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1. Inactivation of Toxoplasma gondii in dry sausage and processed pork, and quantification of the pathogen in pig tissues prior to production

Author: Dámek, Filip, Fremaux, Bastien, Aubert, Dominique, Thoumire, Sandra, Delsart, Maxime, Martin, Jean-Luc, Vuillermet, Sandra, Opsteegh, Marieke, Jokelainen, Pikka, Le Roux, Delphine, Boireau, Pascal, Villena, Isabelle, Blaga, Radu, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut du Porc (IFIP), Epidémiosurveillance de protozooses à transmission alimentaire et vectorielle (ESCAPE), Université de Reims Champagne-Ardenne (URCA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre Hospitalier Universitaire de Reims (CHU Reims), Centre National de Référence (CNR) Toxoplasmose/Toxoplasma Biological Resource Center (BRC) (CNR Toxoplasmose-Toxoplasma BRC), CHU Limoges, Epidémiologie des maladies animales infectieuses (EpiMAI USC), École nationale vétérinaire - Alfort (ENVA)-Epidémiologie (EPI), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Statens Serum Institut [Copenhagen], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), This work was supported by funding from the France-Agri-Mer: contract number 0917003490 and the European Union's Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme (projects ToxSauQMRA and TOXOSOURCES)., and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: [SDV.EE.SANT]Life Sciences [q-bio]/Ecology, environment/Health, meat, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, nitrate, Epidemiology, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, viability, distribution, salt, Parasitology, nitrite
Abstract: Toxoplasma gondiiis an important zoonotic foodborne parasite. Meat of infected animals appears to be a major source of infection in Europe. Pork is the most consumed meat in France, with dry sausages well represented. The risk of transmission via consumption of processed pork products is largely unknown, mainly since processing will affect viability but may not entirely inactivate allT. gondiiparasites. We investigated the presence and concentration ofT. gondiiDNA in the shoulder, breast, ham, and heart of pigs orally inoculated with 1000 oocysts (n= 3) or tissue cysts (n = 3) and naturally infected pigs (n= 2), by means of magnetic capture qPCR (MC-qPCR). Muscle tissues of experimentally infected pigs were further used to evaluate the impact of manufacturing processes of dry sausages, including different concentrations of nitrates (0, 60, 120, 200 ppm), nitrites (0, 60, 120 ppm), and NaCl (0, 20, 26 g/kg), ripening (2 days at 16-24 °C) and drying (up to 30 days at 13 °C), by a combination of mouse bioassay, qPCR and MC-qPCR. DNA ofT. gondiiwas detected in all eight pigs, including in 41.7% (10/24) of muscle samples (shoulder, breast and ham) and 87.5% (7/8) of hearts by MC-qPCR. The number of parasites per gram of tissue was estimated to be the lowest in the hams (arithmetic mean (M) = 1, standard deviation (SD) = 2) and the highest in the hearts (M = 147, SD = 233). However, theT. gondiiburden estimates varied on the individual animal level, the tissue tested and the parasitic stage used for the experimental infection (oocysts or tissue cysts). Of dry sausages and processed pork, 94.4% (51/54) were positive forT. gondiiby MC-qPCR or qPCR, with the meanT. gondiiburden estimate equivalent to 31 parasites per gram (SD = 93). Only the untreated processed pork sample collected on the day of production was positive by mouse bioassay. The results suggest an uneven distribution ofT. gondiiin the tissues examined, and possibly an absence or a concentration below the detection limit in some of them. Moreover, the processing of dry sausages and processed pork with NaCl, nitrates, and nitrites has an impact on the viability ofT. gondiifrom the first day of production. Results are valuable input for future risk assessments aiming to estimate the relative contribution of different sources ofT. gondiihuman infections.
Published: 2023

2. Analyse des risques pour la santé humaine et animale liés aux tiques du genre Hyalomma en France

Author: Bonnet, Sarah, Baize, Sylvain, Bertagnoli, Stéphane, Falchi, Alessandra, Figoni, Julie, Hoch, Thierry, Moutailler, Sara, Raffetin, Alice, René-Martellet, Magalie, Stachurski, Frederic, Vial, Laurence, Vourc’h, Gwenaël, Quillery, Elsa, Fite, Johanna, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie des Infections Virales Émergentes - Biology of Emerging Viral Infections (UBIVE), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Università di Corsica Pasquale Paoli [Université de Corse Pascal Paoli], Partenaires INRAE, Direction santé environnement travail - Santé Publique France, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre Hospitalier Intercommunal Villeneuve-Saint-Georges (CHIV), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Direction de l'Evaluation des Risques (DER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Anses, and Druesne, Christine
Subjects: human health, animal health, Fièvre hémorragique de Crimée-Congo, risk analysis, santé animale, [SDV]Life Sciences [q-bio], agents pathogènes, Hyalomma marginatum, virus, vector-borne disease, vecteur, [SDV] Life Sciences [q-bio], santé humaine, Hyalomma, FHCC, France, Crimean-Congo hemorrhagic fever (CCHF), Tique, tick-borne virus, vector, pathogen agents, maladie vectorielle, Tick, analyse de risque
Abstract: Citation suggérée : Anses. (2022). Analyse des risques pour la santé humaine et animale liés aux tiques du genreHyalomma en France. (Saisine 2020-SA-0039). Maisons-Alfort : Anses, 300 p.; Les populations de tiques du genre Hyalomma sont considérées en augmentation sur unepartie de leur aire de répartition, qui semble s'étendre en Europe depuis la fin du XXe siècle.La tique Hyalomma marginatum est présente en Corse depuis plusieurs décennies (Grech-Angelini et al. 2016). Hyalomma marginatum est considérée comme une espèce de tique invasive en France continentale, de récentes publications confirmant son installation sur le littoral méditerranéen (Vial et al. 2016; Stachurski et Vial 2018; Bahet al. 2022). D’autres espèces de Hyalomma sont également présentes en France, H. scupense en Corse (Grech-Angelini , 2016) et sur le continent (Vial et Stachurski, comm. pers.), et des données récentes montrent que H. lusitanicum serait également installée en France continentale (Stachurski, comm. pers.).Cette évolution est préoccupante, car ces tiques sont vectrices de nombreux agents pathogènes responsables de maladies pour l’être humain (notamment du virus de la fièvre hémorragique de Crimée-Congo – FHCC – ou de Rickettsies) et de maladies animales (notamment Babesia caballi responsable de la piroplasmose équine).Le virus de la FHCC (CCHFV) est responsable, chez l’être humain, de flambées de fièvre hémorragique sévère, dont le taux de létalité varie de 5 à près de 30 % (Spengler, Bergeron,et Spiropoulou 2019). Une séroprévalence du CCHFV de l’ordre de 10 % aurait récemment été mise en évidence chez les ruminants domestiques en Corse, sans qu’aucun cas humain n’ait encore été observé (Grech-Angelini et al. 2020). En 2016, deux cas autochtones de FHCC ont été confirmés à Madrid (Negredo et al. 2017), pour la première fois en Europe de l’Ouest.Une étude rétrospective, menée en 2020, a montré qu'un cas de FHCC était survenu dans la même province en 2013 (Negredo et al 2021). Depuis, des cas de FHCC, dont certains mortels, sont rapportés quasiment tous les ans en Espagne (2018, 2020, 2021, 2022). De plus, la circulation du virus est en recrudescence dans la région des Balkans et en Turquie.Aussi, l’Anses s’est autosaisie le 4 mars 2020 pour analyser les risques pour la santé humaineet animale liés aux tiques du genre Hyalomma en France.
Published: 2023

3. The control of Hyalomma ticks, vectors of the Crimean–Congo hemorrhagic fever virus: Where are we now and where are we going?

Author: Sarah I. Bonnet, Gwenaël Vourc’h, Alice Raffetin, Alessandra Falchi, Julie Figoni, Johanna Fite, Thierry Hoch, Sara Moutailler, Elsa Quillery, Département Santé Animale (DEPT SA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Centre Hospitalier Intercommunal Villeneuve-Saint-Georges (CHIV), Dynamic Microbiology - EA 7380 (DYNAMIC), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est (UPE)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Epidémiologie des maladies animales infectieuses (EpiMAI USC), École nationale vétérinaire - Alfort (ENVA)-Epidémiologie (EPI), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Università di Corsica Pasquale Paoli [Université de Corse Pascal Paoli], Partenaires INRAE, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Direction de l'Evaluation des Risques (DER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Infectious Diseases, Ticks, Ixodidae, Spain, Hemorrhagic Fever Virus, Crimean-Congo, Public Health, Environmental and Occupational Health, Animals, Hemorrhagic Fever, Crimean, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: This review was conducted by the ad hoc subgroup from the working expert group on the risks related to Hyalomma ticks at the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) commissioned by the French authorities.; International audience; At a time of major global, societal, and environmental changes, the shifting distribution of pathogen vectors represents a real danger in certain regions of the world as generating opportunities for emergency. For example, the recent arrival of the Hyalomma marginatum ticks in southern France and the concurrent appearance of cases of Crimean–Congo hemorrhagic fever (CCHF)—a disease vectored by this tick species—in neighboring Spain raises many concerns about the associated risks for the European continent. This context has created an urgent need for effective methods for control, surveillance, and risk assessment for ticks and tick-borne diseases with a particular concern regarding Hyalomma sp. Here, we then review the current body of knowledge on different methods of tick control—including chemical, biological, genetical, immunological, and ecological methods—and the latest developments in the field, with a focus on those that have been tested against ticks from the genus Hyalomma. In the absence of a fully and unique efficient approach, we demonstrated that integrated pest management combining several approaches adapted to the local context and species is currently the best strategy for tick control together with a rational use of acaricide. Continued efforts are needed to develop and implement new and innovative methods of tick control.
Published: 2022

4. Risk of Monkeypox virus (MPXV) transmission through the handling and consumption of food

Author: Estelle Chaix, Mickaël Boni, Laurent Guillier, Stéphane Bertagnoli, Alexandra Mailles, Catherine Collignon, Pauline Kooh, Olivier Ferraris, Sandra Martin-Latil, Jean-Claude Manuguerra, Nadia Haddad, Direction de l'Evaluation des Risques (DER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Cellule d'Intervention Biologique d'Urgence (Centre National de Référence) - Laboratory for Urgent Response to Biological Threats (National Reference Center) (CIBU), Université Paris Cité (UPCité)-Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Microbiology (medical), Infectious Diseases, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Epidemiology, Food, Poxvirus, [SDV]Life Sciences [q-bio], Transmission, Monkeypox, Monkeypox virus, Recommendations
Abstract: This paper was prepared thanks to the collective expertise carried out by the ANSES emergency collective expert appraisal group (GECU) “Monkeypox – Food” (ANSES opinion no 2022-SA-0110), chaired by Nadia Haddad, and whose members are cited in the authors.; International audience; Monkeypox (MPX) is a zoonotic infectious disease caused by Monkeypox virus (MPXV), an enveloped DNA virus belonging to the Poxviridae family and the Orthopoxvirus genus. Since early May 2022, a growing number of human cases of Monkeypox have been reported in non-endemic countries, with no history of contact with animals imported from endemic and enzootic areas, or travel to an area where the virus usually circulated before May 2022. This qualitative risk assessment aimed to investigate the probability that MPXV transmission occurs through food during its handling and consumption. The risk assessment used “top-down” (based on epidemiological data) and “bottom-up” (following the agent through the food chain to assess the risk of foodborne transmission to human) approaches, which were combined. The “top-down” approach first concluded that bushmeat was the only food suspected as a source of contamination in recorded cases of MPXV, by contact or ingestion. The “bottom-up” approach then evaluated the chain of events required for a human to become ill after handling or consuming food. This approach involves several conditions: (i) the food must be contaminated with MPXV (naturally, by an infected handler or after contact with a contaminated surface); (ii) the food must contain viable virus when it reaches the handler or consumer; (iii) the person must be exposed to the virus and; (iv) the person must be infected after exposure. Throughout the risk assessment, some data gaps were identified and highlighted. The conclusions of the top-down and bottom-up approaches are consistent and suggest that the risk of transmission of MPXV through food is hypothetical and that such an occurrence was never reported. In case of contamination, cooking (e.g., 12 min at 70°C) could be considered effective in inactivating Poxviridae in foods. Recommendations for risk management are proposed. To our knowledge, this is the first risk assessment performed on foodborne transmission of MPXV.
Published: 2022

5. WP4_T1. Development of pre-DNA extraction enrichment strategies: Aptamers

Author: Karadjian, Grégory, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018), KARADJIAN, Grégory, and Promoting One Health in Europe through joint actions on foodborne zoonoses, antimicrobial resistance and emerging microbiological hazards. - One Health EJP - - H2020-SFS-2017-1 2018-01-01 - 2022-12-31 - 773830 - VALID
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2022

6. One Health surveillance of West Nile and Usutu viruses

Author: Constant, Orianne, Gil, Patricia, Barthelemy, Jonathan, Bolloré, Karine, Foulongne, Vincent, Desmetz, Caroline, Leblond, Agnès, Desjardins, Isabelle, Pradier, Sophie, Joulié, Aurélien, Sandoz, Alain, Amaral, Rayane, Boisseau, Michel, Rakotoarivony, Ignace, Baldet, Thierry, Marie, Albane, Frances, Benoît, Reboul Salze, Florence, Tinto, Bachirou, van de Perre, Philippe, Salinas, Sara, Beck, Cécile, Lecolinet, Sylvie, Gutierrez, Serafin, Simonin, Yannick, Simonin, Yannick, MUSE - - MUSE2016 - ANR-16-IDEX-0006 - IDEX - VALID, Laboratoires d'excellence - From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow - - EpiGenMed2010 - ANR-10-LABX-0012 - LABX - VALID, Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier]-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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biocommunication en Cardio-Métabolique (BC2M), Université de Montpellier (UM), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), GREMERES ICE, Clinique Vétérinaire Jolimont, Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire Chimie de l'environnement (LCE), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Entente interdépartementale pour la démoustication du littoral méditerranéen [Montpellier] (EID Méditerranée), EID-Méditerranée, This study was funded by the ANR (French National Research Agency, reference ANR-16-IDEX-0006), the KIM RIVE initiative, the Labex EpiGenMed 'Investissements d’avenir' programme (reference ANR- 10-LABX-12-01), and Montpellier University of Excellence (MUSE, ArboSud project). Moreover, SG was recipient of funding from the Direction Générale de l’Alimentation from the French Ministry of Agriculture and Food. Horse serosurveys were funded by the French Horse and Riding Institute, IFCE, and the EPERON fund (Encouragement aux ProjetsEquestres Régionaux Ou Nationaux) (OpIUM project)., ANR-16-IDEX-0006,MUSE,MUSE(2016), and ANR-10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010)
Subjects: [SDV] Life Sciences [q-bio], seroprevalence, [SDV]Life Sciences [q-bio], Usutu virus, One Health surveillance, West Nile virus, co-circulation
Abstract: International audience; Background West Nile virus (WNV) and Usutu virus (USUV), two closely related flaviviruses, mainly follow an enzootic cycle involving mosquitoes and birds, but also infect humans and other mammals. Since 2010, their epidemiological situation may have shifted from irregular epidemics to endemicity in several European regions; this requires confirmation, as it could have implications for risk assessment and surveillance strategies. Aim To explore the seroprevalence in animals and humans and potential endemicity of WNV and USUV in Southern France, given a long history of WNV outbreaks and the only severe human USUV case in France in this region. Methods We evaluated the prevalence of WNV and USUV in a repeated cross-sectional study by serological and molecular analyses of human, dog, horse, bird and mosquito samples in the Camargue area, including the city of Montpellier, between 2016 and 2020. Results We observed the active transmission of both viruses and higher USUV prevalence in humans, dogs, birds and mosquitoes, while WNV prevalence was higher in horses. In 500 human samples, 15 were positive for USUV and 6 for WNV. Genetic data showed that the same lineages, WNV lineage 1a and USUV lineage Africa 3, were found in mosquitoes in 2015, 2018 and 2020. Conclusion These findings support existing literature suggesting endemisation in the study region and contribute to a better understanding of USUV and WNV circulation in Southern France. Our study underlines the importance of a One Health approach for the surveillance of these viruses.
Published: 2022

