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1. Distribution of ticks, tick-borne pathogens and the associated local environmental factors including small mammals and livestock, in two French agricultural sites: the OSCAR database

Author: Isabelle Lebert, Albert Agoulon, Suzanne Bastian, Alain Butet, Bruno Cargnelutti, Nicolas Cèbe, Amélie Chastagner, Elsa Léger, Bruno Lourtet, Sébastien Masseglia, Karen McCoy, Joël Merlet, Valérie Noël, Grégoire Perez, Denis Picot, Angélique Pion, Valérie Poux, Jean-Luc Rames, Yann Rantier, Hélène Verheyden, Gwenael Vourc'h, and Olivier Plantard
Subjects: Ticks, Ixodes ricinus, small mammals, Ap, Biology (General), QH301-705.5
Published: 2020
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2. Oronasal or Intramuscular Immunization with a Thermo-Attenuated ASFV Strain Provides Full Clinical Protection against Georgia 2007/1 Challenge

Author: Olivier Bourry, Evelyne Hutet, Mireille Le Dimna, Pierrick Lucas, Yannick Blanchard, Amélie Chastagner, Frédéric Paboeuf, and Marie-Frédérique Le Potier
Subjects: ASF, live attenuated vaccine, oronasal, intramuscular, Microbiology, QR1-502
Abstract: African swine fever (ASF) is a contagious viral disease of suids that induces high mortality in domestic pigs and wild boars. Given the current spread of ASF, the development of a vaccine is a priority. During an attempt to inactivate the Georgia 2007/1 strain via heat treatment, we fortuitously generated an attenuated strain called ASFV-989. Compared to Georgia, the ASFV-989 strain genome has a deletion of 7458 nucleotides located in the 5′-end encoding region of MGF 505/360, which allowed for developing a DIVA PCR system. In vitro, in porcine alveolar macrophages, the replication kinetics of the ASFV-989 and Georgia strains were identical. In vivo, specific-pathogen-free (SPF) pigs inoculated with the ASFV-989 strain, either intramuscularly or oronasally, exhibited transient hyperthermia and slightly decreased growth performance. Animals immunized with the ASFV-989 strain showed viremia 100 to 1000 times lower than those inoculated with the Georgia strain and developed a rapid antibody and cell-mediated response. In ASFV-989-immunized pigs challenged 2 or 4 weeks later with the Georgia strain, no symptoms were recorded and no viremia for the challenge strain was detected. These results show that the ASFV-989 strain is a promising non-GMO vaccine candidate that is usable either intramuscularly or oronasally.
Published: 2022
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3. Bidirectional Human–Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018

Author: Amélie Chastagner, Vincent Enouf, David Peroz, Séverine Hervé, Pierrick Lucas, Stéphane Quéguiner, Stéphane Gorin, Véronique Beven, Sylvie Behillil, Philippe Leneveu, Emmanuel Garin, Yannick Blanchard, Sylvie van der Werf, and Gaëlle Simon
Subjects: influenza, A(H1N1)pdm09, interspecies transmission, pandemic, zoonotic disease, reverse zoonosis, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: In 2018, a veterinarian became sick shortly after swabbing sows exhibiting respiratory syndrome on a farm in France. Epidemiologic data and genetic analyses revealed consecutive human-to-swine and swine-to-human influenza A(H1N1)pdm09 virus transmission, which occurred despite some biosecurity measures. Providing pig industry workers the annual influenza vaccine might reduce transmission risk.
Published: 2019
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4. Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus

Author: Amélie Chastagner, Emilie Bonin, Christelle Fablet, Stéphane Quéguiner, Edouard Hirchaud, Pierrick Lucas, Stéphane Gorin, Nicolas Barbier, Véronique Béven, Emmanuel Garin, Yannick Blanchard, Nicolas Rose, Séverine Hervé, and Gaëlle Simon
Subjects: Veterinary medicine, SF600-1100
Abstract: Abstract This report describes the detection of a triple reassortant swine influenza A virus of H1avN2 subtype. It evolved from an avian-like swine H1avN1 that first acquired the N2 segment from a seasonal H3N2, then the M segment from a 2009 pandemic H1N1, in two reassortments estimated to have occurred 10 years apart. This study illustrates how recurrent influenza infections increase the co-infection risk and facilitate evolutionary jumps by successive gene exchanges. It recalls the importance of appropriate biosecurity measures inside holdings to limit virus persistence and interspecies transmissions, which both contribute to the emergence of new potentially zoonotic viruses.
Published: 2019
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5. Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

Author: Amélie Chastagner, Séverine Hervé, Stéphane Quéguiner, Edouard Hirchaud, Pierrick Lucas, Stéphane Gorin, Véronique Béven, Nicolas Barbier, Céline Deblanc, Yannick Blanchard, and Gaëlle Simon
Subjects: swine influenza, virus evolution, genetic diversity, antigenic drift, H1N1, H1N2, Microbiology, QR1-502
Abstract: This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1av) and -1B (H1hu), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1avNy and 105 H1huNy strains were submitted to hemagglutination inhibition tests. H1avN1 (66.5%) and H1huN2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named “Δ146-147” harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the “Eurasian avian-like lineage”, with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1av/H1hu strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.
Published: 2020
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6. Evaluation of the Pathogenicity and the Escape from Vaccine Protection of a New Antigenic Variant Derived from the European Human-Like Reassortant Swine H1N2 Influenza Virus

Author: Céline Deblanc, Stéphane Quéguiner, Stéphane Gorin, Amélie Chastagner, Séverine Hervé, Frédéric Paboeuf, and Gaëlle Simon
Subjects: swine influenza virus, H1N2, variant, post-infectious immune response, pathogenesis, vaccine, Microbiology, QR1-502
Abstract: The surveillance of swine influenza A viruses in France revealed the emergence of an antigenic variant following deletions and mutations that are fixed in the HA-encoding gene of the European human-like reassortant swine H1N2 lineage. In this study, we compared the outcomes of the parental (H1huN2) and variant (H1huN2Δ14–147) virus infections in experimentally-inoculated piglets. Moreover, we assessed and compared the protection that was conferred by an inactivated vaccine currently licensed in Europe. Three groups of five unvaccinated or vaccinated piglets were inoculated with H1huN2 or H1huN2Δ14–147 or mock-inoculated, respectively. In unvaccinated piglets, the variant strain induced greater clinical signs than the parental virus, in relation to a higher inflammatory response that involves TNF-α production and a huge afflux of granulocytes into the lung. However, both infections led to similar levels of virus excretion and adaptive (humoral and cellular) immune responses in blood. The vaccinated animals were clinically protected from both infectious challenges and did not exhibit any inflammatory responses, regardless the inoculated virus. However, whereas vaccination prevented virus shedding in H1huN2-infected animals, it did not completely inhibit the multiplication of the variant strain, since live virus particles were detected in nasal secretions that were taken from H1huN2Δ14–147-inoculated vaccinated piglets. This difference in the level of vaccine protection was probably related to the poorer ability of the post-vaccine antibodies to neutralize the variant virus than the parental virus, even though post-vaccine cellular immunity appeared to be equally effective against both viruses. These results suggest that vaccine antigens would potentially need to be updated if this variant becomes established in Europe.
Published: 2020
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7. A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants

