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1. Characterization of internal ribosome entry sites according to secondary structure analysis to classify Border Disease virus strains

Author: Pasquale Turno, Rebecca Strong, Falko Steinbach, Nicola Decaro, Massimo Giangaspero, Lorenzo Domenis, Claudio Apicella, Canio Buonavoglia, Xavier Bailly, Pietro Gargano, Faculty of Veterinary Medicine, Universita degli studi di Teramo - University of Teramo [Italie] (UNITE), Mammalian Virology Group, Virology Department, Animal and Plant Health Agency [Addlestone, UK] (APHA)-Animal and Plant Health Agency [Addlestone, UK] (APHA), Università degli studi di Bari Aldo Moro (UNIBA), Centro di Referenza Nazionale per le Malattie degli Animali, Selvatici ( (CeRMAS)), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta-Liguria e Valle d'Aosta, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Directorate General of Veterinary Public Health, Food and Nutrition, Ministry of Health, and Department for Environment, Food & Rural Affairs (DEFRA) ED1000 1100
Subjects: 0301 basic medicine, Untranslated region, Internal ribosome entry site, 030106 microbiology, Genome, Viral, Internal Ribosome Entry Sites, Biology, Border disease virus, 03 medical and health sciences, Secondary structure, Virology, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Protein secondary structure, Phylogeny, Sequence (medicine), Genetics, Inverted Repeat Sequences, Palindrome, Diagnostic test, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Nucleic Acid Conformation, RNA, Viral, 5' Untranslated Regions
Abstract: Applying palindromic nucleotide substitutions (PNS) method, variable loci of the internal ribosome entry site (IRES) secondary structure in the 5' untranslated region (UTR) of Border disease virus sequences were analysed allowing their allocation into ten IRES classes within the species. Sequence characteristics of Turkish and Chinese strains were highly divergent from other genogroups, indicating geographic segregation and micro-evolutive steps within the species. Observed heterogeneity in the BDV species has to be considered for potential implications on diagnostic tests, control and preventive measures.
Published: 2019
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2. A combined measure of tuberculous lesions for assessing the efficacy of vaccination against tuberculosis (Mycobacterium bovis) in European badgers (Meles meles) supports the 3Rs principle of reduction

Author: Colin P.D. Birch, Sandrine Lesellier, Mark A. Chambers, Animal and Plant Health Agency [Addlestone, UK] (APHA), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and DEFRA grant number SE3247 'Development of an oral BCG vaccine for badgers'
Subjects: MESH: Mycobacterium bovis, Male, Badger, Statistical standardization, [SDV]Life Sciences [q-bio], Disease, 0302 clinical medicine, MESH: Tuberculosis, 030212 general & internal medicine, Mycobacterium bovis, Outbred, biology, Vaccination, Regression, Experimental design, MESH: Mustelidae, 3. Good health, MESH: BCG Vaccine, MESH: Cattle, Infectious Diseases, BCG Vaccine, Molecular Medicine, MESH: Tuberculosis, Bovine, medicine.medical_specialty, Tuberculosis, 030231 tropical medicine, Meles, 03 medical and health sciences, Internal medicine, biology.animal, Covariate, Mustelidae, medicine, Animals, Disease burden, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, General Immunology and Microbiology, business.industry, Public Health, Environmental and Occupational Health, MESH: Vaccination, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, United Kingdom, Cattle, business, Covariates, Tuberculosis, Bovine
Abstract: International audience; BackgroundAn oral vaccine is a potential tool to tackle the reservoir of Mycobacterium bovis in European badgers (Meles meles), which contributes to tuberculosis of cattle in the British Isles. Inferences about vaccine protection against experimental challenge with M. bovis depend on the measurement of tuberculosis. Assessment of tuberculosis in larger species, such as badgers, is typically based on the tuberculous lesions visible at post-mortem examination and histopathology. We have developed a robust scoring system for tuberculous lesions by combining several parallel measures, which we call the “disease burden score” (DBS).MethodsAlternative scoring systems were compared within a regression analysis applied to observations from a total of 168 badgers from eight studies, including 107 badgers subjected to vaccination treatment and 61 non-vaccinated controls. The analysis included incidental observations that were recorded from each badger as potential covariate factors explaining some of the variation among animals sourced from the wild.ResultsDBS was found to be the most accurate and reliable of the scoring systems compared. By taking account of significant covariates affecting disease, application of the DBS reduced residual variance by 22.9%. A previously used measure, based on assessment of visible lesions, was suboptimal due to non-uniform variance that increased with expected value, although square root transformation addressed this issue. The covariate model fitted to DBS included sex (males had higher DBS), weight (negatively associated with DBS) and immunological evidence of prior exposure to Mycobacterium avium (positively associated with DBS).ConclusionsWe identified improved measures of tuberculous disease derived from data already collected. We also demonstrated that the proper scaling of measurements of disease in such models is necessary and can be determined empirically. The covariates which were most strongly associated with the severity of disease are important in experimental studies involving outbred animals with variable background.
Published: 2021
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3. Transmissible spongiform encephalopathy in goats: is PrP rapid test sensitivity affected by genotype?

Author: Simmons, Marion, Thorne, Leigh, Ortiz-Pelaez, Angel, Spiropoulos, John, Georgiadou, Soteria, Papasavva-Stylianou, Penelope, Andreoletti, Olivier, Hawkins, Stephen A.C., Hawkins, Stephen, Meloni, Daniela, Cassar, Claire, Animal and Plant Health Agency [Addlestone, UK] (APHA), European Food Safety Authority (EFSA), Veterinary Services of Cyprus, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), 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-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, and This work was funded by the EC and Defra through the activities of the EURL for TSE at APHA. The UMR INRA ENVT 1225 was funded for this work by the EU FEDER/INTERREG (EFA148/16 REDPRION)
Subjects: goats, Genotype, Prions, 040301 veterinary sciences, [SDV]Life Sciences [q-bio], animal diseases, Population, Scrapie, Disease, Prion Proteins, Epitope, PRNP, 0403 veterinary science, 03 medical and health sciences, medicine, Animals, Full Scientific Reports, education, transmissible spongiform encephalopathy, 030304 developmental biology, 0303 health sciences, education.field_of_study, Goat Diseases, Polymorphism, Genetic, Transmissible spongiform encephalopathy, General Veterinary, biology, scrapie, 04 agricultural and veterinary sciences, medicine.disease, Virology, nervous system diseases, prion protein, biology.protein, ELISA, Antibody
Abstract: Transmissible spongiform encephalopathy (TSE) surveillance in goats relies on tests initially approved for cattle, subsequently assessed for sheep, and approval extrapolated for use in “small ruminants.” The current EU-approved immunodetection tests employ antibodies against various epitopes of the prion protein PrPSc, which is encoded by the host PRNP gene. The caprine PRNP gene is polymorphic, mostly at codons different from the ovine PRNP. The EU goat population is much more heterogeneous than the sheep population, with more PRNP-related polymorphisms, and with marked breed-related differences. The ability of the current tests to detect disease-specific PrPSc generated against these different genetic backgrounds is currently assumed, rather than proven. We examined whether common polymorphisms within the goat PRNP gene might have any adverse effect on the relative performance of EU-approved rapid tests. The sample panel comprised goats from the UK, Cyprus, France, and Italy, with either experimental or naturally acquired scrapie at both the preclinical and/or unknown and clinical stages of disease. Test sensitivity was significantly lower and more variable when compared using samples from animals that were preclinical or of unknown status. However, all of the rapid tests included in our study were able to correctly identify all samples from animals in the clinical stages of disease, apart from samples from animals polymorphic for serine or aspartic acid at codon 146, in which the performance of the Bio-Rad tests was profoundly affected. Our data show that some polymorphisms may adversely affect one test and not another, as well as underline the dangers of extrapolating from other species.
Published: 2020
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4. Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance

Author: Nunez-Garcia, J., AbuOun, M., Storey, N., Brouwer, M.S., Delgado-Blas, J.F., Mo, S.S., Ellaby, N., Veldman, K.T., Haenni, M., Châtre, P., Madec, J.Y., Hammerl, J.A., Serna, C., Getino, M., La Ragione, R., Naas, T., Telke, A.A., Glaser, P., Sunde, M., Gonzalez-Zorn, B., Ellington, M.J., Anjum, M.F., Animal and Plant Health Agency [Addlestone, UK] (APHA), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Norwegian Veterinary Institute [Oslo], Public Health England [London], Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), German Federal Institute for Risk Assessment [Berlin] (BfR), University of Surrey (UNIS), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Écologie et Évolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris-Saclay-Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: ARDIG, Microbial Sensitivity Tests, Antimicrobial resistance, Next generation sequencing, MESH: Anti-Bacterial Agents, MESH: Drug Resistance, Bacterial, Drug Resistance, Bacterial, Escherichia coli, Life Science, Humans, MESH: High-Throughput Nucleotide Sequencing, Escherichia coli Infections, MESH: Escherichia coli Infections, Host Pathogen Interaction & Diagnostics, MESH: Microbial Sensitivity Tests, Multidisciplinary, MESH: Escherichia coli, Bacteriologie, Computational Biology, High-Throughput Nucleotide Sequencing, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Host Pathogen Interactie & Diagnostiek, Anti-Bacterial Agents, Bacteriologie, Host Pathogen Interactie & Diagnostiek, MESH: Computational Biology
Abstract: Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.
Published: 2022
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5. A European multicenter evaluation study to investigate the performance on commercially available selective agar plates for the detection of carbapenemase producing Enterobacteriaceae