7. Multidisciplinary Management of Suspected Lyme Borreliosis: Clinical Features of 569 Patients, and Factors Associated with Recovery at 3 and 12 Months, a Prospective Cohort Study

Author: Alice, Raffetin, Julien, Schemoul, Amal, Chahour, Steve, Nguala, Pauline, Caraux-Paz, Giulia, Paoletti, Anna, Belkacem, Fernanda, Medina, Catherine, Fabre, Sébastien, Gallien, Nicolas, Vignier, Yoann, Madec, On The Behalf Of The Tick-Borne Diseases Reference Center-Paris And Northern Region Working Group, Centre Hospitalier Intercommunal Villeneuve-Saint-Georges (CHIV), ESCMID [Basel], Dynamic Microbiology - EA 7380 (DYNAMIC), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est (UPE)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Groupe de Recherche et d’Etude des Maladies Infectieuses-Paris Sud-Est (GREMLIN), Epidémiologie des maladies animales infectieuses (EpiMAI USC), École nationale vétérinaire - Alfort (ENVA)-Epidémiologie (EPI), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Hôpital Henri Mondor, CHU Henri Mondor [Créteil], Laboratoire éducations et promotion de la santé (LEPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Sorbonne Paris Nord, Centre d'investigation clinique Antilles-Guyane (CIC - Antilles Guyane), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -CHU de la Martinique [Fort de France]-Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), We are grateful to the French Ministry of Health who has provided an annual budget allowance for the development of the TBD-RC since July 2019, and to the Regional Health Agency of Paris region who created a position for an infectious diseases physician to work at the TBD-RC in 2020., and on the behalf of the Tick-Borne Diseases Reference Center-Paris and Northern Region Working Group
Subjects: Microbiology (medical), serial misdiagnosis, Virology, [SDV]Life Sciences [q-bio], lyme borreliosis, multidisciplinary management, Microbiology
Abstract: We are grateful to the following persons for their contribution and support to the TBD-RC and this study: The Tick-Borne Diseases Reference Center-Paris and Northern Region Working Group (Agathe Bounhiol, Kevin Diallo, Danielle Jaafar, Claudine Badr, Soline de Monteynard: Department of Infectious Diseases; Romain Jouenne, Emmanuel Dossou: Department of Internal Medicine; Stéphanie Emilie, Christine Shenouda: Department of Rheumatology; Lydie Lim, Navaneethan Nindulan: Department of Neurology; Sylvie Le Berre, Corinne Canu, Vincent Robin: Department of Algology; Sophie Dellion, Floriane Kouby: Department of Dermatology; Jonas Bantsimba: Department of Geriatrics; Jacques Breuil, Eric Hernandez, Camille Corlouer, Laurence Ghisalberti: Department of Microbiology; Eric Meinadier, Arthur Lefort: Department of Physical Rehabilitation; Aurélie Garraffo, Anne Chace, Emilie Georget: Department of Pediatrics; Ilia Pustilnicov: Department of Health Economics); International audience; Introduction. Because patients with a suspicion of Lyme borreliosis (LB) may have experienced difficult care paths, the Tick-Borne Diseases Reference Center (TBD-RC) was started in 2017. The aim of our study was to compare the clinical features of patients according to their final diagnoses, and to determine the factors associated with recovery in the context of multidisciplinary management for suspected LB. Methods. We included all adult patients who were seen at the TBD-RC (2017\textendash 2020). Four groups were defined: (i) confirmed LB, (ii) possible LB, (iii) Post-Treatment Lyme Disease Syndrome (PTLDS) or sequelae, and (iv) other diagnoses. Their clinical evolution at 3, 6, and 9\textendash 12 months after care was compared. Factors associated with recovery at 3 and at 9\textendash 12 months were identified using logistic regression models. Results. Among the 569 patients who consulted, 72 (12.6%) had confirmed LB, 43 (7.6%) possible LB, 58 (10.2%) PTLDS/sequelae, and 396 (69.2%) another diagnosis. A favorable evolution was observed in 389/569 (68.4%) at three months and in 459/569 (80.7%) at 12 months, independent of the final diagnosis. A longer delay between the first symptoms and the first consultation at the TBD-RC (p = 0.001), the multiplicity of the diagnoses (p = 0.004), and the inappropriate prescription of long-term antibiotic therapy (p = 0.023) were negatively associated with recovery, reflecting serial misdiagnoses. Conclusions. A multidisciplinary team dedicated to suspicion of LB may achieve a more precise diagnosis and better patient-centered medical support in the adapted clinical sector with a shorter delay, enabling clinical improvement and avoiding inappropriate antimicrobial prescription.
Published: 2021

8. Survey of ticks and tick-borne pathogens in wild chimpanzee habitat in Western Uganda

Author: Lacroux, Camille, Bonnet, Sarah, Pouydebat, Emmanuelle, Buysse, Marie, Rahola, Nil, Rakotobe, Sabine, Okimat, John-Paul, Duron, Olivier, Koual, Rachid, Asalu, Edward, Krief, Sabrina, Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Kibale National Park, Mécanismes Adaptatifs et Evolution (MECADEV), La Phocéenne de Cosmétique, Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Département Santé Animale (DEPT SA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Uganda Wildlife Authority (UWA), The Great Ape Conservation Project, the Fondation Ensemble, the Fondation pour la Nature et l’Homme, the Fondation Prince Albert II and the Fonds Français pour l’Environnement Mondial provided financial support for the research conducted at Sebitoli. La Phocéenne de Cosmétique and the Association Nationale de la Recherche et de la Technologie provided funds for the PhD scholarship of Camille Lacroux. This work has benefited from ‘Investissements d’Avenir’ managed by the French Agence Nationale de la Recherche (ANR, Laboratoire d’Excellence CEBA, ref. ANR-10-LABX-25-01)., and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: Vector-borne pathogens, Borrelia, Cryptoplasma, Ehrlichia, MESH: Rickettsia, MESH: Ixodidae, Piroplasmids, MESH: Ixodes, MESH: Tick-Borne Diseases, Infectious Diseases, Ticks, Amblyomma, [SDE]Environmental Sciences, Apes, Kibale, Parasitology, MESH: Tick Infestations, Rickettsia, MESH: Uganda
Abstract: Background Ticks and tick-borne pathogens significantly impact both human and animal health and therefore are of major concern to the scientific community. Knowledge of tick-borne pathogens is crucial for prescription of mitigation measures. In Africa, much research on ticks has focused on domestic animals. Little is known about ticks and their pathogens in wild habitats and wild animals like the endangered chimpanzee, our closest relative. Methods In this study, we collected ticks in the forested habitat of a community of 100 chimpanzees living in Kibale National Park, Western Uganda, and assessed how their presence and abundance are influenced by environmental factors. We used non-invasive methods of flagging the vegetation and visual search of ticks both on human team members and in chimpanzee nests. We identified adult and nymph ticks through morphological features. Molecular techniques were used to detect and identify tick-borne piroplasmids and bacterial pathogens. Results A total of 470 ticks were collected, which led to the identification of seven tick species: Haemaphysalis parmata (68.77%), Amblyomma tholloni (20.70%), Ixodes rasus sensu lato (7.37%), Rhipicephalus dux (1.40%), Haemaphysalis punctaleachi (0.70%), Ixodes muniensis (0.70%) and Amblyomma paulopunctatum (0.35%). The presence of ticks, irrespective of species, was influenced by temperature and type of vegetation but not by relative humidity. Molecular detection revealed the presence of at least six genera of tick-borne pathogens (Babesia, Theileria, Borrelia, Cryptoplasma, Ehrlichia and Rickettsia). The Afrotopical tick Amblyomma tholloni found in one chimpanzee nest was infected by Rickettsia sp. Conclusions In conclusion, this study presented ticks and tick-borne pathogens in a Ugandan wildlife habitat whose potential effects on animal health remain to be elucidated. Graphical Abstract
Published: 2023

9. Novel Chronic Anaplasmosis in Splenectomized Patient, Amazon Rainforest

Author: Olivier Duron, Rachid Koual, Lise Musset, Marie Buysse, Yann Lambert, Benoît Jaulhac, Denis Blanchet, Kinan Drak Alsibai, Yassamine Lazrek, Loïc Epelboin, Pierre Deshuillers, Céline Michaud, Maylis Douine, 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), Institut Pasteur de la Guyane, Réseau International des Instituts Pasteur (RIIP), Laboratoire de Parasitologie [Cayenne, Guyane française], Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre National de Référence du Paludisme [Cayenne, Guyane française] (CNR - laboratoire associé), Centre Collaborateur OMS pour la surveillance de la résistance aux antipaludiques [Cayenne, Guyane française] (CCOMS), Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Centre Hospitalier Andrée Rosemon [Cayenne, Guyane Française], Virulence bactérienne précoce : fonctions cellulaires et contrôle de l'infection aiguë et subaiguë, Université de Strasbourg (UNISTRA), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The research was supported by funding from Investissements d’Avenir grants managed by the Agence Nationale de la Recherche (ANR, France, Laboratoire d’Excellence CEBA, ref. ANR-10-LABX-25-01)., and ANR-10-LABX-0025,CEBA,CEnter of the study of Biodiversity in Amazonia(2010)
Subjects: Microbiology (medical), Anaplasmosis, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Anaplasma, Rainforest, Infectious Diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Epidemiology, Animals, Humans, Rickettsia Infections, Brazil
Abstract: International audience; We report a case of unusual human anaplasmosis in the Amazon rainforest of French Guiana. Molecular typing demonstrated that the pathogen is a novel Anaplasma species, distinct to all known species, and more genetically related to recently described Anaplasma spp. causing infections in rainforest wild fauna of Brazil.
Published: 2022

10. The distribution, phenology, host range and pathogen prevalence of Ixodes ricinus in France: a systematic map and narrative review

Author: Grégoire Perez, Laure Bournez, Nathalie Boulanger, Johanna Fite, Barbara Livoreil, Karen D. McCoy, Elsa Quillery, Magalie René-Martellet, Sarah I. Bonnet, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Cogitamus, Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Virulence bactérienne précoce : fonctions cellulaires et contrôle de l'infection aiguë et subaiguë, Université de Strasbourg (UNISTRA), Centre National de référence des Borrelia (CNR), Les Hôpitaux Universitaires de Strasbourg (HUS), Direction de l'Evaluation des Risques (DER), 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), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and This work is issued from a scientific report commanded by of the Direction Générale de la Santé (Ministry of Health) to ANSES (French Agency for Food, Environmental and Occupational Health & Safety) who delegated through a research and development agreement to the École nationale vétérinaire d’Alfort (national veterinary School of Alfort) and allocated funds to hire GP for a 13 months postdoc contract (the complete report in French is available at https://hal-anses.archives-ouvertes.fr/anses-03263410).
Subjects: Anaplasma, Coxiella, tick-borne encephalitis virus, Borrelia, Theileria, tick-borne diseases, Babesia, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Francisella, Rickettsia, Bartonella, hard tick
Abstract: The tickIxodes ricinusis the most important vector species of infectious diseases in European France. Understanding its distribution, phenology, and host species use, along with the distribution and prevalence of associated pathogens at national scales is essential for developing prevention strategies. The aim of this paper is to provide a systematic map and narrative review of the existing knowledge on the eco-epidemiology ofI.ricinusin France. Using literature published up to 2020, the present paper provides a distribution map for the species and a summary of environmental factors explaining observed geographical differences in phenology and temporal differences in abundance. The diversity of vertebrate host species used by this tick, along with their degree of infestation when available, are presented and discussed with respect to their potential contribution to the population dynamics ofI.ricinusand the circulation of tick-borne zoonotic pathogens. Prevalence data of detected pathogens are summarised in different maps. Results from 187 identified references show that the species is present in most departments, but scarce under Mediterranean climate and in coastal habitats. Its phenology is generally bimodal with variations depending on climate. Abundance seems positively influenced by forest cover and host abundance. Rodents and ruminants are the most studied species groups, but the diversity of sampling protocols (e.g., location, season, exhaustivity of inspection) precluded direct comparisons between species groups. Data on pathogens are patchy, with most studies conducted near research units. Among pathogens,Borrelia burgdorferisensu lato is the most searched for in ticks and seems more prevalent in north-eastern and central France. The review carried out here has made it possible to highlight the gaps in our knowledge of tick-host-pathogen interactions, their ecology and their distribution, and the need to address these gaps in order to optimize tick and tick-borne diseases prevention and control strategies.
Published: 2023

