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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. Pericarditis related to post-acute COVID infection: A case report and review of the literature

Author

Nguyen, Nhu Ngoc, Dudouet, Pierre, Dhiver, Catherine, Gautret, 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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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, [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

International audience; Abstract Cardiovascular involvement has been described in acute and recovered COVID-19 patients. Here, we present a case of symptomatic pericarditis with persistent symptoms for at least six months after the acute infection and report 66 published cases of pericarditis in discharged COVID patients. Patient mean age ± SD was 49.7 ± 13.3 years, ranging from 15 to 75 years and 57.6% were female. A proportion of 89.4% patients reported at least one comorbidity, with autoimmune and allergic disorders, hypertension and dyslipidaemia, as the most frequent. Only 8.3% of patients experienced severe symptoms of acute COVID-19. The time between acute COVID and pericarditis symptoms varied from 14 to 255 days. Chest pain (90.9%), tachycardia (60.0%) and dyspnoea (38.2%) were the most frequent symptoms in post-acute pericarditis. A proportion of 45.5% and 87% of patients had an abnormal electrocardiogram and abnormal transthoracic ultrasound, respectively. Colchicine combined with non-steroidal anti-inflammatory drug (NSAID) or acetylsalicylic acid (aspirin) were prescribed to 39/54 (72%) patients. Of them, 12 were switched to corticosteroid therapy due to non-response to the first-line treatment. Only 6 patients had persisting symptoms and were considered as non-respondent to therapy. Our report highlights that pericarditis should be suspected in COVID-19 patients with persistent chest pain and dyspnoea when pulmonary function is normal. Treatment with non-steroidal anti-inflammatory and colchicine is usually effective but corticosteroids are sometimes required.

Published
2023

9. Updated estimation of cutaneous leishmaniasis incubation period in French Guiana

Author

Blaizot, Romain, Fontaine, Albin, Demar, Magalie, Delon, François, D’oleon, Albane de Bonet, Mayet, Aurélie, de Laval, Franck, de Santi, Vincent Pommier, Briolant, Sébastien, Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Université de Guyane (UG), National Reference Center for Leishmania, Cayenne, 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), Service de Santé des Armées, Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Direction Interarmées du Service de Santé en Guyane, 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), and Centre d'épidémiologie et de santé publique des armées [Marseille] (CESPA)

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, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience; Background The cutaneous leishmaniasis (CL) incubation period (IP) is defined as the time between parasite inoculation by sandfly bite and the onset of the first CL lesion. IP distribution is difficult to assess for CL because the date of exposure to an infectious bite cannot be accurately determined in endemic areas. IP current estimates for CL range from 14 days to several months with a median around 30–60 days, as established by a few previous studies in both New and Old Worlds. Methodology We estimated CL incubation period distribution using time-to-event models adapted to interval-censored data based on declared date of travels from symptomatic military personnel living in non-endemic areas that were exposed during their short stays in French Guiana (FG) between January 2001 and December 2021. Principal findings A total of 180 patients were included, of which 176 were men (97.8%), with a median age of 26 years. When recorded, the parasite species was always Leishmania guyanensis (31/180, 17.2%). The main periods of CL diagnosis spread from November to January (84/180, 46.7%) and over March-April (54/180, 30.0%). The median IP was estimated at 26.2 days (95% Credible Level, 23.8–28.7 days) using a Bayesian accelerated failure-time regression model. Estimated IP did not exceed 62.1 days (95% CI, 56–69.8 days) in 95% of cases (95 th percentile). Age, gender, lesion number, lesion evolution and infection date did not significantly modify the IP. However, disseminated CL was significantly associated with a 2.8-fold shortening of IP. Conclusions This work suggests that the CL IP distribution in French Guiana is shorter and more restricted than anticipated. As the incidence of CL in FG usually peaks in January and March, these findings suggest that patients are contaminated at the start of the rainy season.

Published
2023

10. Roman-era alluvial waste in the Vistre de la Fontaine (Nîmes, southeast France): from a sacred spring to a contaminated river

Author

Flaux, Clément, Save, Sabrina, Scrinzi, Maxime, Minvielle Larousse, Nicolas, Vaschalde, Christophe, Renaud, Audrey, Tillier, Margaux, Guihou, Abel, Deschamps, Pierre, Véron, Alain, Mosaïques Archéologie, SARL Amélie, études environnementales & archéologiques, Société SARL Amélie, études environnementales & archéologiques, Aix Marseille Université (AMU), Ecole française de Rome (EFR), 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), 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), and CEREGE APIC 2021

Subjects
lead, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, palaeopollution, [SDE]Environmental Sciences, waste, Geoarchaeology lead isotopes palaeopollution waste Early Roman Empire, Geoarchaeology, isotopes, Early Roman Empire
Abstract

International audience; Abstract The excavation of a palaeochannel at the Vistre de la Fontaine 2-2 archaeological site, 3 km downstream from the ancient city of Nîmes (southeastern France), provided an accumulation sequence covering the last 2,500 years. Trace metal analyses of these alluvial sediments disclosed lead (Pb) contamination during the Early Roman Empire, with concentrations close to 1,000 ppm, a factor of 100 above the local geochemical background. This excess of Pb shows a uniform isotopic signature that may reflect unchanged ore sources, perhaps from the Massif Central or from Great Britain. The Pb peak accompanied visible waste that was transported in the sediments of the Vistre de la Fontaine at the time of the development of the Nîmes urban water supply and drainage network during the Early Roman Empire. This research shows the bimillennial persistence of palaeo-contamination in a peri-urban alluvial plain and the relevance of fluvial sedimentary archives in documenting ancient waste.

Published
2023

11. Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3‐like editing, gene inactivation, and bacterial agents of skin superinfection

Author

Colson, Philippe, Penant, Gwilherm, Delerce, Jeremy, Boschi, Céline, Wurtz, Nathalie, Bedotto, Marielle, Branger, Stéphanie, Brouqui, Philippe, Parola, Philippe, Lagier, Jean‐christophe, Cassir, Nadim, Tissot-Dupont, Hervé, Million, Matthieu, Aherfi, Sarah, La Scola, Bernard, 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), Centre hospitalier d'Avignon, 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, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience

Published
2023

12. Maliibacterium massiliense gen. nov. sp. nov., Isolated from Human Feces and Proposal of Maliibacteriaceae fam. nov

Author

Sory Ibrahima Traore, Cheikh Ibrahima Lo, Maaloum Mossaab, Guillaume Durand, Jean Christophe Lagier, Didier Raoult, Pierre-Edouard Fournier, Florence Fenollar, 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, Applied Microbiology and Biotechnology, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience

Published
2023

13. Tracking Mycoviruses in Public RNAseq Datasets of Malassezia: Three Original Totiviruses Revealed

Author

Boulanouar, Fatima, Ranque, Stéphane, Levasseur, Anthony, 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), 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, Malassezia, dsRNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, fungal host, skin disorders, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, mycovirus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, transcriptomes, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, fungal evolution, Totivirus
Abstract