Author: Cindy Dierikx, Stefan Börjesson, Agnès Perrin-Guyomard, Marisa Haenni, Madelaine Norström, Hege H. Divon, Hanna Karin Ilag, Sophie A. Granier, Annette Hammerum, Jette Sejer Kjeldgaard, Natalie Pauly, Luke Randall, Muna F. Anjum, Aleksandra Smialowska, Alessia Franco, Kees Veldman, Jannice Schau Slettemeås, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Public Health Agency of Sweden, Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Norwegian Veterinary Institute [Oslo], Statens Serum Institut [Copenhagen], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), German Federal Institute for Risk Assessment [Berlin] (BfR), Animal and Plant Health Agency [Addlestone, UK] (APHA), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: antibiotic resistance, Selective agar, Swine, résistance aux antibiotiques, Salmonella, [SDV.IDA]Life Sciences [q-bio]/Food engineering, ddc:630, animal, résistance, MESH: Enterobacteriaceae Infections, MESH: Swine, bactérie, 2. Zero hunger, MESH: Microbial Sensitivity Tests, 0303 health sciences, Bacteriologie, Enterobacteriaceae Infections, Bacteriology, Host Pathogen Interaction & Diagnostics, IMPART, Carbapenemases, Text, carbapénème, Microbiology (medical), carbapenemases, Carbapenem resistance, carbapenem resistance, entérobactérie, Microbial Sensitivity Tests, MESH: Carbapenem-Resistant Enterobacteriaceae, Sensitivity and Specificity, Microbiology, beta-Lactamases, 03 medical and health sciences, Bacterial Proteins, Enterobacteriaceae, Animals, microbiologie, selective agar, Molecular Biology, 030304 developmental biology, Host Pathogen Interaction & Diagnostics, Bacteriological Techniques, 030306 microbiology, Animal, Bacteriology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Host Pathogen Interactie & Diagnostiek, MESH: Sensitivity and Specificity, Agar, veterinary medicine, Carbapenem-Resistant Enterobacteriaceae, Bacteriologie, Host Pathogen Interactie & Diagnostiek
Abstract: The European Food Safety Authority (EFSA) advised to prioritize monitoring carbapenemase producing Enterobacteriaceae (CPE) in food producing animals. Therefore, this study evaluated the performance of different commercially available selective agars for the detection of CPE using spiked pig caecal and turkey meat samples and the proposed EFSA cultivation protocol. Eleven laboratories from nine countries received eight samples (four caecal and four meat samples). For each matrix, three samples contained approximately 100 CFU/g CPE, and one sample lacked CPE. After overnight enrichment in buffered peptone water, broths were spread upon Brilliance™ CRE Agar (1), CHROMID® CARBA (2), CHROMagar™ mSuperCARBA™ (3), Chromatic™ CRE (4), CHROMID® OXA-48 (5) and Chromatic™ OXA-48 (6). From plates with suspected growth, one to three colonies were selected for species identification, confirmation of carbapenem resistance and detection of carbapenemase encoding genes, by methods available at participating laboratories. Of the eleven participating laboratories, seven reported species identification, susceptibility tests and genotyping on isolates from all selective agar plates. Agars 2, 4 and 5 performed best, with 100% sensitivity. For agar 3, a sensitivity of 96% was recorded, while agar 1 and 6 performed with 75% and 43% sensitivity, respectively. More background flora was noticed for turkey meat samples than pig caecal samples. Based on this limited set of samples, most commercially available agars performed adequately. The results indicate, however, that OXA-48-like and non-OXA-48-like producers perform very differently, and one should consider which CPE strains are of interest to culture when choosing agar type.
Published: 2022
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6. Multicentre evaluation of a selective isolation protocol for detection of mcr-positive E. coli and Salmonella spp. in food-producing animals and meat

Author: Agnès Perrin-Guyomard, Sophie A. Granier, Jannice Schau Slettemeås, Muna Anjum, Luke Randall, Manal AbuOun, Natalie Pauly, Alexandra Irrgang, Jens Andre Hammerl, Jette Sejer Kjeldgaard, Anette Hammerum, Alessia Franco, Magdalena Skarżyńska, Ewelina Kamińska, Dariusz Wasyl, Cindy Dierikx, Stefan Börjesson, Yvon Geurts, Marisa Haenni, Kees Veldman, Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Norwegian Veterinary Institute [Oslo], Animal and Plant Health Agency [Addlestone, UK] (APHA), German Federal Institute for Risk Assessment [Berlin] (BfR), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Statens Serum Institut [Copenhagen], Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT), National Veterinary Research Institute [Pulawy, Pologne] (NVRI), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Public Health Agency of Sweden, Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: viande, Meat, food-borne pathogen, detection, Colistin resistance, Microbial Sensitivity Tests, MESH: Food Safety, Applied Microbiology and Biotechnology, Salmonelle, Salmonella, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Drug Resistance, Bacterial, mcr, Escherichia coli, Animals, microbiologie, MESH: Salmonella, bacteria, sécurité des aliments, bactérie, Host Pathogen Interaction & Diagnostics, MESH: Escherichia coli, Colistin, Escherichia coli Proteins, screening, microbiology, Bacteriologie, E. coli, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, détection, Host Pathogen Interactie & Diagnostiek, pathogénes alimentaires, Anti-Bacterial Agents, animals, food safety, Agar, PCR, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Screening, contaminant, Eschérichia coli, hormones, hormone substitutes, and hormone antagonists, Plasmids
Abstract: This study was conducted to evaluate the performance of a screening protocol to detect and isolate mcr-positive Escherichia coli and Salmonella spp. from animal caecal content and meat samples. We used a multicentre approach involving 12 laboratories from nine European countries. All participants applied the same methodology combining a multiplex PCR performed on DNA extracted from a pre-enrichment step, followed by a selective culture step on three commercially available chromogenic agar plates. The test panel was composed of two negative samples and four samples artificially contaminated with E. coli and Salmonella spp. respectively harbouring mcr-1 or mcr-3 and mcr-4 or mcr-5 genes. PCR screening resulted in a specificity of 100% and a sensitivity of 83%. Sensitivity of each agar medium to detect mcr-positive colistin-resistant E. coli or Salmonella spp. strains was 86% for CHROMID(R)Colistin R, 75% for CHROMagarTM COL-APSE and 70% for COLISTIGRAM. This combined method was effective to detect and isolate most of the E. coli or Salmonella spp. strains harbouring different mcr genes from food-producing animals and food products and might thus be used as a harmonized protocol for the screening of mcr genes in food-producing animals and food products in Europe.
Published: 2022
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7. Estimation of Bait Uptake by Badgers, Using Non-invasive Methods, in the Perspective of Oral Vaccination Against Bovine Tuberculosis in a French Infected Area