11. Development of an aptamer-based test for trichinella detection (AptaTrich)

Author: Brosseau, Noah Emerson, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Vallée Isabelle, Karadjian Grégory, and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: [SDV]Life Sciences [q-bio], Trichinella, aptamères, diagnostique, Trichinella, aptamer, diagnostic
Abstract: Objectives The aim is to develop an innovative and highly specific approach to detect Trichinella infected animals (or humans) based on aptamers directed against Trichinella whole larvae and/or against larval molecules (proteins, carbohydrates, ...). It will allow an early detection of infected animals or patients using blood samples. This in turn will result in: - implementation of serological monitoring programmes to reduce the costs of the current Trichinella testing schemes, and at the same time guarantee removal of infected animals from the food chain ; - early onset therapy in humans avoiding the parasite installation in muscles. Methods An initial random DNA library already available at the French NRL will be used. In order to select specific targets, two selection strategies based on the method of "Systematic Evolution of Ligands by Enrichment" (SELEX) will be adapted to Trichinella. The first is a method of Whole Larvae-SELEX, very innovative since the technique has never been performed on whole larvae; the second is a Protein-SELEX method, already used for the selection of aptamers against protozoa. Two subsequent positive selection steps based on the first strategy (whole larvae-SELEX) will be performed in order to greatly reduce the number of aptamers in the DNA library. Then ten more steps of positive selections will be implemented by decreasing the aptamer quantity and the contact time between the previous aptamers with the larvae to increase specificity. Some aptamers may be able to bind to Trichinella but could also cross-react with other parasites. At each of the 10 positive selection steps, negative selections will be made on other nematodes larvae. Only the aptamers that do not link to these other nematodes will be preserved. Obtaining other species will be easy since the French partner is 1) located on the campus of the National Veterinary School of Alfort and benefits from numerous samples provided by veterinary colleagues (Ascaris suum, Toxocara canis, T. cati, ...); and 2) co-leader of the French Nematode Network (REFNEM). The aptamers selected on whole larvae will be used for the development of serological tests. Nevertheless, there is still a risk of cross-reactions during co-infection with other parasites. These cross-reactions will be tested on patient and pig sera known to be infected with other parasite species but not with Trichinella. If it turns out that false positives are obtained, a Protein-SELEX strategy will be performed. Recombinant proteins specific for Trichinella and expressed early in the infection, such as NBL1, L20HTs1, L20HTs3, but also later proteins such as the p49, 3,6-dideoxy-D-arabino-hexose or beta-tyvelose, a specific carbohydrate of Trichinella, will be targeted by aptamer selections either from the first selected aptamers on whole larvae or from a new library. At least 8 steps of positive selections will be made by decreasing the amount of recombinant proteins and the aptamer-protein contact time to gain specificity. For each strategy, the different aptamers present in the last selection (different nucleotide sequences) may be quite numerous. They will then be identified by cloning/sequencing and / or by NGS. Then, small DNAs corresponding to these sequences will be synthesized in order to carry out the first Aptamer-Based ELISA tests on patient and pig sera that have been collected during infections versus healthy sera. Also, both the French and German NRLs have defined Trichinella positive and negative pig sera available. Different combinations of aptamers will also be tested to gain sensitivity. The selected aptamers and a protocol will be sent to the German (veterinary samples) and Canadian partners (human samples) that will test their available sera in a blinded approach. Test parameters such as sensitivity, specificity, reproducibility and robustness will be determined.; Contexte et enjeux Les travaux de l'équipe Paralim (Parasites transmis par les aliments) relèvent du concept « One World, One health » à l'interface de la santé animale et de la santé humaine. Les objectifs de l'équipe Paralim visent le développement d'outils de détection et d'identification des parasites zoonotiques transmis par l'alimentation et notamment les Nématodes du genre Trichinella. Pour protéger les consommateurs, ces parasites font l'objet d'une réglementation imposant leur détection à l'abattoir par des tests directs qui malheureusement ne permettent pas un suivi épidémiologique des élevages. Par ailleurs, les tests sérologiques actuels ne permettent pas une détection précoce de l'infection ni chez l'animal, chez l'humain. En santé humaine, ce problème retarde la mise en place de traitements qui pourtant pourraient réduire la charge parasitaire finale s'ils étaient administrés plus précocement. En santé animale, l'interprétation d'un test séropositif signifie que l'animal a été exposé à Trichinella mais ne certifie pas que le parasite soit présent dans ses muscles (infection éliminée, échec de l'infection, ) et donc que la viande soit infectieuse pour l'Homme. Développer un test innovant de détection directe du parasite est donc essentiel pour améliorer la détection des animaux vivants présentant un risque pour le consommateur. Nos travaux s'orientent vers l'utilisation des aptamères afin de disposer de tests sérologiques permettant d'identifier la présence du parasite chez son hôte. Objectifs du projet de thèse L'objectif du projet de thèse est de sélectionner des aptamères dirigés contre des larves entières ou contre des molécules (protéines, carbohydrates, ) de Trichinella spp., puis de développer des tests sérologiques de détection de ces molécules dans le sang des animaux (porcs, sangliers), mais également de patients. Approche méthodologique Deux stratégies de sélection basées sur la méthode d'« Evolution Systématique de Ligands par Enrichissement » (SELEX) seront développées à partir d'une librairie initiale composée de petits ADNs de 80 paires de bases. La première est une méthode de Whole Larvae-SELEX, très novatrice puisque la technique n'a encore jamais été réalisée sur larves entières ; la deuxième est une méthode de Protein-SELEX ayant déjà été utilisée pour la sélection d'aptamères dirigés contre des protozoaires. Dix cycles de sélections positives sur des Larves 1 Musculaires (L1M) entières de Trichinella spp, ou de molécules cibles (NBL1, L20HTs1, β-tyvelose,), puis de sélections négatives sur larves de Nématodes autres que Trichinella seront réalisées. Les aptamères seront alors identifiés par clonage-séquençage et/ou par NGS. Puis des petits ADNs correspondants à ces séquences seront synthétisés. Un test Aptamer-Based ELISA sera développé puis utilisé sur des sérums de patients et des sérums de porcs positifs versus sains ou contaminés par d'autres parasites pour déterminer le(s)quel(s) des aptamères sont le(s)plus sensible(s) et le(s) plus spécifique(s). Différentes combinaisons d'aptamères seront également testées pour permettre de gagner en sensibilité. Résultats attendus, livrables 1/ Des aptamères ligands de Trichinella seront sélectionnés et séquencés. 2/ Un (des) test (s) sérologique (s) basé (s) sur ces aptamères sera (ont) développé (s) et optimisés. 3/ Des études épidémiologiques seront initiées au niveau des élevages de porcs (France, Allemagne, Pologne), de la faune sauvage (sangliers : France, Allemagne, Pologne) mais aussi en analyse rétrospectives de patients français et québécois. Collaborations et financement Ce projet s'inscrit dans le cadre d'une collaboration déjà établie avec un partenaire québéquois (Pr Ndao, Univesité McGill), des partenaires européens (Dr A Mayer (BfR, Allemagne) ; Dr M Rosycki (Piwet, Pologne) et partenaire français (Dr H Yéra, Institut Cochin). Une bourse de doctorat est obtenue dans le cadre d'un projet Européen One Health European Join Project (https://onehealthejp.eu/about/) porté par l'Anses.
Published: 2023

12. An update of evidence for pathogen transmission by ticks of the genus Hyalomma

Author: Sarah I. Bonnet, Stéphane Bertagnoli, Alessandra Falchi, Julie Figoni, Johanna Fite, Thierry Hoch, Elsa Quillery, Sara Moutailler, Alice Raffetin, Magalie René-Martellet, Gwenaël Vourc’h, Laurence Vial, Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), EA Bioscope Corse Méditerranée : Dynamique des infections virales en milieu insulaire, Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Direction de l'Evaluation des Risques (DER), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre Hospitalier Intercommunal Villeneuve-Saint-Georges (CHIV), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), 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: Microbiology (medical), Infectious Diseases, General Immunology and Microbiology, vectorial competence, Immunology and Allergy, tick-borne pathogens, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Molecular Biology, Hyalomma sp, ticks
Abstract: This narrative review was conducted by the ad hoc subgroup from the working expert group on the risks related to Hyalomma ticks at the French Agency for Food, Environmental and Occupational Health & Safety (ANSES) commissioned by the French authorities.; International audience; Current and likely future changes in the geographic distribution of ticks belonging to the genus Hyalomma are of concern, as these ticks are believed to be vectors of many pathogens responsible for human and animal diseases. However, we have observed that for many pathogens there are no vector competence experiments, and that the level of evidence provided by the scientific literature is often not sufficient to validate the transmission of a specific pathogen by a specific Hyalomma species. We therefore carried out a bibliographical study to collate the validation evidence for the transmission of parasitic, viral, or bacterial pathogens by Hyalomma spp. ticks. Our results show that there are very few validated cases of pathogen transmission by Hyalomma tick species.
Published: 2023

13. Features of Mycobacterium bovis Complete Genomes Belonging to 5 Different Lineages

Author: Ciriac Charles, Cyril Conde, Fabien Vorimore, Thierry Cochard, Lorraine Michelet, Maria Laura Boschiroli, Franck Biet, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Unité Zoonoses Bactériennes (UZB), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), ANSES, and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: Microbiology (medical), pangenome, mammalian tuberculosis (TB), Virology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], transmission, complete de novo assembly, Mycobacterium bovis, Microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract: Publication on Microorganisms. 11 January 2023. https://www.mdpi.com/2076-2607/11/1/177 Abstract: Mammalian tuberculosis (TB) is a zoonotic disease mainly due toMycobacterium bovis(M. bovis). A current challenge for its eradication is understanding its transmission within multi-host systems. Improvements in long-read sequencing technologies have made it possible to obtain complete bacterial genomes that provide a comprehensive view of species-specific genomic features. In the context of TB, new genomic references based on complete genomes genetically close to field strains are also essential to perform precise field molecular epidemiological studies. A total of 10M. bovisstrains representing each genetic lineage identified in France and in other countries were selected for performing complete assembly of their genomes. Pangenome analysis revealed a “closed” pangenome composed of 3900 core genes and only 96 accessory genes. Whole genomes-based alignment using progressive Mauve showed remarkable conservation of the genomic synteny except that the genomes have a variable number of copies of IS6110. Characteristic genomic traits of each lineage were identified through the discovery of specific indels. Altogether, these results provide new genetic features that improve the description ofM. bovislineages. The availability of new complete representative genomes ofM. boviswill be useful to epidemiological studies and better understand the transmission of this clonal-evolving pathogen.
Published: 2023
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14. First Expert Elicitation of Knowledge on Possible Drivers of Observed Increasing Human Cases of Tick-Borne Encephalitis in Europe

Author: Claude Saegerman, Marie-France Humblet, Marc Leandri, Gaëlle Gonzalez, Paul Heyman, Hein Sprong, Monique L’Hostis, Sara Moutailler, Sarah I. Bonnet, Nadia Haddad, Nathalie Boulanger, Stephen L. Leib, Thierry Hoch, Etienne Thiry, Laure Bournez, Jana Kerlik, Aurélie Velay, Solveig Jore, Elsa Jourdain, Emmanuelle Gilot-Fromont, Katharina Brugger, Julia Geller, Marie Studahl, Nataša Knap, Tatjana Avšič-Županc, Daniel Růžek, Tizza P. Zomer, René Bødker, Thomas F. H. Berger, Sandra Martin-Latil, Nick De Regge, Alice Raffetin, Sandrine A. Lacour, Matthias Klein, Tinne Lernout, Elsa Quillery, Zdeněk Hubálek, Francisco Ruiz-Fons, Agustín Estrada-Peña, Philippe Fravalo, Pauline Kooh, Florence Etore, Céline M. Gossner, Bethan Purse, Fundamental and Applied Research for Animals & Health (FARAH), Faculté de Médecine Vétérinaire [Liège], Université de Liège, SOUtenabilité et RésilienCE (SOURCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut de Recherche pour le Développement (IRD [France-Nord]), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Queen Astrid Military Hospital [Brussels], National Institute for Public Health and the Environment [Bilthoven] (RIVM), Retraité, École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Écologie et Émergence des Pathogènes Transmis par les Arthropodes / Ecology and Emergence of Arthropod-borne Pathogens, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Département Santé Animale (DEPT SA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virulence bactérienne précoce : fonctions cellulaires et contrôle de l'infection aiguë et subaiguë, Université de Strasbourg (UNISTRA), Universität Bern [Bern] (UNIBE), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Department of Epidemiology, Regional Authority of Public Health in Banská Bystrica, Immuno-Rhumatologie Moléculaire, Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Norwegian Institute of Public Health [Oslo] (NIPH), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), GÖG/ÖBIG (Gesundheit Österreich GmbH/Österreichisches Bundesinstitut für Gesundheitswesen)—Health Austria Ltd./Division of the Austrian Federal Institute for Health, National institute for health development Talinn, University of Gothenburg (GU), University of Ljubljana, Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Masaryk University [Brno] (MUNI), Veterinary Research Institute [Brno] (VRI), Lyme Center Apeldoorn, Gelre Hospital, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH), Agroscope, Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Sciensano [Bruxelles], Réseau International des Instituts Pasteur (RIIP), Centre Hospitalier Intercommunal Villeneuve-Saint-Georges (CHIV), Klinikum der Universitat Munchen, Ludwig-Maximilians-Universität München (LMU), Direction de l'Evaluation des Risques (DER), Institute of Vertebrate Biology of the Czech Academy of Sciences (IVB / CAS), Czech Academy of Sciences [Prague] (CAS), Catalonia Institute for Energy Research (IREC), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Metabiot (Metabiot), 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), UK Centre for Ecology & Hydrology, Natural Environment Research Council (NERC), European Centre for Disease Prevention and Control [Stockholm, Sweden] (ECDC), Maastricht University Medical Centre (MUMC), Maastricht University [Maastricht], and This research received no external funding.
Subjects: clustering analysis, Dermacentor reticulatus, genus Ixodes, 610 Medicine & health, drivers, multi-criteria decision analysis (MCDA), MESH: Ixodes, ticks, expert elicitation, TBEV, tick-borne encephalitis (TBE), Infectious Diseases, flavivirus, sensitivity analysis, Virology, MESH: Dermacentor, 570 Life sciences, biology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Europe, uncertainty, 610 Medizin und Gesundheit, MESH: Encephalitis, Tick-Borne, 570 Biowissenschaften, Biologie
Abstract: International audience; Tick-borne encephalitis (TBE) is a viral disease endemic in Eurasia. The virus is mainly transmitted to humans via ticks and occasionally via the consumption of unpasteurized milk products. The European Centre for Disease Prevention and Control reported an increase in TBE incidence over the past years in Europe as well as the emergence of the disease in new areas. To better understand this phenomenon, we investigated the drivers of TBE emergence and increase in incidence in humans through an expert knowledge elicitation. We listed 59 possible drivers grouped in eight domains and elicited forty European experts to: (i) allocate a score per driver, (ii) weight this score within each domain, and (iii) weight the different domains and attribute an uncertainty level per domain. An overall weighted score per driver was calculated, and drivers with comparable scores were grouped into three terminal nodes using a regression tree analysis. The drivers with the highest scores were: (i) changes in human behavior/activities; (ii) changes in eating habits or consumer demand; (iii) changes in the landscape; (iv) influence of humidity on the survival and transmission of the pathogen; (v) difficulty to control reservoir(s) and/or vector(s); (vi) influence of temperature on virus survival and transmission; (vii) number of wildlife compartments/groups acting as reservoirs or amplifying hosts; (viii) increase of autochthonous wild mammals; and (ix) number of tick species vectors and their distribution. Our results support researchers in prioritizing studies targeting the most relevant drivers of emergence and increasing TBE incidence.
Published: 2023
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15. Acquisition of new genetic knowledge on Mycobacterium bovis strains circulating in France through whole genome sequencing

