of the Pro-VC-Be questionnaire

Author

Pierre Verger, Lisa Fressard, Anna Soveri, Nicolas Dauby, Angelo Fasce, Linda Karlsson, Stephan Lewandowsky, Philipp Schmid, Eve Dubé, Arnaud Gagneur, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), University of Turku, Université libre de Bruxelles (ULB), Universidade de Coimbra [Coimbra], University of Bristol [Bristol], The University of Western Australia (UWA), Institute of Inorganic Chemistry, Karlsruhe Institute of Technology (KIT), Institut de Chimie Séparative de Marcoule (ICSM - UMR 5257), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), Université de Montpellier (UM), Institut National de Santé Publique du Québec [Canada] (INSPQ), Université de Sherbrooke (UdeS), Centre de recherche du centre hospitalier de l'Université de Sherbrooke (CR CHUS), European Project: 964728,JITSUVAX, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Health Knowledge, Attitudes, Practice, COVID-19 Vaccines, Health Personnel, education, Immunology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Surveys and Questionnaires, Drug Discovery, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, questionnaire validation, ComputingMilieux_MISCELLANEOUS, vaccination behaviors, Pharmacology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Vaccines, Vaccination, COVID-19, vaccine confidence, TeDCog, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Health care professionals, Cross-Sectional Studies, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, vaccine hesitancy, Molecular Medicine
Abstract

OBJECTIVES The lack of validated instruments assessing vaccine hesitancy/confidence among health care professionals (HCPs) for themselves, and their patients led us to develop and validate the Pro-VC-Be instrument to measure vaccine confidence and other psychosocial determinants of HCPs’ vaccination behavior among diverse HCPs in different countries.METHODS Cross-sectional survey in October-November 2020 among 1,249 GPs in France, 432 GPs in French-speaking parts of Belgium, and 1,055 nurses in Quebec (Canada), all participating in general population immunization. Exploratory and confirmatory factor analyses evaluated the instrument’s construct validity. We used HCPs’ self-reported vaccine recommendations to patients, general immunization activity, self-vaccination, and future COVID-19 vaccine acceptance to test criterion validity.RESULTS The final results indicated a 6-factor structure with good fit: vaccine confidence (combining complacency, perceived vaccine risks, perceived benefit-risk balance, perceived collective responsibility), trust in authorities, perceived constraints, proactive efficacy (combining commitment to vaccination and self-efficacy), reluctant trust, and openness to patients. The instrument showed good convergent and criterion validity and adequate discriminant validity.CONCLUSIONS This study found that the Pro-VC-Be is a valid instrument for measuring psychosocial determinants of HCPs’ vaccination behaviors in different settings. Its validation is currently underway in Europe among various HCPs in different languages.

Published
2022

16. Morphological, Molecular and MALDI-TOF MS Identification of Bedbugs and Associated Wolbachia Species in Rural Senegal

Author

El Hadji Ibrahima Ndiaye, Georges Diatta, Adama Zan Diarra, Jean Michel Berenger, Hubert Bassene, Oleg Mediannikov, Charles Bouganali, Cheikh Sokhna, Philippe Parola, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Maladies infectieuses persistantes et émergentes en Afrique de l’Ouest [Dakar, Sénégal] (Equipe 3 - VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Bedbugs, General Veterinary, fungi, Ectoparasitic Infestations, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Senegal, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Insect Science, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, parasitic diseases, Animals, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Parasitology, Wolbachia
Abstract

Bed bugs are known to carry several microorganisms. The purpose of this study was to assess the prevalence of bed bug infestation in two rural areas of Senegal and determine the species present in the population. A screening was conducted to detect some arthropod associated pathogenic bacteria in bed bugs and to evaluate the prevalence of endosymbiont carriage. One survey took place in 17 villages in Niakhar and two surveys in Dielmo and Ndiop and surroundings area in the same 20 villages. Bed bugs collected were identified morphologically and by MALDI-TOF MS tools. Microorganisms screening was performed by qPCR and confirmed by sequencing. During the survey in the Niakhar region, only one household 1/255 (0.4%) in the village of Ngayokhem was found infested by bed bugs. In a monitoring survey of the surroundings of Dielmo and Ndiop area, high prevalence was found during the two rounds of surveys in 65/314 (21%) in 16/20 villages (January–March) and 93/351 (26%) in 19/20 villages (December). All bed bugs were morphologically identified as the species Cimex hemipterus, of which 285/1,637 (17%) were randomly selected for MALDI-TOF MS analysis and bacteria screening. Among the Bacteria tested only Wolbachia (Alphaproteobacteria, Rickettsiales, Rickettsiaceae) DNA was found in 248/276 (90%) of the bedbugs. We briefly describe a high level of non-generalized bed bug infestation in rural Senegal and the diversity of Wolbachia strains carried by C. hemipterus. This study opens perspectives for raising household awareness of bed bug infestations and possibilities for appropriate control.

Published
2022

17. Characteristics of the first 1119 SARS‐CoV‐2 Omicron variant cases, in Marseille, France, November−December 2021

Author

Linda HOUHAMDI, Van Thuan HOANG, Philippe Gautret, Philippe Colson, Pierre-Edouard Fournier, Didier Raoult, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, COVID-19 Vaccines, SARS-CoV-2, COVID-19, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, France, ComputingMilieux_MISCELLANEOUS
Abstract

One thousand one hundred and nineteen cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant cases have been diagnosed at the Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France, between November 28, 2021, and December 31, 2021. Among the 825 patients with known vaccination status, 383 (46.4%) were vaccinated, of whom 91.9% had received at least two doses of the vaccine. Interestingly, 26.3% of cases developed SARS-CoV-2 infection within 21 days following the last dose of vaccine suggesting possible early production of anti-SARS-CoV-2 facilitating antibodies. Twenty-one patients have been hospitalized, one patient required intensive care, and another patient who received a vaccine booster dose died.

Published
2022

18. Limited spread of a rare spike E484K-harboring SARS-CoV-2 in Marseille, France

Author

Philippe Colson, Jacques Fantini, Nouara Yahi, Jeremy Delerce, Anthony Levasseur, Pierre-Edouard Fournier, Jean-Christophe Lagier, Didier Raoult, Bernard La Scola, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Assistance Publique - Hôpitaux de Marseille (APHM), Unité de Neurobiologie des canaux Ioniques et de la Synapse (UNIS - Inserm U1072), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and COMBE, Isabelle

Subjects
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, Brief Report, COVID-19, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, Mutation, Spike Glycoprotein, Coronavirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, Guinea, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; We detected SARS-CoV-2 of PANGO lineage R.1 with the spike substitution E484K in three patients. Eleven other sequences in France and 8,831 worldwide were available from GISAID, 92% originating from Japan. The three genome sequences from our institute were phylogenetically closest to another from Guinea-Conakry, where one of the patients had travelled. These viruses did not exhibit any unusual features in cell culture. Spike structural predictions indicated a 1.3-time higher transmissibility index than for the globally spread B.1.1.7 variant but also an affinity loss for gangliosides that might have slowed dissemination. The spread of new SARS-CoV-2 mutants/variants is still not well understood and therefore difficult to predict, and this hinders implementation of effective preventive measures, including adapted vaccines.

Published
2022

19. Nucleation in sessile saline microdroplets: induction time measurement via deliquescence–recrystallization cycling

Author

Ruel Cedeno, Romain Grossier, Mehdi Lagaize, David Nerini, Nadine Candoni, Adrian Flood, Stéphane Veesler, Vidyasirimedhi Institute of Science and Technology, Centre Interdisciplinaire de Nanoscience de Marseille (CINaM), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Aix Marseille Université (AMU), Vidyasirimedhi Institute of Science and Technology [Thaïlande] (VISTEC), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), and Eiffel Excellence Scholarship (N°P744524E)

Subjects
optical microscopy, Condensed Matter - Materials Science, 010405 organic chemistry, nucleation, Materials Science (cond-mat.mtrl-sci), FOS: Physical sciences, contraction, 010402 general chemistry, sessile droplets, 01 natural sciences, evaporation, image processing, [SPI.MAT]Engineering Sciences [physics]/Materials, 0104 chemical sciences, induction time, [PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci], Physical and Theoretical Chemistry
Abstract

International audience; Induction time, a measure of how long one will wait for nucleation to occur, is an important parameter in quantifying nucleation kinetics and its underlying mechanisms. Due to the stochastic nature of nucleation, efficient methods for measuring large number of independent induction times are needed to ensure statistical reproducibility. In this work, we present a novel approach for measuring and analyzing induction times in sessile arrays of microdroplets via deliquescence/recrystallization cycling. With the help of a recently developed image analysis protocol, we show that the interfering diffusion-mediated interactions between microdroplets can be eliminated by controlling the relative humidity, thereby ensuring independent nucleation events. Moreover, possible influence of heterogeneities, impurities, and memory effect appear negligible as suggested by our 2-cycle experiment. Further statistical analysis (k-sample Anderson-Darling test) reveals that upon identifying possible outliers, the dimensionless induction times obtained from different datasets (microdroplet lines) obey the same distribution and thus can be pooled together to form a much larger dataset. The pooled dataset showed an excellent fit with the Weibull function, giving a mean supersaturation at nucleation of 1.61 and 1.85 for the 60pL and 4pL microdroplet respectively. This confirms the effect of confinement where smaller systems require higher supersaturations to nucleate. Both the experimental method and the data-treatment procedure presented herein offer promising routes in the study of fundamental aspects of nucleation kinetics, particularly confinement effects, and are adaptable to other salts, pharmaceuticals, or biological crystals of interest.

Published
2022

20. Hepatitis B in Senegal: A Successful Infant Vaccination Program but Urgent Need to Scale Up Screening and Treatment (ANRS 12356 AmBASS survey)

Author

Périères, Lauren, Diallo, Aldiouma, Marcellin, Fabienne, Nishimwe, Marie Libérée, Ba, El Hadji, Coste, Marion, Lo, Gora, Halfon, Philippe, Touré Kane, Coumba, Maradan, Gwenaëlle, Carrieri, Patrizia, Diouf, Assane, Shimakawa, Yusuke, Sokhna, Cheikh, Boyer, Sylvie, Bérenger, Cyril, Bousmah, Marwan al Qays, de Seze, Maëlle, Djaogol, Tchadine, Treibich, Carole, Ba, Elhadji, Dièye, Fambaye, Faye, Elhadji Bilal, Ndiaye, Assane, Sow, Mouhamadou Baba, Ndiaye, Anna Julienne Selbé, Ndiour, Samba, Mohamed, Sofiane, Rouveau, Nicolas, Cortès, Maria‐Camila Calvo, Laborde‐Balen, Gabrièle, Audibert, Martine, Fall, Fatou, Gueye, Ibrahima, Lacombe, Karine, Seydi, Moussa, Tuaillon, Edouard, Vray, Muriel, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Aix-Marseille Sciences Economiques (AMSE), École des hautes études en sciences sociales (EHESS)-Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation [Dakar, Sénégal] (IRESSEF), ALPHABIO - Laboratoire de biologie médicale, Hôpital Européen [Fondation Ambroise Paré - Marseille], Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Université Paris Cité (UPCité)-Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), ANRS 12356 AmBASS Survey Study Group: Cyril Bérenger, Marwan Al Qays Bousmah, Sylvie Boyer, Patrizia Carrieri, Marion Coste, Maëlle de Seze, Tchadine Djaogol, Gwenaëlle Maradan, Fabienne Marcellin, Carole Treibich, Elhadji Ba, Aldiouma Diallo, Fambaye Dièye, Assane Diouf, Elhadji Bilal Faye, Assane Ndiaye, Lauren Périères, Cheikh Sokhna, Mouhamadou Baba Sow, Coumba Touré Kane, Gora Lo, Anna Julienne Selbé Ndiaye, Samba Ndiour, Philippe Halfon, Sofiane Mohamed, Nicolas Rouveau, Maria-Camila Calvo Cortès, Gabrièle Laborde-Balen, Martine Audibert, Fatou Fall, Ibrahima Gueye, Karine Lacombe, Moussa Seydi, Yusuke Shimakawa, Edouard Tuaillon, Muriel Vray, Lhuillier, Elisabeth, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
Adult, Hepatitis B Surface Antigens, Adolescent, Hepatology, Vaccination, Infant, Hepatitis B, [SHS.ECO]Humanities and Social Sciences/Economics and Finance, Senegal, 3. Good health, Young Adult, 03 medical and health sciences, Cross-Sectional Studies, 0302 clinical medicine, Humans, Female, Hepatitis B Vaccines, 030211 gastroenterology & hepatology, 030212 general & internal medicine, [SHS.ECO] Humanities and Social Sciences/Economics and Finance, Child
Abstract