Author: Ariane, Payne, Sandrine, Ruette, Mickaël, Jacquier, Céline, Richomme, Sandrine, Lesellier, Sonya, Middleton, Jeanne, Duhayer, Sophie, Rossi, Office français de la biodiversité (OFB), Groupement de défense sanitaire de Saône et Loire (GDS 71), Fédération nationale des Groupements de Défense Sanitaire (GDS France)-Groupement de Défense Sanitaire de Bourgogne - Franche-Comté (GDS BFC), Fédération nationale des Groupements de Défense Sanitaire (GDS France), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), French Ministry for Agriculture and Food (MAA) (Agreement No. 2017-397), GDS France, GDS 21, Wildlife and Hunting Agency (ONCFS now being called French Office for Biodiversity – OFB), and DEFRA - Bovine Tuberculosis Research Projects (Project SE3247)
Subjects: [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, animal diseases, food and beverages, macromolecular substances, MESH: Vaccination, MESH: Mustelidae, oral vaccination, parasitic diseases, bait deployment, MESH: Biomarkers, badger (Meles meles), biomarker, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, bovine tuberculosis, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, human activities, MESH: Tuberculosis, Bovine, hair trapping
Abstract: Although France is officially declared free of bovine tuberculosis (TB), Mycobacterium bovis infection is still observed in several regions in cattle and wildlife, including badgers (Meles meles). In this context, vaccinating badgers should be considered as a promising strategy for the reduction in M. bovis transmission between badgers and other species, and cattle in particular. An oral vaccine consisting of live Bacille Calmette–Guérin (BCG) contained in bait is currently under assessment for badgers, for which testing bait deployment in the field and assessing bait uptake by badgers are required. This study aimed to evaluate the bait uptake by badgers and determine the main factors influencing uptake in a TB-infected area in Burgundy, north-eastern France. The baits were delivered at 15 different setts located in the vicinity of 13 pastures within a TB-infected area, which has been subject to intense badger culling over the last decade. Pre-baits followed by baits containing a biomarker (Rhodamine B; no BCG vaccine) were delivered down sett entrances in the spring (8 days of pre-baiting and 4 days of baiting) and summer (2 days of pre-baiting and 2 days of baiting) of 2018. The consumption of the marked baits was assessed by detecting fluorescence, produced by Rhodamine B, in hair collected in hair traps positioned at the setts and on the margins of the targeted pastures. Collected hairs were also genotyped to differentiate individuals using 24 microsatellites markers and one sex marker. Bait uptake was estimated as the proportion of badgers consuming baits marked by the biomarker over all the sampled animals (individual level), per badger social group, and per targeted pasture. We found a bait uptake of 52.4% (43 marked individuals of 82 genetically identified) at the individual level and a mean of 48.9 and 50.6% at the social group and pasture levels, respectively. The bait uptake was positively associated with the presence of cubs (social group level) and negatively influenced by the intensity of previous trapping (social group and pasture levels). This study is the first conducted in France on bait deployment in a badger population of intermediate density after several years of intensive culling. The results are expected to provide valuable information toward a realistic deployment of oral vaccine baits to control TB in badger populations.
Published: 2022
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8. Access and benefit-sharing by the European Virus Archive in response to COVID-19

Author: Jan Felix Drexler, Thomas C. Mettenleiter, Antonio Di Caro, Amber Hartman Scholz, Christian Drosten, Carrie Batten, Sven Reiche, Anthony R. Fooks, Bruno Coutard, Boris Klempa, Hervé Bourhy, Carolina dos S. Ribeiro, Florence Komurian-Pradel, Thomas Klimkait, Jean-Louis Romette, George B. Haringhuizen, Marion Koopmans, Christine M.A. Prat, Jean-Claude Manuguerra, Stephan Günther, Maria Serena Beato, Ali Mirazimi, Scarlett Sett, Rémi N. Charrel, David Williams, Chantal Reusken, Tatjana Avšič, Sylvie van der Werf, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Netherlands Center for Infectious Disease Control, Unité des Virus Emergents (UVE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Ljubljana, The Pirbright Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Lyssavirus, épidémiologie et neuropathologie - Lyssavirus Epidemiology and Neuropathology, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Istituto Nazionale di Malattie Infettive 'Lazzaro Spallanzani' (INMI), German Center for Infection Research, Partnersite Munich (DZIF), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Animal and Plant Health Agency [Addlestone, UK] (APHA), Slovak Academy of Science [Bratislava] (SAS), Erasmus University Medical Center [Rotterdam] (Erasmus MC), University of Basel (Unibas), Bernhard Nocht Institute for Tropical Medicine - Bernhard-Nocht-Institut für Tropenmedizin [Hamburg, Germany] (BNITM), German Center for Infection Research - Partner Site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research (DZIF), Cellule d'Intervention Biologique d'Urgence (Centre National de Référence) - Laboratory for Urgent Response to Biological Threats (National Reference Center) (CIBU), Université Paris Cité (UPCité)-Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP), Environnement et Risques infectieux - Environment and Infectious Risks (ERI), Public Health Agency of Sweden, Friedrich-Loeffler-Institut (FLI), Fondation Mérieux, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Aix Marseille Université (AMU), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Australian Centre for Disease Preparedness, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), This publication was supported by the European Virus Archive-GLOBAL project that has received funding from the EU Horizon 2020 research and innovation programme (grantagreement number 871029), The manuscript was written by the European Virus Archive access and benefit-sharing compliance team but would not have been possible without the front-line scientists that built up the European Virus Archive infrastructure and have worked tirelessly over the past year to support the global pandemic response. We welcome the European Virus Archive signatory authors who endorse this publication and its call for a multilateral pathogen genetic resources mechanism tied to a distributed biobanking infrastructure., European Virus Archive principal investigators Slovenia T Avšič (University of Ljubljana, Ljubljana). UK C Batten (The Pirbright Institute, Pirbright), A R Fooks (The Animal and Plant Health Agency, Addlestone). Italy M S Beato (Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro), A Di Caro (Istituto Nazionale Malattie Infettive Lazzaro Spallanzani, Rome). France H Bourhy, J-C Manuguerra, S van der Werf (Institute Pasteur, Paris), R Charrel, J-L Romette, B Coutard (Aix Marseille University, Marseille), F Komurian-Pradel (Fondation Mérieux, Lyon). Germany J F Drexler, C Drosten (Charité–Universitätsmedizin Berlin, Berlin), S Günther (Bernhard Nocht Institute for Tropical Medicine, Hamburg), T C Mettenleiter, S Reiche (Friedrich Loeffler Institute, Greifswald). Slovakia B Klempa (Biomedical Research Center of the Slovak Academy of Sciences, Bratislava). Switzerland T Klimkait (University of Basel, Basel). Sweden A Mirazimi (The Public Health Agency of Sweden, Solna). Netherlands C Reusken (Dutch National Institute for Public Health and the Environment, Bilthoven), M Koopmans (Erasmus Medical Center, Rotterdam). Australia D Williams (Australian Centre for Disease Preparedness, East Geelong, VIC)., and European Project: 871029,H2020,H2020-INFRAIA-2019-1,EVA-GLOBAL(2020)
Subjects: Microbiology (medical), 2019-20 coronavirus outbreak, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], Internet privacy, Microbiology, Corrections, SDG 3 - Good Health and Well-being, Genetic resources, Virology, Pandemic, Humans, Pandemics, Biological Specimen Banks, Personal View, Benefit sharing, business.industry, SARS-CoV-2, DNA Viruses, COVID-19, Biobank, Infectious Diseases, Viruses, Viruses, Unclassified, Business
Abstract: Erratum in Correction to Lancet Microbe 2021; published online Nov 16. https://doi.org/10.1016/S2666-5247(21)00211-1. [No authors listed] Lancet Microbe. 2022 Jan;3(1):e8. doi: 10.1016/S2666-5247(21)00325-6. Epub 2021 Nov 26. PMID: 34870252 Free PMC article.; International audience; Biobanking infrastructures, which are crucial for responding early to new viral outbreaks, share pathogen genetic resources in an affordable, safe, and impartial manner and can provide expertise to address access and benefit-sharing issues. The European Virus Archive has had a crucial role in the global response to the COVID-19 pandemic by distributing EU-subsidised (free of charge) viral resources to users worldwide, providing non-monetary benefit sharing, implementing access and benefit-sharing compliance, and raising access and benefit-sharing awareness among members and users. All currently available SARS-CoV-2 material in the European Virus Archive catalogue, including variants of concern, are not access and benefit-sharing cases per se, but multilateral benefit-sharing has nevertheless occurred. We propose and discuss how a multilateral system enabling access and benefit-sharing from pathogen genetic resources, based on the European Virus Archive operational model, could help bridge the discrepancies between the current bilateral legal framework for pathogen genetic resources and actual pandemic response practices.
Published: 2021
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9. A new model for sensitive detection of zoonotic prions by PrP transgenic Drosophila