Author: Charles, Ciriac, Unité Zoonoses Bactériennes (UZB), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Boschiroli Maria Laura, Biet Franck, and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: Bioinformatics analysis, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Séquençage de génomes complets, Molecular biology, Microbiologie, Whole genome sequencing, Analyse bioinformatique, Tuberculose bovine, Mycobacterium bovis, Microbiology, biologie moléculaire, IS6110, Bovine tuberculosis
Abstract: Mycobacterium bovis (M. bovis) is the etiological agent of bovine tuberculosis (bTB), a zoonotic disease with a high socioeconomic impact. After having reduced the prevalence of this disease below 0.1% for 6 years, France was recognised bTB free in 2001 which is a very advantageous situation for trading. However, this status is threatened in the recent years by the re-emergence of bTB in some French regions. BTB outbreaks are present in very localized areas and are due to persistent M. bovis strains with specific genotypes (defined by spoligotyping and MLVA typing). It is therefore important to understand if among the reasons for bTB increase, genetic factors linked to these dominant genotypes could be included. Furthermore, the transmission link between infected animals (which can involve those of different cattle herds and different wildlife species) remains difficult to establish in regions sharing the same M. bovis genotype. Analysis of whole-genome single nucleotide polymorphisms compared with appropriate reference genomes can accurately differentiate field strains. However, new whole genomes closer to the French field strains are needed to perform these studies.Ten new complete genomes were sequenced using MinION and Illumina technologies. Despite the high stability of M. bovis genome, their characterization and comparison allowed a better description of genetic lineages by defining specific genetic criteria for some of them. The use of complete genomes allows a better genomes annotation which improves our knowledge of the genetic diversity of the M. bovis genomes. The copy number of an insertion sequence, IS6110, was found to be variable between the different complete genomes. This sequence plays an important role in genome plasticity of the human pathogen Mycobacterium tuberculosis and was found in high copy numbers in representative genomes of highly prevalent genotypes whereas M. bovis is considered to have one or very few copies.We therefore studied the abundance and location of IS6110 in a larger panel of M. bovis genomes representative of the French diversity. These results confirmed that the most persistent genotypes were those with multiple copies of IS6110 and that two of the most common genotypes found in France in recent years present a very high copy number (more than 10). Further studies on 3 important genotypes, SB0120-DHV, SB0120-CO and a sub-group of Cluster A/F4 family, which are respectively found in Dordogne and Haute-Vienne, Côte d’Or and Atlantic Pyrenees (French regions), showed a quite high stability of IS6110 number and their insertion site between host species over 6-to-17-year periods. IS6110-related genetic changes did not appear to occur for host adaptation as suggested for highly prevalent Mycobacterium tuberculosis strains.This work has improved our knowledge on the M. bovis lineages circulating in France and worldwide by establishing a list of genetic characteristics specific to them. Some of these, such as IS6110, seem to be correlated with the epidemiological success of certain genotypes. The new genomes will help to better understand the bTB transmission dynamics in multihost systems and to implement more effective control measures to eradicate the disease in these areas.; Mycobacterium bovis (M. bovis) est l’agent étiologique de la tuberculose bovine (bTB) qui est une maladie zoonotique ayant un fort impact socioéconomique. Après avoir réduit la prévalence de cette maladie en dessous de 0,1% pendant 6 ans, la France a été reconnue indemne de bTB en 2001, ce qui est une situation très avantageuse pour le commerce. Ce statut est néanmoins menacé ces dernières années par la réémergence de la bTB dans certaines régions françaises. Ces foyers de bTB présents dans ces régions très localisées sont dus à des génotypes (défini par le profil spoligotype et le typage MLVA) spécifiques et persistants de ces régions. Il est donc important de comprendre si des facteurs génétiques liés à ces génotypes dominants peuvent expliquer leur succès épidémiologique. De plus, le lien de transmission entre les animaux infectés (pouvant impliquer des bovins domestiques et la faune sauvage) reste difficile à établir dans les régions partageant le même génotype de M. bovis. L’analyse des polymorphismes mononucléotidiques du génome entier comparé à des génomes de référence appropriés peut différencier précisément les souches de terrain. Cependant, de nouveaux génomes complets génétiquement plus proches des souches françaises de terrain sont nécessaires pour améliorer ces études.Dix nouveaux génomes complets ont été séquencés avec les technologies MinION et Illumina. Malgré la grande stabilité du génome de M. bovis, la caractérisation et la comparaison des 10 génomes ont permis de mieux décrire les lignées génétiques identifiées en France en définissant des critères génétiques spécifiques pour certaines d'entre elles. L’utilisation de génomes complets permet une meilleure annotation des génomes ce qui améliore nos connaissances sur la diversité génétique des génomes de M. bovis. Le nombre de copies d’une séquence d’insertion, IS6110, s’est avéré variable entre les différents génomes complets. Cette séquence joue un rôle important dans la plasticité du génome de Mycobacterium tuberculosis et a été retrouvée en grand nombre dans des génomes représentatifs de génotype très prévalent alors que M. bovis est considéré comme ayant une ou très peu de copies.Nous avons donc étudié l'abondance et la localisation d'IS6110 dans panel plus large de génomes de M. bovis représentatifs de la diversité française. Ces résultats ont confirmé que les génotypes les plus persistants étaient ceux présentant plusieurs copies d'IS6110 et que deux des génotypes les plus retrouvés en France ces dernières années avaient plus de 10 copies. Des études supplémentaires sur 3 génotypes majoritaires, SB0120-DHV, SB0120-CO et un sous-groupe du cluster A/ famille F4, qui sont respectivement très présents dans les régions françaises de Dordogne et Haute-Vienne, Côte d'Or et Pyrénées-Atlantiques, ont montré une grande stabilité du nombre d'IS6110 et de leur site d’insertion entre les espèces hôtes sur des périodes de 6 à 17 ans. Les changements liés aux IS6110 ne semblent pas se produire lors de changement d’hôte, comme cela était suggéré pour la lignée Beijing de M. tuberculosis. Ce travail a permis d'améliorer nos connaissances des génotypes de M. bovis circulant en France et dans le monde en établissant des listes de caractéristiques génétiques. Certains évènements génétiques, comme l'insertion d’IS6110, semblent être corrélés au succès de certains génotypes. Les nouveaux génomes permettront de mieux comprendre la dynamique de la transmission de la bTB dans les systèmes multi-hôtes et de mettre en place des mesures de contrôle plus efficaces pour éradiquer la maladie dans ces zones.
Published: 2022

16. A large-scale comparative genomics study of human and ruminant strains of Cryptosporidium parvum from Europe

Author: Bellinzona, Greta, Nardi, Tiago, Castelli, Tiago, Autio, Tiina, Blanchard, Yannick, Chalmers, Rachel, Davidson Rebecca, K., de Jong, Anton, Enbom, Tuulia, Karadjian, Grégory, Klotz, Christian, Jokelainen, Pikka, Ostlund, Emma, Plutzer, Judith, Ptochos, Sokratis, Robertson Lucy, J., Robinson, Guy, Sannella Anna, Rosa, Sroka, Jacek, Stensvold Christen, R., Touzain, Fabrice, Troell, Karin, Vatta, Paolo, Sassera, Davide, Caccio Simone, M., Lalle, Marco, Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), Finish Food Safety Authority Evira, Partenaires INRAE, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Swansea University Medical School [Swansea, Royaume-Uni], Swansea University, National Veterinary Institute [Uppsala] (SVA), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Robert Koch Institute [Berlin] (RKI), Statens Serum Institut [Copenhagen], National Institute of Environmental Health, Norwegian Veterinary Institute [Oslo], Singleton Hospital, Istituto Superiore di Sanità (ISS), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2022

17. Development of a multi-locus sequence typing scheme for Cryptosporidium parvum

Author: Chaudhry, Umer, Betson, Martha, Stensvold Christen, Rune, Lalle, Marco, Villena, Isabelle, Chalmers, Rachel, Deksne, Gunita, van der Giessen, Joke, Plutzer, Judith, Mayer-Scholl, Anne, Karadjian, Grégory, Vedel Nielsen, Henrik, Opsteegh, Marieke, Ptochos, Sokratis, Ostlund, Emma, Touzain, Fabrice, Sannella, Anna, Vatta, Paolo, Blanchard, Yannick, Riedel, Hilde, Aesbicher, Toni, Bujila, Ioana, Waap, Helga, Robertson, Lucy, Hellmér, Maria, Sroka, Jacek, Zalewska, Barbora, Franssen, Fritz, Koudela, Bretislav, Schouw, Christian, Aftab, Huma, Engberg, Jorgen, Davidson, Rebecca, Hartmeyer, Gitte, Lejeune Virapin, Manigandan, Jokelainen, Pikka, Klotz, Christian, Caccio, Simone, Troell, Karin, Royal (Dick) School of Veterinary Studies, University of Surrey (UNIS), Statens Serum Institut [Copenhagen], Istituto Superiore di Sanità (ISS), Centre Hospitalier Universitaire de Reims (CHU Reims), Swansea University Medical School [Swansea, Royaume-Uni], Swansea University, Institute of Food Safety, Animal Health and Environment (BIOR), University of Latvia (LU), National Institute for Public Health and the Environment [Bilthoven] (RIVM), National Institute of Environmental Health (NIEH), Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Norwegian Veterinary Institute [Oslo], National Veterinary Institute [Uppsala] (SVA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Uppsala University Hospital, Robert Koch Institute [Berlin] (RKI), Public Health Agency of Sweden, Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), Mammal Research Institute, Polska Akademia Nauk = Polish Academy of Sciences (PAN), University of South Bohemia, Faculty of Science and Biology Centre of the Academy of Sciences of the Czech Republic, Parasitology Institute, Ceske Budejovice, Czech Republic, Zealand University Hospital, University of Calgary, and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2022

18. Development of an aptamer-based test for Trichinella detection

Author: Brosseau, Noah, Vallée, Isabelle, Mayer-Scholl, Anne, Ndao, Momar, Karadjian, Grégory, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Research Institute of the McGill University Health Centre (RI-MUHC), McGill University Health Center [Montreal] (MUHC), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2022

19. Prevalence of major digestive and respiratory helminths in dogs and cats in France: results of a multicenter study

Author: Gilles Bourgoin, Marie-Pierre Callait-Cardinal, Emilie Bouhsira, Bruno Polack, Patrick Bourdeau, Clarisse Roussel Ariza, Lisa Carassou, Emmanuel Lienard, Jason Drake, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Innovations Thérapeutiques et Résistances (InTheRes), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Ecole Nationale Vétérinaire de Nantes
Subjects: Male, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Nematodes, Deworming, Cestodes, Internal parasites, Companion animals, Cat Diseases, Feces, Metastrongyloidea, Dogs, Infectious Diseases, Risk factors, Helminths, Cats, Prevalence, Animals, Female, Parasites, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Parasitology, Dog Diseases, Intestinal Diseases, Parasitic
Abstract: Background The local distribution of helminths in dogs and cats and the evaluation of risk of contamination represent an important challenge for veterinarians due to their effects on animal health and their potential zoonotic risk. The overall goal of this study was to estimate the prevalence of the digestive and respiratory helminths infecting client-owned dogs and cats in France. Methods Faecal samples were collected from 414 pet dogs and 425 pet cats at 20 study sites during 2017–2018 and analysed by coproscopy. The samples included specimens collected from animals of both genders and various breeds and ages from a variety of living environments, and with different lifestyles and feeding regimes. Associations between parasitic infection and qualitative factors were explored. Results Overall, 125 (14.9%) samples (15.2% in dogs and 14.6% in cats) were positive for at least one of the species of helminths identified. Infection rates were highest for Toxocara canis and Toxocara cati (8.5% and 11.3%, respectively), while Toxascaris leonina was found only in one cat (0.2%). The apparent prevalence of Ancylostoma caninum and Uncinaria stenocephala in dogs was 1.7% and 4.3%, respectively. No hookworms were found in cats. Whipworms (Trichuris vulpis) were identified in 2.7% of the dogs. Tapeworms (Dipylidium caninum and Taeniidae) were rarely found (Angiostrongylus vasorum Crenosoma vulpis, and Strongyloides stercoralis in dogs, Aelurostrongylus abstrusus in cats and Eucoleus spp. / Capillaria spp. in both dogs and cats was < 1%. Significantly higher fecal parasite emission rates were identified in young individuals, in animals with outdoor access, in animals living in the countryside and in intact animals (especially in cats). In addition, cats not fed exclusively with commercial diets and living with other animals (dogs and/or cats) were at higher risk for parasites. For dogs, hunting/herding and walking off-leash were found to be additional risk factors. Furthermore, pets with no reported history of deworming or dewormed > 1 year before the study were positive for parasites significantly more often than pets dewormed < 1 year before study participation. Conclusions The overall prevalence of helminths (some of which are zoonotic), the risk factors and the reportedly low deworming frequencies identified in this study (20.5% animals having never been dewormed and only 26.4% dewormed ≥ 3 times/year) illustrate the need for improving pet owners’ adherence to anthelmintic guidelines in France. Graphical Abstract
Published: 2022

20. Design and Planning of a Transdisciplinary Investigation into Farmland Pollinators: Rationale, Co-Design, and Lessons Learned

Author: Simon Hodge, Oliver Schweiger, Alexandra-Maria Klein, Simon G. Potts, Cecilia Costa, Matthias Albrecht, Joachim R. de Miranda, Marika Mand, Pilar De la Rúa, Maj Rundlöf, Eleanor Attridge, Robin Dean, Philippe Bulet, Denis Michez, Robert J. Paxton, Aurélie Babin, Nicolas Cougoule, Marion Laurent, Anne-Claire Martel, Laurianne Paris, Marie-Pierre Rivière, Eric Dubois, Marie-Pierre Chauzat, Karim Arafah, Dalel Askri, Sebastien N. Voisin, Tomasz Kiljanek, Irene Bottero, Christophe Dominik, Giovanni Tamburini, Maria Helena Pereira-Peixoto, Dimitry Wintermantel, Tom D. Breeze, Elena Cini, Deepa Senapathi, Gennaro Di Prisco, Piotr Medrzycki, Steffen Hagenbucher, Anina Knauer, Janine M. Schwarz, Risto Raimets, Vicente Martínez-López, Kjell Ivarsson, Chris Hartfield, Pamela Hunter, Mark J. F. Brown, Jane C. Stout, Trinity College Dublin, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of Freiburg [Freiburg], University of Reading (UOR), Consiglio Nazionale delle Ricerche [Bologna] (CNR), Agroscope, Swedish University of Agricultural Sciences (SLU), Estonian University of Life Sciences (EMU), Universidad de Murcia, Lund University [Lund], The Red Beehive Co. Ltd, Partenaires INRAE, Centre National de la Recherche Scientifique (CNRS), University of Mons [Belgium] (UMONS), Martin-Luther-University Halle-Wittenberg, Unité Pathologie de l'abeille (UPA), Laboratoire de Sophia Antipolis, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), BioPark Archamps (BioPark), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), Swedish Farmers' Foundation for Agricultural Research, National Farmers' Union, British Beekeepers Association, Royal Holloway [University of London] (RHUL), and European Project: 773921,Horizon 2020,PoshBee(2018)
Subjects: landscape ecology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Renewable Energy, Sustainability and the Environment, pan-European, Geography, Planning and Development, Building and Construction, pesticides, Management, Monitoring, Policy and Law, bees, bee pathogens, insect declines, pollinators, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; To provide a complete portrayal of the multiple factors negatively impacting insects in agricultural landscapes it is necessary to assess the concurrent incidence, magnitude, and interactions among multiple stressors over substantial biogeographical scales. Trans-national ecological field investigations with wide-ranging stakeholders typically encounter numerous challenges during the design planning stages, not least that the scientific soundness of a spatially replicated study design must account for the substantial geographic and climatic variation among distant sites. ‘PoshBee’ (Pan-European assessment, monitoring, and mitigation of Stressors on the Health of Bees) is a multi-partner transdisciplinary agroecological project established to investigate the suite of stressors typically encountered by pollinating insects in European agricultural landscapes. To do this, PoshBee established a network of 128 study sites across eight European countries and collected over 50 measurements and samples relating to the nutritional, toxicological, pathogenic, and landscape components of the bees’ environment. This paper describes the development process, rationale, and end-result of each aspect of the of the PoshBee field investigation. We describe the main issues and challenges encountered during the design stages and highlight a number of actions or processes that may benefit other multi-partner research consortia planning similar large-scale studies. It was soon identified that in a multi-component study design process, the development of interaction and communication networks involving all collaborators and stakeholders requires considerable time and resources. It was also necessary at each planning stage to be mindful of the needs and objectives of all stakeholders and partners, and further challenges inevitably arose when practical limitations, such as time restrictions and labour constraints, were superimposed upon prototype study designs. To promote clarity for all stakeholders, for each sub-component of the study, there should be a clear record of the rationale and reasoning that outlines how the final design transpired, what compromises were made, and how the requirements of different stakeholders were accomplished. Ultimately, multi-national agroecological field studies such as PoshBee benefit greatly from the involvement of diverse stakeholders and partners, ranging from field ecologists, project managers, policy legislators, mathematical modelers, and farmer organisations. While the execution of the study highlighted the advantages and benefits of large-scale transdisciplinary projects, the long planning period emphasized the need to formally describe a design framework that could facilitate the design process of future multi-partner collaborations.
Published: 2022
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21. Dermacentor reticulatus - a tick on its way from glacial refugia to a panmictic Eurasian population