International audience; Mycoviruses are viruses that selectively infect and multiply in fungal cells. Malassezia is the most abundant fungus on human skin and is associated with a variety of conditions, including atopic eczema, atopic dermatitis, dandruff, folliculitis, pityriasis versicolor, and seborrheic dermatitis. Here, we conducted mycovirome studies on 194 public transcriptomes of Malassezia (2,568,212,042 paired-end reads) screened against all available viral proteins. Transcriptomic data were assembled de novo resulting in 1,170,715 contigs and 2,995,306 open reading frames (ORFs) that were subsequently tracked for potential viral sequences. Eighty-eight virus-associated ORFs were detected in 68 contigs from 28 Sequence Read Archive (SRA) samples. Seventy-five and thirteen ORFs were retrieved from transcriptomes of Malassezia globosa and Malassezia restricta, respectively. Phylogenetic reconstructions revealed three new mycoviruses belonging to the Totivirus genus and named Malassezia globosa-associated-totivirus 1 (MgaTV1); Malassezia restricta-associated-totivirus 1 (MraTV1) and Malassezia restricta-associated-totivirus 2 (MraTV2). These viral candidates extend our understanding of the diversity and taxonomy of mycoviruses as well as their co-evolution with their fungal hosts. These results reflected the unexpected diversity of mycoviruses hidden in public databases. In conclusion, this study sheds light on the discovery of novel mycoviruses and opens the door to study their impact on disease caused by the host fungus Malassezia and globally, their implication in clinical skin disorders.

Published
2023

14. 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

15. Molecular Survey of Rodent-Borne Infectious Agents in the Ferlo Region, Senegal

Author

Joa Braïthe Mangombi-Pambou, Laurent Granjon, Fabien Flirden, Mamadou Kane, Youssoupha Niang, Bernard Davoust, Florence Fenollar, Oleg Mediannikov, Centre International de Recherches Médicales de Franceville (CIRMF), 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), 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), BIOPASS, ISRA-UCAD, Institut de Recherche pour le Développement (IRD [France-Ouest]), 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), This study was supported by the Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, the French National Research Agency under the Investissements d’avenir programme (reference: ANR-10-IAHU-0003) and the fourth Make Our Planet Great Again programme (MOPGA 4). This work was co-funded by the Labex DRIIHM, the French Investissements d’Avenir programme (ANR-11-LABX-0010), which is managed by the ANR., ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), and ANR-11-LABX-0010,DRIIHM / IRDHEI,Dispositif de recherche interdisciplinaire sur les Interactions Hommes-Milieux(2011)

Subjects
rodents, infectious agents, multiple infections, zoonotic diseases, tick-borne zoonotic disease, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genetics, Genetics (clinical)
Abstract

International audience; Zoonotic pathogens are responsible for most infectious diseases in humans, with rodents being important reservoir hosts for many of these microorganisms. Rodents, thus, pose a significant threat to public health. Previous studies in Senegal have shown that rodents harbour a diversity of microorganisms, including human pathogens. Our study aimed to monitor the prevalence of infectious agents in outdoor rodents, which can be the cause of epidemics. We screened 125 rodents (both native and expanding) from the Ferlo region, around Widou Thiengoly, for different microorganisms. Analysis, performed on rodent spleens, detected bacteria from the Anaplasmataceae family (20%), Borrelia spp. (10%), Bartonella spp. (24%) and Piroplasmida (2.4%). Prevalences were similar between native and the expanding (Gerbillus nigeriae) species, which has recently colonised the region. We identified Borrelia crocidurae, the agent responsible for tick-borne relapsing fever, which is endemic in Senegal. We also identified two other not-yet-described bacteria of the genera Bartonella and Ehrlichia that were previously reported in Senegalese rodents. Additionally, we found a potential new species, provisionally referred to here as Candidatus Anaplasma ferloense. This study highlights the diversity of infectious agents circulating in rodent populations and the importance of describing potential new species and evaluating their pathogenicity and zoonotic potential.

Published
2023

16. Borrelia miyamotoi in wild rodents from four different regions of Turkey

Author

Bekir Çelebi, Derya Karataş Yeni, Yusuf Yılmaz, Ferhat Matur, Cahit Babür, Mehmet Ali Öktem, Mustafa Sözen, Ahmet Karataş, Didier Raoult, Oleg Mediannikov, Pierre Edouard Fournier, Ministry of Health, Zoonotic and Vector-Borne Diseases Departmen, Veterinary Control Central Research Institute, Dokuz Eylül Üniversitesi = Dokuz Eylül University [Izmir] (DEÜ), Zonguldak Bülent Ecevit University (BEU), Niğde Ömer Halisdemir University, 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, 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, Insect Science, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Parasitology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Borrelia miyamotoi is a tick-borne zoonotic agent that causes hard tick-borne relapsing fever, an emerging disease in humans. Some small mammalian and bird species are reported to be reservoirs of B. miyamotoi. This study aims to examine Borrelia species present in rodents captured from rural areas of Turkey. Blood samples of rodents were initially screened with Borrelia 16S rRNA qPCR. The Borrelia flaB gene was subsequently amplified by conventional PCR, after which all positive samples were sequenced. Borrelia miyamotoi was observed in nine out of 536 blood samples (1.7%) collected from wild rodents. Phylogenetic analysis showed that all positive samples belonged to the European genotype clade of B. miyamotoi. PCR positivity was 5.3%, 3.7%, and 1.8% in Apodemus uralensis, Apodemus flavicollis, and Myodes glareolus, respectively. Borrelia burgdorferi sensu lato that causes Lyme borreliosis in humans could not be detected in the rodents. In this study, presence of B. miyamotoi DNA is reported for the first time in rodents in Turkey.

Published
2023

17. Cardiovascular Safety of Hydroxychloroquine–Azithromycin in 424 COVID-19 Patients

Author

Matthieu Million, Jean-Christophe Lagier, Jérôme Hourdain, Frédéric Franceschi, Jean-Claude Deharo, Philippe Parola, Philippe Brouqui, 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), Service de cardiologie, Université de la Méditerranée - Aix-Marseille 2-Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE), 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), 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
COVID-19, SARS-CoV-2, hydroxychloroquine, azithromycin, QTc interval, cardiac rhythm, safety, torsades de pointe, [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

Background and Objectives: Hydroxychloroquine (HCQ) combined with azithromycin (AZM) has been widely administered to patients with COVID-19 despite scientific controversies. In particular, the potential of prolong cardiac repolarization when using this combination has been discussed. Materials and Methods: We report a pragmatic and simple safety approach which we implemented among the first patients treated for COVID-19 in our center in early 2020. Treatment contraindications were the presence of severe structural or electrical heart disease, baseline corrected QT interval (QTc) > 500 ms, hypokalemia, or other drugs prolonging QTc that could not be interrupted. Electrocardiogram and QTc was evaluated at admission and re-evaluated after 48 h of the initial prescription. Results: Among the 424 consecutive adult patients (mean age 46.3 ± 16.1 years; 216 women), 21.5% patients were followed in conventional wards and 78.5% in a day-care unit. A total of 11 patients (2.6%) had contraindications to the HCQ-AZ combination. In the remaining 413 treated patients, there were no arrhythmic events in any patient during the 10-day treatment regimen. QTc was slightly but statistically significantly prolonged by 3.75 ± 25.4 ms after 2 days of treatment (p = 0.003). QTc prolongation was particularly observed in female outpatients 60 ms, and none had QTc > 500 ms. Conclusions: This report does not aim to contribute to knowledge of the efficacy of treating COVID-19 with HCQ-AZ. However, it shows that a simple initial assessment of patient medical history, electrocardiogram (ECG), and kalemia identifies contraindicated patients and enables the safe treatment of COVID-19 patients with HCQ-AZ. QT-prolonging anti-infective drugs can be used safely in acute life-threatening infections, provided that a strict protocol and close collaboration between infectious disease specialists and rhythmologists are applied.