Author: Raymond Bujdoso, John Spiropoulos, Olivier Andreoletti, Alana M. Thackray, Thackray, Alana [0000-0002-2752-1127], Bujdoso, Raymond [0000-0002-5068-3247], Apollo - University of Cambridge Repository, University of Cambridge [UK] (CAM), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), 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-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal and Plant Health Agency [Addlestone, UK] (APHA), and This work was partly funded by the NC3Rs Skills and Knowledge Transfer Grant (Grant NC/R00093X/1) held by R. B. and A. M. T.
Subjects: BSE, bovine spongiform encephalopathy, [SDV]Life Sciences [q-bio], animal diseases, protein misfolding PrPSc, 01 natural sciences, Biochemistry, Animals, Genetically Modified, PrP(Sc), neurodegenerative disease, Bioassay, Drosophila Proteins, protein misfolding, 0303 health sciences, biology, H-type, heavy type, Encephalopathy, Bovine Spongiform, vCJD, variant CJD, Titer, bioassay, Protein Misfolding Cyclic Amplification, Protein folding, Drosophila, Biological Assay, Research Article, Prions, Transgene, Bovine spongiform encephalopathy, infectious disease, 010402 general chemistry, Prion Proteins, prion, 03 medical and health sciences, PK, proteinase K, medicine, Animals, Molecular Biology, mouse, 030304 developmental biology, CJD, Creutzfeldt–Jakob disease, PrP, prion protein, classical and atypical BSE, Cell Biology, Models, Theoretical, Proteinase K, medicine.disease, biology.organism_classification, Virology, 0104 chemical sciences, nervous system diseases, biology.protein, Cattle, L-type, light type, PI, performance index, PMCA, protein misfolding cyclic amplification, PrPSc
Abstract: International audience; Prions are transmissible protein pathogens most reliably detected by a bioassay in a suitable host, typically mice. However, the mouse bioassay is slow and cumbersome, and relatively insensitive to low titers of prion infectivity. Prions can be detected biochemically in vitro by the protein misfolding cyclic amplification (PMCA) technique, which amplifies diseaseassociated prion protein but does not detect bona fide prion infectivity. Here, we demonstrate that Drosophila transgenic for bovine prion protein (PrP) expression can serve as a model system for the detection of bovine prions significantly more efficiently than either the mouse prion bioassay or PMCA. Strikingly, bovine PrP transgenic Drosophila could detect bovine prion infectivity in the region of a 10-12 dilution of classical bovine spongiform encephalopathy (BSE) inoculum, which is 106-fold more sensitive than that achieved by the bovine PrP mouse bioassay. A similar level of sensitivity was observed in the detection of H-type and L-type atypical BSE and sheep-passaged BSE by bovine PrP transgenic Drosophila. Bioassays of bovine prions in Drosophila were performed within 7 weeks, whereas the mouse prion bioassay required at least a year to assess the same inoculum. In addition, bovine PrP transgenic Drosophila could detect classical BSE at a level 105-fold lower than that achieved by PMCA. These data show that PrP transgenic Drosophila represent a new tractable prion bioassay for the efficient and sensitive detection of mammalian prions, including those of known zoonotic potential.
Published: 2021
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10. Editorial: Pathogenomics of the Genus Brucella and Beyond

Author: Adrian M. Whatmore, Michel S. Zygmunt, Holger C. Scholz, Axel Cloeckaert, Nieves Vizcaíno, Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Biological Threats and Special Pathogens [Berlin] (ZBS), Robert Koch Institute [Berlin] (RKI), Departamento de Microbiología y Genética, Universidad de Salamanca, Animal and Plant Health Agency [Addlestone, UK] (APHA), and Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Microbiology (medical), cell envelope, Brucella, Disease, Abortion, Ochrobactrum, Original research, Microbiology, diversity, 03 medical and health sciences, Pathogenomics, evolution, medicine, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Human brucellosis, 2. Zero hunger, Genetics, 0303 health sciences, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, 030306 microbiology, Brucellosis, Genus Brucella, medicine.disease, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, QR1-502, 3. Good health, Brucellaceae, virulence, genetics/genomics
Abstract: Brucellosis, caused by members of the genus Brucella, is an economically important disease in production animals causing abortion and infertility. Human brucellosis is associated with animal reservoirs and transmitted via the food chain or direct contact with diseased animals. This collection of 30 review, opinion and original research articles add to understanding of this group in fundamental areas from emerging genomic approaches and their application, through to knowledge of diverse aspects of lifestyle and pathogenicity.
Published: 2021
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11. The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe

Author: Maria Borowiak, Eva Litrup, Liljana Petrovska, Emeline Cherchame, Arnaud Felten, Sangeeta Banerji, Yue Tang, Pauline Barbet, Michèle Gourmelon, Federique Pasquali, Sabrina Cadel-Six, Sandra Simon, Michel-Yves Mistou, Pierre-Emmanuel Douarre, Nana Mensah, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), Statens Serum Institut [Copenhagen], Robert Koch Institute [Wernigerode], University of Bologna/Università di Bologna, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), IFREMER, Centre de Brest, Plouzane, German Federal Institute for Risk Assessment [Berlin] (BfR), Centre International de Rencontres Mathématiques (CIRM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), European Project: 64E3459(1964), Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Santé, Génétique et Microbiologie des Mollusques (SGMM), Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Project: 643476,H2020,H2020-PHC-2014-single-stage,COMPARE(2014), Cadel-Six, S, Cherchame, E, Douarre, PE, Tang, Y, Felten, A, Barbet, P, Litrup, E, Banerji, S, Simon, S, Pasquali, F, Gourmelon, M, Mensah, N, Borowiak, M, Mistou, MY, and Petrovska, L
Subjects: Microbiology (medical), Salmonella, [SDV]Life Sciences [q-bio], Bayesian analysis, plasmidome, epidemic monophasic Typhimurium, core and accessory genome phylogenetic analyse, Biology, medicine.disease_cause, Microbiology, 03 medical and health sciences, Antibiotic resistance, Plasmid, microevolution European study, Enterotoxigenic Escherichia coli, Genomic island, medicine, resistome, Bayesian analysi, 030304 developmental biology, Original Research, Genetics, 0303 health sciences, 030306 microbiology, biology.organism_classification, QR1-502, Multiple drug resistance, core and accessory genome phylogenetic analyses, Salmonella enterica, Plasmidome, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3′ end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.
Published: 2021
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12. Classical scrapie in small ruminants is caused by at least four different prion strains

Author: Natalia Fernández-Borges, María Zamora-Ceballos, Lorenzo González, Juan Carlos Espinosa, Juan María Torres, Leonor Orge, Patricia Aguilar-Calvo, J.L. Pitarch, Olivier Andreoletti, Romolo Nonno, Alba Marín-Moreno, Centro de Investigacion en Sanidad Animal (INIA-CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), University of California [San Diego] (UC San Diego), University of California (UC), Animal and Plant Health Agency [Addlestone, UK] (APHA), Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Istituto Superiore di Sanità (ISS), This work was funded by European Union Projects [FOOD‑CT‑2006‑36353 GoatBSE] to JMT and OA, and 219235 ERA‑NET EMIDA [GOAT‑TSE‑FREE] to JCE, OA and RN, Spanish Ministerio de Economía Industria y Competitividad [AGL2009‑11553‑C02‑02] to JMT, AEI/FEDER UE [AGL2016‑78054‑R] to JMT and JCE, and fellowship BES‑2010‑ 040922 to PAC, and fellowship Instituto Nacional de Investigación y Tecnología Agraria y Agroalimentaria [INIA‑FPI‑SGIT‑2015‑02] to AMM., European Project: 39519,GOATBSE, European Project: 219235,EC:FP7:KBBE,FP7-ERANET-2007-RTD,EMIDA(2008), University of California, 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-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Istituto Superiore di Sanita [Rome], European Commission, Ministerio de Economía y Competitividad (España), CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Marín-Moreno, Alba [0000-0002-4023-6398], Aguilar-Calvo, Patricia [0000-0001-5859-0240], Espinosa, Juan Carlos [0000-0002-6719-9902], Zamora-Ceballos, María [0000-0002-4694-2365], Pitarch, José Luis [0000-0003-3016-9125], González, Lorenzo [0000-0003-1513-1399], Orge, Leonor [0000-0002-2673-2758], Andréoletti, Olivier [0000-0002-7369-6016], Nonno, Romolo [0000-0001-7556-1564], Torres, Juan María [0000-0003-0443-9232], Marín-Moreno, Alba, Aguilar-Calvo, Patricia, Espinosa, Juan Carlos, Zamora-Ceballos, María, Pitarch, José Luis, González, Lorenzo, Orge, Leonor, Andréoletti, Olivier, Nonno, Romolo, and Torres, Juan María
Subjects: Adverse event, Prions, 040301 veterinary sciences, Bovine spongiform encephalopathy, Veterinary medicine, animal diseases, Sheep Diseases, Scrapie, Biology, Single strain, 0403 veterinary science, 03 medical and health sciences, SF600-1100, medicine, Animals, Small ruminant, Sheep, Domestic, 030304 developmental biology, 0303 health sciences, Sheep disease, Goat Diseases, Transmissible spongiform encephalopathy, Sheep, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, Animal, Goats, 04 agricultural and veterinary sciences, Classical scrapie, medicine.disease, Domestic sheep, Virology, nervous system diseases, Europe, Species barrier, Goat, Prion, Goat disease, Research Article
Abstract: 15 pág. Centro de Investigación en Sanidad Animal (CISA), The diversity of goat scrapie strains in Europe has recently been studied using bioassays in a wide collection of rodent models, resulting in the classification of classical scrapie into four different categories. However, the sole use of the first passage does not lead to isolate adaptation and identification of the strains involved and might therefore lead to misclassification of some scrapie isolates. Therefore, this work reports the complete transmission study of a wide collection of goat transmissible spongiform encephalopathy (TSE) isolates by intracranial inoculation in two transgenic mouse lines overexpressing either small ruminant (TgGoat-ARQ) or bovine (TgBov) PrPC. To compare scrapie strains in sheep and goats, sheep scrapie isolates from different European countries were also included in the study. Once the species barrier phenomenon was overcome, an accurate classification of the isolates was attained. Thus, the use of just two rodent models allowed us to fully differentiate at least four different classical scrapie strains in small ruminants and to identify isolates containing mixtures of strains. This work reinforces the idea that classical scrapie in small ruminants is a prion disease caused by multiple different prion strains and not by a single strain, as is the case for epidemic classical bovine spongiform encephalopathy (BSE-C). In addition, the clear dissimilarity between the different scrapie strains and BSE-C does not support the idea that classical scrapie is the origin of epidemic BSE-C., This work was funded by European Union Projects [FOOD-CT-2006-36353 [GoatBSE] to JMT and OA and 219235 ERA-NET EMIDA [GOAT-TSE-FREE] to JCE, OA and RN], Spanish Ministerio de Economía Industria y Competitividad [AGL2009-11553-C02-02 to JMT, AGL2016-78054-R (AEI/FEDER, UE) to JMT and JCE and fellowship BES-2010- 040922 to PAC], and Instituto Nacional de Investigación y Tecnología Agraria y Agroalimentaria [fellowship INIA-FPI-SGIT-2015-02 to AMM]. The funders had no role in the study design, data collection and interpretation, or the decision to submit the work for publication
Published: 2021
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13. Interferon-γ Response of Mycobacterium avium subsp. paratuberculosis Infected Goats to Recombinant and Synthetic Mycobacterial Antigens