Author: Branka Bilbija, Cäcilia Spitzweg, Ivo Papoušek, Uwe Fritz, Gábor Földvári, Martin Mullett, Flora Ihlow, Hein Sprong, Kristína Civáňová Křížová, Nikolay Anisimov, Oxana A. Belova, Sarah I. Bonnet, Elizabeth Bychkova, Aleksandra Czułowska, Georg G. Duscher, Manoj Fonville, Olaf Kahl, Grzegorz Karbowiak, Ivan S. Kholodilov, Dorota Kiewra, Stjepan Krčmar, Gulzina Kumisbek, Natalya Livanova, Igor Majláth, Maria Teresa Manfredi, Andrei D. Mihalca, Guadalupe Miró, Sara Moutailler, Igor V. Nebogatkin, Snežana Tomanović, Zati Vatansever, Marya Yakovich, Sergio Zanzani, Pavel Široký, University of Veterinary and Pharmaceutical Sciences [Brno] (VFU), Senckenberg Naturhistorische Sammlungen Dresden, Museum für Mineralogie und Geologie, Centre for Ecological Research [Budapest], Eötvös Loránd University (ELTE)-Hungarian Academy of Sciences (MTA), Mendel University in Brno (MENDELU), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Masaryk University [Brno] (MUNI), Tyumen State University, Chumakov Institute of Poliomyelitis and Viral Encephalities [Moscou], Génétique fonctionnelle des maladies infectieuses - Functional Genetics of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Département Santé Animale (DEPT SA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Scientific and Practical Center of the National Academy of Sciences of Belarus on Bioresources [Minsk], University of Wrocław [Poland] (UWr), University of Veterinary Medicine [Vienna] (Vetmeduni), Austrian Agency for Health and Food Safety (AGES), Witold Stefanski Institute of Parasitology, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Chumakov Institute of Poliomyelitis and Viral Encephalitides, Josip Juraj Strossmayer University of Osijek, Al-Farabi Kazakh National University [Almaty] (KazNU), Institute of Systematics and Ecology of Animals, Novosibirsk, Russia., Pavol Jozef Šafárik University, Università degli Studi di Milano = University of Milan (UNIMI), University of Agricultural Sciences and Veterinary Medicine Cluj Napoca = Universitatea de Științe Agricole și Medicină Veterinară Cluj-Napoca, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), I.I. Schmalhausen Institute of Zoology of NASU, National Academy of Sciences of Ukraine (NASU), National center for public health [Hungary], University of Belgrade [Belgrade], Kafkas University, and This study was financed by the University of Veterinary Sciences Brno, Czech Republic, project 2022ITA22. GF was supported by the grant 'In the light of evolution: theories and solutions' (GINOP-2.3.2-15-2016-00057) and by the National Research, Development and Innovation Office in Hungary (RRF-2.3.1-21-2022-00006). This work was supported by the COST Action CA21170 'Prevention, anticipation and mitigation of tick-borne disease risk applying the DAMA protocol (PRAGMATICK)'.
Subjects: MESH: Refugium, Settore VET/06 - Parassitologia e Malattie Parassitarie degli Animali, MESH: Bayes Theorem, [SDV]Life Sciences [q-bio], Multigene sequence analysis, Vectors, Glacial refugia, Divergence, MESH: Dogs, Ixodida, Palaearctic, MESH: Rhipicephalus sanguineus, Infectious Diseases, Microsatellites, MESH: Dermacentor, MESH: Animals, Parasitology, MESH: Phylogeny, Divergence, Ixodida, Glacial refugia, Multigene sequence analysis, Microsatellites, Palaearctic, Vectors
Abstract: International audience; The ornate dog tick (Dermacentor reticulatus) shows a recently expanding geographic distribution. Knowledge on its intraspecific variability, population structure, rate of genetic diversity and divergence, including its evolution and geographic distribution, is crucial to understand its dispersal capacity. All such information would help to evaluate the potential risk of future spread of associated pathogens of medical and veterinary concern. A set of 865 D. reticulatus ticks was collected from 65 localities across 21 countries, from Portugal in the west to Kazakhstan and southern Russia in the east. Cluster analyses of 16 microsatellite loci were combined with nuclear (ITS2, 18S) and mitochondrial (12S, 16S, COI) sequence data to uncover the ticks’ population structures and geographical patterns. Approximate Bayesian computation was applied to model evolutionary relationships among the found clusters. Low variability and a weak phylogenetic signal showing an east–west cline were detected both for mitochondrial and nuclear sequence markers. Microsatellite analyses revealed three genetic clusters, where the eastern and western cluster gradient was supplemented by a third, northern cluster. Alternative scenarios could explain such a tripartite population structure by independent formation of clusters in separate refugia, limited gene flow connected with isolation by distance causing a “bipolar pattern”, and the northern cluster deriving from admixture between the eastern and western populations. The best supported demographic scenario of this tick species indicates that the northern cluster derived from admixture between the eastern and western populations 441 (median) to 224 (mode) generations ago, suggesting a possible link with the end of the Little Ice Age in Europe.
Published: 2022

22. Diagnosis of animal trypanosomoses: proper use of current tools and future prospects

Author: Marc Desquesnes, Alireza Sazmand, Marisa Gonzatti, Alain Boulangé, Géraldine Bossard, Sophie Thévenon, Geoffrey Gimonneau, Philippe Truc, Stéphane Herder, Sophie Ravel, Denis Sereno, Etienne Waleckx, Vincent Jamonneau, Philippe Jacquiet, Sathaporn Jittapalapong, David Berthier, Philippe Solano, Laurent Hébert, Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (UMR INTERTRYP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université de Bordeaux (UB), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Bu-Ali Sina University, Universidad Simon Bolivar (USB), Centre international de recherche-développement sur l'élevage en zone sub-humide (CIRDES), Universidad Autónoma de Yucatán, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kasetsart University (KU), Physiopathologie et épidémiologie des maladies équines (PhEED), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Subjects: Pan-trypanosome ELISA, Trypanosoma, Trypanosoma cruzi, MESH: Africa, L73 - Maladies des animaux, Trypanosome, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Trypanosomiasis, Trypanosomose, Integrative trypanosomosis diagnosis, Animals, Surveillance épidémiologique, MESH: Animals, MESH: Animals, Domestic, MESH: Chagas Disease, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Chagas Disease, Diagnostic, POCD, Maladie de chagas, PSR, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Trypanosomosis, Contrôle de maladies, Dourine, L70 - Sciences et hygiène vétérinaires - Considérations générales, Trypanosomose africaine, Infectious Diseases, Maladie des animaux, Animals, Domestic, Africa, Parasitology, MESH: Trypanosomiasis, MESH: Trypanosoma cruzi, MESH: Trypanosoma
Abstract: Reliable diagnostic tools are needed to choose the appropriate treatment and proper control measures for animal trypanosomoses, some of which are pathogenic.Trypanosoma cruzi, for example, is responsible for Chagas disease in Latin America. Similarly, pathogenic animal trypanosomoses of African origin (ATAO), including a variety ofTrypanosomaspecies and subspecies, are currently found in Africa, Latin America and Asia. ATAO limit global livestock productivity and impact food security and the welfare of domestic animals. This review focusses on implementing previously reviewed diagnostic methods, in a complex epizootiological scenario, by critically assessing diagnostic results at the individual or herd level. In most cases, a single diagnostic method applied at a given time does not unequivocally identify the various parasitological and disease statuses of a host. These include “non-infected”, “asymptomatic carrier”, “sick infected”, “cured/not cured” and/or “multi-infected”. The diversity of hosts affected by these animal trypanosomoses and their vectors (or other routes of transmission) is such that integrative, diachronic approaches are needed that combine: (i) parasite detection, (ii) DNA, RNA or antigen detection and (iii) antibody detection, along with epizootiological information. The specificity of antibody detection tests is restricted to the genus or subgenus due to cross-reactivity with otherTrypanosomaspp. and Trypanosomatidae, but sensitivity is high. The DNA-based methods implemented over the last three decades have yielded higher specificity and sensitivity for active infection detection in hosts and vectors. However, no single diagnostic method can detect all active infections and/or trypanosome species or subspecies. The proposed integrative approach will improve the prevention, surveillance and monitoring of animal trypanosomoses with the available diagnostic tools. However, further developments are required to address specific gaps in diagnostic methods and the sustainable control or elimination of these diseases.Graphical Abstract
Published: 2022

23. IS6110 Copy Number in Multi-Host Mycobacterium bovis Strains Circulating in Bovine Tuberculosis Endemic French Regions

Author: Ciriac Charles, Cyril Conde, Franck Biet, Maria Laura Boschiroli, Lorraine Michelet, Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: MESH: Mycobacterium bovis, Microbiology (medical), insertion sequence (IS), bovine tuberculosis (bTB), [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Mycobacterium bovis, Microbiology, MESH: France, MESH: DNA Transposable Elements, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], France, MESH: Tuberculosis, Bovine, IS6110
Abstract: Publication onFront. Microbiol., 23 June 2022 Sec.Evolutionary and Genomic Microbiology https://www.frontiersin.org/articles/10.3389/fmicb.2022.891902/full Abstract IS6110is an insertion sequence found in theMycobacterium tuberculosiscomplex, to whichMycobacterium bovisbelongs, which can play a role in genome plasticity and in bacterial evolution. In this study, the abundance and location of IS6110onM. bovisgenomic data of French animal field strains were studied. A first analysis was performed on a panel of 81 strains that reflect the nationalM. bovispopulation’s genetic diversity. The results show that more than one-third of them are IS6110multicopy and that 10% have IS6110in a high copy number (more than 6 copies). Multicopy strains are those circulating in the regions where prevalence was above the national average. Further study of 93 such strains, with an IS6110copy number of 10-12, showed stability of IS6110copy number and genome location over time and between host species. The correlation betweenM. bovismulticopy strains and high bovine tuberculosis (bTB) prevalence leads us to consider whether their epidemiological success could be partly due to genetic changes originated by IS6110transposition.
Published: 2022
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24. Mycobacterial infection of precision cut lung slices reveals type 1 interferon pathway is locally induced by Mycobacterium bovis but not M. tuberculosis

Author: Remot, Aude, Carreras, Florence, Doz-Deblauwe, Emilie, Boschiroli, Maria-Laura, Browne, John, Gordon W, Stephen, Winter, Nathalie, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Zoonoses Bactériennes (UZB), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), University College Dublin [Dublin] (UCD), This work was supported by the Veterinary Biocontained research facility Network (VETBIONET), the ANR EpiLungCell (grant ANR-17-CE20-0018) and FEDER/Region Centre Val de Loire ANIMALT grant (FEDER convention number EX007516, Region Centre convention number 2019-00134936, research program number AE-2019-1850). Mobilities between France and Irland were supported by the 'ONE-TB' project (PHC Ulysses, funded by Campus France and the Irish Research Council), and the Fédération de Recherche en Infectiologie du Centre Val de Loire (FéRI)., ANR-17-CE20-0018,EpiLungCell,Etablissement de lignées cellulaires de ruminants pour la réplication et l'étude de pathogènes(2017), and European Project: 731014,VetBioNet(2017)
Subjects: cattle, [SDV]Life Sciences [q-bio], ex vivo, [SDV.IMM]Life Sciences [q-bio]/Immunology, One Health, innate immunity, Mycobacterium bovis
Abstract: International audience; Objective: Mycobacterium bovis (Mb) responsible for bovine TB, and Mycobacterium tuberculosis (Mtb) for human TB, are greater than 99.9% identical at the genetic level. It has been shown that the human pathogen, Mtb, shows reduced ability to cause disease in cattle (PMID: 20049086); furthermore, epidemiological studies have shown that Mb is less able to cause disease in humans (PMID: 5297551). However, the genetic reason(s) why one is an animal pathogen and the other human pathogen is not known. If we were able to determine the basis for the ability of these pathogens to cause disease, we would be able to develop better control tools, such as vaccines and diagnostics, to control these diseases in both humans and animals. Mb causes a chronic infection preferentially targeting the lung. The early steps after infection that influence the physiopathology of the disease are still poorly understood. We aim to get a deeper understanding of the physiopathology of bTB in the target species i.e. bovine and in the target organ, the lung. We compared the host tissue responses after Mb and Mtb infection. Such comparative study of human and animal pathogens is a key example of the One Health concept that explores the interrelation of human and animal health.Key findings: We set up a protocol for ex vivo infection of bovine lungs (Precision-cut lung slices; PCLS) that helps deciphering early steps following infection in the natural environment.We performed in situ imaging of PCLS infected with a fluorescent Mb strain, and localized our bacilli in the alveolar compartment, in contact with pneumocytes, near or inside alveolar macrophages. We analyzed the global tissue signature following infection by two Mb strains (AF2122 and Mb3601) and two Mtb strains (H37Rv and BTB1558). We performed a transcriptomic analysis using two different technologies, NanoString nCounter Analysis System and Fluidigm Biomark; and measured cytokines/chemokines in culture supernatant using a bovine 15-plex assay. We measured induction of inflammatory genes and chemokines for granulocyte recruitment. Tissue responses were higher at day 2 than day 1 post infection, and different between two breeds. Strikingly, the type I interferon pathway was only induced by Mb but not Mtb strains indicating that this pathway may be involved in mycobacterial virulence and host tropism. Impact: We aim to improve our comprehension of host-pathogen interactions ex vivo while reducing reliance on animal experiments, and contribute to future disease control strategies through a One Health approach.
Published: 2022

25. Low prevalence of hepatitis E virus in the liver of Corsican pigs slaughtered after 12 months despite high antibody seroprevalence

Author: Marie Pellerin, Bastien Trabucco, Lisandru Capai, Morgane Laval, Oscar Maestrini, Ferran Jori, Alessandra Falchi, Virginie Doceul, François Charrier, François Casabianca, Nicole Pavio, Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Systèmes d'Elevage Méditerranéens et Tropicaux - Laboratoire de Recherche sur le Développement de l'Elevage (SELMET-LRDE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), EA Bioscope Corse Méditerranée : Dynamique des infections virales en milieu insulaire, Université Pascal Paoli (UPP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Interdisciplinaire Sciences, Innovations, Sociétés (LISIS), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Gustave Eiffel, and Doceul, Virginie
Subjects: Swine, viruses, Corsica, L73 - Maladies des animaux, Âge, Porcin, liver contamination, Seroepidemiologic Studies, Prévention des maladies, Hepatitis E virus, Prevalence, Animals, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Swine Diseases, Élevage extensif, General Veterinary, General Immunology and Microbiology, pig extensive breeding, virus diseases, Contamination biologique, General Medicine, Morbidité, digestive system diseases, Virus, Hepatitis E, Maladie du foie, Liver, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, S50 - Santé humaine, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, RNA, RNA, Viral, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Hépatite
Abstract: International audience; Hepatitis E virus (HEV) infection can be acute and benign or evolve to chronic hepatitis with rapid progression toward cirrhosis or liver failure in humans. Hence, Hepatitis E (HE) disease is a major public health concern. In countries where pig populations are highly contaminated with HEV, human cases of HE are mainly foodborne, occurring frequently after consumption of raw or undercooked pork products or liver. Among factors associated to the presence of HEV in pork livers from intensive rearing systems, early slaughter (≤6 months) seems to be major. In Corsica, local pigs are raised in extensive farming systems and slaughtered after 12 months. To evaluate if slaughter of pigs over 12 months reduces the risk of HEV presence in livers, 1 197 liver samples were randomly collected in 2 Corsican slaughterhouses. Presence of HEV RNA was detected in liver and HEV seroprevalence was determined in paired serum. The sampling included 1,083 livers from animals between 12 and 48 months and 114 livers from animals < 12 months. The samples were predominantly from semi-extensive and extensive farms (n = 1 ,154). Estimated HEV seroprevalence was high, > 88% and HEV RNA prevalence in adult pig livers (>12-month-old) was low 0.18 %. However, in livers from younger animals (< 12 months), including piglets below 6-month-old, 5.3% (6/114) of the samples were positive for HEV RNA. Sequences recovered from positive livers belonged to HEV genotype 3c and 3f. The presence of infectious HEV was confirmed in 2 livers by the detection of HEV replication in HepaRG cell cultures. Thus, this study, demonstrates the low prevalence of HEV in livers of pigs over 12 months, even in farms with high HEV circulation. This observation may open new perspectives on the preferential use of livers from animals older than 12 months in raw pork liver products.
Published: 2022