International audience; Senegal introduced the infant hepatitis B virus (HBV) vaccination in 2004 and recently committed to eliminating hepatitis B by 2030. Updated epidemiological data are needed to provide information on the progress being made and to develop new interventions. We estimated the prevalence of hepatitis B surface antigen (HBsAg) in children and adults living in rural Senegal and assessed hepatitis B treatment eligibility. A cross-sectional population-based serosurvey of HBsAg was conducted in 2018-2019 in a large sample (n = 3,118) of residents living in the Niakhar area (Fatick region, Senegal). Individuals positive for HBsAg subsequently underwent clinical and biological assessments. Data were weighted for age and sex and calibrated to be representative of the area's population. Among the 3,118 participants, 206 were HBsAg positive (prevalence, 6.9%; 95% confidence interval [CI], 5.6-8.1). Prevalence varied markedly according to age group in individuals aged 0-4, 5-14, 15-34, and >= 35 years as follows: 0.0% (95% CI, 0.00-0.01); 1.5% (95% CI, 0.0-2.3); 12.4% (95% CI, 9.1-15.6); and 8.8% (95% CI, 6.1-11.5), respectively. Of those subsequently assessed, 50.9% (95% CI, 41.8-60.0) had active HBV infection; 4 (2.9%; 95% CI, 0.9-9.4) were eligible for hepatitis B treatment. Conclusion: In this first population-based serosurvey targeting children and adults in rural Senegal, HBsAg prevalence was very low in the former, meeting the World Health Organization's (WHO) < 1% HBsAg 2020 target; however, it was high in young adults (15-34 years old) born before the HBV vaccine was introduced in 2004. To reach national and WHO hepatitis elimination goals, general population testing (particularly for adolescents and young adults), care, and treatment scale-up need to be implemented.

Published
2021

21. Estimating fundamental parameters of nearby M dwarfs from SPIRou spectra

Author

P I Cristofari, J-F Donati, T Masseron, P Fouqué, C Moutou, X Delfosse, E Artigau, C P Folsom, A Carmona, E Gaidos, J-D do Nascimento, F Jahandar, G Hébrard, Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Universidad de La Laguna [Tenerife - SP] (ULL), Instituto de Astrofisica de Canarias (IAC), Institut de Planétologie et d'Astrophysique de Grenoble (IPAG), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire des Sciences de l'Univers de Grenoble (OSUG ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France -Institut national des sciences de l'Univers (INSU - CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Météo-France, Université de Montréal (UdeM), University of Tartu, University of Hawai‘i [Mānoa] (UHM), Universidade Federal do Rio Grande do Norte [Natal] (UFRN), Institut d'Astrophysique de Paris (IAP), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Observatoire de Haute-Provence (OHP), Institut Pythéas (OSU PYTHEAS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-18-CE31-0019,SPlaSH,Recherche de planètes habitables avec SPIRou(2018), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Canada-France-Hawaii Telescope Corporation (CFHT), and National Research Council of Canada (NRC)-Centre National de la Recherche Scientifique (CNRS)-University of Hawai'i [Honolulu] (UH)

Subjects
Astrophysics - Solar and Stellar Astrophysics, [SDU]Sciences of the Universe [physics], stars: low-mass, [SDU.ASTR.SR]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Solar and Stellar Astrophysics [astro-ph.SR], Space and Planetary Science, FOS: Physical sciences, Astronomy and Astrophysics, stars: fundamental parameters, infrared: stars, Solar and Stellar Astrophysics (astro-ph.SR), techniques: spectroscopic, [SDU.ASTR.IM]Sciences of the Universe [physics]/Astrophysics [astro-ph]/Instrumentation and Methods for Astrophysic [astro-ph.IM]
Abstract

We present the results of a study aiming at retrieving the fundamental parameters of M dwarfs from spectra secured with SPIRou, the near-infrared high-resolution spectropolarimeter installed at the Canada-France-Hawaii Telescope (CFHT), in the framework of the SPIRou Legacy Survey (SLS). Our study relies on comparing observed spectra with two grids of synthetic spectra, respectively computed from PHOENIX and MARCS model atmospheres, with the ultimate goal of optimizing the precision at which fundamental parameters can be determined. In this first step, we applied our technique to 12 inactive M dwarfs with effective temperatures ($T_{\rm eff}$) ranging from 3000 to 4000 K. We implemented a benchmark to carry out a comparison of the two models used in this study. We report that the choice of model has a significant impact on the results and may lead to discrepancies in the derived parameters of 30 K in $T_{\rm eff}$ and 0.05 dex to 0.10 dex in surface gravity ($\log{g}$) and metallicity ([M/H]), as well as systematic shifts of up to 50 K in $T_{\rm eff}$ and 0.4 dex $\log{g}$ and [M/H]. The analysis is performed on high signal-to-noise ratio template SPIRou spectra, averaged over multiple observations corrected from telluric absorption features and sky lines, using both a synthetic telluric transmission model and principal component analysis. With both models, we retrieve $T_{\rm eff}$ , $\log{g}$ and [M/H] estimates in good agreement with reference literature studies, with internal error bars of about 30 K, 0.05 dex and 0.1 dex, respectively., Comment: 20 pages, plus supplementary material, accepted for publication in MNRAS

Published
2021

22. Real-time whole genome sequencing direct diagnosis of Streptococcus pneumoniae meningitis: A case report

Author

Michel Drancourt, Sophie Amrane, Madjid Morsli, P.-E. Fournier, P. Parola, Q. Kerharo, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)

Subjects
Microbiology (medical), Whole genome sequencing, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, medicine.disease_cause, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Streptococcus pneumoniae, medicine, Point of care poc, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, business, Meningitis, Streptococcus pneumoniae Meningitis
Abstract

International audience

Published
2021

23. Observational Cohort Study of Evolving Epidemiologic, Clinical, and Virologic Features of Monkeypox in Southern France

Author

Nadim Cassir, Florian Cardona, Hervé Tissot-Dupont, Christiane Bruel, Barbara Doudier, Salima Lahouel, Karim Bendamardji, Céline Boschi, Sarah Aherfi, Sophie Edouard, Jean-Christophe Lagier, Philippe Colson, Philippe Gautret, Pierre-Edouard Fournier, Philippe Parola, Philippe Brouqui, Bernard La-Scola, Matthieu Million, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Agence Régionale de la Santé (ARS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
Male, Adult, Cohort Studies, Microbiology (medical), Sexual and Gender Minorities, Infectious Diseases, Epidemiology, [SDV]Life Sciences [q-bio], Sexually Transmitted Diseases, Humans, Female, Monkeypox, Homosexuality, Male
Abstract

We enrolled 136 patients with laboratory-confirmed monkeypox during June 4-August 31, 2022, at the University Hospital Institute Méditerranée Infection in Marseille, France. The median patient age was 36 years (interquartile range 31-42 years). Of 136 patients, 125 (92%) were men who have sex with men, 15 (11%) reported previous smallpox vaccinations, and 21 (15.5%) were HIV-positive. The most frequent lesion locations were the genitals (68 patients, 53%), perianal region (65 patients, 49%), and oral/perioral area (22 patients, 17%). Lesion locations largely corresponded with the route of contamination. Most (68%) patients had isolated anal, genital, or oral lesions when they were first seen, including 56 (61%) who had1 positive site without a visible lesion. Concurrent sexually transmitted infections were diagnosed in 19 (15%) patients, and 7 patients (5%) were asymptomatic. We recommend vaccination campaigns, intensified testing for sexually transmitted infections, and increased contact tracing to control the ongoing monkeypox outbreak.

Published
2022

24. Diagnosis and management of rabies encephalitis in two patients in northwest Africa: A case series

Author

Boushab Mohamed Boushab, Hacen Ahmed Benane, Sidi El‐Wafi Ould Baba, Leonardo K. Basco, Kiffa Regional Hospital Assaba, Faculty of Medicine University of Nouakchott Al-Aasriya, WorldWide Antimalarial Resistance Network Falciparum Haematology Study Group, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Kiffa Regional Hospital Center, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)

Subjects
[SDV]Life Sciences [q-bio], General Medicine
Abstract

International audience

Published
2022

25. An absolute radiocarbon chronology for the world heritage site of Sarvestan (SW Iran): A late Sasanian heritage in early Islamic era

Author

Morteza Djamali, Manuela Capano, Nicolas Faucherre, Thibaut Tuna, Alastair Northedge, Alireza Askari-Chaverdi, Edouard Bard, Frédéric Guibal, Elnaz Rashidian, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), History Department, Shiraz University, Shiraz, Iran, Laboratoire d'Archéologie Médiévale et Moderne en Méditerranée (LA3M), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Université Paris 1 Panthéon-Sorbonne (UP1), Chaire Evolution du climat et de l'océan, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-14-CE35-0026,PaleoPersepolis,The Persepolis Basin (SW Iran): a System Model to investigate Human-Climate-Ecosystem interactions during the Holocene(2014), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Collège de France - Chaire Evolution du climat et de l'océan

Subjects
010506 paleontology, Archeology, History, Ancient history, 01 natural sciences, Islamic architecture, law.invention, Late Antiquity, law, Fars, 0601 history and archaeology, Radiocarbon dating, 0105 earth and related environmental sciences, 060102 archaeology, radiocarbon dating, Sasanian architecture, Islam, 06 humanities and the arts, tree rings, Absolute (philosophy), World heritage, [SDE]Environmental Sciences, Chronology
Abstract

International audience; This study presents a new precise radiocarbon chronology for the World Heritage site of Sarvestan (SW Iran). The monument is a key construction in the history of architecture because it is a typical Sasanian construction built during the late Sasanian or early Islamic period. Previous attempts to date the monument have suggested the ages ranging from the middle Sasanian (fifth century CE) to early Abbasid (ninth century CE) era. These age estimations are based on the analysis of architectural plans and techniques, and a few radiocarbon dates with very large age uncertainties. This paper presents the results of a systematic radiocarbon dating of timbers in the walls and charcoals in plaster mortars used in the main dome of the monument. It further applies wiggle matching technique and R_Combine function to substantially reduce the age uncertainties in wood sections. The results indicate that a major construction work was undertaken sometime between 658 and 683 CE, the century of the invasion of Fars by Muslim Arabs. This finding pushes back the age of Sarvestan for two centuries and suggests that the monument was built at the transitional period between Sasanian to Islamic era. Sarvestan would have been an architectural project designed andpossibly initiated during the late Sasanian period but mainly accomplished during the second half of the seventh century CE. It can thus be considered a late Sasanian heritage in early Islamic period. Its construction at a time of political unrest further suggests that some areas of Fars may have benefited from certain socio-political stabilities during the expansion of Islaminto the east at mid- to late seventh century CE

Published
2021

26. Fatal Cowpox Virus Infection in Human Fetus, France, 2017

Author

Sandrine Henard, Isabelle Drouet, Evelyne Schvoerer, Christophe N. Peyrefitte, Olivier Ferraris, Estelle Mosca, Gaelle Frenois-Veyrat, Fanny Jarjaval, Laetitia Boutin, Hawa Timera, Audrey Ferrier, Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Laboratoire de Chimie Physique et Microbiologie pour les Matériaux et l'Environnement (LCPME), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Service de Virologie [CHRU Nancy], Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Service des Maladies Infectieuses et Tropicales [CHRU Nancy], Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), and Service de Santé des Armées

Subjects
Microbiology (medical), Epidemiology, viruses, cowpox virus, orthopoxvirus, Infectious and parasitic diseases, RC109-216, fetal mortality, Virus, Young Adult, chemistry.chemical_compound, Fetus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Animals, Humans, Fatal Cowpox Virus Infection in Human Fetus, France, 2017, Smallpox, Orthopoxvirus, Fetal Death, Pregnancy, biology, business.industry, Research, Cowpox virus, Cowpox, virus diseases, biology.organism_classification, medicine.disease, Virology, infection, Vaccination, Infectious Diseases, chemistry, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Medicine, Female, France, Variola virus, Vaccinia, business
Abstract

Cowpox virus (CPXV) has an animal reservoir and is typically transmitted to humans by contact with infected animals. In 2017, CPXV infection of a pregnant woman in France led to the death of her fetus. Fetal death after maternal orthopoxvirus (smallpox) vaccination has been reported; however, this patient had not been vaccinated. Investigation of the patient’s domestic animals failed to demonstrate prevalence of CPXV infection among them. The patient’s diagnosis was confirmed by identifying CPXV DNA in all fetal and maternal biopsy samples and infectious CPXV in biopsy but not plasma samples. This case of fetal death highlights the risk for complications of orthopoxvirus infection during pregnancy. Among orthopoxviruses, fetal infection has been reported for variola virus and vaccinia virus; our findings suggest that CPXV poses the same threats for infection complications as vaccinia virus.