Author: Köhler, Heike, Liebler-Tenorio, Elisabeth, Hughes, Valerie, Stevenson, Karen, Bakker, Douwe, Willemsen, Peter, Bay, Sylvie, Ganneau, Christelle, Biet, Franck, Vordermeier, H.M., Friedrich-Loeffler-Institut (FLI), Moredun Research Institute [Penicuik, UK] (MRI), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Chimie des Biomolécules - Chemistry of Biomolecules, Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Infectiologie et Santé Publique (UMR ISP), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal and Plant Health Agency [Addlestone, UK] (APHA), ANR-11-EMID-0005,MYCOBACTDIAGNOSIS(2011), European Project: 23106,Paratbtools, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Mycobacterium avium subsp. paratuberculosis (MAP), [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV]Life Sciences [q-bio], goat, Bacteriology, Host Pathogen Interaction & Diagnostics, recombinant proteins, Mycobacterium avium subsp. hominissuis (MAH), experimental infection, Bacteriologie, Host Pathogen Interactie & Diagnostiek, IFN-gamma response, Veterinary Science, synthetic lipopetides, Original Research
Abstract: International audience; Despite its potential for early diagnosis of Mycobacterium avium subsp. paratuberculosis (MAP) infection, the IFN-γ release assay is not used routinely, because of low specificity of the established crude antigen preparation Johnin (PPDj). Limited data are available assessing the potential of MAP-derived protein and lipopeptide antigens to replace PPDj in assays for goats, while cattle and sheep have been studied more extensively. Furthermore, MAP infection is claimed to interfere with the diagnosis of bovine tuberculosis when other crude antigen preparations (PPDb, PPDa) are applied. In this study, the diagnostic potential of MAP-derived recombinant protein antigens, synthetic MAP lipopentapeptides and of Mycobacterium bovis-specific peptide cocktails was assessed compared to crude mycobacterial antigen preparations in experimentally infected goats. Goats were inoculated with MAP, or Mycobacterium avium subsp. hominissuis (MAH) as surrogate for environmental mycobacteria, non-exposed animals served as controls. Mycobacterium avium Complex-specific antibody and PPDj-induced IFN-γ responses were monitored in vivo. Infection status was assessed by pathomorphological findings and bacteriological tissue culture at necropsy 1 year after inoculation. The IFN-γ response to 13 recombinant protein antigens of MAP, two synthetic MAP lipopentapeptides and three recombinant peptide cocktails of Mycobacterium bovis was investigated at three defined time points after infection. At necropsy, MAP or MAH infection was confirmed in all inoculated goats, no signs of infection were found in the controls. Antibody formation was first detected 3-6 weeks post infection (wpi) in MAH-inoculated and 11-14 wpi in the MAP-inoculated goats. Maximum PPDj-induced IFN-γ levels in MAH and MAP exposed animals were recorded 3-6 and 23-26 wpi, respectively. Positive responses continued with large individual variation. Antigens Map 0210c, Map 1693c, Map 2020, Map 3651cT(it), and Map 3651c stimulated increased whole blood IFN-γ levels in several MAP-inoculated goats compared to MAH inoculated and control animals. These IFN-γ levels correlated with the intensity of the PPDj-induced responses. The two synthetic lipopentapeptides and the other MAP-derived protein antigens had no discriminatory potential. Stimulation with Mycobacterium bovis peptide cocktails ESAT6-CFP10, Rv3020c, and Rv3615c did not elicit IFN-γ production. Further work is required to investigate if test sensitivity will increase when mixtures of the MAP-derived protein antigens are applied.
Published: 2021
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14. Comparison of Phenotypical Antimicrobial Resistance between Clinical and Non-Clinical E. coli Isolates from Broilers, Turkeys and Calves in Four European Countries

Author: Agnès Perrin-Guyomard, Octavio Mesa-Varona, Martina Velasova, Bernd-Alois Tenhagen, Mirjam Grobbel, Muna F. Anjum, Heike Kaspar, Sophie A. Granier, Madelaine Norström, Eric Jouy, R. Mader, Jean-Yves Madec, Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Unité Antibiorésistance et Virulence Bactériennes, Laboratoire de Lyon [ANSES], 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), Animal and Plant Health Agency [Addlestone, UK] (APHA), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Norwegian Veterinary Institute [Oslo], Federal Office of Consumer Protection and Food Safety, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], This work was carried out within the framework of the ARDIG project, the European Joint Programme (EJP) on AMU and AMR in humans, food and animals. ARDIG project has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No 773830., European Project: 773830, Unité Antibiorésistance et Virulence Bactériennes (AVB), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: 0301 basic medicine, Veterinary medicine, dinde, antibiotic resistance, Nalidixic acid, résistance aux antibiotiques, veterinary drug, E. coli, Ampicillin, AMR, animal, bacteria, lcsh:QH301-705.5, agriculture, bactérie, veau, Antimicrobial, 3. Good health, Europe, phénotype, Gentamicin, Livestock, medicine.drug, Microbiology (medical), médicament vétérinaire, Tetracycline, clinical isolates, 030106 microbiology, poulet, Biology, broiler, Article, 03 medical and health sciences, Antibiotic resistance, résistance aux antimicrobiens, Virology, phentoype, medicine, Escherichia coli, turkey, antimicrobial resistance, microbiologie, calf, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, business.industry, microbiology, Broiler, élevage, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, livestock, 030104 developmental biology, lcsh:Biology (General), non-clinical isolates, business
Abstract: International audience; Livestock data on antimicrobial resistance (AMR) are commonly collected from bacterial populations of clinical and non-clinical isolates. In contrast to data on non-clinical isolates from livestock, data on clinical isolates are not harmonized in Europe. The Normalized Resistance Interpretation (NRI) method was applied to overcome the lack of harmonization of laboratory methods and interpretation rules between monitoring systems. Statistical analyses were performed to identify associations between the isolate type (clinical vs. non-clinical) and resistance to four antimicrobials (ampicillin, tetracycline, gentamicin, and nalidixic acid) per animal category in Germany and France. Additional statistical analyses comparing clinical and non-clinical isolates were performed with the available data on the same antimicrobial panel and animal categories from the UK and Norway. Higher resistance prevalence was found in clinical isolates compared to non-clinical isolates from calves to all antimicrobials included in Germany and France. It was also found for gentamicin in broilers from France. In contrast, in broilers and turkeys from Germany and France and in broilers from the UK, a higher resistance level to ampicillin and tetracycline in non-clinical isolates was encountered. This was also found in resistance to gentamicin in isolates from turkeys in Germany. Resistance differed within countries and across years, which was partially in line with differences in antimicrobial use patterns. Differences in AMR between clinical and non-clinical isolates of Escherichia coli are associated with animal category (broiler, calf, and turkey) and specific antimicrobials. The NRI method allowed comparing results of non-harmonized AMR systems and might be useful until international harmonization is achieved.
Published: 2021
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15. Dialogue moléculaire entre les virus de l’encéphalite à tiques et louping ill et leur arthropode vecteur, la tique Ixodes ricinus

Author: Lemasson, Manon, Caignard, Grégory, Unterfinger, Yves, Attoui, Houssam, Bell-Sakyi, Lesley, Hirchaud, Edouard, Moutailler, Sara, Johnson, Nick, VITOUR, Damien, Richardson, Jennifer, Lacour, Sandrine, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire d'Alfort (ENVA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), Virologie UMR1161 (VIRO), and École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

16. Comparative mapping of protein-protein interactions between tick-borne flaviviruses and their mammalian hosts reveals potential virus- and mammalian host-specific interactions

Author: Sourisseau, Marion, Lemasson, Manon, Unterfinger, Yves, Caignard, Grégory, Piumi, François, Moutailler, Sara, Johnson, Nick, Coulpier, Muriel, VITOUR, Damien, Lacour, Sandrine, Richardson, Jennifer, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire d'Alfort (ENVA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), Virologie UMR1161 (VIRO), and École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