Published
2023

18. 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

19. 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

20. 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

21. 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

22. Tracking the Source of Human Q Fever from a Southern French Village: Sentinel Animals and Environmental Reservoir

Author

Younes Laidoudi, Elodie Rousset, Anne-Sophie Dessimoulie, Myriam Prigent, Alizée Raptopoulo, Quentin Huteau, Elisabeth Chabbert, Catherine Navarro, Pierre-Edouard Fournier, Bernard Davoust, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Laboratoire de Sophia Antipolis, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire d'Analyses Médicales Biomed 34, Mireval, Laboratoire d'Etude des Mécanismes Cognitifs (EMC), Université Lumière - Lyon 2 (UL2), 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 Référence des Rickettsies, Coxiella et Bartonella

Subjects
Microbiology (medical), [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, Virology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, One Health, Coxiella burnetii, Q fever, sentinels, epidemiology, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

International audience; Coxiella burnetii, also known as the causal agent of Q fever, is a zoonotic pathogen infecting humans and several animal species. Here, we investigated the epidemiological context of C. burnetii from an area in the Hérault department in southern France, using the One Health paradigm. In total, 13 human cases of Q fever were diagnosed over the last three years in an area comprising four villages. Serological and molecular investigations conducted on the representative animal population, as well as wind data, indicated that some of the recent cases are likely to have originated from a sheepfold, which revealed bacterial contamination and a seroprevalence of 47.6%. However, the clear-cut origin of human cases cannot be ruled out in the absence of molecular data from the patients. Multi-spacer typing based on dual barcoding nanopore sequencing highlighted the occurrence of a new genotype of C. burnetii. In addition, the environmental contamination appeared to be widespread across a perimeter of 6 km due to local wind activity, according to the seroprevalence detected in dogs (12.6%) and horses (8.49%) in the surrounding populations. These findings were helpful in describing the extent of the exposed area and thus supporting the use of dogs and horses as valuable sentinel indicators for monitoring Q fever. The present data clearly highlighted that the epidemiological surveillance of Q fever should be reinforced and improved.

Published
2023

23. Contamination of planktonic food webs in the Mediterranean Sea: Setting the frame for the MERITE-HIPPOCAMPE oceanographic cruise (spring 2019)

Author

Marc Tedetti, Jacek Tronczynski, François Carlotti, Marc Pagano, Sana Ben Ismail, Cherif Sammari, Malika Bel Hassen, Karine Desboeufs, Charlotte Poindron, Sandrine Chifflet, Amel Bellaaj Zouari, Moufida Abdennadher, Sirine Amri, Daniela Bănaru, Lotfi Ben Abdallah, Nagib Bhairy, Ismail Boudriga, Aude Bourin, Christophe Brach-Papa, Nicolas Briant, Léa Cabrol, Cristele Chevalier, Lassaad Chouba, Sylvain Coudray, Mohamed Nejib Daly Yahia, Thibault de Garidel-Thoron, Aurélie Dufour, Jean-Claude Dutay, Boris Espinasse, Pamela Fierro-González, Michel Fornier, Nicole Garcia, Franck Giner, Catherine Guigue, Loïc Guilloux, Asma Hamza, Lars-Eric Heimbürger-Boavida, Stéphanie Jacquet, Joel Knoery, Rim Lajnef, Nouha Makhlouf Belkahia, Deny Malengros, Pauline L. Martinot, Anthony Bosse, Jean-Charles Mazur, Marouan Meddeb, Benjamin Misson, Olivier Pringault, Marianne Quéméneur, Olivier Radakovitch, Patrick Raimbault, Christophe Ravel, Vincent Rossi, Chaimaa Rwawi, Asma Sakka Hlaili, Javier Angel Tesán-Onrubia, Bastien Thomas, Melilotus Thyssen, Noureddine Zaaboub, Cédric Garnier, 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 Interuniversitaire des Systèmes Atmosphériques (LISA (UMR_7583)), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Nord Europe), Institut Mines-Télécom [Paris] (IMT), Qatar University, 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), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation du climat (CLIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), The Arctic University of Norway [Tromsø, Norway] (UiT), 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), Faculté des Sciences de Bizerte [Université de Carthage], Université de Carthage - University of Carthage, Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-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), ANR-19-CE34-0001,CONTAMPUMP,Plancton: pompe biologique de contaminants dans les écosystèmes marins (CONTAMPUMP)?(2019), ANR-11-LABX-0005,Cappa,Physiques et Chimie de l'Environnement Atmosphérique(2011), and Institut de Recherche pour le Développement (IRD)

Subjects
bioaccumulation, atmospheric deposition, plankton, size fractions, [SDE]Environmental Sciences, Mediterranean Sea, contaminants, Aquatic Science, Oceanography, Pollution
Abstract

International audience; This paper looks at experiential feedback and the technical and scientific challenges tied to the MERITE-HIPPOCAMPE cruise that took place in the Mediterranean Sea in spring 2019. This cruise proposes an innovative approach to investigate the accumulation and transfer of inorganic and organic contaminants within the planktonic food webs. We present detailed information on how the cruise worked, including 1) the cruise track and sampling stations, 2) the overall strategy, based mainly on the collection of plankton, suspended particles and water at the deep chlorophyll maximum, and the separation of these particles and planktonic organisms into various size fractions, as well as the collection of atmospheric deposition, 3) the operations performed and material used at each station, and 4) the sequence of operations and main parameters analysed. The paper also provides the main environmental conditions that were prevailing during the campaign. Lastly, we present the types of articles produced based on work completed by the cruise that are part of this special issue.