Published
2021

27. Congenital Infection of Severe Acute Respiratory Syndrome Coronavirus 2 With Intrauterine Fetal Death: A Clinicopathological Study With Molecular Analysis

Author

Soraya Mezouar, Sophie Collardeau-Frachon, Laurent Daniel, Florence Bretelle, Delphine Sirgant, Julia Torrents, Emmanuelle Lesieur, Hubert Lepidi, Christine Zandotti, Radia Fritih, Frédéric Fina, Jean-Louis Mege, Myriem Otmani Idrissi, Celine Gazin, Julie Blanc, Hôpital Saint-Joseph [Marseille], Hôpital de la Timone [CHU - APHM] (TIMONE), Service d'Anatomie Pathologique et de Neuropathologie, Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d'études et de recherche sur les services de santé et la qualité de vie (CEReSS), Aix Marseille Université (AMU), Département de Pathologie [CHU Lyon-Sud - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Aix-Marseille Université - École de médecine (AMU SMPM MED), Aix-Marseille Université - Faculté des sciences médicales et paramédicales (AMU SMPM), Aix Marseille Université (AMU)-Aix Marseille Université (AMU), Centre recherche en CardioVasculaire et Nutrition = Center for CardioVascular and Nutrition research (C2VN), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Assistance Publique - Hôpitaux de Marseille (APHM), Department of Obstetrics and Gynecology, Nord Hospital, Assistance Publique - Hopitaux de Marseille, Chemin des Bourrely, Marseille, France, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Microbiology (medical), Pathology, medicine.medical_specialty, Necrosis, Placenta, miscarriage, Communicable Diseases, Infant, Newborn, Diseases, Virus, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Pregnancy, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Immunochemistry, Major Article, medicine, Humans, in utero x death, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Pregnancy Complications, Infectious, Fetal Death, Pathological, reproductive and urinary physiology, In utero foetal death, Histiocyte, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Fetus, SARS-CoV-2, business.industry, Infant, Newborn, COVID-19, Stillbirth, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, female genital diseases and pregnancy complications, Infectious Disease Transmission, Vertical, congenital infection, Fetal Diseases, AcademicSubjects/MED00290, Infectious Diseases, In utero, embryonic structures, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Gestation, Female, medicine.symptom, business
Abstract

Background Observations of vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection from mother to fetus have recently been described in the literature. However, the consequences of such transmission, whether fetal or neonatal, are poorly understood. Methods From a case of in utero fetal death at 24+2 weeks of gestation that occurred 7 days after the diagnosis of symptomatic SARS-CoV-2 infection in the mother, we isolated the incriminating virus by immunochemistry and molecular techniques in several fetal tissues, with a variant analysis of the SARS-CoV-2 genome. Results The fetal demise could be explained by the presence of placental histological lesions, such as histiocytic intervillositis and trophoblastic necrosis, in addition to fetal tissue damage. We observed mild fetal growth retardation and visceral damage to the liver, causing hepatocellular damage and hemosiderosis. To the best of our knowledge, this is the first report in the literature of fetal demise secondary to maternal–fetal transmission of SARSCoV- 2 with a congenital infection and a pathological description of placental and fetal tissue damage. Conclusions SARS-CoV-2 was identified in both specimens using 3 independent techniques (immunochemistry, real-time quantitative polymerase chain reaction, and realtime digital polymerase chain reaction). Furthermore, the incriminating variant has been identified.

Published
2021

28. Overview of the Instrumentation for the Dark Energy Spectroscopic Instrument

Author

DESI Collaboration, Abareshi, B., Aguilar, J., Ahlen, S., Alam, Shadab, Alexander, David M., Alfarsy, R., Allen, L., Prieto, C. Allende, Alves, O., Ameel, J., Armengaud, E., Asorey, J., Aviles, Alejandro, Bailey, S., Balaguera-Antolínez, A., Ballester, O., Baltay, C., Bault, A., Beltran, S. F., Benavides, B., BenZvi, S., Berti, A., Besuner, R., Beutler, Florian, Bianchi, D., Blake, C., Blanc, P., Blum, R., Bolton, A., Bose, S., Bramall, D., Brieden, S., Brodzeller, A., Brooks, D., Brownewell, C., Buckley-Geer, E., Cahn, R. N., Cai, Z., Canning, R., Capasso, R., Rosell, A. Carnero, Carton, P., Casas, R., Castander, F. J., Cervantes-Cota, J. L., Chabanier, S., Chaussidon, E., Chuang, C., Circosta, C., Cole, S., Cooper, A. P., Costa, L. Da, Cousinou, M.-C., Cuceu, A., Davis, T. M., Dawson, K., Cruz-Noriega, R. De La, Macorra, A. De La, Mattia, A. De, Costa, J. Della, Demmer, P., Derwent, M., Dey, A., Dey, B., Dhungana, G., Ding, Z., Dobson, C., Doel, P., Donald-McCann, J., Donaldson, J., Douglass, K., Duan, Y., Dunlop, P., Edelstein, J., Eftekharzadeh, S., Eisenstein, D. J., Enriquez-Vargas, M., Escoffier, S., Evatt, M., Fagrelius, P., Fan, X., Fanning, K., Fawcett, V. A., Ferraro, S., Ereza, J., Flaugher, B., Font-Ribera, A., Forero-Romero, J. E., Frenk, C. S., Fromenteau, S., Gänsicke, B. T., Garcia-Quintero, C., Garrison, L., Gaztañaga, E., Gerardi, F., Gil-Marín, H., A Gontcho, S. Gontcho, Gonzalez-Morales, Alma X., Gonzalez-De-Rivera, G., Gonzalez-Perez, V., Gordon, C., Graur, O., Green, D., Grove, C., Gruen, D., Gutierrez, G., Guy, J., Hahn, C., Harris, S., Herrera, D., Herrera-Alcantar, Hiram K., Honscheid, K., Howlett, C., Huterer, D., Iršič, V., Ishak, M., Jelinsky, P., Jiang, L., Jimenez, J., Jing, Y. P., Joyce, R., Jullo, E., Juneau, S., Karaçaylı, N. G., Karamanis, M., Karcher, A., Karim, T., Kehoe, R., Kent, S., Kirkby, D., Kisner, T., Kitaura, F., Koposov, S. E., Kovács, A., Kremin, A., Krolewski, Alex, L’Huillier, B., Lahav, O., Lambert, A., Lamman, C., Lan, Ting-Wen, Landriau, M., Lane, S., Lang, D., Lange, J. U., Lasker, J., Guillou, L. Le, Leauthaud, A., Van Suu, A. Le, Levi, Michael E., Li, T. S., Magneville, C., Manera, M., Manser, Christopher J., Marshall, B., Martini, Paul, McCollam, W., McDonald, P., Meisner, Aaron M., Mena-Fernández, J., Meneses-Rizo, J., Mezcua, M., Miller, T., Miquel, R., Montero-Camacho, P., Moon, J., Moustakas, J., Mueller, E., Muñoz-Gutiérrez, Andrea, Myers, Adam D., Nadathur, S., Najita, J., Napolitano, L., Neilsen, E., Newman, Jeffrey A., Nie, J. D., Ning, Y., Niz, G., Norberg, P., Noriega, Hernán E., O’Brien, T., Obuljen, A., Palanque-Delabrouille, N., Palmese, A., Zhiwei, P., Pappalardo, D., PENG, X., Percival, W. J., Perruchot, S., Pogge, R., Poppett, C., Porredon, A., Prada, F., Prochaska, J., Pucha, R., Pérez-Fernández, A., Pérez-Ràfols, I., Rabinowitz, D., Raichoor, A., Ramirez-Solano, S., Ramírez-Pérez, César, Ravoux, C., Reil, K., Rezaie, M., Rocher, A., Rockosi, C., Roe, N. A., Roodman, A., Ross, A. J., Rossi, G., Ruggeri, R., Ruhlmann-Kleider, V., Sabiu, C. G., Safonova, S., Said, K., Saintonge, A., Catonga, Javier Salas, Samushia, L., Sanchez, E., Saulder, C., Schaan, E., Schlafly, E., Schlegel, D., Schmoll, J., Scholte, D., Schubnell, M., Secroun, A., Seo, H., Serrano, S., Sharples, Ray M., Sholl, Michael J., Silber, Joseph Harry, Silva, D. R., Sirk, M., Siudek, M., Smith, A., Sprayberry, D., Staten, R., Stupak, B., Tan, T., Tarlé, Gregory, Tie, Suk Sien, Tojeiro, R., Ureña-López, L. A., Valdes, F., Valenzuela, O., Valluri, M., Vargas-Magaña, M., Verde, L., Walther, M., Wang, B., Wang, M. S., Weaver, B. A., Weaverdyck, C., Wechsler, R., Wilson, Michael J., Yang, J., Yu, Y., Yuan, S., Yèche, Christophe, Zhang, H., Zhang, K., Zhao, Cheng, Zhou, Rongpu, Zhou, Zhimin, Zou, H., Zou, J., Zou, S., Zu, Y., Aguilar, J. [0000-0003-0822-452X], Ahlen, S. [0000-0001-6098-7247], Alam, Shadab [0000-0002-3757-6359], Alexander, David M. [0000-0002-5896-6313], Allen, L. [0000-0002-7789-5119], Prieto, C. Allende [0000-0002-0084-572X], Ameel, J. [0000-0003-3638-2584], Asorey, J. [0000-0002-6211-499X], Bailey, S. [0000-0003-4162-6619], Balaguera-Antolínez, A. [0000-0001-5028-3035], Ballester, O. [0000-0002-7126-5300], Bault, A. [0000-0002-9964-1005], Beltran, S. F. [0000-0001-6324-4019], Berti, A. [0000-0003-3582-6649], Beutler, Florian [0000-0003-0467-5438], Bose, S. [0000-0002-0974-5266], Brieden, S. [0000-0003-3896-9215], Brodzeller, A. [0000-0002-8934-0954], Brooks, D. [0000-0002-8458-5047], Cahn, R. N. [0000-0003-2748-0641], Cai, Z. [0000-0001-8467-6478], Capasso, R. [0000-0002-3083-6840], Rosell, A. Carnero [0000-0003-3044-5150], Castander, F. J. [0000-0001-7316-4573], Cervantes-Cota, J. L. [0000-0002-3057-6786], Chabanier, S. [0000-0002-5692-5243], Chaussidon, E. [0000-0001-8996-4874], Chuang, C. [0000-0002-3882-078X], Cole, S. [0000-0002-5954-7903], Cooper, A. P. [0000-0001-8274-158X], Cuceu, A. [0000-0002-2169-0595], Davis, T. M. [0000-0002-4213-8783], Dawson, K. [0000-0002-0553-3805], Costa, J. Della [0000-0003-0928-2000], Dey, A. [0000-0002-4928-4003], Dey, B. [0000-0002-5665-7912], Dhungana, G. [0000-0002-5402-1216], Ding, Z. [0000-0002-3369-3718], Douglass, K. [0000-0002-9540-546X], Duan, Y. [0000-0002-2611-0895], Eisenstein, D. J. [0000-0002-2929-3121], Escoffier, S. [0000-0002-2847-7498], Fan, X. [0000-0003-3310-0131], Fawcett, V. A. [0000-0003-1251-532X], Ereza, J. [0000-0002-0194-4017], Frenk, C. S. [0000-0002-2338-716X], Gänsicke, B. T. [0000-0002-2761-3005], Garrison, L. [0000-0002-9853-5673], Gaztañaga, E. [0000-0001-9632-0815], Gonzalez-Morales, Alma X. [0000-0003-4089-6924], Gonzalez-de-Rivera, G. [0000-0003-4452-743X], Gonzalez-Perez, V. [0000-0001-9938-2755], Graur, O. [0000-0002-4391-6137], Green, D. [0000-0002-0676-3661], Gruen, D. [0000-0003-3270-7644], Hahn, C. [0000-0003-1197-0902], Herrera, D. [0000-0003-2092-6727], Herrera-Alcantar, Hiram K. [0000-0002-9136-9609], Huterer, D. [0000-0001-6558-0112], Iršič, V. [0000-0002-5445-461X], Ishak, M. [0000-0002-6024-466X], Jiang, L. [0000-0003-4176-6486], Jing, Y. P. [0000-0002-4534-3125], Joyce, R. [0000-0003-0201-5241], Jullo, E. [0000-0002-9253-053X], Juneau, S. [0000-0002-0000-2394], Karaçaylı, N. G. [0000-0001-7336-8912], Karamanis, M. [0000-0001-9489-4612], Karim, T. [0000-0002-5652-8870], Kehoe, R. [0000-0002-7101-697X], Kent, S. [0000-0003-4207-7420], Kirkby, D. [0000-0002-8828-5463], Kisner, T. [0000-0003-3510-7134], Koposov, S. E. [0000-0003-2644-135X], Kovács, A. [0000-0002-5825-579X], Kremin, A. [0000-0001-6356-7424], L’Huillier, B. [0000-0003-2934-6243], Landriau, M. [0000-0003-1838-8528], Lang, D. [0000-0002-1172-0754], Lasker, J. [0000-0003-2999-4873], Guillou, L. Le [0000-0001-7178-8868], Leauthaud, A. [0000-0002-3677-3617], Van Suu, A. Le [0000-0001-5488-783X], Levi, Michael E. [0000-0003-1887-1018], Li, T. S. [0000-0002-9110-6163], Manser, Christopher J. [0000-0003-1543-5405], Martini, Paul [0000-0002-0194-4017], McDonald, P. [0000-0001-8346-8394], Meisner, Aaron M. [0000-0002-1125-7384], Mena-Fernández, J. [0000-0001-9497-7266], Meneses-Rizo, J. [0000-0003-3201-9788], Miquel, R. [0000-0002-6610-4836], Moustakas, J. [0000-0002-2733-4559], Nadathur, S. [0000-0001-9070-3102], Neilsen, E. [0000-0002-7357-0317], Newman, Jeffrey A. [0000-0001-8684-2222], Nie, J. D. [0000-0001-6590-8122], Ning, Y. [0000-0001-9442-1217], Niz, G. [0000-0002-1544-8946], Norberg, P. [0000-0002-5875-0440], Noriega, Hernán E. [0000-0002-3397-3998], Obuljen, A. [0000-0002-9012-6621], Palanque-Delabrouille, N. [0000-0003-3188-784], PENG, X. [0000-0002-3784-830X], Percival, W. J. [0000-0002-0644-5727], Pogge, R. [0000-0003-1435-3053], Porredon, A. [0000-0002-2762-2024], Prada, F. [0000-0001-7145-8674], Prochaska, J. [0000-0002-7738-6875], Pucha, R. [0000-0002-4940-3009], Pérez-Ràfols, I. [0000-0001-6979-0125], Rabinowitz, D. [0000-0003-4961-7653], Raichoor, A. [0000-0001-5999-7923], Rezaie, M. [0000-0001-5589-7116], Rockosi, C. [0000-0002-6667-7028], Roodman, A. [0000-0001-5326-3486], Sabiu, C. G. [0000-0002-5513-5303], Safonova, S. [0000-0002-2240-7421], Said, K. [0000-0002-1809-6325], Saintonge, A. [0000-0003-4357-3450], Samushia, L. [0000-0002-1609-5687], Sanchez, E. [0000-0002-9646-8198], Saulder, C. [0000-0002-0408-5633], Schaan, E. [0000-0002-4619-8927], Schlegel, D. [0000-0002-5042-5088], Secroun, A. [0000-0003-0505-3710], Seo, H. [0000-0002-6588-3508], Sharples, Ray M. [0000-0003-3449-8583], Silber, Joseph Harry [0000-0002-3461-0320], Silva, D. R. [0000-0002-7678-2155], Sprayberry, D. [0000-0001-7583-6441], Tarlé, Gregory [0000-0003-1704-0781], Tie, Suk Sien [0000-0002-5249-1353], Valdes, F. [0000-0001-5567-1301], Valenzuela, O. [0000-0002-0523-5509], Valluri, M. [0000-0002-6257-2341], Verde, L. [0000-0003-2601-8770], Walther, M. [0000-0002-1748-3745], Wang, B. [0000-0003-4877-1659], Wang, M. S. [0000-0002-2652-4043], Wechsler, R. [0000-0003-2229-011X], Yang, J. [0000-0001-5287-4242], Yu, Y. [0000-0002-9359-7170], Yuan, S. [0000-0002-5992-7586], Yèche, Christophe [0000-0001-5146-8533], Zhang, H. [0000-0001-6847-5254], Zhang, K. [0000-0002-9808-3646], Zhao, Cheng [0000-0002-1991-7295], Zhou, Rongpu [0000-0001-5381-4372], Zhou, Zhimin [0000-0002-4135-0977], Zou, H. [0000-0002-6684-3997], Zou, J. [0000-0001-9189-0368], Zou, S. [0000-0002-3983-6484], Zu, Y. [0000-0001-6966-6925], Apollo - University of Cambridge Repository, University of St Andrews. School of Physics and Astronomy, Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Observatoire de Haute-Provence (OHP), Institut Pythéas (OSU PYTHEAS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Centre National de la Recherche Scientifique (CNRS), Centre de Physique des Particules de Marseille (CPPM), Aix Marseille Université (AMU)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Astrophysique de Marseille (LAM), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique Nucléaire et de Hautes Énergies (LPNHE (UMR_7585)), Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), DESI, HEP, INSPIRE, and Ministerio de Ciencia e Innovación (España)