17. Exploration of binary protein-protein interactions between tick-borne flaviviruses and Ixodes ricinus

Author: Manon LEMASSON, Grégory CAIGNARD, Yves UNTERFINGER, Houssam ATTOUI, Lesley BELL-SAKYI, Edouard HIRCHAUD, Sara MOUTAILLER, Nicholas JOHNSON, Damien VITOUR, Jennifer RICHARDSON, Sandrine A. LACOUR, Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Infection and Global Health [University of Liverpool, UK], University of Liverpool, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie moléculaire et immunologie parasitaires et fongiques (BIPAR), École nationale vétérinaire d'Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal and Plant Health Agency [Addlestone, UK] (APHA), French Agency for Food, Environmental and Occupational Health & Safety (ANSES, Grant No. PHD2017‑2020)., National Research Institute for Agriculture, Food and Environment (INRAE)., French Agency for Food, Environmental and Occupational Health & Safety (ANSES), National Veterinary School of Maisons‑Alfort (ENVA), United Kingdom Biotechnology and Biological Sciences Research Council Grant Number BB/P024270/1, Department for Environment, Food and Rural Affairs (Defra), Scottish and Welsh Governments through project SV3045, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and École nationale vétérinaire - Alfort (ENVA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Dozulé
Subjects: Host Microbial Interactions, Ixodes, viruses, Research, lcsh:Infectious and parasitic diseases, Arthropod Proteins, Encephalitis Viruses, Tick-Borne, Open Reading Frames, Viral Proteins, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, parasitic diseases, Animals, lcsh:RC109-216, Female, Protein Interaction Domains and Motifs, Gene Library
Abstract: BackgroundLouping ill virus (LIV) and tick-borne encephalitis virus (TBEV) are tick-borne flaviviruses that are both transmitted by the major European tick, Ixodes ricinus. Despite the importance of I. ricinus as an arthropod vector, its capacity to acquire and subsequently transmit viruses, known as vector competence, is poorly understood. At the molecular scale, vector competence is governed in part by binary interactions established between viral and cellular proteins within infected tick cells.MethodsTo investigate virus-vector protein-protein interactions (PPIs), the entire set of open reading frames for LIV and TBEV was screened against an I. ricinus cDNA library established from three embryonic tick cell lines using yeast two-hybrid methodology (Y2H). PPIs revealed for each viral bait were retested in yeast by applying a gap repair (GR) strategy and notably against the cognate protein of both viruses, to determine whether the PPIs were specific for a single virus or common to both. The interacting tick proteins were identified by automatic BLASTX and in silico analyses were performed to expose the biological processes targeted by LIV and TBEV.ResultsFor each virus, we identified 24 different PPIs involving six viral proteins and 22 unique tick proteins, with all PPIs being common to both viruses. According to our data, several viral proteins (pM, M, NS2A, NS4A, 2K and NS5) target multiple tick protein modules implicated in critical biological pathways. Of note, the NS5 and pM viral proteins establish PPI with several tumor necrosis factor (TNF) receptor-associated factor (TRAF) proteins, which are essential adaptor proteins at the nexus of multiple signal transduction pathways.ConclusionWe provide the first description of the TBEV/LIV-I. ricinus PPI network, and indeed of any PPI network involving a tick-borne virus and its tick vector. While further investigation will be needed to elucidate the role of each tick protein in the replication cycle of tick-borne flaviviruses, our study provides a foundation for understanding the vector competence of I. ricinus at the molecular level. Indeed, certain PPIs may represent molecular determinants of vector competence of I. ricinus for TBEV and LIV, and potentially for other tick-borne flaviviruses.
Published: 2020
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18. Characterization of goat prions demonstrates geographical variation of scrapie strains in Europe and reveals the composite nature of prion strains

Author: Lucien van Keulen, Patricia Aguilar-Calvo, John Spiropoulos, Claudia D'Agostino, Christine Fast, Pier Luigi Acutis, Penelope Papasavva-Stylianou, Alex Bossers, Romolo Nonno, Frédéric Lantier, Olivier Andreoletti, Gabriele Vaccari, Isabelle Lantier, Jorge G Jacobs, Juan María Torres, Jan P. M. Langeveld, Martin H. Groschup, Umberto Agrimi, Juan Carlos Espinosa, Cristina Acín, Barbara Chiappini, Theodoros Sklaviadis, Michele Angelo Di Bari, Laura Pirisinu, Alba Marín-Moreno, Istituto Superiore di Sanità (ISS), Centro de Investigacion en Sanidad Animal (INIA-CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Institute of Novel and Emerging Infectious Diseases (INNT), Friedrich-Loeffler-Institut (FLI), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Animal and Plant Health Agency [Addlestone, UK] (APHA), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aristotle University of Thessaloniki, Veterinary Services of Cyprus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, This work was funded by the European Union (FOOD-CT-2006-36353 to AB, JPML, OA, JMT, CA, MHG, PLA, UA, TS, and ERA-NET EMIDA GOAT-TSE-FREE to JPML, LVK, PLA, OA, JCE, CA, CF), the Dutch Ministry of Agriculture (project WOT-01-002-001.01 to JPML), the Spanish Ministerio de ciencia innovacion y universidades (AGL201678054-R [AEI/FEDER, UE] and AGL2012-37988-C04-04 to JMT), the Italian Ministry of Health (RF-20091474624 to RN). AMM was supported by a fellowship from the INIA (FPI-SGIT-2015-02). PAC was supported by a fellowship from the Spanish Ministerio de Economia y Competitividad (BES-2010-040922)., European Project: 36353,GOATBSE, Istituto Superiore di Sanita [Rome], Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Prion diseases, Prions, [SDV]Life Sciences [q-bio], animal diseases, Bovine spongiform encephalopathy, lcsh:Medicine, Prion strain, Scrapie, Biology, Prion Proteins, Article, Mice, 03 medical and health sciences, 0302 clinical medicine, Animal model, Biological property, medicine, Animals, Life Science, Neurodegeneration, lcsh:Science, Host Pathogen Interaction & Diagnostics, Genetics, Goat Diseases, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Multidisciplinary, Goats, Strain (biology), lcsh:R, Bacteriologie, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, Limiting, medicine.disease, Host Pathogen Interactie & Diagnostiek, nervous system diseases, Encephalopathy, Bovine Spongiform, Europe, Experimental models of disease, 030104 developmental biology, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Infectious diseases, Cattle, lcsh:Q, 030217 neurology & neurosurgery
Abstract: Bovine Spongiform Encephalopathy (BSE) is the only animal prion which has been recognized as a zoonotic agent so far. The identification of BSE in two goats raised the need to reliably identify BSE in small ruminants. However, our understanding of scrapie strain diversity in small ruminants remains ill-defined, thus limiting the accuracy of BSE surveillance and spreading fear that BSE might lurk unrecognized in goats. We investigated prion strain diversity in a large panel of European goats by a novel experimental approach that, instead of assessing the neuropathological profile after serial transmissions in a single animal model, was based on the direct interaction of prion isolates with several recipient rodent models expressing small ruminants or heterologous prion proteins. The findings show that the biological properties of scrapie isolates display different patterns of geographical distribution in Europe and suggest that goat BSE could be reliably discriminated from a wide range of biologically and geographically diverse goat prion isolates. Finally, most field prion isolates showed composite strain features, with discrete strain components or sub-strains being present in different proportions in individual goats or tissues. This has important implications for understanding the nature and evolution of scrapie strains and their transmissibility to other species, including humans.
Published: 2020
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19. Bioreactor-Grown Bacillus of Calmette and Guérin (BCG) Vaccine Protects Badgers against Virulent Mycobacterium bovis When Administered Orally: Identifying Limitations in Baited Vaccine Delivery