Published
2023

24. SARS-CoV-2 Reinfection and Severity of the Disease: A Systematic Review and Meta-Analysis

Author

Nhu Ngoc Nguyen, Y Ngoc Nguyen, Van Thuan Hoang, Matthieu Million, 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), Hoan My Sai Gon Hospital, Ho Chi Minh City, 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, SARS-CoV-2, coronavirus, COVID-19, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, reinfection, Infectious Diseases, variant, [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, second infection
Abstract

International audience; Since the discovery of SARS-CoV-2, changes in genotype and reinfection with different variants have been observed in COVID-19-recovered patients, raising questions around the clinical pattern and severity of primary infection and reinfection. In this systematic review, we summarize the results of 23 studies addressing SARS-CoV-2 reinfections. A total of 23,231 reinfected patients were included, with pooled estimated reinfection rates ranging from 0.1 to 6.8%. Reinfections were more prevalent during the Omicron variant period. The mean age of reinfected patients was 38.0 ± 6. years and females were predominant among reinfected patients (M/F = 0.8). The most common symptoms during the first and second infection were fever (41.1%), cough (35.7% and 44.6%), myalgia (34.5% and 33.3%), fatigue (23.8% and 25.6%), and headaches (24.4% and 21.4%). No significant differences of clinical pattern were observed between primary infection and reinfection. No significant differences in the severity of infection were observed between primary infection and reinfection. Being female, being a patient with comorbidities, lacking anti-nucleocapsid IgG after the first infection, being infected during the Delta and Omicron wave, and being unvaccinated were associated with a higher risk of reinfection. Conflicting age-related findings were found in two studies. Reinfection with SARS-CoV-2 suggests that natural immunity is not long-lasting in COVID-19 patients.

Published
2023

25. A Repertoire of Clinical Non-Dermatophytes Moulds

Author

Estelle Menu, Quentin Filori, Jean-Charles Dufour, Stéphane Ranque, Coralie L’Ollivier, 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), 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), Biostatistique et technologies de l'information et de la communication (BioSTIC) - [Hôpital de la Timone - APHM] (BiosTIC ), and Assistance Publique - Hôpitaux de Marseille (APHM)- Hôpital de la Timone [CHU - APHM] (TIMONE)

Subjects
Microbiology (medical), mould, [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, filamentous fungi, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, repertoire, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Plant Science, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Ecology, Evolution, Behavior and Systematics
Abstract

International audience; Humans are constantly exposed to micromycetes, especially filamentous fungi that are ubiquitous in the environment. In the presence of risk factors, mostly related to an alteration of immunity, the non-dermatophyte fungi can then become opportunistic pathogens, causing superficial, deep or disseminated infections. With new molecular tools applied to medical mycology and revisions in taxonomy, the number of fungi described in humans is rising. Some rare species are emerging, and others more frequent are increasing. The aim of this review is to (i) inventory the filamentous fungi found in humans and (ii) provide details on the anatomical sites where they have been identified and the semiology of infections. Among the 239,890 fungi taxa and corresponding synonyms, if any, retrieved from the Mycobank and NCBI Taxonomy databases, we were able to identify 565 moulds in humans. These filamentous fungi were identified in one or more anatomical sites. From a clinical point of view, this review allows us to realize that some uncommon fungi isolated in non-sterile sites may be involved in invasive infections. It may present a first step in the understanding of the pathogenicity of filamentous fungi and the interpretation of the results obtained with the new molecular diagnostic tools.

Published
2023

26. Circulation of SARS-CoV-2 virus among pilgrims at the 2022 Grand Magal of Touba

Author

Coumba Diouf, Ihssane Ouaddane, Ndiaw Goumballa, Masse Sambou, Hubert Bassène, Mamadou Dieng, Philippe Gautret, Cheikh Sokhna, 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, [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; Among pilgrims departing from two villages in South Senegal who participated to the event, 45% had respiratory symptoms and 7% acquired SARS-CoV-2 nasopharyngeal carriage. Among patients with respiratory symptoms sampled at a health care centre close to Touba, 5% tested positive. In contrast, no SARS-CoV-2 infection was observed in 2020–21.

Published
2023

27. Limitations of Serological Diagnosis of Typical Cat Scratch Disease and Recommendations for the Diagnostic Procedure

Author

Myrto Koutantou, Konstantinos Kambas, Sofia Makka, Pierre-Edouard Fournier, Didier Raoult, Emmanouil Angelakis, Diagnostic Department and Public Health Laboratories, Hellenic Pasteur Institute, Athens 11521, Greece., Laboratory of Molecular Genetics, Hellenic Pasteur Institute, Athens 11521, Greece., 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
Microbiology (medical), [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, [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; Introduction. Cat scratch disease (CSD) is the most common cause of bacterial infectious lymphadenopathy, especially in children, but its diagnosis still remains challenging. Serological assays are widely applied due to their simplicity and the non-invasive sampling. However, these techniques present several limitations, including not well-defined antigen preparation, assay conditions and cutoff titers, severe cross-reactions with other species and organisms, and the notably ranging seroprevalence in the normal population. The objective of this study is to review the literature in order to determine the best diagnostic procedure for the diagnosis of CSD. Methods. Databases including PubMed, Medline, Google Scholar, and Google were searched to determine the best diagnostic procedure for the diagnosis of CSD. A total of 437 papers were identified and screened, and after exclusion of papers that did not fulfill the including criteria, 63 papers were used. Results. It was revealed that sensitivities of serological assays varied from 10% to 100%. Indeed, more than half of the studies reported a sensitivity lower than 70%, while 71% of them had a sensitivity lower than 80%. Moreover, specificities of serological assays ranged from 15% to 100%, with 25 assays reporting a specificity lower than 90%. Conclusion. It is considered that molecular assays should be the gold standard technique for CSD confirmation, and physicians are reinforced to proceed to lymph node biopsy in suspicious CSD cases.

Published
2023

28. High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol

Author

Nasserdine Papa Mze, Idir Kacel, Mamadou Beye, Raphael Tola, Mariéma Sarr, Leonardo Basco, Hervé Bogreau, Philippe Colson, Pierre-Edouard Fournier, 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), Ctr Hosp Versailles, Hop Mignot, Serv Biol, Unite Microbiol, Le Chesnay, 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 de la Timone [CHU - APHM] (TIMONE), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), and ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, clade, SARS-CoV-2, MiSeq, sequencing, Illumina, [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.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genetics, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Genetics (clinical)
Abstract

International audience; The emergence of the Coronavirus Disease 2019 (COVID-19) pandemic has fostered the use of high-throughput techniques to sequence the entire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome and track its evolution. The present study proposes a rapid and relatively less expensive sequencing protocol for 384 samples by adapting the use of an Illumina NovaSeq library to an Illumina MiSeq flow cell instrument. The SARS-CoV-2 genome sequences obtained with Illumina NovaSeq and those obtained using MiSeq instruments were compared with the objective to validate the new, modified protocol. A total of 356 (94.6%) samples yielded interpretable sequences using the modified Illumina COVIDSeq protocol, with an average coverage of 91.6%. By comparison, 357 (94.9%) samples yielded interpretable sequences with the standard COVIDSeq protocol, with an average coverage of 95.6%. Our modified COVIDSeq protocol could save 14,155 euros per run and yield results from 384 samples in 53.5 h, compared to four times 55.5 h with the standard Illumina MiSeq protocol. The modified COVIDSeq protocol thus provides high quality results comparable to those obtained with the standard COVIDSeq protocol, four times faster, while saving money.