26. Meteorological and climatic variables predict the phenology of Ixodes ricinus nymph activity in France, accounting for habitat heterogeneity

Author: Phrutsamon Wongnak, Séverine Bord, Maude Jacquot, Albert Agoulon, Frédéric Beugnet, Laure Bournez, Nicolas Cèbe, Adélie Chevalier, Jean-François Cosson, Naïma Dambrine, Thierry Hoch, Frédéric Huard, Nathalie Korboulewsky, Isabelle Lebert, Aurélien Madouasse, Anders Mårell, Sara Moutailler, Olivier Plantard, Thomas Pollet, Valérie Poux, Magalie René-Martellet, Muriel Vayssier-Taussat, Hélène Verheyden, Gwenaël Vourc’h, Karine Chalvet-Monfray, Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Boehringer Ingelheim Animal Health, Partenaires INRAE, Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Ecosystèmes forestiers (UR EFNO), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroclim (AGROCLIM), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Most tick observatories were supported by the CC-EID and Climatick projects: 'Adaptation of Agriculture and Forests to Climate Change' metaprogramme of the French National Research Institute for Agriculture, Food and Environment (INRAE). The observatory of Les Bordes was installed and equipped by the Centre Val-de-Loire region, the Loiret and the French National Forest Office. We also would like to thank the TEMPO French Network (https://tempo.pheno.fr/) for providing resources to support this study. The Les Bordes site belongs to the French national research infrastructure, ANAEE-F (http://www.anaee-france.fr/fr/), and is also included in the SOERE TEMPO (https://tempo.pheno.fr/).The Les Bordes site is also part of the framework of the ZAL (LTSER Zone Atelier Loire) and the GIS Coop network (https://www6.inra.fr/giscoop/), which is supported by the French Ministry for Agriculture and Food. This study was partially funded by EU grant 874850 MOOD and is catalogued as MOOD 040. The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Finally, PW is grateful for a grant from the Association Nationale de la Recherche et de la Technologie, bourse CIFRE (no 2019/0393)., European Project: 874850,H2020-SC1-2019-Single-Stage-RTD,MOOD(2020), and École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé
Subjects: Ecological epidemiology, Nymph, 2. Zero hunger, Lyme Disease, Multidisciplinary, Ixodes, Ixodes ricinus ticks, [SDV]Life Sciences [q-bio], Forests, 15. Life on land, Habitat characteristics, Phenological patterns, 13. Climate action, Questing activity, Meteorological conditions, Animals, Humans, Seasons, Entomology, Ecosystem, Ecological modelling
Abstract: Ixodes ricinus ticks (Acari: Ixodidae) are the most important vector for Lyme borreliosis in Europe. As climate change might affect their distributions and activities, this study aimed to determine the effects of environmental factors, i.e., meteorological, bioclimatic, and habitat characteristics on host-seeking (questing) activity of I. ricinus nymphs, an important stage in disease transmissions, across diverse climatic types in France over 8 years. Questing activity was observed using a repeated removal sampling with a cloth-dragging technique in 11 sampling sites from 7 tick observatories from 2014 to 2021 at approximately 1-month intervals, involving 631 sampling campaigns. Three phenological patterns were observed, potentially following a climatic gradient. The mixed-effects negative binomial regression revealed that observed nymph counts were driven by different interval-average meteorological variables, including 1-month moving average temperature, previous 3-to-6-month moving average temperature, and 6-month moving average minimum relative humidity. The interaction effects indicated that the phenology in colder climates peaked differently from that of warmer climates. Also, land cover characteristics that support the highest baseline abundance were moderate forest fragmentation with transition borders with agricultural areas. Finally, our model could potentially be used to predict seasonal human-tick exposure risks in France that could contribute to mitigating Lyme borreliosis risk.
Published: 2022

27. Building composite indices in the age of big data – Application to honey bee exposure to infectious and parasitic agents

Author: Huyen Ton Nu Nguyet, Minh, Bougeard, Stéphanie, Babin, Aurélie, Dubois, Eric, Druesne, Christine, Rivière, Marie-Pierre, Laurent, Marion, Chauzat, Marie-Pierre, Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Unité Pathologie de l'abeille (UPA), Laboratoire de Sophia Antipolis, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Direction du financement de la Recherche et Veille scientifique (DfRV), and European Project: 773921,Horizon 2020,PoshBee(2018)
Subjects: Multidisciplinary, Honey bee health, [SDV]Life Sciences [q-bio], Stress exposure, Summarizing big datasets, Factor analysis, Synthetic indices
Abstract: International audience; Pollinator insects play a crucial role in maintaining biodiversity and agricultural production worldwide. Yet they are subject to various infectious and parasitic agents (IPAs). To better assess their exposure to IPAs, discriminative and quantitative molecular methods have been developed. These tools produce large datasets that need to be summarised so as to be interpreted. In this paper, we described the calculation of three types of composite indices (numerical, ordinal, nominal) to characterize the honey bee exposure to IPAs in 128 European sites. Our summarizing methods are based on component-based factorial analyses. The indices summarised the dataset of eight IPAs quantified at two sampling times, into synthetic values providing different yet complementary information. Because our dataset included two sampling times, we used Multiple Factor Analysis (MFA) to synthetize the information. More precisely, the numerical and ordinal indices were generated from the first component of MFA, whereas the nominal index used the first main components of MFA combined with a clustering analysis (Hierarchical Clustering on components). The numerical index was easy to calculate and to be used in further statistical analyses. However, it contained only about 20% of the original information. Containing the same amount of original information, the ordinal index was much easier to interpret. These two indices summarised information in a unidimensional manner. Instead, the nominal index summarised information in a multidimensional manner, which retained much more information (94%). In the practical example, the three indices showed an antagonistic relationship between N. ceranae and DWV-B. These indices represented a toolbox where scientists could pick one composite index according to the aim pursued. Indices could be used in further statistical analyses but could also be used by policy makers and public instances to characterize a given sanitary situation at a site level for instance.
Published: 2023

28. West Nile, Sindbis and Usutu Viruses: Evidence of Circulation in Mosquitoes and Horses in Tunisia

Author: Youmna M’ghirbi, Laurence Mousson, Sara Moutailler, Sylvie Lecollinet, Rayane Amaral, Cécile Beck, Hajer Aounallah, Meriem Amara, Ahmed Chabchoub, Adel Rhim, Anna-Bella Failloux, Ali Bouattour, Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP), Université de Tunis El Manar (UTM), Arbovirus et Insectes Vecteurs - Arboviruses and Insect Vectors, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de la Manouba [Tunisie] (UMA), and This study was funded by Pasteur Institute of Tunis, Tunisia and Pasteur Institute of Paris, France in the frame of MATI project-ENVIRONMOS, and the laboratory of Viruses, Vectors and Hosts (LR20IPT02) funded by the Ministry of Higher Education and Scientific Research of Tunisia.
Subjects: Microbiology (medical), microsphere immunoassay, [SDV]Life Sciences [q-bio], Virus de sindbis, L73 - Maladies des animaux, Immunology and Allergy, Surveillance épidémiologique, Molecular Biology, Transmission des maladies, horses, mosquito-borne-viruses, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Immunology and Microbiology, virus du Nil occidental, high-throughput real-time PCR, Maladie transmise par vecteur, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, seroneutralization test, cELISA assay, Equus caballus, L72 - Organismes nuisibles des animaux, Cheval
Abstract: International audience; Mosquito-borne diseases have a significant impact on humans and animals and this impact is exacerbated by environmental changes. However, in Tunisia, surveillance of the West Nile virus (WNV) is based solely on the surveillance of human neuroinvasive infections and no study has reported mosquito-borne viruses (MBVs), nor has there been any thorough serological investigation of anti-MBV antibodies in horses. This study therefore sought to investigate the presence of MBVs in Tunisia. Among tested mosquito pools, infections by WNV, Usutu virus (USUV), and Sindbis virus (SINV) were identified in Cx. perexiguus. The serosurvey showed that 146 of 369 surveyed horses were positive for flavivirus antibodies using the cELISA test. The microsphere immunoassay (MIA) showed that 74 of 104 flavivirus cELISA-positive horses were positive for WNV, 8 were positive for USUV, 7 were positive for undetermined flaviviruses, and 2 were positive for tick-borne encephalitis virus (TBEV). Virus neutralization tests and MIA results correlated well. This study is the first to report the detection of WNV, USUV and SINV in Cx. perexiguus in Tunisia. Besides, it has shown that there is a significant circulation of WNV and USUV among horses, which is likely to cause future sporadic outbreaks. An integrated arbovirus surveillance system that includes entomological surveillance as an early alert system is of major epidemiological importance.
Published: 2023

29. Genomic epidemiology of Cryptosporidiump arvum in Europe

Author: Bellinzona, Greta, Nardi, Tiago, Castelli, Michele, Autio, Tiina, Blanchard, Yannick, Chalmers, Rachel, Davidson, Rebecca, de Jong, Anton, Embom, Tuulia, Gomes, Jacinto, Karadjian, Gregory, Klotz, Christian, Jokelainen, Pikka, Östlund, Emma, Plutzer, Judith, Robertson Lucy, J., Robinson, Guy, Sannella, Rosa Anna, Sroka, Jacek, Stensvold Christens, Rune, Troell, Karin, Vatta, Paolo, Sassera, Davide, Cacciò Simone, M., Dipartimento di Biologia e Biotecnologie 'Lazzaro Spallanzani' = Department of Biology and Biotechnology [Univ di Pavia] (DBB UNIPV), Università degli Studi di Pavia = University of Pavia (UNIPV), Finish Food Safety Authority Evira, Partenaires INRAE, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Swansea University Medical School [Swansea, Royaume-Uni], Swansea University, National Veterinary Institute [Uppsala] (SVA), Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Robert Koch Institute [Berlin] (RKI), Statens Serum Institut [Copenhagen], National Institute of Environmental Health, Norwegian Veterinary Institute [Oslo], Singleton Hospital, Istituto Superiore di Sanità (ISS), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), Dipartimento di Chimica = Department of Chemistry [Univ Pavia] (UNIPV), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: International audience
Published: 2022

30. A One-Health Approach to Investigating an Outbreak of Alimentary Tick-Borne Encephalitis in a Non-endemic Area in France (Ain, Eastern France): A Longitudinal Serological Study in Livestock, Detection in Ticks, and the First Tick-Borne Encephalitis Virus Isolation and Molecular Characterisation

Author: Gaëlle Gonzalez, Laure Bournez, Rayane Amaral Moraes, Dumarest Marine, Clémence Galon, Fabien Vorimore, Maxime Cochin, Antoine Nougairède, Catherine Hennechart-Collette, Sylvie Perelle, Isabelle Leparc-Goffart, Guillaume André Durand, Gilda Grard, Thomas Bénet, Nathalie Danjou, Martine Blanchin, Sandrine A. Lacour, Boué Franck, Guillaume Chenut, Catherine Mainguet, Catherine Simon, Laurence Brémont, Stephan Zientara, Sara Moutailler, Sandra Martin-Latil, Nolwenn M. Dheilly, Cécile Beck, Sylvie Lecollinet, Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Agence régionale de santé Auvergne Rhône Alpes (ARS), DDPP - Direction départementale de la protection des populations [Ain], Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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: Microbiology (medical), tick-borne encephalitis virus, Microbiology, Fromage de chèvre, one health, Maladie de l'homme, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Encéphalite à tiques, Surveillance épidémiologique, S30 - Régimes alimentaires et maladies nutritionnelles, Maladie transmissible par tiques, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, outbreak, Aliment biologique pour homme, Lait cru, environmental investigation, Enquête pathologique, alimentary route, S50 - Santé humaine, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: International audience; Tick-borne encephalitis virus’ (TBEV) geographic range and the human incidence are increasing throughout Europe, putting a number of non-endemic regions and countries at risk of outbreaks. In spring 2020, there was an outbreak of tick-born encephalitis (TBE) in Ain, Eastern France, where the virus had never been detected before. All patients but one had consumed traditional unpasteurised raw goat cheese from a local producer. We conducted an investigation in the suspected farm using an integrative One Health approach. Our methodology included (i) the detection of virus in cheese and milk products, (ii) serological testing of all animals in the suspected farm and surrounding farms, (iii) an analysis of the landscape and localisation of wooded area, (iv) the capture of questing ticks and small mammals for virus detection and estimating enzootic hazard, and (v) virus isolation and genome sequencing. This approach allowed us to confirm the alimentary origin of the TBE outbreak and witness in real-time the seroconversion of recently exposed individuals and excretion of virus in goat milk. In addition, we identified a wooded focus area where and around which there is a risk of TBEV exposure. We provide the first TBEV isolate responsible for the first alimentary-transmitted TBE in France, obtained its full-length genome sequence, and found that it belongs to the European subtype of TBEV. TBEV is now a notifiable human disease in France, which should facilitate surveillance of its incidence and distribution throughout France.
Published: 2022
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31. New Mycobacterium bovis complete genomes of different clonal complexes to improve molecular epidemiology of french field strains

Author: Charles, Ciriac, Michelet, Lorraine, Vorimore, Fabien, Conde, Cyril, Cochard, Thierry, Biet, Franck, Boschiroli, Maria‐laura, Unité Zoonoses Bactériennes (UZB), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Est (UPE), Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), One health EJP, and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: mycobacterium bovis, lineages, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], genome
Abstract: International audience; Bovine Tuberculosis (bTB) is a zoonotic disease due to Mycobacterium bovis (M. bovis). France has a bTB-free status, but the disease has not been eradicated yet and a worryingly steady increase of bTB outbreaks has been observed in some regions (1). This could be explained by the detection of bTB in wildlife that spills it back to livestock in the same territories. The transmission link within these multi-host systems remains difficult to establish given that they share the same M. bovis genotypes (2). Obtaining new reference genomes for each of these genotypes could improve the knowledge of clonal groups and refine molecular field epidemiology studies based on whole genome sequencing.
Published: 2022