Author: Thibaud Dugat, Amélie Chastagner, Anne-Claire Lagrée, Elisabeth Petit, Benoît Durand, Simon Thierry, Fabien Corbière, Hélène Verheyden, Luc Chabanne, Xavier Bailly, Agnès Leblond, Gwenaël Vourc’h, Henri-Jean Boulouis, Renaud Maillard, and Nadia Haddad
Subjects: Anaplasma phagocytophilum, MLVA, VNTR, Epidemiology, Reservoir, Wild ruminants, Infectious and parasitic diseases, RC109-216
Abstract: Abstract Background Anaplasma phagocytophilum is a tick-borne intragranulocytic alpha-proteobacterium. It is the causative agent of tick-borne fever in ruminants, and of human granulocytic anaplasmosis in humans, two diseases which are becoming increasingly recognized in Europe and the USA. However, while several molecular typing tools have been developed over the last years, few of them are appropriate for in-depth exploration of the epidemiological cycle of this bacterium. Therefore we have developed a Multiple-Locus Variable number tandem repeat (VNTR) Analysis typing technique for A. phagocytophilum. Methods Five VNTRs were selected based on the HZ human-derived strain genome, and were tested on the Webster human-derived strain and on 123 DNA samples: 67 from cattle, 7 from sheep, 15 from roe deer, 4 from red deer, 1 from a reindeer, 2 from horses, 1 from a dog, and 26 from ticks. Results From these samples, we obtained 84 different profiles, with a diversity index of 0.96 (0.99 for vertebrate samples, i.e. without tick samples). Our technique confirmed that A. phagocytophilum from roe deer or domestic ruminants belong to two different clusters, while A. phagocytophilum from red deer and domestic ruminants locate within the same cluster, questioning the respective roles of roe vs red deer as reservoir hosts for domestic ruminant strains in Europe. As expected, greater diversity was obtained between rather than within cattle herds. Conclusions Our technique has great potential to provide detailed information on A. phagocytophilum isolates, improving both epidemiological and phylogenic investigations, thereby helping in the development of relevant prevention and control measures.
Published: 2014
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8. Single Genotype of Anaplasma phagocytophilum Identified from Ticks, Camargue, France

Author: Amélie Chastagner, Xavier Bailly, Agnès Leblond, Sophie Pradier, and Gwenaël Vourc’h
Subjects: Anaplasma phagocytophilum, Ixodes ricinus, Rhipicephalus bursa, Rhipicephalus sanguineus, Rhipicephalus turanicus, Dermacentor marginatus, Medicine, Infectious and parasitic diseases, RC109-216
Published: 2013
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9. Bidirectional Human–Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018

Author: Sylvie Behillil, Véronique Béven, Emmanuel Garin, Séverine Hervé, Stéphane Quéguiner, Yannick Blanchard, Amélie Chastagner, David Peroz, Gaëlle Simon, Pierrick Lucas, Philippe Leneveu, Vincent Enouf, Sylvie van der Werf, Stéphane Gorin, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Institut Pasteur [Paris] (IP), Atlantic Vétérinaires [Ancenis], CEVA Santé Animale [Libourne, France] (Laboratoire Vétérinaire Pharmaceutique), Coop de France, and Plateforme Epidémiosurveillance Santé Animale [Lyon]
Subjects: Veterinary medicine, Epidemiology, Swine, [SDV]Life Sciences [q-bio], animal diseases, Biosecurity, influenza A(H1N1)pdm09, lcsh:Medicine, Bidirectional Human–Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018, Disease Outbreaks, zoonotic disease, Seasonal influenza, 0302 clinical medicine, Influenza A Virus, H1N1 Subtype, Zoonoses, Pandemic, 030212 general & internal medicine, Phylogeny, reverse zoonosis, Swine Diseases, Transmission (medicine), H1N1, Dispatch, transmission, farms, 3. Good health, Infectious Diseases, A(H1N1)pdm09, Female, France, influenza, Microbiology (medical), Influenza vaccine, 030231 tropical medicine, human–swine transmission, interspecies transmission, Biology, Virus, swine–human transmission, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, respiratory infections, Orthomyxoviridae Infections, Influenza, Human, case report, Animals, Humans, viruses, lcsh:RC109-216, human, H1N1pdm09, pandemic, lcsh:R, Influenza a, Herd, biosecurity
Abstract: International audience; In 2018, a veterinarian became sick shortly after swabbing sows exhibiting respiratory syndrome on a farm in France. Epidemiologic data and genetic analyses revealed consecutive human-to-swine and swine-to-human influenza A(H1N1)pdm09 virus transmission, which occurred despite some biosecurity measures. Providing pig industry workers the annual influenza vaccine might reduce transmission risk.
Published: 2019

10. Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus

Author: Séverine Hervé, Emilie Bonin, Gaëlle Simon, Stéphane Quéguiner, Yannick Blanchard, Véronique Béven, Emmanuel Garin, Amélie Chastagner, Stéphane Gorin, Pierrick Lucas, Nicolas Rose, Nicolas Barbier, Christelle Fablet, and Edouard Hirchaud
Subjects: 0301 basic medicine, Human influenza, Swine, [SDV]Life Sciences [q-bio], viruses, 030106 microbiology, Biosecurity, Reassortment, Sus scrofa, Short Report, Biology, medicine.disease_cause, Virus, 03 medical and health sciences, Influenza A Virus, H1N1 Subtype, Influenza A Virus, H1N2 Subtype, Pandemic, Influenza A virus, medicine, Animals, 2. Zero hunger, Swine Diseases, lcsh:Veterinary medicine, General Veterinary, Influenza A Virus, H3N2 Subtype, Virology, 030104 developmental biology, Herd, lcsh:SF600-1100, France, Viral persistence, Reassortant Viruses
Abstract: This report describes the detection of a triple reassortant swine influenza A virus of H1avN2 subtype. It evolved from an avian-like swine H1avN1 that first acquired the N2 segment from a seasonal H3N2, then the M segment from a 2009 pandemic H1N1, in two reassortments estimated to have occurred 10 years apart. This study illustrates how recurrent influenza infections increase the co-infection risk and facilitate evolutionary jumps by successive gene exchanges. It recalls the importance of appropriate biosecurity measures inside holdings to limit virus persistence and interspecies transmissions, which both contribute to the emergence of new potentially zoonotic viruses.
Published: 2019

11. Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

Author: Séverine Hervé, Nicolas Barbier, Véronique Béven, Stéphane Gorin, Céline Deblanc, Gaëlle Simon, Amélie Chastagner, Stéphane Quéguiner, Yannick Blanchard, Pierrick Lucas, and Edouard Hirchaud
Subjects: 0301 basic medicine, Lineage (genetic), Genotype, Swine, 030106 microbiology, lcsh:QR1-502, matrix protein, Virulence, Hemagglutinin (influenza), Neuraminidase, Hemagglutinin Glycoproteins, Influenza Virus, Antigenic drift, Virus, lcsh:Microbiology, Article, Evolution, Molecular, 03 medical and health sciences, Influenza A Virus, H1N1 Subtype, Virology, Eurasian avian-like lineage, Animals, Humans, Phylogeny, antigenic drift, virus evolution, swine influenza, biology, Sequence Analysis, RNA, Influenza A Virus, H3N2 Subtype, H1N2, H1N1, Sequence Analysis, DNA, genetic diversity, Hemagglutination Inhibition Tests, 030104 developmental biology, Infectious Diseases, Influenza A virus, Viral evolution, biology.protein, surveillance, RNA, Viral, France
Abstract: This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1av) and -1B (H1hu), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1avNy and 105 H1huNy strains were submitted to hemagglutination inhibition tests. H1avN1 (66.5%) and H1huN2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named &ldquo, &Delta, 146-147&rdquo, harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the &ldquo, Eurasian avian-like lineage&rdquo, with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1av/H1hu strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.
Published: 2020

12. Evaluation of the Pathogenicity and the Escape from Vaccine Protection of a New Antigenic Variant Derived from the European Human-Like Reassortant Swine H1N2 Influenza Virus