Published
2023

29. Monkeypox clinical disease: Literature review and a tool proposal for the monitoring of cases and contacts

Author

Emilie Javelle, Cécile Ficko, Hélène Savini, Marie Mura, Olivier Ferraris, Jean Nicolas Tournier, Franck de Laval, 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), Hôpital d'Instruction des Armées Laveran, Service de Santé des Armées, Hôpital d'Instruction des Armées Begin, École du Val de Grâce (EVDG), Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Laboratoire d’innovation : vaccins – Innovation lab : vaccines, Institut Pasteur [Paris] (IP), Centre d'épidémiologie et de santé publique des armées [Marseille] (CESPA), Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Surveillance, Follow-up, Public Health, Environmental and Occupational Health, Epidemic, Outbreak, Emergence, [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, Clinical questionnaire, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology
Abstract

International audience; The human monkeypox disease has mainly been described in Western and Central Africa. Since May 2022, the monkeypox virus has been spreading worldwide in a new epidemiological pattern, where cases result from person-to-person transmission, and develop clinically milder or less typical illness than during previous outbreaks in endemic areas. The newly-emerging monkeypox disease needs to be described over the long term, to improve cases definitions, to implement prompt control measures against epidemics, and to provide supportive care. Hence, we first conducted a review of historical and recent outbreaks to define the full clinical spectrum of the monkeypox disease and its course known so far. Then, we built a self-administrated questionnaire collecting daily symptoms of the monkeypox infection to follow cases and their contacts, even remotely. This tool will assist in the management of cases, the surveillance of contacts, and the conduct of clinical studies.

Published
2023

30. The sponge Oscarella lobularis (Porifera, Homoscleromorpha) as a suitable biomonitor of metallic contamination in Mediterranean coastal ecosystems

Author

Kassandra de Pao Mendonca, Bernard Angeletti, Aurélie Dufour, Carole Borchiellini, Lars-Eric Heimbürger-Boavida, Emmanuelle Renard, Julien Issartel, 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), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-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), Institut méditerranéen d'océanologie (MIO), and 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)

Subjects
[SDE]Environmental Sciences, Aquatic Science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Oceanography, Pollution
Abstract

International audience

Published
2023

31. 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

32. Current controversies on mechanisms controlling soil carbon storage: implications for interactions with practitioners and policy-makers. A review

Author

Delphine Derrien, Pierre Barré, Isabelle Basile-Doelsch, Lauric Cécillon, Abad Chabbi, Alexandra Crème, Sébastien Fontaine, Ludovic Henneron, Noémie Janot, Gwenaëlle Lashermes, Katell Quénéa, Frédéric Rees, Marie-France Dignac, Unité de recherche Biogéochimie des Ecosystèmes Forestiers (BEF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-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), Plateforme de géochimie isotopique ASTER-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), Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Etude et Compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Interactions Sol Plante Atmosphère (UMR ISPA), Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fractionnement des AgroRessources et Environnement (FARE), Université de Reims Champagne-Ardenne (URCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sorbonne Université (SU), Institut d'écologie et des sciences de l'environnement de Paris (iEES Paris ), and Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Carbon storage, POM, InaccessibilityModels, Big data, Environmental Engineering, Management practices, [SDE]Environmental Sciences, Chemical recalcitrance, Biomass use, Agronomy and Crop Science
Abstract

There is currently an intense debate about the potential for additional organic carbon storage in soil, the strategies by which it may be accomplished and what the actual benefits might be for agriculture and the climate. Controversy forms an essential part of the scientific process, but on the topic of soil carbon storage, it may confuse the agricultural community and the general public and may delay actions to fight climate change. In an attempt to shed light on this topic, the originality of this article lies in its intention to provide a balanced description of contradictory scientific opinions on soil carbon storage and to examine how the scientific community can support decision-making despite the controversy. In the first part, we review and attempt to reconcile conflicting views on the mechanisms controlling organic carbon dynamics in soil. We discuss the divergent opinions about chemical recalcitrance, the microbial or plant origin of persistent soil organic matter, the contribution of particulate organic matter to additional organic carbon storage in soil, and the spatial and energetic inaccessibility of soil organic matter to decomposers. In the second part, we examine the advantages and limitations of big data management and modeling, which are essential tools to link the latest scientific theories with the actions taken by stakeholders. Finally, we show how the analysis and discussion of controversies can guide scientists in supporting stakeholders for the design of (i) appropriate trade-offs for biomass use in agriculture and forestry and (ii) climate-smart management practices, keeping in mind their still unresolved effects on soil carbon storage.

Published
2023

33. 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

34. 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

35. 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

36. 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

37. 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

38. 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

39. Carbonyl Cyanide 3-Chloro Phenyl Hydrazone (CCCP) Restores the Colistin Sensitivity in Brucella intermedia

Author

Malak Zoaiter, Zaher Zeaiter, Oleg Mediannikov, Cheikh Sokhna, Pierre-Edouard Fournier, 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), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)

Subjects
[SDV]Life Sciences [q-bio], Organic Chemistry, synergy, General Medicine, intrinsic colistin resistance, Catalysis, Computer Science Applications, Inorganic Chemistry, carbonyl cyanide 3-chloro phenyl hydrazone, CO-MIC, biofilm formation, efflux pump, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, efflux pump inhibitors
Abstract

Brucella intermedia (formerly Ochrobactrum intermedium), a non-fermentative bacterium, has been isolated from animals and human clinical specimens. It is naturally resistant to polymyxins, including colistin (CO), and may cause opportunistic infections in humans. We isolated six Brucella intermedia strains from Senegalese monkey stool. In order to determine whether an efflux pump mechanism was involved in CO resistance in B. intermedia, we evaluated the effects of verapamil (VRP), reserpine (RSP), phe-arg β-naphthylamide dihydrochloride (PAβN) and carbonyl cyanide 3-chloro phenyl hydrazone (CCCP), four efflux pump inhibitors, on these colistin-resistant strains. Using the broth microdilution method, a CO and CCCP combination of 2 µg/mL and 10 µg/mL, respectively, significantlyreduced the CO minimal inhibitory concentration (MIC) of B. intermedia, supporting an efflux pump mechanism. In contrast, VRP, PAβN and RSP did not restore CO susceptibility. A time kill assay showed a bactericidal effect of the CO–CCCP combination. Genomic analysis revealed a potential implication in the CO resistance mechanism of some conserved efflux pumps, such as YejABEF, NorM and EmrAB, as previously reported in other bacteria. An inhibitory effect of the CO–CCCP combination was observed on biofilm formation using the crystal violet method. These results suggest that the intrinsic CO resistance in Brucella intermedia is linked to an efflux pump mechanism and that the synergistic effect of CO–CCCP may open a new field to identify new treatments to restore antibiotic efficacy in humans.