Subjects
Cosmology and Nongalactic Astrophysics (astro-ph.CO), FOS: Physical sciences, redshift 0.6, Settore FIS/05 - Astronomia e Astrofisica, QB Astronomy, [PHYS.PHYS.PHYS-INS-DET]Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], Instrumentation and Methods for Astrophysics (astro-ph.IM), QC, QB, MCC, Astronomy and Astrophysics, DAS, space, distortions, peak, Laboratory Astrophysics, Instrumentation, Software, and Data, QC Physics, Space and Planetary Science, [PHYS.PHYS.PHYS-INS-DET] Physics [physics]/Physics [physics]/Instrumentation and Detectors [physics.ins-det], astro-ph.CO, galaxy sample, power-spectrum, Astrophysics - Instrumentation and Methods for Astrophysics, [PHYS.ASTR] Physics [physics]/Astrophysics [astro-ph], [PHYS.ASTR]Physics [physics]/Astrophysics [astro-ph], growth-rate, Astrophysics - Cosmology and Nongalactic Astrophysics, astro-ph.IM
Abstract

Full list of authors: Abareshi, B.; Aguilar, J.; Ahlen, S.; Alam, Shadab; Alexander, David M.; Alfarsy, R.; Allen, L.; Allende Prieto, C.; Alves, O.; Ameel, J.; Armengaud, E.; Asorey, J.; Aviles, Alejandro; Bailey, S.; Balaguera-Antolinez, A.; Ballester, O.; Baltay, C.; Bault, A.; Beltran, S. F.; Benavides, B.; BenZvi, S.; Berti, A.; Besuner, R.; Beutler, Florian; Bianchi, D.; Blake, C.; Blanc, P.; Blum, R.; Bolton, A.; Bose, S.; Bramall, D.; Brieden, S.; Brodzeller, A.; Brooks, D.; Brownewell, C.; Buckley-Geer, E.; Cahn, R. N.; Cai, Z.; Canning, R.; Capasso, R.; Carnero Rosell, A.; Carton, P.; Casas, R.; Castander, F. J.; Cervantes-Cota, J. L.; Chabanier, S.; Chaussidon, E.; Chuang, C.; Circosta, C.; Cole, S.; Cooper, A. P.; da Costa, L.; Cousinou, M-C; Cuceu, A.; Davis, T. M.; Dawson, K.; De la Cruz-Noriega, R.; de la Macorra, A.; de Mattia, A.; Della Costa, J.; Demmer, P.; Derwent, M.; Dey, A.; Dey, B.; Dhungana, G.; Ding, Z.; Dobson, C.; Doel, P.; Donald-McCann, J.; Donaldson, J.; Douglass, K.; Duan, Y.; Dunlop, P.; Edelstein, J.; Eftekharzadeh, S.; Eisenstein, D. J.; Enriquez-Vargas, M.; Escoffier, S.; Evatt, M.; Fagrelius, P.; Fan, X.; Fanning, K.; Fawcett, V. A.; Ferraro, S.; Ereza, J.; Flaugher, B.; Font-Ribera, A.; Forero-Romero, J. E.; Frenk, C. S.; Fromenteau, S.; Gansicke, B. T.; Garcia-Quintero, C.; Garrison, L.; Gaztanaga, E.; Gerardi, F.; Gil-Marin, H.; Gontcho, S. Gontcho A.; Gonzalez-Morales, Alma X.; Gonzalez-de-Rivera, G.; Gonzalez-Perez, V; Gordon, C.; Graur, O.; Green, D.; Grove, C.; Gruen, D.; Gutierrez, G.; Guy, J.; Hahn, C.; Harris, S.; Herrera, D.; Herrera-Alcantar, Hiram K.; Honscheid, K.; Howlett, C.; Huterer, D.; Irsic, V; Ishak, M.; Jelinsky, P.; Jiang, L.; Jimenez, J.; Jing, Y. P.; Joyce, R.; Jullo, E.; Juneau, S.; Karacayli, N. G.; Karamanis, M.; Karcher, A.; Karim, T.; Kehoe, R.; Kent, S.; Kirkby, D.; Kisner, T.; Kitaura, F.; Koposov, S. E.; Kovacs, A.; Kremin, A.; Krolewski, Alex; L'Huillier, B.; Lahav, O.; Lambert, A.; Lamman, C.; Lan, Ting-Wen; Landriau, M.; Lane, S.; Lang, D.; Lange, J. U.; Lasker, J.; Le Guillou, L.; Leauthaud, A.; Suu, A. Le Van; Levi, Michael E.; Li, T. S.; Magneville, C.; Manera, M.; Manser, Christopher J.; Marshall, B.; Martini, Paul; McCollam, W.; McDonald, P.; Meisner, Aaron M.; Mena-Fernandez, J.; Meneses-Rizo, J.; Mezcua, M.; Miller, T.; Miquel, R.; Montero-Camacho, P.; Moon, J.; Moustakas, J.; Mueller, E.; Munoz-Gutierrez, Andrea; Myers, Adam D.; Nadathur, S.; Najita, J.; Napolitano, L.; Neilsen, E.; Newman, Jeffrey A.; Nie, J. D.; Ning, Y.; Niz, G.; Norberg, P.; Noriega, Hernan E.; O'Brien, T.; Obuljen, A.; Palanque-Delabrouille, N.; Palmese, A.; Zhiwei, P.; Pappalardo, D.; Peng, X.; Percival, W. J.; Perruchot, S.; Pogge, R.; Poppett, C.; Porredon, A.; Prada, F.; Prochaska, J.; Pucha, R.; Perez-Fernandez, A.; Perez-Rafols, I; Rabinowitz, D.; Raichoor, A.; Ramirez-Solano, S.; Ramirez-Perez, Cesar; Ravoux, C.; Reil, K.; Rezaie, M.; Rocher, A.; Rockosi, C.; Roe, N. A.; Roodman, A.; Ross, A. J.; Rossi, G.; Ruggeri, R.; Ruhlmann-Kleider, V; Sabiu, C. G.; Safonova, S.; Said, K.; Saintonge, A.; Catonga, Javier Salas; Samushia, L.; Sanchez, E.; Saulder, C.; Schaan, E.; Schlafly, E.; Schlegel, D.; Schmoll, J.; Scholte, D.; Schubnell, M.; Secroun, A.; Seo, H.; Serrano, S.; Sharples, Ray M.; Sholl, Michael J.; Silber, Joseph Harry; Silva, D. R.; Sirk, M.; Siudek, M.; Smith, A.; Sprayberry, D.; Staten, R.; Stupak, B.; Tan, T.; Tarle, Gregory; Tie, Suk Sien; Tojeiro, R.; Urena-Lopez, L. A.; Valdes, F.; Valenzuela, O.; Valluri, M.; Vargas-Magana, M.; Verde, L.; Walther, M.; Wang, B.; Wang, M. S.; Weaver, B. A.; Weaverdyck, C.; Wechsler, R.; Wilson, Michael J.; Yang, J.; Yu, Y.; Yuan, S.; Yeche, Christophe; Zhang, H.; Zhang, K.; Zhao, Cheng; Zhou, Rongpu; Zhou, Zhimin; Zou, H.; Zou, J.; Zou, S.; Zu, Y.; DESI Collaboration.--This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited., The Dark Energy Spectroscopic Instrument (DESI) embarked on an ambitious 5 yr survey in 2021 May to explore the nature of dark energy with spectroscopic measurements of 40 million galaxies and quasars. DESI will determine precise redshifts and employ the baryon acoustic oscillation method to measure distances from the nearby universe to beyond redshift z > 3.5, and employ redshift space distortions to measure the growth of structure and probe potential modifications to general relativity. We describe the significant instrumentation we developed to conduct the DESI survey. This includes: a wide-field, 3fdg2 diameter prime-focus corrector; a focal plane system with 5020 fiber positioners on the 0.812 m diameter, aspheric focal surface; 10 continuous, high-efficiency fiber cable bundles that connect the focal plane to the spectrographs; and 10 identical spectrographs. Each spectrograph employs a pair of dichroics to split the light into three channels that together record the light from 360–980 nm with a spectral resolution that ranges from 2000–5000. We describe the science requirements, their connection to the technical requirements, the management of the project, and interfaces between subsystems. DESI was installed at the 4 m Mayall Telescope at Kitt Peak National Observatory and has achieved all of its performance goals. Some performance highlights include an rms positioner accuracy of better than 0farcs1 and a median signal-to-noise ratio of 7 of the [O ii] doublet at 8 × 10−17 erg s−1 cm−2 in 1000 s for galaxies at z = 1.4–1.6. We conclude with additional highlights from the on-sky validation and commissioning, key successes, and lessons learned. © 2022. The Author(s). Published by the American Astronomical Society., This research is supported by the Director, Office of Science, Office of High Energy Physics of the U.S. Department of Energy under contract No. DE-AC02-05CH11231, and by the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility under the same contract. Additional support for DESI is provided by the U.S. National Science Foundation, Division of Astronomical Sciences under contract No. AST-0950945 to the NSF's National Optical-Infrared Astronomy Research Laboratory; the Science and Technologies Facilities Council of the United Kingdom; the Gordon and Betty Moore Foundation; the Heising–Simons Foundation; the French Alternative Energies and Atomic Energy Commission (CEA); the National Council of Science and Technology of Mexico (CONACYT); the Ministry of Science and Innovation of Spain, and by the DESI Member Institutions: Aix-Marseille University; Argonne National Laboratory; Barcelona-Madrid Regional Participation Group; Brookhaven National Laboratory; Boston University; Brazil Regional Participation Group; Carnegie Mellon University; CEA-IRFU, Saclay; China Participation Group; Cornell University; Durham University; École Polytechnique Fédérale de Lausanne; Eidgenössische Technische Hochschule, Zürich; Fermi National Accelerator Laboratory; Granada-Madrid-Tenerife Regional Participation Group; Harvard University; Kansas State University; Korea Astronomy and Space Science Institute; Korea Institute for Advanced Study; Lawrence Berkeley National Laboratory; Laboratoire de Physique Nucléaire et de Hautes Energies; Ludwig Maximilians University; Max Planck Institute; Mexico Regional Participation Group; New York University; NSF's National Optical-Infrared Astronomy Research Laboratory; Ohio University; Perimeter Institute; Shanghai Jiao Tong University; Siena College; SLAC National Accelerator Laboratory; Southern Methodist University; Swinburne University; The Ohio State University; Universidad de los Andes; University of Arizona; University of Barcelona; University of California, Berkeley; University of California, Irvine; University of California, Santa Cruz; University College London; University of Florida; University of Michigan at Ann Arbor; University of Pennsylvania; University of Pittsburgh; University of Portsmouth; University of Queensland; University of Rochester; University of Toronto; University of Utah; University of Waterloo; University of Wyoming; University of Zurich; UK Regional Participation Group; and Yale University. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC; https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement., With funding from the Spanish government through the Severo Ochoa Centre of Excellence accreditation SEV-2017-0709.