Author: Gareth A. Williams, Joanna Bacon, Claire McKenna, Colin P.D. Birch, Sarah E. Beatham, Dipesh Davé, Roland Ashford, Jason Sawyer, Stephen Powell, Jordan Pascoe, Sandrine Lesellier, Deanna Dalley, Charlotte L. Hendon-Dunn, S. Palmer, John Spiropoulos, Ute Weyer, A. Núñez, Sonya Gowtage, Pedro J. Sánchez-Cordón, Mark A. Chambers, Julia Coats, Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), Animal and Plant Health Agency [York], Public Health England [Salisbury] (PHE), and University of Surrey (UNIS)
Subjects: 0301 basic medicine, Tuberculosis, Badger, animal diseases, Pharmaceutical Science, lcsh:RS1-441, Context (language use), Meles, Article, lcsh:Pharmacy and materia medica, 03 medical and health sciences, 0302 clinical medicine, Immune system, biology.animal, Oral vaccine, Medicine, BCG, 030212 general & internal medicine, Mycobacterium bovis, Bait, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, business.industry, bacterial infections and mycoses, medicine.disease, biology.organism_classification, Virology, 3. Good health, Vaccination, 030104 developmental biology, Fermentation, [SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology, business, BCG vaccine, Badgers
Abstract: Bovine tuberculosis (TB) in Great Britain adversely affects animal health and welfare and is a cause of considerable economic loss. The situation is exacerbated by European badgers (Meles meles) acting as a wildlife source of recurrent Mycobacterium bovis infection to cattle. Vaccination of badgers against TB is a possible means to reduce and control bovine TB. The delivery of vaccine in oral bait holds the best prospect for vaccinating badgers over a wide geographical area. There are practical limitations over the volume and concentration of Bacillus of Calmette and Gu&eacute, rin (BCG) that can be prepared for inclusion in bait. The production of BCG in a bioreactor may overcome these issues. We evaluated the efficacy of oral, bioreactor-grown BCG against experimental TB in badgers. We demonstrated repeatable protection through the direct administration of at least 2.0 &times, 108 colony forming units of BCG to the oral cavity, whereas vaccination via voluntary consumption of bait containing the same preparation of BCG did not result in demonstrable protection at the group-level, although a minority of badgers consuming bait showed immunological responses and protection after challenge equivalent to badgers receiving oral vaccine by direct administration. The need to deliver oral BCG in the context of a palatable and environmentally robust bait appears to introduce such variation in BCG delivery to sites of immune induction in the badger as to render experimental studies variable and inconsistent.
Published: 2020
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20. Inter-laboratory comparison of 2 ELISA kits used for foot-and-mouth disease virus nonstructural protein serology

Author: Santina Grazioli, Anna B. Ludi, Lynne Hendry, Donald P. King, Antonello Di Nardo, Anthony Relmy, Emiliana Brocchi, Tim Pollard, Clare Browning, P.L. Eblé, Aurore Romey, Lissie Henry, Institute for Animal Health, the Pirbright Institute, Animal and Plant Health Agency [Addlestone, UK] (APHA), Virologie UMR1161 (VIRO), École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna 'Bruno Ubertini' (IZSLER), and DEFRA (Department for Environment, Food Rural Affairs) SE1129SV3022UK Research & Innovation (UKRI)Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/I/00007035BBS/E/I/00007036
Subjects: 040301 veterinary sciences, Cattle Diseases, serology, Enzyme-Linked Immunosorbent Assay, Viral Nonstructural Proteins, Antibodies, Viral, Screen test, Sensitivity and Specificity, Virus, Serology, 0403 veterinary science, 03 medical and health sciences, inter-laboratory study, Animals, Medicine, 030304 developmental biology, 0303 health sciences, Disease surveillance, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, General Veterinary, biology, business.industry, foot-and-mouth disease virus, Reproducibility of Results, Outbreak, 04 agricultural and veterinary sciences, biology.organism_classification, Virology, 3. Good health, Virology & Molecular Biology, Virologie & Moleculaire Biologie, Vaccination, Foot-and-Mouth Disease, biology.protein, Cattle, ELISA, Antibody, Foot-and-mouth disease virus, Brief Communications, business
Abstract: International audience; Serologic assays used to detect antibodies to nonstructural proteins (NSPs) of foot-and-mouth disease virus (FMDV) are used for disease surveillance in endemic countries, and are essential to providing evidence for freedom of the disease with or without vaccination and to recover the free status of a country after an outbreak. In a 5-site inter-laboratory study, we compared the performance of 2 commercial NSP ELISA kits (ID Screen FMD NSP ELISA single day [short] and overnight protocols, ID.Vet; PrioCHECK FMDV NS antibody ELISA, Thermo Fisher Scientific). The overall concordance between the PrioCHECK and ID Screen test was 93.8% (95% CI: 92.0–95.2%) and 94.8% (95% CI: 93.1–96.1%) for the overnight and short ID Screen incubation protocols, respectively. Our results indicate that the assays (including the 2 different formats of the ID Screen test) can be used interchangeably in post-outbreak serosurveillance.
Published: 2020
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21. Protective Effect of Oral BCG and Inactivated Mycobacterium bovis Vaccines in European Badgers (Meles meles) Experimentally Infected With M. bovis

Author: Ana Balseiro, José Miguel Prieto, Vega Álvarez, Sandrine Lesellier, Dipesh Davé, Francisco J. Salguero, Iker A. Sevilla, José Antonio Infantes-Lorenzo, Joseba M. Garrido, Hans Adriaensen, Ramón A. Juste, Marta Barral, CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Principado de Asturias, European Commission, Eusko Jaurlaritza, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Balseiro Morales, Ana María, Balseiro Morales, Ana María [0000-0002-5121-7264], Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Centro de Biotecnologia Animal-SERIDA, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), Public Health England, Instituto Vasco de Investigación y Desarrollo Agrario [Derio] (NEIKER), Centro de Vigilancia Sanitaria, Partenaires INRAE, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: vaccin, Tuberculosis, Badger, Efficacy, 040301 veterinary sciences, animal diseases, meles meles, Meles, tuberculosis, badger, BCG vaccine, Mycobacterium bovis heat-inactivated (HIMB) vaccine, efficacy, 0403 veterinary science, 03 medical and health sciences, Wild boar, biology.animal, medicine, 030304 developmental biology, 0303 health sciences, Mycobacterium bovis, lcsh:Veterinary medicine, General Veterinary, biology, Microbiology and Parasitology, Tuberculosis, badger, BCG vccine, Mycobacterium bovis heat-inactivatede (HIMB) vaccine, efficacy, 04 agricultural and veterinary sciences, biology.organism_classification, medicine.disease, Virology, Microbiologie et Parasitologie, 3. Good health, Vaccination, mycobacterium bovis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Inactivated vaccine, tuberculose bovine, lcsh:SF600-1100, bcg, test d'efficacite, efficacité du traitement
Abstract: 13 páginas, 4 figuras, 1 tabla., This study was funded by a grant from Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), reference number RTA2014-00002-C02 (FEDER co-funded), the Principado de Asturias, PCTI 2018–2020 (GRUPIN: IDI2018-000237 and FEDER), and Departamento de Desarrollo Económico e Infraestructuras del Gobierno Vasco. This study was also funded by Ministerio de Ciencia, Innovación y Universidades (MCIU), the Agencia Estatal de Investigación (AEI) reference project RTI2018-096010-B-C21 and Fondo Europeo de Desarrollo Regional (FEDER). DEFRA also funded APHA staff for their participation in the study and for the purchase of BCG from Statens Serum Institute (Copenhagen, Denmark).
Published: 2020
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22. Comparative mapping of protein-protein interactions between tick-borne flaviviruses and their mammalian hosts reveals virus-specific interactions

Author: Sourisseau, Marion, Lemasson, Manon, Unterfinger, Yves, Caignard, Grégory, Piumi, François, Johnson, Nick, VITOUR, Damien, Estrada-Pena, Agustin, Jouvenet, Nolwenn, Coulpier, Muriel, Lacour, Sandrine, Richardson, Jennifer, Richardson, Jennifer, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale vétérinaire d'Alfort (ENVA), Animal and Plant Health Agency [Addlestone, UK] (APHA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre National de la Recherche Scientifique (CNRS), Virologie UMR1161 (VIRO), and École nationale vétérinaire d'Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BBM.MN] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

23. Four types of scrapie in goats differentiated from each other and bovine spongiform encephalopathy by biochemical methods