Published
2023
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40. Aetiology of Acute Undifferentiated Fever Among Children Under the Age of Five in Vietnam: A Prospective Study

Author

Xuan Duong Tran, Van Thuan Hoang, Thi Thuy Duong Dang, Thi Phuong Vu, Minh Manh To, Trong Kiem Tran, Manh Dung Do, Duy Cuong Nguyen, Quoc Tien Nguyen, Philippe Colson, Philippe Parola, Pierre Marty, Philippe Gautret, Thai Binh University of Medecine and Pharmacy, 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), Thai Binh Paediatric Hospital, Thai Binh, Thai Binh Pediatric Hospital, Institut Charles Delaunay (ICD), Université de Technologie de Troyes (UTT)-Centre National de la Recherche Scientifique (CNRS), Thai Binh University of Medicine and Pharmacy, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), and Centre Hospitalier Universitaire de l’Archet

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, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Background To investigate the aetiology of acute undifferentiated fever (AUF) among children under the age of five in Vietnam. Methods This prospective study was conducted in the Thai Binh paediatric hospital, between July 2020 and July 2021 among children with AUF at admission. Real-time PCR testing 18 microbial pathogens were done on blood samples. Results 286 children were included, with median age of 16 months. 64.7% were male. 53.9% were positive for at least one pathogen by PCR. Enterovirus, human herpesvirus 6, adenovirus, and varicella zoster virus PCR were positive for 31.1, 12.6, 1.4, and 1.0% patients, respectively. Other pathogens tested negative by PCR. During the hospital stay, based on clinical criteria 47.2% children secondarily presented with signs of respiratory tract infections, 18.9% had hand, foot and mouth disease, 4.6% had chickenpox. 4.2% presented signs of central nervous system infections, 1.0% had dengue (antigenic test) and 1.0% had signs of gastrointestinal infection. Finally, 23.1% patients presented a fever with or without a rash and no other symptoms and ultimately received a diagnosis of AUF. Conclusion Real-time PCR of blood is useful for detecting pathogens and diagnosing infectious causes of AUF. Further prospective studies with blood and urine culture testing and PCR investigation of not only blood but also cerebrospinal fluid, throat, and skin samples according to symptoms would be of interest to confirm the predominance of viral infections in children with AUF and to guide therapeutic options.

Published
2023

41. Lice and lice-borne diseases in humans in Africa: A narrative review

Author

Basma Ouarti, Descartes Maxime Mbogning Fonkou, Linda Houhamdi, Oleg Mediannikov, 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), 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, Insect Science, Veterinary (miscellaneous), [SDV]Life Sciences [q-bio], Africa, Pediculus, Animals, Humans, Parasitology, Lice Infestations, Child, Trench Fever, Typhus, Epidemic Louse-Borne
Abstract

Lice are host-specific insects. Human lice include Pediculus humanus (body lice) which are known to be vectors of serious human bacterial infectious diseases including epidemic typhus, relapsing fever, trench fever and plague; Pediculus humanus capitis (head lice) that frequently affect children; and Pthirus pubis, commonly known as crab lice. In Africa, human infections transmitted by lice remained poorly known and therefore, underestimated, perhaps due to the lack of diagnostic tools and professional knowledge. In this paper we review current knowledge of the microorganisms identified in human lice in the continent of Africa, in order to alert health professionals to the importance of recognizing the risk of lice-related diseases.

Published
2023

42. Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing

Author

Harilanto Felana Andrianjakarivony, Yvan Bettarel, Fabrice Armougom, Christelle Desnues, 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
virome, Infectious Diseases, phage-host interaction, 16S rRNA metabarcoding, Virology, host prediction, bacteria, metagenomic, lagoon, [SDE.MCG]Environmental Sciences/Global Changes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage–host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages’ bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.

Published
2023

43. Streptococcus bouchesdurhonensis sp. nov. isolated from a bronchoalveolar lavage of a patient with pneumonia

Author

Malak Zoaiter, Reham Magdy Wasfy, Aurelia Caputo, Florence Fenollar, Zaher Zeaiter, Pierre-Edouard Fournier, Linda Houhamdi, 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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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
DNA, Bacterial, [SDV]Life Sciences [q-bio], Streptococcus, General Medicine, Pneumonia, Biochemistry, Microbiology, Bronchoalveolar Lavage, RNA, Ribosomal, 16S, Genetics, Humans, Molecular Biology, Phylogeny, Genome, Bacterial, Aged
Abstract

Strain Marseille-Q6994 was isolated from a 72-year-old patient with pneumonia from Bouches-du-Rhône department, in France. Cells were Gram positive, non-motile, catalase and oxidase-negative cocci. The major fatty acids were hexadecanoic (47.4%) and tetradecanoic acids (28.3%). 16S rRNA gene sequence comparison suggested that strain Marseille-Q6994 was affiliated to the Streptococcus genus. GroEL phylogenetic analysis separated strain Marseille-Q6994 in a distinct branch from the closely related Streptococcus-type strains with standing in nomenclature. Whole genome sequencing-based methods (OrthoAverage Nucleotide Identity, digital DNA-DNA hybridization and pangenome analysis) supported the classification of the strain into a novel species. Therefore, based on the phenotypic, genomic, and phylogenetic analyses, we propose the name Streptococcus bouchesdurhonensis sp. nov for which strain Marseille-Q6994

Published
2023

44. Evidence of Antibodies against the West Nile Virus and the Usutu Virus in Dogs and Horses from the Southeast of France

Author

Younes Laidoudi, Guillaume Durand, Stéphanie Watier-Grillot, Anne-Sophie Dessimoulie, Claire Labarde, Thomas Normand, Virginie Andréo, Patrick Guérin, Gilda Grard, Bernard Davoust, 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), 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), Centre d'épidémiologie et de santé publique des armées [Marseille] (CESPA), Service de Santé des Armées, Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), and SOS Médecins Nantes

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, General Veterinary, General Immunology and Microbiology, Article Subject, [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; Every year, the world faces vector-borne diseases including arboviral (arthropod-borne viral) diseases caused by several, possibly fatal flaviviruses. The way they spread is related to a complex episystem involving several elements including vector abundance, animal carriers, and the flavivirus itself, which makes the disease difficult to manage. Here, we serologically screened 556 animals (358 dogs and 198 horses) using ELISA and a serum neutralisation test (SNT) for the anti-IgG antibodies directed against the West Nile (WNV) and Usutu (USUV) viruses. The animals investigated were split into two groups according to their exposure to the risk linked to the abundance of mosquitoes and migratory birds as well as the geographical distribution of arbovirus cases (458 animals from areas exposed to risk and 98 not exposed to risk). Overall, 25/310 dogs (8.1%) and 2/148 horses (1.3%) tested positive for SNT WNV and/or USUV in geographically exposed areas. Animals in unexposed areas were all negative. The geographical distribution of WNV seroprevalence in dogs was the same as the distribution of reported autochthonous human cases. Interestingly, a non-negligible seroprevalence caused by an as yet unidentified flavivirus other than WNV, USUV, or tick-borne encephalitis virus (TBEV) was detected in 18.6% (28/150) and 3.7% (4/106) of the investigated dogs and horses from the Hérault department, in the southeast of France, respectively. These data highlight the role of outdoor dogs as suitable sentinels for the evidence of WNV and USUV circulation in each area. In addition, the serological detection of an as yet unidentified flavivirus circulating in the Hérault department deserves greater attention, as this may constitute a serious threat to public and animal health.