Author: Amélie Chastagner, Gaëlle Simon, Frédéric Paboeuf, Séverine Hervé, Céline Deblanc, Stéphane Quéguiner, and Stéphane Gorin
Subjects: 0301 basic medicine, Cellular immunity, Swine, 030106 microbiology, lcsh:QR1-502, Antibodies, Viral, Virus, lcsh:Microbiology, Article, 03 medical and health sciences, Immune system, swine influenza virus, Antigen, Orthomyxoviridae Infections, Virology, vaccine, Influenza A Virus, H1N2 Subtype, Animals, Viral shedding, post-infectious immune response, Antigens, Viral, Swine Diseases, biology, H1N2, pathogenesis, Vaccination, Antibodies, Neutralizing, 030104 developmental biology, Infectious Diseases, variant, Influenza Vaccines, Inactivated vaccine, Mutation, biology.protein, France, Antibody
Abstract: The surveillance of swine influenza A viruses in France revealed the emergence of an antigenic variant following deletions and mutations that are fixed in the HA-encoding gene of the European human-like reassortant swine H1N2 lineage. In this study, we compared the outcomes of the parental (H1huN2) and variant (H1huN2&Delta, 146-147) virus infections in experimentally-inoculated piglets. Moreover, we assessed and compared the protection that was conferred by an inactivated vaccine currently licensed in Europe. Three groups of five unvaccinated or vaccinated piglets were inoculated with H1huN2 or H1huN2&Delta, 146-147 or mock-inoculated, respectively. In unvaccinated piglets, the variant strain induced greater clinical signs than the parental virus, in relation to a higher inflammatory response that involves TNF-&alpha, production and a huge afflux of granulocytes into the lung. However, both infections led to similar levels of virus excretion and adaptive (humoral and cellular) immune responses in blood. The vaccinated animals were clinically protected from both infectious challenges and did not exhibit any inflammatory responses, regardless the inoculated virus. However, whereas vaccination prevented virus shedding in H1huN2-infected animals, it did not completely inhibit the multiplication of the variant strain, since live virus particles were detected in nasal secretions that were taken from H1huN2&Delta, 146-147-inoculated vaccinated piglets. This difference in the level of vaccine protection was probably related to the poorer ability of the post-vaccine antibodies to neutralize the variant virus than the parental virus, even though post-vaccine cellular immunity appeared to be equally effective against both viruses. These results suggest that vaccine antigens would potentially need to be updated if this variant becomes established in Europe.
Published: 2020

13. Relationships between landscape structure and the prevalence of two tick-borne infectious agents, Anaplasma Phagocytophilum and Borrelia burgdorferi sensu lato, in small mammal communities

Author: Grégoire Perez, Olivier Plantard, Amélie Chastagner, Albert Agoulon, Gwenaël Vourc’h, Alain Butet, Yann Rantier, Suzanne Bastian, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Épidémiologie des Maladies Animales et Zoonotiques - UMR 346 (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), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Région Bretagne, ANR-11-Agro-001-04, Agence National de la Recherche, ANR-11-AGRO-0001,OSCAR,Outil de Simulation Cartographique à l'échelle du paysage Agricole du Risque acarologique(2011), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0106 biological sciences, Economics, Geography, Planning and Development, Small mammal community, Woodland, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, medicine, Tick-borne diseases, Borrelia burgdorferi, Biology, Nature and Landscape Conservation, Tick-borne disease, 0303 health sciences, Ecology, Community, biology, 030306 microbiology, Physics, 010604 marine biology & hydrobiology, Ecotone, 15. Life on land, medicine.disease, biology.organism_classification, Anaplasma phagocytophilum, Bank vole, Graph theory, Chemistry, Wood mouse, Least cost paths, Apodemus, Landscape ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Landscape connectivity, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: ContextBy modifying ecosystems, land cover changes influence the emergence, the spread and the incidence of vector-borne diseases.ObjectiveThis study aimed at identifying associations between landscape structure and the prevalence of two tick-borne infectious agents, Anaplasma phagocytophilum and Borrelia burgdorferi s.l., in small mammal communities.MethodsSmall mammals were sampled in 24 sites along a gradient of woodland fragmentation and hedgerow network density, and screened for infectious agents with real-time PCR techniques. For each site, structural variables (composition and configuration) of the surrounding landscape at various scales (0-500 m) and variables of wooded habitats connectivity based on graph theory and least cost path distances for the two dominant species, bank voles (Myodes glareolus) and wood mice (Apodemus sylvaticus), were computed.ResultsThe A. phagocytophilum prevalence increased with wooded habitats cover (0-500 m), likely through host population size, and increased slightly with bank vole abundance, which has a higher reservoir competence than wood mouse. The B. burgdorferi s.l. prevalence increased with wooded ecotones only at local scales (50-100 m). Wooded habitats connectivity measures did not improve models built with simple land cover variables. A more marked spatial pattern was observed for the prevalence of A. phagocytophilum than B. burgdorferi s.l..ConclusionsThis study highlights the interest of considering together the ecology of infectious agents (e.g. host specificity) and the host species community ecology to better understand the influence of the landscape structure on the spatial distribution of vector-borne infectious agents.
Published: 2020

14. Evaluation of un-methylated DNA enrichment in sequencing of African swine fever virus complete genome

Author: Amélie Chastagner, Yannick Blanchard, Marie-Frédérique Le Potier, Laurence Vial, Pierrick Lucas, Rémi Pereira De Oliveira, Claire de Boisséson, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), 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), and European Project: 643476,H2020,H2020-PHC-2014-single-stage,COMPARE(2014)
Subjects: 0301 basic medicine, Swine, Virus peste porcine africaine, [SDV]Life Sciences [q-bio], 030106 microbiology, Sus scrofa, Genome, Viral, Biology, Tick, L73 - Maladies des animaux, African swine fever virus, Genome, Methylation, Virus, 03 medical and health sciences, chemistry.chemical_compound, Séquence d'ADN, Virology, Méthylation, Animals, Vector (molecular biology), African Swine Fever, Ornithodoros, Whole genome sequencing, Génome, Whole Genome Sequencing, DNA Methylation, biology.organism_classification, L10 - Génétique et amélioration des animaux, African Swine Fever Virus, 3. Good health, 030104 developmental biology, chemistry, Enrichment, NGS, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, DNA, Viral, DNA
Abstract: International audience; African swine fever is a febrile hemorrhagic fever disease that is caused by the African swine fever virus (ASFV) and is lethal for domestic pigs and wild boar. ASFV also infects soft ticks of the genus Ornithodoros, some species of which can act as a vector for ASFV. Whole genome sequencing of ASFV is a challenge because, due to the size difference of the host genome versus the viral genome, the higher proportion of host versus virus DNA fragments renders the virus sequencing poorly efficient. A novel approach of DNA enrichment, based on the separation of methylated and un-methylated DNA, has been reported but without an evaluation of its efficacy. In this study, the efficiency of the un-methylated DNA enrichment protocol was evaluated for pig and tick samples infected by ASFV. As expected, fewer reads corresponding to ASFV were found in the methylated fraction compared to the un-methylated fraction. However, the sequencing coverage of the un-methylated fraction was not improved compared to the untreated DNA. In our hands, the ASFV DNA enrichment was inefficient for tick samples and very limited for pig samples. This enrichment process represents extra work and cost without a significant improvement of ASFV genome coverage. The efficiency of this enrichment approach and the cost/benefit ratio are discussed
Published: 2020

15. Host specificity, pathogen exposure, and superinfections impact the distribution of Anaplasma phagocytophilum genotypes in ticks, roe deer, and livestock in a fragmented agricultural landscape