32. Anti-Microbiota Vaccine Reduces Avian Malaria Infection Within Mosquito Vectors

Author: Justė Aželytė, Alejandra Wu-Chuang, Rita Žiegytė, Elena Platonova, Lourdes Mateos-Hernandez, Jennifer Maye, Dasiel Obregon, Vaidas Palinauskas, Alejandro Cabezas-Cruz, National Research Centre Lithuania, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), SEPPIC, University of Guelph, Bioénergétique et Ingénierie des Protéines (BIP ), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Plasmodium, Vaccines, Canaries, Malaria, Avian, fungi, Immunology, Oocysts, Mosquito Vectors, digestive system, anti-microbiota vaccines, Birds, Culicidae, networks, parasitic diseases, Escherichia coli, microbiota, Animals, avian malaria, [SDV.IMM]Life Sciences [q-bio]/Immunology, Immunology and Allergy, mosquitoes
Abstract: Animal and human pathogens that are transmitted by arthropods are a global concern, particularly those vectored by mosquitoes (e.g., Plasmodium spp. and dengue virus). Vector microbiota may hold the key to vector-borne pathogen control, as mounting evidence suggests that the contributions of the vector microbiota to vector physiology and pathogen life cycle are so relevant that vectorial capacity cannot be understood without considering microbial communities within the vectors. Anti-tick microbiota vaccines targeting commensal bacteria of the vector microbiota alter vector feeding and modulate the taxonomic and functional profiles of vector microbiome, but their impact on vector-borne pathogen development within the vector has not been tested. In this study, we tested whether anti-microbiota vaccination in birds targeting Enterobacteriaceae within mosquito midguts modulates the mosquito microbiota and disrupt Plasmodium relictum development in its natural vector Culex quinquefasciatus. Domestic canaries (Serinus canaria domestica) were experimentally infected with P. relictum and/or immunized with live vaccines containing different strains of Escherichia coli. Immunization of birds induced E. coli-specific antibodies. The midgut microbial communities of mosquitoes fed on Plasmodium-infected and/or E. coli-immunized birds were different from those of mosquitoes fed on control birds. Notably, mosquito midgut microbiota modulation was associated with a significant decrease in the occurrence of P. relictum oocysts and sporozoites in the midguts and salivary glands of C. quinquefasciatus, respectively. A significant reduction in the number of oocysts was also observed. These findings suggest that anti-microbiota vaccines can be used as a novel tool to control malaria transmission and potentially other vector-borne pathogens.
Published: 2022
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33. Specific detection and quantification of three microsporidia infecting bees, Nosema apis, Nosema ceranae, and Nosema bombi, using probe-based real-time PCR

Author: Aurélie Babin, Frank Schurr, Marie-Pierre Rivière, Marie-Pierre Chauzat, Eric Dubois, Laboratoire de Sophia Antipolis, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, and European Project: 773921,Horizon 2020,PoshBee(2018)
Subjects: Honey bee, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Real-time qPCR, Nosema, Nosema apis, RPB1 gene, Animals, Bees, Real-Time Polymerase Chain Reaction, Microbiology, Nosema ceranae, Nosema bombi, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Among stressors affecting bee health, Nosema microsporidia are prevalent intracellular parasites. Nosema apis and Nosema ceranae have been described in honey bees (Apis spp.), while Nosema bombi has been described in bumble bees (Bombus spp.). Although available molecular methods serve as a complement to microscopic diagnosis of nosemosis, they do not enable accurate quantification of these three Nosema species. We developed three quantitative real-time PCRs (qPCRs) starting from in silico design of specific primers, probes, and recombinant plasmids, to target the RNA polymerase II subunit B1 (RPB1) gene in the three species. The complete methods, including bee grinding, DNA purification, and qPCR, were validated in honey bee (Apis mellifera) homogenate. Specificity was assessed in silico and in vitro with several types of bee samples. The limit of detection was estimated at 4 log10 copies/honey bee. A small, systematic method bias was corrected for accurate quantification up to 10 log10 copies/honey bee. Method accuracy was also verified in bumble bee (Bombus terrestris) and mason bee (Osmia bicornis) homogenates in the range of 5 to 10 log10 copies/bee. These validated qPCR methods open perspectives in nosemosis diagnosis and in the study of the parasite’s eco-dynamics in managed and wild bees.
Published: 2022

34. Demande d’avis sur l’évaluation du risque relatif à l’enfouissement de cadavres issus d’animaux d’élevage et/ou de la faune sauvage: Avis complété de l’Anses Rapport complété d’expertise collective

Author: Peroz-Sapede, Carole, Mialet, Sylvie, Boulouis, Henri-Jean, Charabidzé, Damien, Chevrier, Boris, Decors, Anouk, Giraud, Etienne, Martin, Clément, Ponsart, Claire, Souillard, Rozenn, Vaillancourt, Jean-Pierre, Corre, Justine, Etore, Florence, Attig, Isabelle, Jaffal, Ali, École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), École nationale vétérinaire - Alfort (ENVA), Université de Lille, Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Office français de la biodiversité (OFB), Innovations Thérapeutiques et Résistances (InTheRes), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Liège, Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Université de Montréal (UdeM), Direction de l'Evaluation des Risques (DER), Direction de l'évaluation des produits réglementés (DEPR), and Anses
Subjects: Chaux (oxyde de calcium), Heat wave, Lime (calcium oxide), Carcass disposal, Elimination de cadavres, [SDV]Life Sciences [q-bio], Enfouissement de cadavres, Canicule, Carcass burial, Epizootie, Livestock diseases
Abstract: Citation suggérée :Anses. (2022). Rapport relatif à l’évaluation du risque relatif à l’enfouissement des cadavres issus d’animaux d’élevage et/ou de la faune sauvage (saisine 2020-SA-0011). Maisons-Alfort : Anses, 134 p; L’évaluation demandée porte sur le risque de propagation de microorganismes potentiellement pathogènes par les cadavres et les sous-produits d’animaux d’élevage ou de la faune sauvage, lors de leur stockage ou de leur enfouissement (en utilisant ou non de la chaux). Cette demande s’inscrit dans le cadre de la découverte de cadavres qui ne peuvent pas être collectés et/ou acheminés dans la filière de transformation des sous-produits animaux, ou dans celui de surmortalité importante : - dans un contexte sans cause infectieuse identifiée (e.g. canicule, inondation). En effet, pendant les derniers épisodes de canicule en 2019-2020, les capacités des usines d’équarrissage ont été dépassées et ces dernières se sont trouvées dans l’incapacité de fonctionner normalement. Si un dépeuplement par abattage est planifié, les usines d’équarrissage ont la capacité de s’organiser et de prendre en charge la transformation de tous les cadavres. Le contexte est différent en cas de canicule où beaucoup d’animaux meurent brutalement dans un laps de temps très court, sans planification possible. De plus, en cas de forte chaleur, les cadavres d’animaux laissés à température ambiante se dégradent très rapidement. C’est notamment le cas des cadavres de volailles, les cadavres se liquéfiant et devenant difficiles à manipuler et à transporter. Par ailleurs, les cadavres trop dégradés ne peuvent pas être éliminés au niveau d’une usine d’équarrissage, les matières trop liquides ayant tendance à bloquer le processus; - dans un contexte sanitaire défavorable. Certains agents pathogènes peuvent entraîner des mortalités importantes au sein d’un élevage ou même d’une filière de production. En plus des mortalités directes induites par l’agent pathogène, des mesures de dépeuplement peuvent également être instaurées afin de maîtriser la diffusion de l’infection (e.g. influenza aviaire ou fièvre aphteuse). Dans une telle situation, les capacités de traitement des usines d’équarrissage peuvent aussi être dépassées et nécessiter la mise en place de mesures alternatives de gestion des cadavres. Par rapport à la situation précédente (sans cause infectieuse particulière), le risque de diffusion de l’agent pathogène est à prendre en compte.
Published: 2022

35. Melatonin drugs inhibit SARS-CoV-2 entry into the brain and virus-induced damage of cerebral small vessels

Author: Erika Cecon, Daniela Fernandois, Nicolas Renault, Caio Fernando Ferreira Coelho, Jan Wenzel, Corentin Bedart, Charlotte Izabelle, Sarah Gallet, Sophie Le Poder, Bernard Klonjkowski, Markus Schwaninger, Vincent Prevot, Julie Dam, Ralf Jockers, Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Lille Neurosciences & Cognition - U 1172 (LilNCog), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire [Lille] (CHRU Lille), CHU Lille, FHU 1,000 Days for Health [Lille], Université de Lille, Institute for Translational Research in Inflammation - U 1286 (INFINITE (Ex-Liric)), German Center for Cardiovascular Research (DZHK), Berlin Institute of Health (BIH), Universität zu Lübeck = University of Lübeck [Lübeck], Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANRS (Grant No ANRS 0167), ERC Synergy WATCH, No. 810331, Deutsche Forschungsgemeinschaft (WE 6456/1–1, INSERM, CNRS, Fondation de la Recherche Médicale (Equipe FRM DEQ20130326503), La Ligue Contre le Cancer N/Ref: RS19/75–127, Association France Alzheimer (grant No. 2042), Fondation de France, ANR-20-COV4-0001,MELATOVID,Mélatonine et médicaments mélatoninergiques pour la prévention et le traitement de COVID-19(2020), ANR-19-CE16-0025,mitoGPCR,Les récepteurs couplés aux protéines G mitochondriaux en neuroprotection(2019), ANR-16-CE18-0013,Tbeta-ORPH,Nouvelles fonctions pour les récepteurs orphelins couplés aux protéines G – formation d'un complexe entre le récepteur TGFß et GPR50(2016), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cecon, Erika, Mélatonine et médicaments mélatoninergiques pour la prévention et le traitement de COVID-19 - - MELATOVID2020 - ANR-20-COV4-0001 - COVID-19 - VALID, Les récepteurs couplés aux protéines G mitochondriaux en neuroprotection - - mitoGPCR2019 - ANR-19-CE16-0025 - AAPG2019 - VALID, and Nouvelles fonctions pour les récepteurs orphelins couplés aux protéines G – formation d'un complexe entre le récepteur TGFß et GPR50 - - Tbeta-ORPH2016 - ANR-16-CE18-0013 - AAPG2016 - VALID
Subjects: [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Drug repurposing, Mice, Transgenic, Peptidyl-Dipeptidase A, MESH: Brain, Cellular and Molecular Neuroscience, Mice, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: COVID-19, Animals, MESH: SARS-CoV-2, MESH: Endothelial Cells, Molecular Biology, MESH: Melatonin, Melatonin, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Pharmacology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, [SDV.NEU.NB] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, COVID-19, Brain, Endothelial Cells, Cell Biology, Brain infection, COVID-19 Drug Treatment, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Molecular Medicine, Angiotensin-Converting Enzyme 2, Neuro-vasculature
Abstract: International audience; COVID-19 is a complex disease with short- and long-term respiratory, inflammatory and neurological symptoms that are triggered by the infection with SARS-CoV-2. Invasion of the brain by SARS-CoV-2 has been observed in humans and is postulated to be involved in post-COVID state. Brain infection is particularly pronounced in the K18-hACE2 mouse model of COVID-19. Prevention of brain infection in the acute phase of the disease might thus be of therapeutic relevance to prevent long-lasting symptoms of COVID-19. We previously showed that melatonin or two prescribed structural analogs, agomelatine and ramelteon delay the onset of severe clinical symptoms and improve survival of SARS-CoV-2-infected K18-hACE2 mice. Here, we show that treatment of K18-hACE2 mice with melatonin and two melatonin-derived marketed drugs, agomelatine and ramelteon, prevents SARS-CoV-2 entry in the brain, thereby reducing virus-induced damage of small cerebral vessels, immune cell infiltration and brain inflammation. Molecular modeling analyses complemented by experimental studies in cells showed that SARS-CoV-2 entry in endothelial cells is prevented by melatonin binding to an allosteric-binding site on human angiotensin-converting enzyme 2 (ACE2), thus interfering with ACE2 function as an entry receptor for SARS-CoV-2. Our findings open new perspectives for the repurposing of melatonergic drugs and its clinically used analogs in the prevention of brain infection by SARS-CoV-2 and COVID-19-related long-term neurological symptoms
Published: 2022

36. One Health surveillance of West Nile and Usutu viruses

Author: Orianne Constant, Patricia Gil, Jonathan Barthelemy, Karine Bolloré, Vincent Foulongne, Caroline Desmetz, Agnès Leblond, Isabelle Desjardins, Sophie Pradier, Aurélien Joulié, Alain Sandoz, Rayane Amaral, Michel Boisseau, Ignace Rakotoarivony, Thierry Baldet, Albane Marie, Benoît Frances, Florence Reboul Salze, Bachirou Tinto, Philippe Van de Perre, Sara Salinas, Cécile Beck, Sylvie Lecollinet, Serafin Gutierrez, Yannick Simonin, Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier]-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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Biocommunication en Cardio-Métabolique (BC2M), Université de Montpellier (UM), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), 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), GREMERES ICE, Clinique Vétérinaire Jolimont, Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Laboratoire Chimie de l'environnement (LCE), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Entente interdépartementale pour la démoustication du littoral méditerranéen [Montpellier] (EID Méditerranée), EID-Méditerranée, This study was funded by the ANR (French National Research Agency, reference ANR-16-IDEX-0006), the KIM RIVE initiative, the Labex EpiGenMed 'Investissements d’avenir' programme (reference ANR- 10-LABX-12-01), and Montpellier University of Excellence (MUSE, ArboSud project). Moreover, SG was recipient of funding from the Direction Générale de l’Alimentation from the French Ministry of Agriculture and Food. Horse serosurveys were funded by the French Horse and Riding Institute, IFCE, and the EPERON fund (Encouragement aux ProjetsEquestres Régionaux Ou Nationaux) (OpIUM project)., ANR-16-IDEX-0006,MUSE,MUSE(2016), and ANR-10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010)
Subjects: Epidemiology, viruses, [SDV]Life Sciences [q-bio], L73 - Maladies des animaux, Flavivirus Infections, Virus des animaux, Birds, Dogs, Endémie, Seroepidemiologic Studies, Virology, Animals, Humans, Surveillance épidémiologique, Horses, One Health, Usutu virus, Transmission des maladies, seroprevalence, virus du Nil occidental, Flavivirus, Public Health, Environmental and Occupational Health, virus diseases, Morbidité, Cross-Sectional Studies, Culicidae, S50 - Santé humaine, France, One Health surveillance, West Nile virus, West Nile Fever, co-circulation
Abstract: Background West Nile virus (WNV) and Usutu virus (USUV), two closely related flaviviruses, mainly follow an enzootic cycle involving mosquitoes and birds, but also infect humans and other mammals. Since 2010, their epidemiological situation may have shifted from irregular epidemics to endemicity in several European regions; this requires confirmation, as it could have implications for risk assessment and surveillance strategies. Aim To explore the seroprevalence in animals and humans and potential endemicity of WNV and USUV in Southern France, given a long history of WNV outbreaks and the only severe human USUV case in France in this region. Methods We evaluated the prevalence of WNV and USUV in a repeated cross-sectional study by serological and molecular analyses of human, dog, horse, bird and mosquito samples in the Camargue area, including the city of Montpellier, between 2016 and 2020. Results We observed the active transmission of both viruses and higher USUV prevalence in humans, dogs, birds and mosquitoes, while WNV prevalence was higher in horses. In 500 human samples, 15 were positive for USUV and 6 for WNV. Genetic data showed that the same lineages, WNV lineage 1a and USUV lineage Africa 3, were found in mosquitoes in 2015, 2018 and 2020. Conclusion These findings support existing literature suggesting endemisation in the study region and contribute to a better understanding of USUV and WNV circulation in Southern France. Our study underlines the importance of a One Health approach for the surveillance of these viruses.
Published: 2022