Published
2023
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45. A RESPONSE TO COMMUNITY QUESTIONS ON THE MARINE20 RADIOCARBON AGE CALIBRATION CURVE: MARINE RESERVOIR AGES AND THE CALIBRATION OF 14C SAMPLES FROM THE OCEANS

Author

T J Heaton, E Bard, C Bronk Ramsey, M Butzin, C Hatté, K A Hughen, P Köhler, P J Reimer, 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), Collège de France - 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), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agence Nationale de la Recherche, ANR, Bundesministerium für Bildung und Forschung, BMBF: 01LP1505B, 01LP1919A, P. Köhler and M. Butzin are supported by the German Federal Ministry of Education and Research (BMBF), as Research for Sustainability initiative (FONA), ANR-10-EQPX-0024,ASTER-CEREGE,PLATEFORME DE GEOCHIMIE ISOTOPIQUE ASTER/CEREGE(2010), and ANR-21-CE01-0023,MARCARA,Variabilité de l'âge radiocarbone du réservoir marin et ses implications en paléocéanographie, paléoclimatologie et géochronologie(2021)

Subjects
Archeology, Marine20, Archaeology, marine calibration, radiocarbon, General Earth and Planetary Sciences, Earth and Planetary Sciences(all), calibration, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, dating
Abstract

Radiocarbon (14C) concentrations in the oceans are different from those in the atmosphere. Understanding these ocean-atmospheric 14C differences is important both to estimate the calendar ages of samples which obtained their 14C in the marine environment, and to investigate the carbon cycle. The Marine20 radiocarbon age calibration curve is created to address these dual aims by providing a global-scale surface ocean record of radiocarbon from 55,000–0 cal yr BP that accounts for the smoothed response of the ocean to variations in atmospheric 14C production rates and factors out the effect of known changes in global-scale palaeoclimatic variables. The curve also serves as a baseline to study regional oceanic 14C variation. Marine20 offers substantial improvements over the previous Marine13 curve. In response to community questions, we provide a short intuitive guide, intended for the lay-reader, on the construction and use of the Marine20 calibration curve. We describe the choices behind the making of Marine20, as well as the similarities and differences compared with the earlier Marine calibration curves. We also describe how to use the Marine20 curve for calibration and how to estimate ΔR—the localized variation in the oceanic 14C levels due to regional factors which are not incorporated in the global-scale Marine20 curve. To aid understanding, illustrative worked examples are provided.

Published
2023

46. Not out of the Mediterranean: Atlantic populations of the gorgonian Paramuricea clavata are a separate sister species under further lineage diversification

Author

Márcio A. G. Coelho, Gareth A. Pearson, Joana R. H. Boavida, Diogo Paulo, Didier Aurelle, Sophie Arnaud‐Haond, Daniel Gómez‐Gras, Nathaniel Bensoussan, Paula López‐Sendino, Carlo Cerrano, Silvija Kipson, Tatjana Bakran‐Petricioli, Eliana Ferretti, Cristina Linares, Joaquim Garrabou, Ester A. Serrão, Jean‐Baptiste Ledoux, Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], 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 de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Ecologie Marine et BIOdiversité (EMBIO), 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 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), Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain] (IRBio UB), Universitat de Barcelona (UB), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Consorzio Nazionale Interuniversitario per le Scienze del Mare [Rome, Italie] (CoNISma), University of Zagreb, Australian Institute of Marine Science (AIMS), This work was funded by program BIOMARES, a Pew Marine Fellowship, and FCT – Foundation for Science and Technology UIDB/04326/2020, UIDP/04326/2020, LA/P/0101/2020, PTDC/BIA-CBI/6515/2020, EU-BiodivERsA BiodivRestore-253 (FCT: DivRestore/0013/2020), EU Horizon 2020 research and innovation program (MERCES: Grant no. 689518), as well as the Inaqua Conservation Fund (Oceanário de Lisboa and National Geographic Channel) and National Geographic Society/Waitt Grant no. W153-11., BIOMARES, Foundation for Science and Technology, European Commission, Inaqua Conservation Fund, National Geographic Society, European Maritime and Fisheries Fund, Ministério da Economia (Portugal), and Agencia Estatal de Investigación (España)

Subjects
Incomplete lineage sorting, Atlantic-Mediterranean transition, cryptic diversity, incomplete lineage sorting, Octocorallia, phylotranscriptomics, species delimitation, Atlantic-Mediterranean transition, Ecology, Cryptic diversity, Species delimitation, Octocorallia, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Phylotranscriptomics, Conserve and sustainably use the oceans, seas and marine resources for sustainable development, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

21 pages, 4 figures, 1 table, supporting information https://doi.org/10.1002/ece3.9740.-- Data Availability Statement: Raw RNA-seq data and mt-mutS sequences have been uploaded to NCBI's SRA (BioProject ID: PRJNA847883) and GenBank databases (Accessions numbers: ON804207-ON804214), respectively. Final sequence alignments and microsatellite data are available on DRYAD (https://doi.org/10.5061/dryad.r7sqv9sfm), The accurate delimitation of species boundaries in nonbilaterian marine taxa is notoriously difficult, with consequences for many studies in ecology and evolution. Anthozoans are a diverse group of key structural organisms worldwide, but the lack of reliable morphological characters and informative genetic markers hampers our ability to understand species diversification. We investigated population differentiation and species limits in Atlantic (Iberian Peninsula) and Mediterranean lineages of the octocoral genus Paramuricea previously identified as P. clavata. We used a diverse set of molecular markers (microsatellites, RNA-seq derived single-copy orthologues [SCO] and mt-mutS [mitochondrial barcode]) at 49 locations. Clear segregation of Atlantic and Mediterranean lineages was found with all markers. Species-tree estimations based on SCO strongly supported these two clades as distinct, recently diverged sister species with incomplete lineage sorting, P. cf. grayi and P. clavata, respectively. Furthermore, a second putative (or ongoing) speciation event was detected in the Atlantic between two P. cf. grayi color morphotypes (yellow and purple) using SCO and supported by microsatellites. While segregating P. cf. grayi lineages showed considerable geographic structure, dominating circalittoral communities in southern (yellow) and western (purple) Portugal, their occurrence in sympatry at some localities suggests a degree of reproductive isolation. Overall, our results show that previous molecular and morphological studies have underestimated species diversity in Paramuricea occurring in the Iberian Peninsula, which has important implications for conservation planning. Finally, our findings validate the usefulness of phylotranscriptomics for resolving evolutionary relationships in octocorals, This work was funded by program BIOMARES, a Pew Marine Fellowship, and FCT – Foundation for Science and Technology UIDB/04326/2020, UIDP/04326/2020, LA/P/0101/2020, PTDC/BIA-CBI/6515/2020; EU-BiodivERsA BiodivRestore-253 (FCT: DivRestore/0013/2020); EU Horizon 2020 research and innovation program (MERCES: Grant no. 689518); as well as the Inaqua Conservation Fund (Oceanário de Lisboa and National Geographic Channel) and National Geographic Society/Waitt Grant no. W153-11. This article is also a product of the French network on Marine Connectivity (GDR MarCo). M.C. was supported by postdoctoral fellowships of projects HABMAR (Grant no. MAR-01.04.02-FEAMP-0018) co-financed by the European Maritime and Fisheries Fund of the Operational Program MAR 2020 for Portugal (Portugal 2020), and BiodivAMP (Grant no. FA_06_2017_045) financed by the Directorate-General for Sea Policy of the Ministry of Economy and Sea for Portugal under the Operational Program Fundo Azul. JBL was funded by assistant researcher contract framework of the RD Unit—UID/Multi/04423/2019 – Interdisciplinary Centre of Marine and Environmental Research—financed by the European Regional Development Fund (ERDF) through COMPETE2020—Operational Program for Competitiveness and Internationalization (POCI) and national funds through FCT/MCTES (PIDDAC). JB was funded by a FCT PhD scholarship SFRH/BD/72501/2010, With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)