Published
2022

29. PCR investigation of infections in patients consulting at a healthcare centre over a four-year period during the Grand Magal of Touba

Author

Ndiaw Goumballa, Masse Sambou, Diouf Fatou Samba, Hubert Bassene, Marielle Bedotto, Adama Aidara, Mamadou Dieng, Van Thuan Hoang, Philippe Parola, Cheikh Sokhna, Philippe Gautret, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Maladies infectieuses persistantes et émergentes en Afrique de l’Ouest [Dakar, Sénégal] (Equipe 3 - VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Infectious Diseases, [SDV]Life Sciences [q-bio], Public Health, Environmental and Occupational Health
Abstract

Respiratory and gastrointestinal symptoms and febrile illness are the most common complaints among ill pilgrims attending the Grand Magal of Touba (GMT) in Senegal.Patients presenting with respiratory or gastrointestinal symptoms or febrile systemic illnesses were recruited between 2018 and 2021 at a healthcare centre close to Touba. Respiratory, gastrointestinal and blood samples were tested for potential pathogens using qPCR.538 patients were included. 45.5% of these were female, with a median age of 17 years. Of the 326 samples collected from patients with a cough, 62.8% tested positive for at least one virus, including influenza viruses (33.1%). A high positivity rate of bacterial carriage was observed for Haemophilus influenzae (72.7%), Streptococcus pneumoniae (51.2%) and Moraxella catarrhalis (46.0%). Of the 95 samples collected from patients with diarrhoea, 71.3% were positive, with high rates of bacterial carriage, ranging from 4.2% for Tropheryma whipplei to 45.3% for Entero-pathogenic Escherichia coli. Of the 141 blood samples collected from patients with fever, 31.9% were positive including Plasmodium falciparum (21.3%), Borrelia sp. (5.7%) and dengue virus (5.0%).This study provides insight into the aetiology of most common infections at the GMT on which to base therapeutic options.

Published
2022

30. Sodium Oxybate for Alcohol Dependence: A Network Meta-Regression Analysis Considering Population Severity at Baseline and Treatment Duration

Author

Julien Guiraud, Giovanni Addolorato, Henri-Jean Aubin, Sylvie Bachelot, Philippe Batel, Andrea de Bejczy, Amine Benyamina, Fabio Caputo, Monique Couderc, Maurice Dematteis, Anna E Goudriaan, Antoni Gual, Sylvie Lecoustey, Otto-Michael Lesch, Icro Maremmani, David J Nutt, François Paille, Pascal Perney, Jürgen Rehm, Benjamin Rolland, Bruno Scherrer, Nicolas Simon, Bo Söderpalm, Lorenzo Somaini, Wolfgang H Sommer, Rainer Spanagel, Henriette Walter, Wim van den Brink, University of Amsterdam [Amsterdam] (UvA), Università cattolica del Sacro Cuore = Catholic University of the Sacred Heart [Roma] (Unicatt), Fondazione Policlinico Universitario A. Gemelli [Rome] (FPUAG), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Hôpital Paul Brousse, D&A Pharma Paris - Laboratoires pharmaceutiques (DAPP), University of Gothenburg (GU), Università degli Studi di Ferrara = University of Ferrara (UniFE), Université Grenoble Alpes - UFR Médecine (UGA UFRM), Université Grenoble Alpes (UGA), CHU Grenoble, Amsterdam Public Health Research Institute [The Netherlands], Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona (UB), Medizinische Universität Wien = Medical University of Vienna, University of Pisa - Università di Pisa, Imperial College London, Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Centre Hospitalier Universitaire de Nîmes (CHU Nîmes), Centre for Addiction and Mental Health [Toronto] (CAMH), Technische Universität Dresden = Dresden University of Technology (TU Dresden), I.M. Sechenov First Moscow State Medical University [Moscow, Russia] (MSMU), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Bruno Scherrer Conseil [Saint Arnoult en Yvelines] (BSC), 'Cancer, Biomedicine & Society' group (SESSTIM - U1252 INSERM - AMU - UMR 259 IRD), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hôpital Sainte-Marguerite [CHU - APHM] (Hôpitaux Sud ), Addiction Treatment Center [ASL Biella, Italy] (ATC - Local Health Unit), and Universität Heidelberg [Heidelberg] = Heidelberg University

Subjects
[SDV]Life Sciences [q-bio], General Medicine
Abstract

AimsThe estimated effect of sodium oxybate (SMO) in the treatment of alcohol dependence is heterogeneous. Population severity and treatment duration have been identified as potential effect modifiers. Population severity distinguishes heavy drinking patients with MethodsNetwork meta-regression allows for testing potential effect modifiers. It was selected to investigate the effect of the above factors on SMO efficacy defined as continuous abstinence (abstinence rate) and the percentage of days abstinent (PDA). Randomized controlled trials for alcohol dependence with at least one SMO group conducted in high-severity and mild-severity populations were assigned to a high-severity and mild-severity group of studies, respectively.ResultsEight studies (1082 patients) were retained: four in the high-severity group and four in the mild-severity group. The high-severity group was associated with larger SMO effect sizes than the mild-severity group: abstinence rate risk ratio (RR) 3.16, P = 0.004; PDA +26.9%, P ConclusionsIn the retained studies with alcohol-dependent patients, high-severity population and longer treatment duration were associated with larger SMO effect sizes.

Published
2022

31. MALDI-TOF MS Identification of Dromedary Camel Ticks and Detection of Associated Microorganisms, Southern Algeria

Author

Fatima Zohra Hamlili, Laroche Maureen, Adama Zan Diarra, Ismail Lafri, Brahim Gassen, Boubaker Boutefna, Bernard Davoust, Idir Bitam, Philippe Parola, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Institut des Sciences Vétérinaires, Laboratoire des Biotechnologies liée à la Reproduction Animale (LBRA), Université Saâd Dahlab Blida 1 (UB1), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), LMI REMEDIER, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Université des Sciences et de la Technologie Houari Boumediene = University of Sciences and Technology Houari Boumediene [Alger] (USTHB)

Subjects
Gassen, Microbiology (medical), [SDV]Life Sciences [q-bio], Laroche, I, Microbiology, Hamlili, M, ticks, I. MALDI-TOF MS ticks Hyalomma camels Anaplasma platys Coxiella burnetii Algeria, Hyalomma, Virology, camels, Diarra, MALDI-TOF MS, A.Z, M. Diarra, A.Z. Lafri, Boutefna, B. Bitam, Davoust, F.Z. Laroche, B. Davoust, Anaplasma platys, B. Boutefna, B, Bitam, Coxiella burnetii, Lafri, Algeria, F.Z, I. Gassen
Abstract

International audience; This study used MALDI-TOF MS and molecular tools to identify tick species infesting camels from Tamanrasset in southern Algeria and to investigate their associated microorganisms. Ninety-one adult ticks were collected from nine camels and were morphologically identified as Hyalomma spp., Hyalomma dromedarii, Hyalomma excavatum, Hyalomma impeltatum and Hyalomma anatolicum. Next, the legs of all ticks were subjected to MALDI-TOF MS, and 88/91 specimens provided good-quality MS spectra. Our homemade MALDI-TOF MS arthropod spectra database was then updated with the new MS spectra of 14 specimens of molecularly confirmed species in this study. The spectra of the remaining tick specimens not included in the MS database were queried against the upgraded database. All 74 specimens were correctly identified by MALDI-TOF MS, with logarithmic score values ranging from 1.701 to 2.507, with median and mean values of 2.199 and 2.172 ± 0.169, respectively. One H. impeltatum and one H. dromedarii (2/91; 2.20%) tested positive by qPCR for Coxiella burnetii, the agent of Q fever. We also report the first detection of an Anaplasma sp. close to A. platys in H. dromedarii in Algeria and a potentially new Ehrlichia sp. in H. impeltatum.