Author: Xavier Bailly, Olivier Plantard, Karen D. McCoy, Valérie Poux, Denis Picot, Gwenaël Vourc’h, Hélène Verheyden, Emilie Bard, Bruno Cargnelutti, Angélique Pion, Agnès Leblond, Amélie Chastagner, Bruno Lourtet, Unité de recherche d'Épidémiologie Animale (UEA), Institut National de la Recherche Agronomique (INRA), Evolutionary Ecology Group, Department of Biology, University of Antwerp (UA), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), UMR 1300 Biologie, Epidémiologie et Analyse du Risque, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Biologie, Epidémiologie et Analyse du Risque (BioEpAR)-Santé animale (S.A.), Université de Montpellier (UM), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Épidémiologie des Maladies Animales et Zoonotiques - UMR 346 (EPIA), Institut National de la Recherche Agronomique (INRA)-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), Evolution of host-microbe communities (MIVEGEC-EVCO), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), This work was supported by the French National Research Agency (OSCAR project, ANR-11-AGRO-001-04, 2011) and the French National Institute for Agricultural Research (Bioressources, P030006, 2012). We also received funding from the Tick and Tick-Borne Diseases (TMT) group, which is part of the Research Consortium on Biological Interactions (GdR REID), and Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], animal diseases, Animal Diseases, Ticks, Prevalence, host specificity, Pathogen, Phylogeny, biology, superinfections, Ecology, Ricinus, Agriculture, Bacterial Typing Techniques, 3. Good health, Roe deer, Infectious Diseases, Livestock, Microbiology (medical), Ixodes ricinus, Genotype, 030106 microbiology, Zoology, Tick, within-host diversity, Microbiology, 03 medical and health sciences, biology.animal, parasitic diseases, Genetics, Animals, Humans, infection risk, Nymph, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Disease Reservoirs, business.industry, Deer, anaplasma phagocytophilum, Ehrlichiosis, Environmental Exposure, biology.organism_classification, Anaplasma phagocytophilum, 030104 developmental biology, exposure, Superinfection, Human medicine, business
Abstract: Anaplasma phagocytophilum is a bacterial pathogen mainly transmitted by Ixodes ricinus ticks in Europe. It infects wild mammals, livestock, and, occasionally, humans. Roe deer are considered to be the major reservoir, but the genotypes they carry differ from those that are found in livestock and humans. Here, we investigated whether roe deer were the main source of the A. phagocytophilum genotypes circulating in questing I. ricinus nymphs in a fragmented agricultural landscape in France. First, we assessed pathogen prevalence in 1837 I. ricinus nymphs ?(sampled along georeferenced transects) and 79 roe deer. Prevalence was dramatically different between ticks and roe deer: 1.9% versus 76%, respectively. Second, using high-throughput amplicon sequencing, we characterized the diversity of the A. phagocytophilum genotypes found in 22 infected ticks and 60 infected roe deer; the aim was to determine the frequency of co-infections. Only 22.7% of infected ticks carried genotypes associated with roe deer. This finding fits with others suggesting that cattle density is the major factor explaining infected tick density. To explore epidemiological scenarios capable of explaining these patterns, we constructed compartmental models that focused on how A. phagocytophilum exposure and infection dynamics affected pathogen prevalence in roe deer. At the exposure levels predicted by the results of this study and the literature, the high prevalence in roe deer was only seen in the model in which superinfections could occur during all infection phases and when the probability of infection post exposure was above 0.43. We then interpreted these results from the perspective of livestock and human health.
Published: 2017

16. Ecological factors influencing small mammal infection byAnaplasma phagocytophilumandBorrelia burgdorferis.l. in agricultural and forest landscapes

Author: Suzanne Bastian, Gwenaël Vourc’h, Albert Agoulon, Grégoire Perez, Olivier Plantard, Alain Butet, and Amélie Chastagner
Subjects: 0301 basic medicine, Ixodes ricinus, biology, Ecology, animal diseases, 030231 tropical medicine, 15. Life on land, Tick, bacterial infections and mycoses, biology.organism_classification, Microbiology, Anaplasma phagocytophilum, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Abundance (ecology), parasitic diseases, Apodemus, Borrelia burgdorferi, Nymph, Pathogen, Ecology, Evolution, Behavior and Systematics
Abstract: Summary Small mammals are key components of numerous tick-borne disease systems, as hosts for immature ticks and pathogen reservoirs. To study the factors influencing tick-borne infection in small mammals, we trapped small mammals and collected questing ticks in spring and autumn in 2012 and 2013 at 24 sites in a 10x15 km rural landscapes (Brittany, France). Tissue samples were screened by real-time PCR for Anaplasma phagocytophilum and Borrelia burgdorferi sensu lato. Of the two dominant small mammal species captured, bank voles (Myodes glareolus) had higher prevalence than wood mice (Apodemus sylvaticus) for both infections, presumably because of specific differences in immunological defenses. Prevalence of infections was higher in 2013 than in 2012, likely because small mammals were fivefold less abundant in 2013, favoring tick aggregation. Bacterial prevalence, which was higher in autumn, was not associated to questing Ixodes ricinus nymph abundance which was 6 times higher in spring, but rather to the structure of the small mammal community. These findings suggest the involvement of endophilic tick species, I. trianguliceps and/or I. acuminatus, in bacterial transmission. Our study highlights that the entire community of hosts and vectors, and their interactions, should be considered to fully understand the epidemiology of vector-borne diseases. This article is protected by copyright. All rights reserved.
Published: 2017

17. Why such a contrast between the low prevalence of zoonotic pathogens in questing ticks and the high prevalence in their verterbrate reservoir hosts?

Author: Suzanne Bastian, Albert Agoulon, Xavier Bailly, Alain Butet, Amélie Chastagner, Thierry Hoch, Maggy Jouglin, Laurence Malandrin, Mccoy, Karen D., Grégoire Perez, Olivier Plantard, Hélène Verheyden, Gwenaël Vourc'h, UMR 1300 Biologie, Epidémiologie et Analyse du Risque, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Biologie, Epidémiologie et Analyse du Risque (BioEpAR)-Santé animale (S.A.), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA), Evolution of host-microbe communities (MIVEGEC-EVCO), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Unité de recherche d'Épidémiologie Animale (UEA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Laboratoire de Comportement et d'Ecologie de la Faune Sauvage, INRA, 31326 Castanet-Tolosan cedex, France, Épidémiologie des Maladies Animales et Zoonotiques - UMR 346 (EPIA), ProdInra, Migration, Université de Rennes (UNIV-RENNES), Evolutionary Ecology Group, University of Antwerp (UA), Université de Montpellier (UM), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR), Laboratoire Chrono-environnement (UMR 6249) (LCE), and Briand, Valerie
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV] Life Sciences [q-bio], Diversity, Ticks, [SDV]Life Sciences [q-bio], parasitic diseases, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Tick‐borne infections, ComputingMilieux_MISCELLANEOUS, Meta‐communities, Reservoir
Abstract: International audience; In a context of emerging or re‐emerging tick‐borne diseases, many studies have measured the prevalence of zoonotic agents in hosts and vectors, using cross‐sectional protocols at different spatial scales. Surprisingly, a frequent contrast occurs between a high prevalence in the vertebrate hosts and a low prevalence in questing ticks. Furthermore, investigations on the species of the genera Anaplasma, Babesia and Borrelia have shown that several taxa co‐circulate and are maintained in vertebrate host populations. Indeed, the co‐infection of the individual vertebrate host by several taxa and genetic variants is the rule, rather than the exception. Based on a review of recent papers on ticks and tick‐borne diseases, we hypothesize that high and repeated exposure to ticks under natural conditions causes the frequent re‐infection of vertebrates with a diversity of tick‐transmitted taxa, leading to a high overall prevalence of infections and co‐infections. However, the immunity induced by this frequent exposure could keep the intensity of co‐infections by different strains of the same taxa at a low level within individual hosts, which in turn could lead to a low frequency of acquisition by the ticks during bloodmeals. Furthermore, in order to complete their life‐cycle, the tick‐transmitted organisms need also to resist the tick innate immunity, to compete with its microbiote and to be able to colonize the salivary glands of the vector. Facing these successive selective pressures, the maintenance of the infections in the host populations can be achieved only if ticks are abundant, to compensate for a low prevalence in tick populations. We argue that a meta‐community approach taking into account the functional traits of the different pathogen taxa and their intra‐taxa diversity is required to fully understand the dynamic interplay between the actors of the pathosystem and the potential emergence of pathogenic strains
Published: 2018

18. Spatiotemporal Distribution and Evolution of the A/H1N1 2009 Pandemic Influenza Virus in Pigs in France from 2009 to 2017: Identification of a Potential Swine-Specific Lineage