Published
2023

47. Infection and Persistence of Coxiella burnetii Clinical Isolate in the Placental Environment

Author

Sandra Madariaga Zarza, Muriel Militello, Laetitia Gay, Anthony Levasseur, Hubert Lepidi, Yassina Bechah, Soraya Mezouar, Jean-Louis Mege, 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), Assistance Publique - Hôpitaux de Marseille (APHM), Laboratoire d'Immunologie [Hôpital de la Conception - APHM], and Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital de la Conception [CHU - APHM] (LA CONCEPTION)-Centre National de la Recherche Scientifique (CNRS)

Subjects
placenta, [SDV]Life Sciences [q-bio], Organic Chemistry, General Medicine, Catalysis, Computer Science Applications, Inorganic Chemistry, trophoblasts, Coxiella burnetii, pregnancy, placental macrophages, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy
Abstract

Infection by Coxiella burnetii, the etiological agent of Q fever, poses the risk of causing severe obstetrical complications in pregnant women. C. burnetii is known for its placental tropism based on animal models of infection. The Nine Mile strain has been mostly used to study C. burnetii pathogenicity but the contribution of human isolates to C. burnetii pathogenicity is poorly understood. In this study, we compared five C. burnetii isolates from human placentas with C. burnetii strains including Nine Mile (NM) as reference. Comparative genomic analysis revealed that the Cb122 isolate was distinct from other placental isolates and the C. burnetii NM strain with a set of unique genes involved in energy generation and a type 1 secretion system. The infection of Balb/C mice with the Cb122 isolate showed higher virulence than that of NM or other placental isolates. We evaluated the pathogenicity of the Cb122 isolate by in vitro and ex vivo experiments. As C. burnetii is known to infect and survive within macrophages, we isolated monocytes and placental macrophages from healthy donors and infected them with the Cb122 isolate and the reference strain. We showed that bacteria from the Cb122 isolate were less internalized by monocyte-derived macrophages (MDM) than NM bacteria but the reference strain and the Cb122 isolate were similarly internalized by placental macrophages. The Cb122 isolate and the reference strain survived similarly in the two macrophage types. While the Cb122 isolate and the NM strain stimulated a poorly inflammatory program in MDM, they elicited an inflammatory program in placenta macrophages. We also reported that the Cb122 isolate and NM strain were internalized by trophoblastic cell lines and primary trophoblasts without specific replicative profiles. Placental explants were then infected with the Cb122 isolate and the NM strain. The bacteria from the Cb122 isolate were enriched in the chorionic villous foetal side. It is likely that the Cb122 isolate exhibited increased virulence in the multicellular environment provided by explants. Taken together, these results showed that the placental isolate of C. burnetii exhibits a specific infectious profile but its pathogenic role is not as high as the host immune response in pregnant women.

Published
2023

48. Spectral wave dissipation over a roughness‐varying barrier reef

Author

Damien Sous, Kévin Martins, Marion Tissier, Frédéric Bouchette, Samuel Meulé, Laboratoire des Sciences de l'Ingénieur Appliquées à la Mécanique et au génie Electrique (SIAME), Université de Pau et des Pays de l'Adour (UPPA), 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), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of New South Wales [Sydney] (UNSW), Delft University of Technology (TU Delft), Géosciences Montpellier, Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Université de Montpellier (UM), Centre européen de recherche et d'enseignement des géosciences de l'environnement (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)

Subjects
Geophysics, [SDU.STU.GP]Sciences of the Universe [physics]/Earth Sciences/Geophysics [physics.geo-ph], spectral dissipation, General Earth and Planetary Sciences, coral reef, bottom friction, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience; The present paper reports on a field experiment performed over a shallow, roughness-varying barrier reef at Maupiti island, French Polynesia. The spectral wave energy balance is examined, outside the breaking zone and accounting for non-linear transfers and mean current, to estimate the wave friction factor. This latter varies from 0.05 to 4, with dependence on the ratio between near-bed orbital amplitude and roughness height well predicted by an adjusted parameterization from Madsen (1995). The present results are discussed with respect to other field data recovered on coral and rocky grounds.

Published
2023

49. Phytoplankton reaction to an intense storm in the north-western Mediterranean Sea

Author

Stéphanie Barrillon, Robin Fuchs, Anne A. Petrenko, Caroline Comby, Anthony Bosse, Christophe Yohia, Jean-Luc Fuda, Nagib Bhairy, Frédéric Cyr, Andrea M. Doglioli, Gérald Grégori, Roxane Tzortzis, Francesco d'Ovidio, Melilotus Thyssen, 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 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), Fisheries and Oceans Canada (DFO), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre d'océanologie de Marseille (COM), and Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU]Sciences of the Universe [physics], [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Earth-Surface Processes
Abstract

The study of extreme weather events and their impact on ocean physics and biogeochemistry is challenging due to the difficulty involved with collecting in situ data. However, recent research has pointed out the major influence of such physical forcing events on microbiological organisms. Moreover, the occurrence of such intense events may increase in the future in the context of global change. In May 2019, an intense storm occurred in the Ligurian Sea (north-western Mediterranean Sea) and was captured during the FUMSECK (Facilities for Updating the Mediterranean Submesoscale – Ecosystem Coupling Knowledge) cruise. In situ multi-platform (vessel-mounted acoustic Doppler current profiler, thermosalinometer, fluorometer, flow cytometer, a moving vessel profiler equipped with a multi-sensor towed vehicle, and a glider) measurements along with satellite data and a 3D atmospheric model were used to characterise the fine-scale dynamics occurring in the impacted oceanic zone. The most affected area was marked by a lower water temperature (1 ∘C colder), a factor of 2 increase in surface chlorophyll a, and a factor of 7 increase in the nitrate concentration, exhibiting strong gradients with respect to the surrounding waters. Our results show that this storm led to a deepening of the mixed-layer depth from 15 to 50 m and a dilution of the deep chlorophyll maximum. As a result, the surface biomass of most phytoplankton groups identified by automated flow cytometry increased by up to a factor of 2. Conversely, the carbon / chlorophyll ratio of most phytoplankton groups decreased by a factor of 2, evidencing significant changes in the phytoplankton cell composition. These results suggest that the role of storms on the biogeochemistry and ecology of the Mediterranean Sea may be underestimated and highlight the need for high-resolution measurements during these events coupling physics and biology.

Published
2023

50. 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

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