Published
2022

32. Dynamics of mud banks and sandy urban beaches in French Guiana, South America

Author

Morgane Jolivet, Edward J. Anthony, Antoine Gardel, Tanguy Maury, Sylvain Morvan, Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens (LEEISA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS), Plateforme de géochimie isotopique ASTER-CEREGE, Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Géographie de l'environnement (GEODE), Université Toulouse - Jean Jaurès (UT2J), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Global and Planetary Change, Mud banks, Beach management, [SDE]Environmental Sciences, Beach rotation, Beach erosion, Amazon mud, French Guiana
Abstract

International audience; Beach rotation is a widely described process characterized by periodic alternations in sediment transport involving erosion at one end of the beach and accretion at the other. The 1500-km-long coast of the Guianas, South America, is a unique system dominated by large migrating mud banks, muddy, mangrove-rich shorelines, and rare sandy beaches. Interactions between waves and the rare beaches on this coast are affected by the mud banks which are separated by 'inter-bank' areas. Kourou beach is situated near the site of the European Space Agency's satellite-launching pad in French Guiana. The beach has maintained multi-decadal stability, but its interaction with mud banks has led to phases of severe erosion. To understand these changes, which constitute a risk for the urban front of Kourou, we combined a mesoscale temporal (1950-2017) analysis of shoreline fluctuations with a short-term approach based on photogrammetric monitoring of beach change conducted in 2017-2018 and on bathymetric surveys of the nearshore zone. The results show that Kourou beach evolves in a context of 'rotation', a process involving periodic alternations in beach erosion and recovery. Rotation is characterized during interbank phases by 'normal' sand transport to the northwest generated by the prevailing NE waves, and during mud-bank phases by drift reversal to the southeast generated by refraction of these waves at the leading front of a bank. Due to the aperiodic nature of these bank and inter-bank phases, erosion and accretion involved in beach rotation may prevail over variable periods of time (several years to decades). The large mud banks migrating from east to west first protect the southeastern sector of the beach, blocking the 'normal' northwestward longshore sand transport, but generating, through differential refraction, southeastward counter-drift. These processes and the irregular timescale of beach rotation they entail have not been compatible with the recent urbanization of the beach front in the southeastern sector, resulting in erosion and a sense of threat to beachfront property. Insight gained from an understanding of the rotation process and its irregular timescales should contribute to better beach-front management. Keywords Beach rotation • Beach erosion • Amazon mud • Mud banks • Beach management • French Guiana

Published
2022

33. Diversity of attitudes towards complementary and alternative medicine (CAM) and vaccines: A representative cross-sectional study in France

Author

Jeremy K. Ward, Fatima Gauna, Michael J. Deml, Norah MacKendrick, Patrick Peretti-Watel, CERMES3 - Centre de recherche Médecine, sciences, santé, santé mentale, société (CERMES3 - UMR 8211 / U988 / UM 7), École des hautes études en sciences sociales (EHESS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Institute of Sociological Research, Department of Sociology, University of Geneva, Department of Sociology, Rutgers University, Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Health (social science), [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, History and Philosophy of Science, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience

Published
2023

34. Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal

Author

Anna Julienne Selbé Ndiaye, Mamadou Beye, Gora Lo, Idir Kacel, Aissatou Sow, Nafissatou Leye, Abdou Padane, Aminata Mboup, Halimatou Diop-Ndiaye, Cheikh Sokhna, Coumba Touré Kane, Philippe Colson, Florence Fenollar, Souleymane Mboup, Pierre-Edouard Fournier, Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation [Dakar, Sénégal] (IRESSEF), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Hôpital Aristide-Le-Dantec, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and CHU Aristide Le Dantec

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Senegal, SARS-CoV-2, genomic, epidemiology, SNPs, COVIDSeq, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience; We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic—from March to April 2021—in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.

Published
2023

35. Glutamate optimizes enzymatic activity under high hydrostatic pressure in Desulfovibrio species: effects on the ubiquitous thioredoxin system

Author

H. Gaussier, Corinne Sebban-Kreuzer, Alain Dolla, Olivier Bornet, Nathalie Pradel, E. Champaud, Christian Tamburini, Laetitia Pieulle, Marc Garel, Matthieu Nouailler, Edwige B. Garcin, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Laboratoire d'ingénierie des systèmes macromoléculaires (LISM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Aix Marseille Université (AMU), Aix Marseille Université (AMU), Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de chimie bactérienne (LCB), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), and Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], Thioredoxin reductase, Hydrostatic pressure, Glutamic Acid, glutamate, Microbiology, 03 medical and health sciences, Thioredoxins, 0302 clinical medicine, Protein structure, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, chemistry.chemical_classification, 0303 health sciences, Strain (chemistry), Chemistry, thioredoxin, General Medicine, Adaptation, Physiological, Amino acid, Isoelectric point, Cytoplasm, 030220 oncology & carcinogenesis, Biophysics, hydrostatic pressure, Molecular Medicine, Desulfovibrio, Thioredoxin, co-solute
Abstract

International audience; In piezophilic microorganisms, enzymes are optimized to perform under high hydrostatic pressure. The two major reported mechanisms responsible for such adaptation in bacterial species are changes in amino acids in the protein structure, favoring their activity and stability under high-pressure conditions, and the possible accumulation of micromolecular co-solutes in the cytoplasm. Recently, the accumulation of glutamate in the cytoplasm of piezophilic Desulfovibrio species has been reported under high pressure growth conditions. In this study, analysis of the effect of glutamate on the enzymatic activity of the thioredoxin reductase/thioredoxin enzymatic complex of either a piezosensitive or a piezophilic microorganism confirms its role as a protective co-solute. Analysis of the thioredoxin structures suggests an adaptation both to the presence of glutamate and to high hydrostatic pressure in the enzyme from the piezophilic strain. Indeed, the presence of large surface pockets could counterbalance the overall compression that occurs at high hydrostatic pressure to maintain enzymatic activity. A lower isoelectric point and a greater dipolar moment than that of thioredoxin from the piezosensitive strain would allow the protein from the piezophilic strain to compensate for the presence of the charged amino acid glutamate to interact with its partner.

Published
2021

36. Maternal Age at First Childbirth and Geographical Variation in Hepatitis B Virus Prevalence in Cameroon: Important Role of Mother-to-Child Transmission

Author

Jude Moutchia, Camille Besombes, Gaëtan Texier, Yusuke Shimakawa, Richard Njouom, Arnaud Fontanet, Eva Rumpler, Pascal Crépey, Mathurin Cyrille Tejiokem, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Recherche en Pharmaco-épidémiologie et Recours aux Soins (REPERES), Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP), Centre Pasteur du Cameroun, Réseau International des Instituts Pasteur (RIIP), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), École des Hautes Études en Santé Publique [EHESP] (EHESP), Département Méthodes quantitatives en santé publique (METIS), Centre de Recherches sur l'Action Politique en Europe (ARENES), Université de Rennes (UR)-Institut d'Études Politiques [IEP] - Rennes-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Centre National de la Recherche Scientifique (CNRS), Recherche sur les services et le management en santé (RSMS), Université de Rennes (UR)-École des Hautes Études en Santé Publique [EHESP] (EHESP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 12289, Agence Nationale de Recherches sur le Sida et les Hépatites Virales, Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École des Hautes Études en Santé Publique [EHESP] (EHESP), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)

Subjects
Adult, Male, 0301 basic medicine, Microbiology (medical), Hepatitis B virus, HBsAg, spatial analysis, [SDV]Life Sciences [q-bio], Population, medicine.disease_cause, 03 medical and health sciences, 0302 clinical medicine, Pregnancy, Prevalence, medicine, Humans, Childbirth, demographic health survey (DHS), Cameroon, Pregnancy Complications, Infectious, education, Hepatitis, education.field_of_study, Hepatitis B Surface Antigens, business.industry, Transmission (medicine), Confounding, mother-to-child transmission, virus diseases, Hepatitis B, medicine.disease, Infectious Disease Transmission, Vertical, 3. Good health, 030104 developmental biology, Infectious Diseases, Africa, Female, 030211 gastroenterology & hepatology, business, Maternal Age, Demography
Abstract

Background The prevalence of hepatitis B virus (HBV) infection varies geographically around the world. Yet, its underlying mechanisms are unknown. Using a nationally representative population-based sample from all 58 administrative divisions in Cameroon, we examined the association between median maternal age at first childbirth in a preceding generation, a proxy for the frequency of mother-to-child transmission (MTCT) of HBV in a region, and the risk of chronic HBV infection, defined as positive surface antigen (HBsAg), in the index generation. Methods We estimated a division-specific median maternal age at first childbirth using Demographic Health Surveys (DHSs) conducted in 1991, 1998, 2004, and 2011. We tested HBsAg in 2011 DHS participants. We used maps to display spatial variation. Results In 14 150 participants (median age, 27 years; 51% females), the overall weighted prevalence of HBsAg was 11.9% (95% confidence interval [CI], 11.0 to 12.8), with a wide geographical variation across the divisions (range, 6.3%–23.7%). After adjusting for confounders and spatial dependency, lower maternal age at first childbirth was significantly associated with positive HBsAg at the division level (β, 1.89; 95% CI, 1.26 to 2.52) and at the individual level (odds ratio, 1.20; 95% CI, 1.04 to 1.39). A similar ecological correlation was observed across other African countries. Conclusions The significant association between the maternal age at first childbirth and HBsAg positivity suggests a crucial role of MTCT in maintaining high HBV endemicity in some areas in Cameroon. This underlines an urgent need to effectively prevent MTCT in sub-Saharan Africa.

Published
2021

37. Enteric pathogenic bacteria and resistance gene carriage in the homeless population in Marseille, France

Author

Ly, Tran Duc Anh, Hadjadj, Linda, Hoang, van Thuan, Goumbala, Ndiaw, Dao, Thi Loi, Badiaga, Sekene, Tissot-Dupont, Herve, Brouqui, Philippe, Raoult, Didier, Rolain, Jean-Marc, Gautret, Philippe, Bosson-Vanga, Henriette, Primas, Nicolas, Franetich, Jean-François, Lavazec, Catherine, Gomez, Lina, Ashraf, Kutub, Tefit, Maurel, Soulard, Valérie, Dereuddre-Bosquet, Nathalie, Le Grand, Roger, Donnette, Mélanie, Mustière, Romain, Amanzougaghene, Nadia, Tajeri, Shahin, Suzanne, Peggy, Malzert-Fréon, Aurélie, Rault, Sylvain, Vanelle, Patrice, Hutter, Sébastien, Cohen, Anita, Snounou, Georges, Roques, Pierre, Azas, Nadine, Lagardère, Prisca, Lisowski, Vincent, Masurier, Nicolas, Nguyen, Michel, Paloque, Lucie, Benoit-Vical, Françoise, Verhaeghe, Pierre, Mazier, Dominique, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Thai Binh University of Medicine and Pharmacy, Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
medicine.disease_cause, Microbiology, law.invention, Tropheryma whipplei, 03 medical and health sciences, 0302 clinical medicine, Antibiotic resistance, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, Escherichia coli, Gene, Polymerase chain reaction, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, General Immunology and Microbiology, biology, 030306 microbiology, 1. No poverty, Pathogenic bacteria, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Carriage, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Antibiotic resistance genes
Abstract

We aimed to assess the prevalence of pathogenic bacteria and resistance genes in rectal samples collected among homeless persons in Marseille, France. In February 2014 we enrolled 114 sheltered homeless adults who completed questionnaires and had rectal samples collected. Eight types of enteric bacteria and 15 antibiotic resistance genes (ARGs) were sought by real-time polymerase chain reaction (qPCR) performed directly on rectal samples. ARG-positive samples were further tested by conventional PCR and sequencing. We evidenced a 17.5% prevalence of gastrointestinal symptoms, a 9.6% prevalence of enteric pathogenic bacteria carriage, including Escherichia coli pathotypes (8.7%) and Tropheryma whipplei (0.9%). Only 2 persons carried blaCTX-M-15 resistance genes (1.8%), while other genes, including carbapenemase-encoding genes and colistin-resistance genes, (mcr-1 to mcr-6, mcr-8) were not detected. Our results suggest that sheltered homeless persons in Marseille do not have a high risk of harbouring gastrointestinal antibiotic resistant bacteria.