Author: Stéphane Quéguiner, Yannick Blanchard, Nicolas Barbier, Véronique Béven, Amélie Chastagner, Stéphane Gorin, Gaëlle Simon, Edouard Hirchaud, Séverine Hervé, Dinah Henritzi, Emilie Bonin, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Bretagne Loire (COMUE) (UBL), and Friedrich-Loeffler-Institut (FLI)
Subjects: 0301 basic medicine, pig, Swine, viruses, Reassortment, zoonotic infection, medicine.disease_cause, molecular epidemiology, Influenza A Virus, H1N1 Subtype, Influenza A virus, Phylogeny, 2. Zero hunger, Swine Diseases, education.field_of_study, genetic diversity, 3. Good health, orthomyxoviridae, Hemagglutinins, Population Surveillance, France, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Immunology, Population, Orthomyxoviridae, Neuraminidase, cat, regional pattern, Biology, Microbiology, Virus, Antigenic drift, Evolution, Molecular, 03 medical and health sciences, Viral Proteins, Spatio-Temporal Analysis, Orthomyxoviridae Infections, Virology, Reassortant Viruses, medicine, Animals, education, Pandemics, antigenic drift, Whole Genome Sequencing, pandemic, Outbreak, influenza A virurs, biology.organism_classification, 030104 developmental biology, Genetic Diversity and Evolution, Insect Science
Abstract: International audience; The H1N1 influenza virus responsible for the most recent pandemic in 2009 (H1N1pdm) has spread to swine populations worldwide while it replaced the previous seasonal H1N1 virus in humans. In France, surveillance of swine influenza A viruses in pig herds with respiratory outbreaks led to the detection of 44 H1N1pdm strains between 2009 and 2017, regardless of the season, and findings were not correlated with pig density. From these isolates, 17 whole-genome sequences were obtained, as were 6 additional hemagglutinin (HA)/neuraminidase (NA) sequences, in order to perform spatial and temporal analyses of genetic diversity and to compare evolutionary patterns of H1N1pdm in pigs to patterns for human strains. Following mutation accumulation and fixation over time, phylogenetic analyses revealed for the first time the divergence of a swine-specific genogroup within the H1N1pdm lineage. The divergence is thought to have occurred around 2011, although this was demonstrated only through strains isolated in 2015 to 2016 in the southern half of France. To date, these H1N1pdm swine strains have not been related to any increased virulence in swine herds and have not exhibited any antigenic drift compared to seasonal human strains. However, further monitoring is encouraged, as diverging evolutionary patterns in these two species, i.e., swine and humans, may lead to the emergence of viruses with a potentially higher risk to both animal and human health. Pigs are a "mixing vessel" for influenza A viruses (IAVs) because of their ability to be infected by avian and human IAVs and their propensity to facilitate viral genomic reassortment events. Also, as IAVs may evolve differently in swine and humans, pigs can become a reservoir for old human strains against which the human population has become immunologically naive. Thus, viruses from the novel swine-specific H1N1pdm genogroup may continue to diverge from seasonal H1N1pdm strains and/or from other H1N1pdm viruses infecting pigs and lead to the emergence of viruses that would not be covered by human vaccines and/or swine vaccines based on antigens closely related to the original H1N1pdm virus. This discovery confirms the importance of encouraging swine IAV monitoring because H1N1pdm swine viruses could carry an increased risk to both human and swine health in the future as a whole H1N1pdm virus or gene provider in subsequent reassortant viruses.
Published: 2018

19. Le projet OSCAR : prendre en compte l’hétérogénéité spatiale du paysage pour comprendre les déterminants de la distribution du risque lié aux maladies à tiques

Author: Olivier Plantard, David Abrial, Albert Agoulon, Xavier Bailly, Suzanne Bastian, Alain Butet, Agnès Bouju-Albert, Nicolas Cebe, Amélie Chastagner, Axelle Durand, Mark Hewison, Thierry Hoch, Isabelle Lebert, Elsa Léger, Maggy Jouglin, Karen Mccoy, Sébastien Masséglia, Nicolas Morrelet, Valérie Noël, Grégoire Perez, Denis Picot, Angelique Pion, Valérie Poux, Elsa Quillery, Yann Rantier, Hélène Verheyden, Gwenaël Vourc'H, UMR 1300 Biologie, Epidémiologie et Analyse du Risque, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Biologie, Epidémiologie et Analyse du Risque (BioEpAR)-Santé animale (S.A.), Unité d'épidémiologie animale, Institut National de la Recherche Agronomique (INRA), Unité de Recherche d'Épidémiologie Animale (UR EpiA), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Centre de Recherche en Transplantation et Immunologie (U1064 Inserm - CRTI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5), Fonctionnement et évolution des systèmes écologiques (FESE), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution Théorique et Expérimentale (MIVEGEC-ETE), Perturbations, Evolution, Virulence, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Institut National de la Recherche Agronomique (INRA)-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)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Evolution of host-microbe communities (MIVEGEC-EVCO), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Perturbations, Evolution, Virulence (PEV), Unité de recherche d'Épidémiologie Animale (UEA), École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Épidémiologie des Maladies Animales et Zoonotiques - UMR 346 (EPIA), ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Faune domestique, Micromammifères, Borrelia, [SDV]Life Sciences [q-bio], Landscape ecology, Ixodes ricinus, Babesia, Maladies vectorielles, Landscape genetics, [SDV] Life Sciences [q-bio], Chevreuil, Landscape epidemiology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, Anaplasma phagocytophilum
Abstract: International audience; Les tiques sont des vecteurs majeurs de maladies à la fois animales et humaines (la plupart étant zoonotiques) et dans l'hémisphère nord, elles sont considérées comme les vecteurs les plus importants en santé humaine en raison notamment de la maladie de lyme. Même si l'espèce la plus fréquente en Europe - Ixodes ricinus - est d'abord forestière en raison de l'hygrométrie importante qu'elle exige, on la retrouve cependant dans d'autres biotopes (bordures de prairies, haies, landes...) où elle exploite une grande diversité d'hôtes à la fois dans la faune sauvage (rongeurs, cervidés...) et domestique (bovins, ovins...), qui sont éventuellement des réservoirs d'agents pathogènes. En raison de l'hétérogénéité spatiale de ces différents milieux à l'échelle du paysage, on ne peut pas comprendre la propagation dans l'espace et dans le temps de ces maladies au sein des agro-écosystèmes sans prendre en compte la répartition de ces biotopes ainsi que la distribution et les mouvements des animaux. Le projet OSCAR (Outil de Simulation Cartographique à l'échelle du paysage Agricole du Risque acarologique ; ANR Agrobiosphère, 2012-2016) a pour objectif d'analyser la distribution observée du risque acarologique (défini comme le produit de la densité de tiques par la prévalence des agents pathogènes au sein des tiques), de mieux comprendre la dynamique spatio-temporelle des populations de tiques et d'établir des cartes prédictives du risque acarologique basées sur des scénarios de changement de structure du paysage. Il implique 5 laboratoires (2 du DSA, 1 d'EFPA et 2 du CNRS), qui ont participé aux travaux de collecte d'informations (présence d'animaux domestiques dans les parcelles, localisation de chevreuils équipés de colliers GPS, abondance des micromammifères estimée par piégeage, caractérisation des biotopes étudiés...) et de matériels biologiques (tiques, sangs...) dans 2 zones d'études (les zones Atelier Armorique et Vallons et Côteaux de Gascogne). Des travaux de biologie moléculaire ont permis de caractériser la variabilité génétique au sein des populations de tiques et de rechercher la présence de 3 agents pathogènes dans ces échantillons (Anaplasma phagocytophilum, Borrelia spp. et Babesia spp.). L'analyse des densités de tiques sur la végétation a montré de fortes variations à l'échelle du paysage (avec une absence de tiques en bordure de pâtures lorsque les haies sont trop réduites par exemple). Concernant l'abondance des micromammifères, nous avons observé qu'un réseau de haies et de bosquets plus dense est plus favorable aux mulots sylvestres, tandis que les campagnols roussâtres sont plus abondants dans les habitats boisés isolés. Les importantes fluctuations d'abondance interannuelles de ces rongeurs entraînent de fortes fluctuations des densités du stade nymphal des tiques sur la végétation une saison plus tard. Les prévalences (dans les tiques collectées sur la végétation) des 3 agents pathogènes étudiés se sont avérées faibles (2 à 5 %). Les prévalences d'A. phagocytophilum et de Babesia (B. venatorum et B. capreoli) dans les chevreuils se sont quant à elles révélées importantes (de 65 % à 85 %). L'analyse de la variabilité génétique d'A. phagocytophilum a montré l'existence de plusieurs clades génétiquement distants dont un plus particulièrement associé au chevreuil. Les analyses de génétique des populations des tiques à l'échelle du paysage ont révélé d'importants flux de gènes et une absence de structuration entre populations, suggérant une importante dispersion via les mouvements des hôtes. La dernière année du projet est consacrée à la réalisation d'un modèle spatialisé prenant de compte l'hétérogénéité du paysage afin de prédire les densités de tiques en fonction des différents éléments qui le composent et explorer ainsi par simulation comment la modification de la structure du paysage impactera les densités de tiques
Published: 2016