37. Mechanistic models of Rift Valley fever virus transmission: A systematic review

Author: Hélène, Cecilia, Alex, Drouin, Raphaëlle, Métras, Thomas, Balenghien, Benoit, Durand, Véronique, Chevalier, Pauline, Ezanno, METRAS, Raphaelle, Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), 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), Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Surveillance et modélisation des maladies transmissibles [iPLesp] (SUMO), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), London School of Hygiene and Tropical Medicine (LSHTM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Agronomique et Vétérinaire Hassan II (IAV Hassan II), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), and This work was part of the FORESEE project funded by INRAE metaprogram GISA (Integrated Management of Animal Health). HC was funded by INRAE, Région Pays de la Loire, CIRAD.
Subjects: [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, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Rift Valley Fever, Epidemiology, Arabia, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [MATH] Mathematics [math], Arbovirosis, MESH: Pregnancy, Pregnancy, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Africa, Rift Valley Fever Virus, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, MESH: Rift Valley Fever, Animals, MESH: Rift Valley fever virus, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [MATH]Mathematics [math], MESH: Female, Ecosystem
Abstract: Code used to produce figures and summary statistics is available in Github public repository; International audience; Rift Valley fever (RVF) is a zoonotic arbovirosis which has been reported across Africa including the northernmost edge, South West Indian Ocean islands, and the Arabian Peninsula. The virus is responsible for high abortion rates and mortality in young ruminants, with economic impacts in affected countries. To date, RVF epidemiological mechanisms are not fully understood, due to the multiplicity of implicated vertebrate hosts, vectors, and ecosystems. In this context, mathematical models are useful tools to develop our understanding of complex systems, and mechanistic models are particularly suited to data-scarce settings. Here, we performed a systematic review of mechanistic models studying RVF, to explore their diversity and their contribution to the understanding of this disease epidemiology. Researching Pubmed and Scopus databases (October 2021), we eventually selected 48 papers, presenting overall 49 different models with numerical application to RVF. We categorized models as theoretical, applied, or grey, depending on whether they represented a specific geographical context or not, and whether they relied on an extensive use of data. We discussed their contributions to the understanding of RVF epidemiology, and highlighted that theoretical and applied models are used differently yet meet common objectives. Through the examination of model features, we identified research questions left unexplored across scales, such as the role of animal mobility, as well as the relative contributions of host and vector species to transmission. Importantly, we noted a substantial lack of justification when choosing a functional form for the force of infection. Overall, we showed a great diversity in RVF models, leading to important progress in our comprehension of epidemiological mechanisms. To go further, data gaps must be filled, and modelers need to improve their code accessibility.
Published: 2022

38. Climate change alone cannot explain altered tick distribution across Europe: A spotlight on endemic and invasive tick species

Author: Stachurski, Frederic, Boulanger, Nathalie, Blisnick, Adrien, Vial, Laurence, Bonnet, Sarah, 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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Virulence bactérienne précoce : fonctions cellulaires et contrôle de l'infection aiguë et subaiguë, Université de Strasbourg (UNISTRA), Institut Pasteur [Paris] (IP), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, and Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV]Life Sciences [q-bio]
Abstract: The effect of climate on the evolution of tick populations remains difficult to disentangle from other possible causes and undoubtedly varies depending on the region concerned and local tick species. Large-scale, long-term monitoring is, therefore, necessary to accurately assess climatic impact on tick populations. Climate change can alter tick populations, either indirectly by affecting vertebrate host populations or directly by increasing or decreasing their numbers. These ectoparasites, and in particular hard ticks, spend almost their entire life cycle in the external environment, thus climatic conditions influence their activity, viability and distribution. This expert opinion aims to illustrate the impact of climate change, and its association with other variables, on the distribution and abundance of tick populations in Europe using Ixodes ricinus and Hyalomma marginatum as typical examples of endemic and invasive species, respectively.
Published: 2022

39. The Use of Flocked Swabs with a Protective Medium Increases the Recovery of Live Brucella spp. and DNA Detection

Author: Freddi, Luca, Djokic, Vitomir, Petot-Bottin, Fathia, Girault, Guillaume, Perrot, Ludivine, Ferreira Vicente, Acacia, Ponsart, Claire, Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Paris-Est (UPE), European Union Reference Laboratory for Brucellosis (EURL Brucellosis) (grant agreement no. SI2.801943), One Health EJP project (no. 773830): JRP-17 – 'Identification of emerging Brucella species: new threats for human and animals' (IDEMBRU), European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018), and Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie
Subjects: DNA, Bacterial, Microbial Viability, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, storage condition, Brucella suis, swab, Brucella, bacteriology, qPCR, recovery, Brucella abortus, Polymerase Chain Reaction, Microbiology, Brucellosis, QR1-502, Specimen Handling, Zoonoses, Brucella melitensis, Animals, Humans, Research Article
Abstract: Brucellosis is a worldwide zoonosis caused by bacteria from the genus Brucella. Once established, it is very hard to eradicate this disease, since it contaminates animals, the environment, and humans, causing problems for veterinary and public health as well as wildlife protection programs. Swabs are used for sampling in bacteriological and/or molecular diagnostics, from seropositive animals with disease symptoms, from genitalia or tissue lesions, as well as from contaminated environments. The aim of this study was to compare main of the commercially used swab types for sampling and diagnostics of Brucella spp. and determine the optimal storage conditions and time frame for testing. To achieve this, we tested bacterial and molecular methods for detection of Brucella abortus, Brucella melitensis, and Brucella suis using nine swab types, all with different tip materials, treated immediately after spiking, after 72 h at +4°C, and after 72 h at -20°C. Flocked swabs showed the highest capacity to preserve bacterial viability and DNA quality, regardless the storage conditions. Flocked swabs immersed in a protective medium provided the best conditions for Brucella survival in all three storage conditions. At the same time, the efficacy of quantitative PCR (qPCR) detection for all swabs, including the positive control, was above 50%, irrespective of the storage conditions, while bacterial survival was significantly lowered when swabs were kept at +4°C or -20°C for 72 h (48.2% and 27.5%, respectively). Compared to the positive control and other types, the flocked swabs maintained higher reproducibility regarding their capacity to preserve live bacteria in all three storage conditions. IMPORTANCE In order to protect public and veterinary health from highly zoonotic bacteria such as members of the genus Brucella and prevent their dissemination into the environment, direct diagnostics are of utmost importance. However, in addition to the highly specific diagnostic tests, the sampling methods, time necessary for specimens to reach the laboratories, and transport conditions are important factors to consider in order to increase the sensitivity of performed tests, especially bacterial culturing and qPCR. This paper shows how different swab types and storage conditions influence classical bacteriological diagnostics of the most prevalent Brucella species - B. melitensis, B. abortus, and B. suis - but have little impact on molecular methods. The presented results highlight (i) the choice of swab regarding the storage and transport conditions, (ii) the importance of immediate swab treatment upon sampling, and (iii) that molecular methods do not depend on storage conditions, unlike classical bacteriological isolation.
Published: 2021

40. Cerebral organoids and their potential for studies of brain diseases in domestic animals

Author: Muriel Coulpier, Bertrand Pain, Camille Baquerre, Institut cellule souche et cerveau (U846 Inserm - UCBL1), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA), Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011), Institut cellule souche et cerveau / Stem Cell and Brain Research Institute (U1208 Inserm - UCBL1 / SBRI - USC 1361 INRAE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), PAIN, Bertrand, and Infrastructures - Réseau de Centres de Ressources Biologiques pour les animaux domestiques - - CRB-Anim2011 - ANR-11-INBS-0003 - INBS - VALID
Subjects: 0301 basic medicine, Brain development, Veterinary medicine, [SDV]Life Sciences [q-bio], Review, Biology, Neurotropic virus, 03 medical and health sciences, 0302 clinical medicine, Pluripotent stem cells, SF600-1100, Organoid, Animals, Humans, Cerebral organoids, Brain Diseases, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Brain, [SDV] Life Sciences [q-bio], Organoids, Domestic animals, 030104 developmental biology, Animals, Domestic, Encephalitis, Neuroscience, 030217 neurology & neurosurgery
Abstract: The brain is a complex organ and any model for studying it in its normal and pathological aspects becomes a tool of choice for neuroscientists. The mastering and dissemination of protocols allowing brain organoids development have paved the way for a whole range of new studies in the field of brain development, modeling of neurodegenerative or neurodevelopmental diseases, understanding tumors as well as infectious diseases that affect the brain. While studies are so far limited to the use of human cerebral organoids, there is a growing interest in having similar models in other species. This review presents what is currently developed in this field, with a particular focus on the potential of cerebral organoids for studying neuro-infectious diseases in human and domestic animals.
Published: 2021

41. Differential neurovirulence of Usutu viruslineages in mice and neuronal cells

Author: Clé, Marion, Constant, Orianne, Barthelemy, Jonathan, Desmetz, Caroline, Martin, Marie France, Lapeyre, Lina, Cadar, Daniel, Savini, Giovanni, Teodori, Liana, Monaco, Federica, Schmidt-Chanasit, Jonas, Saiz, Juan-Carlos, Gonzales, Gaëlle, Lecollinet, Sylvie, Beck, Cécile, Gosselet, Fabien, van de Perre, Philippe, Foulongne, Vincent, Salinas, Sara, Simonin, Yannick, Pathogenesis and Control of Chronic and Emerging Infections (PCCEI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Université des Antilles (UA)-Etablissement français du don du sang [Montpellier], Biocommunication en Cardio-Métabolique (BC2M), Université de Montpellier (UM), Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), OIE Reference Centre for West NileDisease, Istituto Zooprofilattico Sperimentale'G. Caporale, Universität Hamburg (UHH), Instituto Nacional de Investigación Agropecuaria (INIA), Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Physiopathologie de la Barrière Hémato-Encéphalique (LBHE), Université d'Artois (UA), CHU Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), and BONIZEC, Sandrine
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract: International audience; No abstract available
Published: 2021

42. Constitutive IFNα protein production in bats

Author: S. Le Poder, R. Wedlarski, Darragh Duffy, Vincent Bondet, D. Le Roux, Thierry Petit, Alexis Lécu, M. Le Baut, Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris], BioPôle Alfort, École nationale vétérinaire d'Alfort (ENVA), Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Muséum national d'Histoire naturelle (MNHN), Parc Zoologique de La Palmyre, Bioparc de Doué-la-Fontaine, Partenaires INRAE, Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was funded by the Agence Nationale pour la Recherche (ANR), grant number CE17001002, We thank the ProteoGenix company (Schiltigheim, France) for the production of the bIFNα ELISA assay calibrator, Marielle Cochet for technical help, Florence Va, Dr Vitomir Djokic and Isabelle Badreau for helping in RT-qPCR datas analysis, the technical staff of the zoos and the Association Française des Vétérinaires de Parcs Zoologiques. We thank the CBUTechS platform of the Institut Pasteur for access to the Simoa instrument., Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), École nationale vétérinaire - Alfort (ENVA), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Pasteur [Paris]-Université Paris Cité (UPC), and École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé
Subjects: Transcription, Genetic, [SDV]Life Sciences [q-bio], Immunology, bats, Enzyme-Linked Immunosorbent Assay, Disease, Biology, Cell Line, 03 medical and health sciences, Antiviral immunity, Extant taxon, Species Specificity, Interferon, Chiroptera, Protein biosynthesis, medicine, Immunology and Allergy, Animals, Simoa digital ELISA, Symbiosis, 030304 developmental biology, Original Research, Genetics, 0303 health sciences, Chiroptera species, Innate immune system, Ifn response, 030306 microbiology, Interferon-alpha, Immunity, Innate, antiviral immunity, Gene Expression Regulation, protein levels, Host-Pathogen Interactions, Viruses, type I IFN, medicine.drug
Abstract: Posté sur bioRxiv le 22 juin 2021.; International audience; Bats are the only mammals with self-powered flight and account for 20% of all extant mammalian diversity. In addition, they harbor many emerging and reemerging viruses, including multiple coronaviruses, several of which are highly pathogenic in other mammals, but cause no disease in bats. How this relationship between bats and viruses exists is not yet fully understood. Existing evidence supports a specific role for the innate immune system, in particular type I interferon (IFN) responses, a major component of antiviral immunity. Previous studies in bats have shown that components of the IFN pathway are constitutively activated at the transcriptional level. In this study, we tested the hypothesis that the type I IFN response in bats is also constitutively activated at the protein level. For this we utilized highly sensitive Single Molecule (Simoa) digital ELISA assays, previously developed for humans that we adapted to bat samples. We prospectively sampled four non-native chiroptera species from French zoos. We identified a constitutive expression of IFNα protein in the circulation of healthy bats, and concentrations that are physiologically active in humans. Expression levels differed according to the species examined, but was not associated with age, sex, or health status suggesting constitutive IFNα protein expression independent of disease. These results confirm a unique IFN response in bat species that may explain their ability to coexist with multiple viruses in the absence of pathology. These results may help to manage potential zoonotic viral reservoirs and potentially identify new anti-viral strategies.
Published: 2021

43. Experimental Infection of Ticks: An Essential Tool for the Analysis of Babesia Species Biology and Transmission

Author: Bonnet, Sarah, Nadal, Clémence, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Santé Animale (DEPT SA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), École nationale vétérinaire - Alfort (ENVA), Ecole Nationale Vétérinaire de Nantes, Institut Pasteur [Paris] (IP), Institut de Recherche pour le Développement (IRD [France-Sud]), Centre interuniversitaire de recherche et d'ingenierie des matériaux (CIRIMAT), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, Génétique fonctionnelle des maladies infectieuses - Functional Genetics of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Est Créteil Val-de-Marne - Faculté de médecine (UPEC Médecine), Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and The PhD of CN is funded by the Institut Français du Cheval et de l’Equitation (IFCE) and by the Fonds Eperon.
Subjects: [SDV]Life Sciences [q-bio], biological cycle, experimental models, Babesia sp, ticks Babesia sp. biological cycle experimental transmission experimental models, ticks, experimental transmission
Abstract: International audience; Babesiosis is one of the most important tick-borne diseases in veterinary health, impacting mainly cattle, equidae, and canidae, and limiting the development of livestock industries worldwide. In humans, babesiosis is considered to be an emerging disease mostly due to Babesia divergens in Europe and Babesia microti in America. Despite this importance, our knowledge of Babesia sp. transmission by ticks is incomplete. The complexity of vectorial systems involving the vector, vertebrate host, and pathogen, as well as the complex feeding biology of ticks, may be part of the reason for the existing gaps in our knowledge. Indeed, this complexity renders the implementation of experimental systems that are as close as possible to natural conditions and allowing the study of tick-host-parasite interactions, quite difficult. However, it is unlikely that the development of more effective and sustainable control measures against babesiosis will emerge unless significant progress can be made in understanding this tripartite relationship. The various methods used to date to achieve tick transmission of Babesia spp. of medical and veterinary importance under experimental conditions are reviewed and discussed here.
Published: 2021

44. [Cell hijacking by a tick-borne flavivirus: dangerous linkages between viral RNA and cellular proteins in humans and the tick Ixodes ricinus].

Author: Grot A, Unterfinger Y, Lacour S, Bell-Sakyi L, Attoui H, Richardson J, and Sourisseau M
Subjects: Animals, Humans, RNA, Viral, Ixodes genetics, Encephalitis Viruses, Tick-Borne genetics
Published: 2023
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