Published
2021

38. Emergence and outcomes of the SARS-CoV-2 ‘Marseille-4’ variant

Author

Christian Devaux, Jean-Christophe Lagier, Didier Raoult, Lucile Pinault, Marielle Bedotto, Florence Fenollar, Philippe Colson, Anthony Levasseur, Philippe Gautret, Ludivine Brechard, Pierre-Edouard Fournier, Jeremy Delerce, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Microbiology (medical), [SDV]Life Sciences [q-bio], Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Spike, Infectious and parasitic diseases, RC109-216, Genome, Viral, medicine.disease_cause, Genome, Article, 03 medical and health sciences, 0302 clinical medicine, biology.animal, medicine, Animals, Humans, 030212 general & internal medicine, Variant, Mink, Epidemics, Clade, Phylogeny, Whole genome sequencing, Mutation, Whole Genome Sequencing, biology, Molecular epidemiology, SARS-CoV-2, COVID-19, Outbreak, General Medicine, Virology, 3. Good health, Marseille-4, Infectious Diseases, Reinfection, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, France, Mutations
Abstract

International audience; Background: In Marseille, France, following a first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in March-May 2020, a second epidemic phase occurred from June, involving 10 new variants. The Marseille-4 variant caused an epidemic that started in August and is still ongoing. Methods: The 1038 SARS-CoV-2 whole genome sequences obtained in our laboratory by next-generation sequencing with Illumina technology were analysed using Nextclade and nextstrain/ncov pipelines and IQ-TREE. A Marseille-4-specific qPCR assay was implemented. Demographic and clinical features were compared between patients with the Marseille-4 variant and those with earlier strains. Results: Marseille-4 harbours 13 hallmark mutations. One leads to an S477N substitution in the receptor binding domain of the spike protein targeted by current vaccines. Using a specific qPCR, it was observed that Marseille-4 caused 12-100% of SARS-CoV-2 infections in Marseille from September 2020, being involved in 2106 diagnoses. This variant was more frequently associated with hypoxemia than were clade 20A strains before May 2020. It caused a re-infection in 11 patients diagnosed with different SARS-CoV-2 strains before June 2020, suggesting either short-term protective immunity or a lack of cross-immunity. Conclusions: Marseille-4 should be considered as a major SARS-CoV-2 variant. Its sudden appearance points towards an animal reservoir, possibly mink. The protective role of past exposure and current vaccines against this variant should be evaluated.

Published
2021

39. Self-Peptidome Variation Shapes Individual Immune Responses

Author

Laurent Abi-Rached, Jung-Hua Yeh, Julien Paganini, Pierre Pontarotti, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Opinion, [SDV]Life Sciences [q-bio], T cell, Receptors, Antigen, T-Cell, Peptide, Immune responses, Human genetic variation, Disease, Human leukocyte antigen, Biology, Epitope, Epitopes, 03 medical and health sciences, 0302 clinical medicine, Immune system, Genetics, medicine, Humans, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Polymorphism, Genetic, Histocompatibility Antigens Class I, T-cell receptor, Histocompatibility Antigens Class II, Immunity, 3. Good health, HLA, medicine.anatomical_structure, [SDV.IMM.IA]Life Sciences [q-bio]/Immunology/Adaptive immunology, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, chemistry, Inherent Modulator Epitopes, Disease Susceptibility, T cell receptor, Peptides, TCR, 030217 neurology & neurosurgery
Abstract

The relationship between human genetic variation and disease has not been fully elucidated. According to the present view on infectious diseases pathogen resistance is linked to human leukocyte antigen (HLA) class I/II variants and their individual capacity to present pathogen-derived peptides. Yet, T cell education in the thymus occurs through negative and positive selection, and both processes are controlled by a combination of HLA class I/II variants and peptides from the self. Therefore, the capacity of given HLA class I/II variants to bind pathogen-derived peptides is only one part of the selective process to generate effective immune responses. We thus propose that peptidome variation contributes to shaping T cell receptor (TCR) repertoires and hence individual immune responses, and that this variation represents inherent modulator epitopes., Highlights TCR repertoires emerge in the thymus in each individual as T cells undergo positive and negative selection. T cell education is controlled by the combination of HLA class I/II molecules and their peptide pools (peptidome). HLA class I/II molecules are highly plastic in human populations but the peptidome is also a source of variation. Hence combined diversity of HLA class I/II molecules and of self-peptides shapes individual immune responses. Self-peptide variants that affect T cell repertoires represent inherent modulator epitopes.

Published
2021

40. The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule

Author

Philippe Colson, Philippe Gautret, Jeremy Delerce, Hervé Chaudet, Pierre Pontarotti, Patrick Forterre, Raphael Tola, Marielle Bedotto, Léa Delorme, Wahiba Bader, Anthony Levasseur, Jean‐Christophe Lagier, Matthieu Million, Nouara Yahi, Jacques Fantini, Bernard La Scola, Pierre‐Edouard Fournier, Didier Raoult, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Hôpital de la Timone [CHU - APHM] (TIMONE), Unité de Neurobiologie des canaux Ioniques et de la Synapse (UNIS - Inserm U1072), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), This work was supported by the French Government under the 'Investments for the Future' program managed by the National Agency for Research (ANR) (Méditerranée-Infection 10-IAHU-03), by the Région Provence Alpes Côte d'Azur and European funding FEDER PRIMMI (Fonds Européen de Développement Régional-Plateformes de Recherche et d'Innovation Mutualisées Méditerranée Infection) (FEDER PA 0000320 PRIMMI), and by the French Ministry of Higher Education, Research and Innovation (Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation) and the French Ministry of Solidarity and Health (Ministère des Solidarités et de la Santé)., ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), Pontarotti, Pierre, Instituts Hospitalo-Universitaires - I.H.U. Méditerranée Infection - - Méditerranée Infection2010 - ANR-10-IAHU-0003 - IAHU - VALID, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, variants, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, ORF8, Pangolin B.1.1.160, epidemic, SARS‐CoV‐2, Infectious Diseases, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Marseille‐4, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract

International audience; The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS-CoV-2 variants causing successive waves are complex. We determined the kinetics of the most common French variant (“Marseille-4”) for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next-generation sequencing. We identified two subvariants, Marseille-4A, which contains 22 different lineages of at least 50 genomes, and Marseille-4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell-shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille-4B emerged when the other Marseille-4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS-CoV-2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak.

Published
2022

41. SARS-CoV-2 quasi-species analysis from patients with persistent nasopharyngeal shedding

Author

Pierre Dudouet, Philippe Colson, Sarah Aherfi, Anthony Levasseur, Mamadou Beye, Jeremy Delerce, Emilie Burel, Philippe Lavrard, Wahiba Bader, Jean-Christophe Lagier, Pierre-Edouard Fournier, Bernard La Scola, Didier Raoult, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
Quasispecies, Multidisciplinary, SARS-CoV-2, [SDV]Life Sciences [q-bio], Humans, COVID-19, Prospective Studies
Abstract

At the time of a new and unprecedented viral pandemic, many questions are being asked about the genomic evolution of SARS-CoV-2 and the emergence of different variants, leading to therapeutic and immune evasion and survival of this genetically highly labile RNA virus. The nasopharyngeal persistence of infectious virus beyond 17 days proves its constant interaction with the human immune system and increases the intra-individual mutational possibilities. We performed a prospective high-throughput sequencing study (ARTIC Nanopore) of SARS-CoV-2 from so-called "persistent" patients, comparing them with a non-persistent population, and analyzing the quasi-species present in a single sample at time t. Global intra-individual variability in persistent patients was found to be higher than in controls (mean 5.3%, Standard deviation 0.9 versus 4.6% SD 0.3, respectively, p

Published
2022

42. Distribution and accumulation of metals and metalloids in planktonic food webs of the Mediterranean Sea (MERITE-HIPPOCAMPE campaign)

Author

Sandrine Chifflet, Nicolas Briant, Javier Angel Tesán-Onrubia, Noureddine Zaaboub, Sirine Amri, Olivier Radakovitch, Daniela Bǎnaru, Marc Tedetti, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut National des Sciences et Technologies de la Mer [Salammbô] (INSTM), Laboratoire de recherche sur les transferts des radionucléides dans les écosystèmes aquatiques (IRSN/PSE-ENV/SRTE/LRTA), Service de recherche sur les transferts et les effets des radionucléides sur les écosystèmes (IRSN/PSE-ENV/SRTE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN)-Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MERITE-HIPPOCAMPE project, ANR-19-CE34-0001,CONTAMPUMP,Plancton: pompe biologique de contaminants dans les écosystèmes marins (CONTAMPUMP)?(2019), Aix Marseille Université (AMU), and The MERITE-HIPPOCAMPE project was initiated and funded by the cross-disciplinary 'Pollution & Contaminants' axis of the CNRS-INSU MISTRALS program (joint action of the MERMEX-MERITE and CHARMEX subprograms). The project also received the financial support from the Franco-Tunisian International Joint Laboratory (LMI) COSYS-Med.

Subjects
Metals and metalloids, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, [SDE.MCG]Environmental Sciences/Global Changes, [SDE]Environmental Sciences, Mediterranean Sea, Contamination, planktonic food webs, Aquatic Science, [CHIM.INOR]Chemical Sciences/Inorganic chemistry, Oceanography, Pollution, Biomagnification
Abstract

International audience; Particle-size classes (7 fractions from 0.8 to 2000 µm) were collected in the deep chlorophyll maximum along a Mediterranean transect including the northern coastal zone (bays of Toulon and Marseilles, France), the offshore zone (near the North Balearic Thermal Front), and the southern coastal zone (Gulf of Gabès, Tunisia). Concentrations of biotic metals and metalloids (As, Cd, Cr, Cu, Fe, Mn, Ni, Sb, V, Zn) bound to living or dead organisms and faecal pellets were assessed by phosphorus normalisation. Biotic metals and metalloids concentrations (except Cr, Mn, and V) were higher in the offshore zone than in the coastal zones. In addition, biotic Sb and V concentrations appeared to be affected by atmospheric deposition, and biotic Cr concentrations appeared to be affected by local anthropogenic inputs. Essential elements (Cd, Cu, Fe, Mn, Ni, V, Zn) were very likely controlled both by the metabolic activity of certain organisms (nanoeukaryotes, copepods) and trophic structure. In the northern coastal zone, biomagnification of essential elements was controlled by copepods activities. In the offshore zone, metals and metalloids were not biomagnified probably due to homeostasis regulatory processes in organisms. In the southern coastal zone, biomagnification of As, Cu, Cr, Sb could probably induce specific effects within the planktonic network.

Published
2022

43. Viral life strategies in a heavily anthropized tropical lagoon

Author

Harilanto Felana Andrianjakarivony, Christelle Desnues, Philippe Cecchi, Yvan Bettarel, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Institut de Recherche pour le Développement (IRD)

Subjects
Bacteria, [SDE.MCG]Environmental Sciences/Global Changes, Ammonium Compounds, Viruses, Genetics, Water, Eutrophication, Molecular Biology, Microbiology
Abstract

Ecological traits of aquatic microorganisms have been poorly investigated in tropical latitudes, especially in lagoons, which are often subjected to strong anthropogenic influence, conducive to microbial development. In this study, we examined the abundance of both viral and bacterial communities, as well as their interactions (lytic and lysogenic infections) in the water and sediment of seven main stations of the Ebrié Lagoon (Ivory Coast) with contrasting levels of eutrophication. The highest bacterial and viral concentrations in both planktonic and benthic samples were found in the most eutrophicated stations, where viral lytic infections also exhibited their highest values. Conversely, the highest fractions of inducible lysogens were measured in the most oligotrophic stations, suggesting that these two main viral life strategies are mutually exclusive in this lagoon. Our findings also revealed the importance that nutrients (especially ammonium) play as drivers of the interactions between viruses and their bacterial hosts in tropical lagoons.