20. Les caractéristiques d'un paysage agricole influencent-elles la relation rongeur-tique ?

Author: Amélie Chastagner, Gwenaël Vourc’h, Dugat, T., Hélène Verheyden, Laurent Legrand, Bachy, V., Chabanne, L., Joncour, G., Maillard, R., Haddad, N., Boulouis, H. J., Olivier Plantard, Albert Agoulon, Suzanne Bastian, Laurence Malandrin, Thierry Hoch, Maggy Jouglin, Agnès Bouju, Axelle Durand, Quillery, E., Mohamed Lemine Brahim, Hélène Mahé, Alain Butet, Yann Rantier, Grégoire Perez, David Abrial, Patrick Gasqui, Isabelle Lebert, Nelly Dorr, Sébastien Masseglia, Mccoy, Karen D., Valérie Noël, Elsa Léger, Mark Hewison, Nicolas Morellet, Jean-Marc Angibault, Nicolas Cebe, Denis Picot, Leblond, A., Xavier Bailly, Unité de recherche d'Épidémiologie Animale (UEA), Institut National de la Recherche Agronomique (INRA), Épidémiologie des Maladies Animales et Zoonotiques - UMR 346 (EPIA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Comportement et d'Ecologie de la Faune Sauvage, INRA, 31326 Castanet-Tolosan cedex, France, Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE - UMR 8587), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), USTBH, Algeria, UMR 1300 Biologie, Epidémiologie et Analyse du Risque, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Biologie, Epidémiologie et Analyse du Risque (BioEpAR)-Santé animale (S.A.), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Centre de Recherche en Transplantation et Immunologie (U1064 Inserm - CRTI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Unité d'épidémiologie animale, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5), Laboratoire de Comportement et d'Ecologie de la Faune Sauvage, Institut National de la Recherche Agronomique, BP 27, 31326 Castanet Tolosan cedex, France, Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Unité de Recherche d'Épidémiologie Animale (UR EpiA), Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Evolution of host-microbe communities (MIVEGEC-EVCO), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Evolution Théorique et Expérimentale (MIVEGEC-ETE), Perturbations, Evolution, Virulence (PEV), Butet, Alain, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), 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), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2), and Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2015

21. Diversité génétique d’Anaplasma phagocytophilum, agent de l’anaplasmose granulocytaire, conséquences épidemiologiques et implications pour le contrôle en France

Author: Nadia Haddad, Thibaud Dugat, Amélie Chastagner, Gwenaëlle Vourc’h, Henri-Jean Boulouis, Agnès Leblond, Renaud Maillard, Luc Chabanne, Unité de Recherche d'Épidémiologie Animale (UR EpiA), Institut National de la Recherche Agronomique (INRA), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), 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)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, 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)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: Veterinary medicine, animal diseases, [SDV]Life Sciences [q-bio], Multiple Loci VNTR Analysis, Intergenic region, biology.animal, parasitic diseases, medicine, hôte réservoir, bovins, chevreuils, cerf, A. phagocytophilum, MLVA, MLSA, épidémiologie moléculaire, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Genetics, Genetic diversity, General Veterinary, Molecular epidemiology, biology, cattle, red deer, roe deer, reservoir host, molecular epidemiology, medicine.disease, biology.organism_classification, bacterial infections and mycoses, Anaplasma phagocytophilum, 3. Good health, Roe deer, Variable number tandem repeat, bacteria, Anaplasmosis
Abstract: Genetic diversity of anaplasma phagocytophilum, the causative agent of granulocytic anaplasmosis, implications for epidemiology and control in France. Anaplasma phagocytophilum is a tick-borne bacterium and the etiologic agent of granulocytic anaplasmosis, an emerging disease that affects a wide range of mammals. In this paper, we present the recent knowledge gained from studies on the genetic diversity of this pathogen in France. Multilocus sequence analysis (MLSA) was used to characterize the genetic diversity of A. phagocytophilum in populations of French cattle, horses, dogs, and roe deer. MLSA was based on nine loci (ankA, msp4, groESL, typA, pled, gyrA, recG, polA, and an intergenic region). Phylogenic analysis revealed three genetic clusters of bacterial variants in domesticated animals. The two principal clusters included 98% of the bacterial genotypes found in cattle, which were only distantly related to those in roe deer. One cluster comprised only cattle genotypes, while the second contained genotypes from cattle, horses, and dogs. The third contained all roe deer genotypes and three cattle genotypes. These results suggest that roe deer do not contribute to the spread of A. phagocytophilum in cattle in France. A Multiple-Locus Variable number tandem repeat (VNTR) Analysis typing technique was developed for A. phagocytophilum. Five VNTRs were selected based on the HZ human-derived strain genome, and were tested on the Webster human-derived strain and on 123 DNA samples. This study confirmed that A. phagocytophilum from roe deer or domestic ruminants belong to two different clusters, while A. phagocytophilum from red deer and domestic ruminants locate within the same cluster, questioning the respective roles of roe vs red deer as reservoir hosts for domestic ruminant strains in Europe. The molecular techniques recently developed have great potential to provide detailed information on A. phagocytophilum isolates, improving both epidemiological and phylogenic investigations, thereby helping in the development of relevant prevention and control measures., A. phagocytophilum, bactérie transmise par les tiques, est responsable de l’anaplasmose granulocytaire, une maladie émergente qui infecte une large gamme de mammifères dont l’homme. L’objectif de cet article est de présenter les nouvelles connaissances acquises sur la diversité génétique d’A. phagocytophilum chez différentes espèces d’hôtes en France, afin de déterminer quelles espèces participent au même cycle épidémiologique. Une analyse par séquençage multi-locus (MLSA) a été effectuée dans des populations de bovins, chevaux, chiens et chevreuils. Trois groupes de génotypes infectant les bovins ont été identifiés. Les deux groupes principaux incluent 98% des génotypes bactériens trouvés chez les bovins et sont éloignés de ceux des chevreuils. Un cluster ne comprenait que les génotypes de bovins, tandis que le second génotype contenant des bovins comprenait également des chevaux et des chiens. Le troisième cluster contenait tous les génotypes de chevreuils et trois génotypes de bovins. Ces résultats suggèrent que les chevreuils ne contribuent pas à la propagation d’A. phagocytophilum chez les bovins en France. Puis, une technique MLVA (Multiple Loci VNTR Analysis) a été développée pour A. phagocytophilum. Cinq VNTR ont été sélectionnés sur la base du génome de la souche d’origine humaine HZ, et ont été testés sur 123 échantillons d’ADN provenant d’animaux domestiques ou sauvages. Cette étude a confirmé que les souches d’A. phagocytophilum retrouvées chez les chevreuils et les ruminants domestiques appartiennent à deux groupes différents, alors que les souches identifiées chez les cerfs et les ruminants domestiques sont localisées dans le même cluster. Ces résultats remettent en question les rôles respectifs des chevreuils et des cerfs comme hôtes réservoirs pour les souches d’A. phagocytophilum de ruminants domestiques en Europe. Ces techniques moléculaires ont un grand potentiel pour améliorer nos connaissances sur les cycles épidémiologiques d’A. phagocytophilum, contribuant ainsi à l’élaboration de mesures de prévention et de contrôle pertinents., Chastagner Amélie Pierrette, Dugat Thibaud, Vourc’h Gwenaëlle, Chabanne Luc, Maillard Renaud, Boulouis Henri-Jean, Haddad Nadia, Leblond Agnès. Diversité génétique d’Anaplasma Phagocytophilum, agent de l’anaplasmose granulocytaire, conséquences épidemiologiques et implications pour le contrôle en France. In: Bulletin de l'Académie Vétérinaire de France tome 168 n°1, 2015. pp. 25-37.
Published: 2015

22. Multilocus sequence analysis of Anaplasma phagocytophilum reveals three distinct lineages with different host ranges in clinically ill French cattle

Author: Henri-Jean Boulouis, Thibaud Dugat, Hélène Verheyden, Renaud Maillard, Xavier Bailly, Véronique Bachy, Gwenaël Vourc’h, Nadia Haddad, Guy Joncour, Luc Chabanne, Agnès Leblond, Amélie Chastagner, Loïc Legrand, Unité de Recherche d'Épidémiologie Animale (UR EpiA), Institut National de la Recherche Agronomique (INRA), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: Veterinary medicine, Anaplasmosis, animal diseases, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Zoology, Cattle Diseases, Biology, 03 medical and health sciences, Dogs, Bacterial Proteins, biology.animal, Genetic variation, parasitic diseases, medicine, Animals, Dog Diseases, Horses, Phylogeny, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, General Veterinary, Molecular epidemiology, 030306 microbiology, Research, Deer, Genetic Variation, Sequence Analysis, DNA, biology.organism_classification, medicine.disease, Anaplasma phagocytophilum, veterinary(all), Roe deer, Multilocus sequence typing, Cattle, Horse Diseases, France, Multilocus Sequence Typing
Abstract: Molecular epidemiology represents a powerful approach to elucidate the complex epidemiological cycles of multi-host pathogens, such as Anaplasma phagocytophilum. A. phagocytophilum is a tick-borne bacterium that affects a wide range of wild and domesticated animals. Here, we characterized its genetic diversity in populations of French cattle; we then compared the observed genotypes with those found in horses, dogs, and roe deer to determine whether genotypes of A. phagocytophilum are shared among different hosts. We sampled 120 domesticated animals (104 cattle, 13 horses, and 3 dogs) and 40 wild animals (roe deer) and used multilocus sequence analysis on nine loci (ankA, msp4, groESL, typA, pled, gyrA, recG, polA, and an intergenic region) to characterize the genotypes of A. phagocytophilum present. Phylogenic analysis revealed three genetic clusters of bacterial variants in domesticated animals. The two principal clusters included 98% of the bacterial genotypes found in cattle, which were only distantly related to those in roe deer. One cluster comprised only cattle genotypes, while the second contained genotypes from cattle, horses, and dogs. The third contained all roe deer genotypes and three cattle genotypes. Geographical factors could not explain this clustering pattern. These results suggest that roe deer do not contribute to the spread of A. phagocytophilum in cattle in France. Further studies should explore if these different clusters are associated with differing disease severity in domesticated hosts. Additionally, it remains to be seen if the three clusters of A. phagocytophilum genotypes in cattle correspond to distinct epidemiological cycles, potentially involving different reservoir hosts. Electronic supplementary material The online version of this article (doi:10.1186/s13567-014-0114-7) contains supplementary material, which is available to authorized users.
Published: 2014

23. A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants

Author: Elisabeth Petit, Fabien Corbière, Thibaud Dugat, Nadia Haddad, Hélène Verheyden, Renaud Maillard, Simon Thierry, Benoit Durand, Luc Chabanne, Agnès Leblond, Henri-Jean Boulouis, Anne-Claire Lagrée, Amélie Chastagner, Gwenaël Vourc’h, Xavier Bailly, Biologie Moléculaire et Immunologie Parasitaires et Fongiques, École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-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), Unité de Recherche d'Épidémiologie Animale (UR EpiA), Institut National de la Recherche Agronomique (INRA), Laboratoire de santé animale, Unité d’épidémiologie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Santé animale, Unité Zoonoses Bactériennes, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Ecole Nationale Vétérinaire de Toulouse (ENVT), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-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), Unité Zoonoses Bactériennes (UZB), 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), and Maillard, Renaud
Subjects: Disease reservoir, Epidemiology, VNTR, animal diseases, [SDV]Life Sciences [q-bio], Minisatellite Repeats, Cluster Analysis, Phylogeny, Genetics, 0303 health sciences, Tick-borne disease, Geography, biology, Ruminants, Bacterial Typing Techniques, 3. Good health, Roe deer, Variable number tandem repeat, Infectious Diseases, Tandem Repeat Sequences, Tick-Borne Diseases, Animals, Domestic, France, Anaplasma phagocytophilum, Human granulocytic anaplasmosis, Molecular Sequence Data, Zoology, Animals, Wild, Multiple Loci VNTR Analysis, Tick, 03 medical and health sciences, biology.animal, parasitic diseases, medicine, Animals, Humans, Wild ruminants, Domestic ruminants, Reservoir, Disease Reservoirs, 030304 developmental biology, Base Sequence, 030306 microbiology, Research, MLVA, Ehrlichiosis, Genetic Variation, Sequence Analysis, DNA, medicine.disease, biology.organism_classification, bacterial infections and mycoses, Genetic Loci, Parasitology
Abstract: Background Anaplasma phagocytophilum is a tick-borne intragranulocytic alpha-proteobacterium. It is the causative agent of tick-borne fever in ruminants, and of human granulocytic anaplasmosis in humans, two diseases which are becoming increasingly recognized in Europe and the USA. However, while several molecular typing tools have been developed over the last years, few of them are appropriate for in-depth exploration of the epidemiological cycle of this bacterium. Therefore we have developed a Multiple-Locus Variable number tandem repeat (VNTR) Analysis typing technique for A. phagocytophilum. Methods Five VNTRs were selected based on the HZ human-derived strain genome, and were tested on the Webster human-derived strain and on 123 DNA samples: 67 from cattle, 7 from sheep, 15 from roe deer, 4 from red deer, 1 from a reindeer, 2 from horses, 1 from a dog, and 26 from ticks. Results From these samples, we obtained 84 different profiles, with a diversity index of 0.96 (0.99 for vertebrate samples, i.e. without tick samples). Our technique confirmed that A. phagocytophilum from roe deer or domestic ruminants belong to two different clusters, while A. phagocytophilum from red deer and domestic ruminants locate within the same cluster, questioning the respective roles of roe vs red deer as reservoir hosts for domestic ruminant strains in Europe. As expected, greater diversity was obtained between rather than within cattle herds. Conclusions Our technique has great potential to provide detailed information on A. phagocytophilum isolates, improving both epidemiological and phylogenic investigations, thereby helping in the development of relevant prevention and control measures. Electronic supplementary material The online version of this article (doi:10.1186/1756-3305-7-439) contains supplementary material, which is available to authorized users.
Published: 2014