Published
2022

44. First glacial chronology in Corsica (Western Mediterranean Sea) based on 10Be moraine dating: evidence of two glacier extents since the Last Glacial Maximum

Author

Chenet, Marie, Brunstein, Daniel, Jomelli, Vincent, Team, Aster, Chenet, Marie, Laboratoire de géographie physique : Environnements Quaternaires et Actuels (LGP), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne - UFR Géographie (UP1 UFR08), Université Paris 1 Panthéon-Sorbonne (UP1), Lieux, Identités, eSpaces, Activités (LISA), Université Pascal Paoli (UPP)-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plateforme de géochimie isotopique ASTER-CEREGE, and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDU.STU.GM] Sciences of the Universe [physics]/Earth Sciences/Geomorphology, [SDU.STU.GM]Sciences of the Universe [physics]/Earth Sciences/Geomorphology, [SDU.STU.GL]Sciences of the Universe [physics]/Earth Sciences/Glaciology, [SDU.STU.GL] Sciences of the Universe [physics]/Earth Sciences/Glaciology
Abstract

The timing of past glacier fluctuations is poorly constrained in Corsica island (Western Mediterranean Sea). Although several glacial landforms and deposits were described, there are no absolute glacial chronology. We will present 19 new 10Be cosmic-ray exposure ages (CRE) of boulders collected from 4 moraines located in the area of the Bastani Lake (Monte Renoso, Northern Corsica). For the first time on a Mediterranean island, mountain glacier fluctuations are documented from moraine CRE for the Lateglacial Period. Two main glacier advances since the Last Glacial Maximum are identified. 12 boulders of three moraines dated between 14.98 ± 0.89 ka BP and 18.88 ± 1.04 ka BP reveal a glacier extent during the Oldest Dryas (Heinrich Stadial 1 - HS1). 5 boulders of one moraine dated between 12.13 ± 0.69 ka BP and 13.93 ± 0.79 ka BP are attributed to the Late Glacial–Younger Dryas transition. Results and associated past Equilibrium Line Altitude will be compared with those in the Mediterranean mountain ranges. Implications for regional climatic conditions will be discussed.

Published
2022

45. Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon

Author

Sonia Etenna Lekana-Douki, Nadine N'dilimabaka, Anthony Levasseur, Philippe Colson, Julia Cyrielle Andeko, Ornella Zong Minko, Octavie Banga Mve-Ella, Pierre-Edouard Fournier, Christian Devaux, Bertrand Mve Ondo, Falone Larissa Akombi, Laurianne Yacka Mouele Bolo, Audrey Michel Ngonga Dikongo, Abdoulaye Diané, Arsène Mabika Mabika, Jenny Francine Mathouet, Cresh Dzembo, Nick Chenis Atiga, Anicet Mouity Matoumba, Nal Kennedy Ndjangangoye, Ludivine Bréchard, Marielle Bedotto-Buffet, Joa Braithe Mangombi Pambou, Marisca Kandet Yattara, Elvire Anita Mbongo Nkama, Armel Mintsa Ndong, Ayola Akim Adegnika, Didier Raoult, Florence Fenollar, Jean-Bernard Lekana-Douki, Centre International de Recherches Médicales de Franceville (CIRMF), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience; Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.

Published
2022

46. Diagnostic Accuracy of LDBIO-Toxo II IgG and IgM Western Blot in Suspected Seroconversion in Pregnancy: A Multicentre Study

Author

Valeria Meroni, Francesca Genco, Luigia Scudeller, Marie-Pierre Brenier-Pinchart, Hélène Fricker-Hidalgo, Coralie L’Ollivier, Luc Paris, Hervé Pelloux, Università degli Studi di Pavia = University of Pavia (UNIPV), Fondazione IRCCS Policlinico San Matteo [Pavia], Sant'Orsola-Malpighi Hospital [Bologna, Italy], Centre Hospitalier Universitaire [Grenoble] (CHU), Université Grenoble Alpes (UGA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Sorbonne Université (SU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Service de Parasitologie - Mycologie [CHU Pitié-Salpétrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and COMBE, Isabelle

Subjects
[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Microbiology (medical), [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, IgM, western blot, General Immunology and Microbiology, IgG, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC] Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, toxoplasmosis, seroconversion, pregnancy, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Immunology and Allergy, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Biology, [SDV.MP.PAR] Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Abstract

International audience; The high sensitivity of the automated tests used for Toxoplasma gondii serology can yield false-positive IgM results due to aspecific reactions. On the other hand, specific therapy can delay IgG production and, therefore, the diagnosis of seroconversion. There is a need for confirmation tests to early detect seroconversions during pregnancy. We conducted a multicentre study to evaluate the diagnostic accuracy of the Toxo II IgG and a new, not yet commercialised Toxo II IgM western blot (WB) (LDBio diagnostics Lyon France) on 229 sera corresponding to 93 patients with seroconversions and 158 sera corresponding to 68 patients with nonspecific IgM. Sensitivity was 97.8% for IgM WB and 98.9% for IgG WB. Specificity was 89.7% and 100%, respectively. The concordance between IgM and IgG Toxo WB with the final diagnosis was very good, K = 0.89 and K = 0.99, respectively. In 5 cases (5.4%), the appearance of IgM, and in 55 cases (59.1%), the appearance of IgG was recorded by WB earlier than by traditional tests. In 10 cases (10.8%), IgM was detected after the traditional tests and in 2 cases (2.2%) for IgG. The association of IgG and IgM WB on the same sample not only detected all seroconversions but also correctly identified most of the false-positive results.

Published
2022

47. Helicobacter pylori outer membrane vesicles induce expression and secretion of oncostatin M in AGS gastric cancer cells

Author

Fadi Abdel-Sater, Bassam Badran, Zaher Zeaiter, Roudaina Nasser, Rouba Hage-Sleiman, Malak Zoaiter, Lebanese University [Beirut] (LU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
Chemokine, medicine.medical_treatment, Population, Oncostatin M, Adenocarcinoma, Microbiology, Helicobacter Infections, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Stomach Neoplasms, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Media Technology, medicine, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Secretion, education, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Oncostatin M Receptor beta Subunit, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, education.field_of_study, Helicobacter pylori, biology, 030306 microbiology, Bacterial and Fungal Pathogenesis - Research Paper, Stomach, fungi, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular biology, 3. Good health, Bacterial Outer Membrane, Cytokine, medicine.anatomical_structure, Gastric Mucosa, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, Gastritis, medicine.symptom, Signal Transduction
Abstract

Helicobacter pylori, a human pathogen that colonizes the stomach of 50% of the world's population, is associated with gastritis, gastric adenocarcinoma, and mucosa-associated lymphoid tissue (MALT) lymphoma. Diseases are characterized by severe inflammatory responses in the stomach that are induced by various chemokines and cytokines. Recently, oncostatin M (OSM), an IL-6 family cytokine, was detected in early gastric cancer biopsies. In this study, we showed that Helicobacter pylori induced secretion of OSM and overexpression of its type II receptor OSMRβ (OSM/OSMRβ) in a human gastric adenocarcinoma cell line (AGS) over 24 h of infection. Furthermore, we showed that the induction of OSM and OSMRβ was carried out by heat-sensitive Helicobacter pylori outer membrane vesicle (OMV) protein. Collectively, our results established, for the first time, a direct relation between Helicobacter pylori OMVs and the OSM/OSMRβ signaling axis.

Published
2021

48. Vaccine Hesitancy, Acceptance, and Anti-Vaccination: Trends and Future Prospects for Public Health

Author

Noni E. MacDonald, Eve Dubé, Pierre Verger, Jeremy K. Ward, Institut National de Santé Publique du Québec [Canada] (INSPQ), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Dalhousie University [Halifax], and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
medicine.medical_specialty, Resistance (psychoanalysis), Terminology, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, 030225 pediatrics, Political science, Medical consensus, Global health, medicine, Humans, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, Vaccines, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, Public health, Vaccination, Public Health, Environmental and Occupational Health, General Medicine, Public relations, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Immunization, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Anti vaccination, Public Health, business, Forecasting
Abstract

International audience; An often-stated public health comment is that “vaccination is a victim of its own success.” While the scientific and medical consensus on the benefits of vaccination is clear and unambiguous, an increasing number of people are perceiving vaccines as unsafe and unnecessary. The World Health Organization identified “the reluctance or refusal to vaccinate despite availability of vaccines” as one of the 10 threats to global health in 2019. The negative influence of anti-vaccination movements is often named as a cause of increasing vaccine resistance in the public. In this review, we give an overview of the current literature on the topic, beginning by agreeing on terminology and concepts before looking at potential causes, consequences, and impacts of resistance to vaccination.

Published
2021

49. Screening of SARS-CoV-2 among homeless people, asylum-seekers and other people living in precarious conditions in Marseille, France, March–April 2020

Author

Tran Duc Anh Ly, Pierre-Edouard Fournier, Ndiaw Goumballa, Meriem Louni, Kevin Bardy, Hacène Medkour, Thi Loi Dao, Véronique Filosa, Oleg Mediannikov, Vera Esteves-Vieira, Bernard Davoust, Naomie Canard, Philippe Gautret, Van Thuan Hoang, Audrey Borg, Didier Raoult, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, 0301 basic medicine, [SDV]Life Sciences [q-bio], real-time polymerase chain reaction (qPCR), Infectious and parasitic diseases, RC109-216, Real-time polymerase chain reaction, 0302 clinical medicine, Medicine, 030212 general & internal medicine, Child, Aged, 80 and over, Refugees, 1. No poverty, Homelessness, General Medicine, Middle Aged, Systematic testing, 3. Good health, precarious conditions, Infectious Diseases, Child, Preschool, Ill-Housed Persons, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, France, Accommodation, Adult, Microbiology (medical), Asylum-seekers, precarious conditions, Adolescent, Acceptance rate, Refugee, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Article, Young Adult, 03 medical and health sciences, Environmental health, Humans, Aged, SARS-CoV-2, business.industry, Asylum-seekers, Infant, Newborn, Infant, COVID-19, Odds ratio, Confidence interval, Cross-Sectional Studies, Carriage, business, 030217 neurology & neurosurgery, Demography
Abstract

International audience; Background: Surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among sheltered homeless and other vulnerable people might provide the information needed to prevent its spread within accommodation centres. Methods: Data were obtained from 698 participants in different accommodation centres (411 homeless individuals, 77 asylum-seekers, 58 other people living in precarious conditions and 152 employees working in these accommodation centres) who completed questionnaires and had nasal samples collected between 26 March and 17 April 2020. SARS-CoV-2 carriage was assessed by quantitative PCR. Results: We found a high acceptance rate (78.9%) for testing. Overall, 49 people (7.0%) were positive for SARS-CoV-2, including 37 homeless individuals (of 411, 9.0%) and 12 employees (of 152, 7.9%). SARS-CoV-2 positivity correlated with symptoms, although 51% of patients who tested positive did not report respiratory symptoms or fever. Among homeless people, being young (18-34 years) (odds ratio 3.83, 95% confidence interval 1.47-10.0, p = 0.006) and being housed in one specific shelter (odds ratio 9.13, 95% confidence interval 4.09-20.37, p < 0.001) were independent factors associated with SARS-CoV-2 positivity (rates of 11.4% and 20.6%, respectively). Discussion: Symptom screening alone is insufficient to prevent SARS-CoV-2 transmission in vulnerable sheltered people. Systematic testing should be promoted.

Published
2021

50. Science under Covid-19’s magnifying glass: Lessons from the first months of the chloroquine debate in the French press

Author

Émilien Schultz, Jeremy K. Ward, 'Cancer, Biomedicine & Society' group (SESSTIM - U1252 INSERM - AMU - UMR 259 IRD), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), CERMES3 - Centre de recherche Médecine, sciences, santé, santé mentale, société (CERMES3 - UMR 8211 / U988 / UM 7), École des hautes études en sciences sociales (EHESS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and ANR-20-COVI-0102,TRACTRUST (Tracking Trust),Surveiller la confiance et la méfiance: analyser les médias sociaux pour soutenir la réponse de santé publique au Covid-19(2020)

Subjects
2019-20 coronavirus outbreak, [SHS.SOCIO]Humanities and Social Sciences/Sociology, Magnifying glass, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 05 social sciences, 050801 communication & media studies, General Medicine, Ancient history, 050905 science studies, law.invention, 0508 media and communications, Qualitative analysis, law, Pandemic, French press, Sociology, 0509 other social sciences
Abstract

International audience; Since the beginning of the Covid-19 pandemic, all hopes are turned towards science. In this article, we put forward a qualitative analysis of how the French national press covered the issue of chloroquine and hydroxychloroquine during the first months, with a focus on the descriptions of the scientific world. We show that during epidemic outbreaks the various tensions existing within the scientific world are more likely to be presented to the public. In their coverage of hydroxychloroquine, journalists shed light on a variety of aspects of contemporary medical research, ranging from the way scientists approach a given drug, the stages of research on medical treatments, the types of proofs used and the institutional make-up of biomedical research. But in doing so they also presented a series of tensions and disagreements which devolved into public accusations of scientific misconduct and anti-science behaviours.

Published
2021

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