24. Single genotype of Anaplasma phagocytophilum identified from ticks, Camargue, France

Author: Xavier Bailly, Gwenaël Vourc’h, Agnès Leblond, Sophie Pradier, Amélie Chastagner, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), 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)-Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Chastagner, Amélie, École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-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), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, and École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie
Subjects: Veterinary medicine, Letter, Epidemiology, [SDV]Life Sciences [q-bio], Ixodes ricinus, lcsh:Medicine, Hyalomma marginatum, Polymerase Chain Reaction, MESH: Genotype, 0302 clinical medicine, Rhipicephalus turanicus, RNA, Ribosomal, 16S, characterization, MESH: Animals, bacteria, MESH: Phylogeny, MESH: Bacterial Proteins, Phylogeny, ComputingMilieux_MISCELLANEOUS, tickborne, 0303 health sciences, biology, 3. Good health, Rhipicephalus, MESH: RNA, Ribosomal, 16S, Infectious Diseases, PCR, Rhipicephalus bursa, MESH: Ehrlichiosis, France, MESH: Tick Infestations, Dermacentor, Anaplasma phagocytophilum, Microbiology (medical), Genotype, Rhipicephalus sanguineus, 030231 tropical medicine, Tick, MESH: Genetic Loci, lcsh:Infectious and parasitic diseases, ticks, 03 medical and health sciences, Bacterial Proteins, parasitic diseases, medicine, Animals, Humans, lcsh:RC109-216, Anaplasma, Horses, Letters to the Editor, MESH: Horses, MESH: Ticks, MESH: Humans, 030306 microbiology, lcsh:R, Ehrlichiosis, MESH: Polymerase Chain Reaction, bacterial infections and mycoses, biology.organism_classification, medicine.disease, Tick Infestations, zoonoses, MESH: France, Genetic Loci, Ixodes, Dermacentor marginatus, Anaplasmosis, MESH: Anaplasma phagocytophilum
Abstract: To the Editor: Granulocytic anaplasmosis is a tickborne zoonosis caused by Anaplasma phagocytophilum bacteria, which are emerging in Europe. Besides infecting humans, A. phagocytophilum infect a wide range of wild and domestic mammals (1). In Europe, the Ixodes ricinus tick is the main vector for the bacteria, but A. phagocytophilum has also been detected in association with Rhipicephalus and Dermacentor spp. ticks (2). The climate and biotopes of the Mediterranean region are particularly favorable for several species of ticks and, therefore, for tickborne diseases. Although I. ricinus ticks are rare or absent in the Mediterranean Basin, serosurveys performed on equine populations in Camargue, southern France, indicated an A. phagocytophilum seroprevalence of ≈10% (3). To investigate the prevalence and diversity of A. phagocytophilum bacteria in ticks in Camargue, we collected questing ticks from horse pastures and feeding ticks from horses. Ticks feeding on horses were collected in randomly selected stables during 2007 (84 stables), 2008 (72 stable), and 2010 (19 stables). The stables were chosen among those where evidence of A. phagocytophilum seroconversion in horses had been previously found (3). In 2008 and 2010, questing ticks were collected by the dragging method in 19 pastures, around bushes, and in areas where horses spent the most time. Surveys were conducted in the spring, which represents the peak activity time of Ixodes ticks. A total of 406 adult ticks were collected, representing 6 species: Rhipicephalus bursa, R. sanguineus, R. turanicus, R. pusillus, Dermacentor marginatus, and Hyalomma marginatum. Tick species were identified by morphologic criteria and molecular analyses based on mitochondrial 12S rDNA sequences (4). Total DNA was extracted from the ticks by using the NucleoSpin Tissue Kit (Macherey-Nagel, Duren, Germany) (5). A. phagocytophilum was detected by nested PCR targeting the 16S rDNA (Technical Appendix 1). Of the 406 ticks, 40 were infected with A. phagocytophilum. The infected group included ticks from all 6 collected species except R. pusillus. Infection rates among the species ranged from 0 to 22% (Technical Appendix 2). The prevalence of A. phagocytophilum infection did not differ significantly between species (logistic regression model, p = 0.76) but was higher among questing ticks than feeding ticks (p
Published: 2013

25. La prévalence de l’anaplamose dans le sud de la France

Author: Agnès Leblond, Amélie Chastagner, Sophie Pradier, Xavier Bailly, Sébastien Masséglia, Gwenaël Vourc’h, Unité de Recherche d'Épidémiologie Animale (UR EpiA), Institut National de la Recherche Agronomique (INRA), Ecole Nationale Vétérinaire, and ProdInra, Migration
Subjects: [SDV] Life Sciences [q-bio], VIRUS DE WEST NILE, zoonose, Ixodes, SYNDROME NERVEUX, [SDV]Life Sciences [q-bio], Rhipicephalus, équidés, ComputingMilieux_MISCELLANEOUS, Anaplasma phagocytophilum
Abstract: National audience

26. Taking into account the spatial heterogeneity of agricultural landscapes to explain densities and movements of Ixodes ricinus and prevalence of its associated pathogens

Author: Olivier Plantard, Albert Agoulon, Suzanne Bastian, Thierry Hoch, Elsa Quillery, Alain Butet, Grégoire Perez, Yann Rantier, Mccoy, Karen D., Elsa Léger, Hélène Verheyden, Mark Hewison, Jodie Martin, Nicolas Morellet, David Abrial, Xavier Bailly, Amélie Chastagner, Isabelle Lebert, Robin Loche, Gwenaël Vourc'H, Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Evolution of host-microbe communities (MIVEGEC-EVCO), Processus Écologiques et Évolutifs au sein des Communautés (PEEC), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Université de Montpellier (UM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UR)
Subjects: [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], parasitic diseases, bacterial infections and mycoses
Abstract: International audience; While most studies on Ixodes ricinus to date have focused on forest habitats, the main European tick species is also widely found in agricultural landscapes including pastures, hedgerows and small woods. Because wildlife and domestic fauna share these habitats and are both feeding hosts for ticks and reservoirs for numerous tick-borne infectious agents, understanding of the epidemiology of associated diseases must explicitly take into account the spatial arrangement of these different biotopes. During the OSCAR project (https://www6.inra.fr/oscar/), we have investigated two comparable agricultural landscapes located in France to analyse the potential importance of this landscape interface on Anaplasma phagocytophilum, Borrelia spp. and Babesia spp. prevalence. In the ecotones between pastures and wooded areas, tick density was linked to wood mouse abundance (Apodemus sylvaticus) the previous year. The A. phagocytophilum prevalence was higher in roe deer (75%) than in rodents (6.9%) or in tick nymphs sampled on the vegetation (1.9%), with density of cattle being positively linked to this last prevalence. Using both SNP and microsatellite genotyping of individual ticks, extensive gene flow was reported among landscape components within each study site probably linked to tick dispersal via host movements. Indeed, GPS analyses of collared roe deer revealed the use of almost all landscape components by these tick hosts. Finally, a landscape simulator was built, and based on information from a model explaining tick density in relation to different landscape features, tick density was mapped on simulated landscapes allowing to investigate how land use changes affect tick density.

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26 results on '"Amélie Chastagner"'

1. Distribution of ticks, tick-borne pathogens and the associated local environmental factors including small mammals and livestock, in two French agricultural sites: the OSCAR database

2. Oronasal or Intramuscular Immunization with a Thermo-Attenuated ASFV Strain Provides Full Clinical Protection against Georgia 2007/1 Challenge

3. Bidirectional Human–Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018

4. Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus

5. Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

6. Evaluation of the Pathogenicity and the Escape from Vaccine Protection of a New Antigenic Variant Derived from the European Human-Like Reassortant Swine H1N2 Influenza Virus

7. A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants

8. Single Genotype of Anaplasma phagocytophilum Identified from Ticks, Camargue, France

9. Bidirectional Human–Swine Transmission of Seasonal Influenza A(H1N1)pdm09 Virus in Pig Herd, France, 2018

10. Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus

11. Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

12. Evaluation of the Pathogenicity and the Escape from Vaccine Protection of a New Antigenic Variant Derived from the European Human-Like Reassortant Swine H1N2 Influenza Virus

13. Relationships between landscape structure and the prevalence of two tick-borne infectious agents, Anaplasma Phagocytophilum and Borrelia burgdorferi sensu lato, in small mammal communities

14. Evaluation of un-methylated DNA enrichment in sequencing of African swine fever virus complete genome

15. Host specificity, pathogen exposure, and superinfections impact the distribution of Anaplasma phagocytophilum genotypes in ticks, roe deer, and livestock in a fragmented agricultural landscape

16. Ecological factors influencing small mammal infection byAnaplasma phagocytophilumandBorrelia burgdorferis.l. in agricultural and forest landscapes

17. Why such a contrast between the low prevalence of zoonotic pathogens in questing ticks and the high prevalence in their verterbrate reservoir hosts?

18. Spatiotemporal Distribution and Evolution of the A/H1N1 2009 Pandemic Influenza Virus in Pigs in France from 2009 to 2017: Identification of a Potential Swine-Specific Lineage

19. Le projet OSCAR : prendre en compte l’hétérogénéité spatiale du paysage pour comprendre les déterminants de la distribution du risque lié aux maladies à tiques

20. Les caractéristiques d'un paysage agricole influencent-elles la relation rongeur-tique ?

21. Diversité génétique d’Anaplasma phagocytophilum, agent de l’anaplasmose granulocytaire, conséquences épidemiologiques et implications pour le contrôle en France

22. Multilocus sequence analysis of Anaplasma phagocytophilum reveals three distinct lineages with different host ranges in clinically ill French cattle

23. A new multiple-locus variable-number tandem repeat analysis reveals different clusters for Anaplasma phagocytophilum circulating in domestic and wild ruminants

24. Single genotype of Anaplasma phagocytophilum identified from ticks, Camargue, France

25. La prévalence de l’anaplamose dans le sud de la France

26. Taking into account the spatial heterogeneity of agricultural landscapes to explain densities and movements of Ixodes ricinus and prevalence of its associated pathogens

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26 results on '"Amélie Chastagner"'

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