Author: Cristina Acín, John Spiropoulos, Laura Pirisinu, J. G. Jacobs, Christine Fast, Jan P. M. Langeveld, Romolo Nonno, Frédéric Lantier, Olivier Andreoletti, Loukia V. Ekateriniadou, Umberto Agrimi, Elena Esposito, Stéphanie Simon, Maria Mazza, Alex Bossers, Martin H. Groschup, Isabelle Lantier, Theodoros Sklaviadis, Wilfred Goldmann, Pier Luigi Acutis, Penelope Papasavva-Stylianou, Lucien van Keulen, Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Istituto Superiore di Sanita [Rome], Istituto Zooprofilattico Sperimentale del Piemonte, IZSPLVA, Italian Reference Centre for Animal TSE, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Commissariat à l’Energie Atomique, Gif-sur-Yvette, France, 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, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Institute of Novel and Emerging Infectious Diseases (INNT), Friedrich-Loeffler-Institut (FLI), University of Edinburgh, Royal Dick Sch Vet Studies, Roslin BioCtr, Roslin EH25 9PS, Animal and Plant Health Agency [Addlestone, UK] (APHA), Aristotle University of Thessaloniki, Hellenic Agricultural Organization Demeter (HAO Demeter), Veterinary Services of Cyprus, Ministry of Agriculture Rural Development and Environment, Partenaires INRAE, This work was supported by the European Commission: NeuroPrion [EC FOOD‑CT‑2004‑506579], GoatBSE [EC FOOD‑CT‑2006‑36353], GOAT‑TSE‑FREE [ERA‑NET EMIDA] and by National fundings: Netherlands—Ministry of Agriculture, Nature and Food Quality [WOT 01‑002‑001.01], Italy—Italian Ministry of Health [RF‑2009‑1474624], Spain—Ministry of Economy and Competitiveness [AGL2012‑40071], United Kingdom—Department for Environment, Food and Rural Affairs [SE2018] [SE1961], Biotechnology and Biological Sciences Research Council [BB/J004332/1], Greece—Greek Ministry of Education, and France—Institut National de la Recherche Agronomique TRANSPRION [EFA282/13], REDPRION [EFA148/16], European Project, European Project: 26570,NEUROPRION, European Project: 39519,GOATBSE, European Project: 36353,GOATBSE, European Project: 219235,EC:FP7:KBBE,FP7-ERANET-2007-RTD,EMIDA(2008), Langeveld, Jan P M, Istituto Superiore di Sanità (ISS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: 0301 basic medicine, 040301 veterinary sciences, Bovine spongiform encephalopathy, [SDV]Life Sciences [q-bio], animal diseases, Blotting, Western, Scrapie, Enzyme-Linked Immunosorbent Assay, polymorphisme, Biology, 0403 veterinary science, prion, 03 medical and health sciences, Protease resistant, medicine, Life Science, biochimie des protéines, Animals, Typing, Prion protein, Host Pathogen Interaction & Diagnostics, Transmissible spongiform encephalopathy, lcsh:Veterinary medicine, Goat Diseases, General Veterinary, tremblante, Goats, Bacteriologie, Bacteriology, 04 agricultural and veterinary sciences, Bacteriology, Host Pathogen Interaction & Diagnostics, Classical scrapie, medicine.disease, Virology, Host Pathogen Interactie & Diagnostiek, encéphalopathie spongiforme bovine, nervous system diseases, Europe, 030104 developmental biology, Bacteriologie, Host Pathogen Interactie & Diagnostiek, lcsh:SF600-1100, Infectious agent, Research Article
Abstract: Scrapie in goats has been known since 1942, the archetype of prion diseases in which only prion protein (PrP) in misfolded state (PrPSc) acts as infectious agent with fatal consequence. Emergence of bovine spongiform encephalopathy (BSE) with its zoonotic behaviour and detection in goats enhanced fears that its source was located in small ruminants. However, in goats knowledge on prion strain typing is limited. A European-wide study is presented concerning the biochemical phenotypes of the protease resistant fraction of PrPSc (PrPres) in over thirty brain isolates from transmissible spongiform encephalopathy (TSE) affected goats collected in seven countries. Three different scrapie forms were found: classical scrapie (CS), Nor98/atypical scrapie and one case of CH1641 scrapie. In addition, CS was found in two variants—CS-1 and CS-2 (mainly Italy)—which differed in proteolytic resistance of the PrPresN-terminus. Suitable PrPres markers for discriminating CH1641 from BSE (C-type) appeared to be glycoprofile pattern, presence of two triplets instead of one, and structural (in)stability of its core amino acid region. None of the samples exhibited BSE like features. BSE and these four scrapie types, of which CS-2 is new, can be recognized in goats with combinations of a set of nine biochemical parameters.
Published: 2019
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24. Dermaseptins as potential antirabies compounds

Author: Guillaume Castel, Karen L. Mansfield, Anthony R. Fooks, Mohamed Ben Mechlia, Khaled Hani, Corinne Jallet, Noël Tordo, Afifa Belaid, Stratégies antivirales, Institut Pasteur [Paris] (IP), Université de Sousse, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Animal and Plant Health Agency [Addlestone, UK] (APHA), Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Université Gamal Abdel Nasser de Conakry, This work was supported by the EU grant FP7-60282 Asklepios 'Advanced Studies towards Knowledge on Lyssavirus Encephalitis Pathogenesis Improving Options for Survival'. Mohamed Chteoui (MC) was recipient of a fellowship of Fondation Merieux, 17, rue Bourgelat, Lyon. Guillaume Castel (GC) was recipient of fellowships of the University Paris VI of Institut Pasteur. The imaging and quantifications have been performed at the Imagopole-CiTech. The Imagopole is part of the France BioImaging infrastructure supported by the French National Research Agency (ANR-10-INBS-00004 'Investments for the future' and is gratefully supported by Conseil de la Region Ile-de-France (program Sesame 2007, projet Imagopole, S. Shorte) and by the Fondation Francaise pour la Recherche Medicale (FRM, Programme Grands Equipements to N. Aulner)., ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 602825,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,ASKLEPIOS(2013), Institut Pasteur [Paris], and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: Cell Survival, Rabies, 030231 tropical medicine, Biology, Antiviral Agents, Injections, Intramuscular, Virus, Amphibian Proteins, Microbiology, Cell Line, 03 medical and health sciences, Mice, Structure-Activity Relationship, Dermaseptin, 0302 clinical medicine, In vivo, Immunity, Cricetinae, Animals, 030212 general & internal medicine, Antiviral, Innate immune system, General Veterinary, General Immunology and Microbiology, Dose-Response Relationship, Drug, [SDV.BA]Life Sciences [q-bio]/Animal biology, Public Health, Environmental and Occupational Health, Antimicrobial, In vitro, 3. Good health, Infectious Diseases, Mutation, biology.protein, Molecular Medicine, Female, Antibody, Antimicrobial Cationic Peptides
Abstract: International audience; Over the last 20 years, natural peptides playing a key role in defense mechanisms and innate immunity have been isolated from unicellular organisms. Amphibian skin secretes dermaseptins, 24–34 amino acids in length that have a wide antimicrobial spectrum incorporating yeast, fungi, protozoa, bacteria and enveloped viruses. The anti-rabies virus (RABV) activity of dermaseptins S3 (30aa) and S4 (28aa) from Phyllomedusa sauvagei has been investigated, and further dissected its molecular basis by comparing punctual mutation or deletion of S4 analogues. The results showed that: (1) S4 is more active than S3 against RABV infection, 89% versus 38% inhibition at 7.5 lM; (2) the 5 NH2-aa of S4 are crucial for its inhibitory potential (S46–28 lost any inhibition) but the COOH terminus stabilizes the inhibitory potential (S41–16 showed only 23% inhibition at 7.5 lM); (3) there is a correlation between viral inhibition and dermaseptin cytotoxicity, which remains however moderated for BSR cells (12% at 10 lM). A single mutation in position 4 (S4M4K) slightly reduced cytotoxicity while keeping its antiviral activity, 97% at 7.5 lM. S4 and S4M4K showed an antiviral activity in vitro when provided 1 h after infection. In vivo experiments in mice by intramuscular injection of non-toxic doses of dermaseptin S4M4K 1 h post-infection by a lethal dose of RABV at the same site allowed more than 50% improvement in mice survival. This study highlights the potential interest of dermaseptins as non-expansive alternatives to rabies immunoglobulins for the treatment of rabies that continues to claim about 60,000 human lives per year worldwide, almost exclusively in developing countries.
Published: 2019
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25. In vitro and in vivo evaluation of a single chain antibody fragment generated in planta with potent rabies neutralisation activity

Author: Phoolcharoen, Waranyoo, Banyard, Ashley, Préhaud, Christophe, Selden, David, Wu, Guanghui, Birch, Colin P.D., Szeto, Tim, Lafon, Monique, Fooks, Anthony, Ma, Julian K.-C., Institute for Infection and Immunity [Londres, UK], St George's, University of London, Faculty of Pharmaceutical Sciences [Bangkok], Chulalongkorn University [Bangkok], Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal and Plant Health Agency [Addlestone, UK] (APHA), Neuro-Immunologie Virale, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Biomathematics and Risk Research Group, This work was supported by the Royal Society (Newton International fellowship to W. Phoolcharoen), a Wellcome Trust grant (WT093092MA), the Hotung Foundation and an ERC award (ERC-2010-AdG_20100317). The studies undertaken at APHA received partial financial support from the EU FP7 project (ASKLEPIOS 602825) and by the UK Department for Environment, Food and Rural Affairs (Defra projects SE0426 and SE0431)., European Project: 602825,EC:FP7:HEALTH,FP7-HEALTH-2013-INNOVATION-1,ASKLEPIOS(2013), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: N-acetylcholine receptor, Rabies, Single-chain antibody (ScFv), [SDV]Life Sciences [q-bio], Blotting, Western, Clinical disease, respiratory system, Antibodies, Neutralizing, Article, Cell Line, Mice, Rabies Vaccines, Blood-Brain Barrier, Rabies virus, Blood brain barrier (BBB), Immunoglobulin, Nicotiana benthamiana, Animals, Humans, Electrophoresis, Polyacrylamide Gel, Single-Chain Antibodies
Abstract: International audience; Rabies causes more than 60,000 human deaths annually in areas where the virus is endemic. Importantly, rabies is one of the few pathogens for which there is no treatment following the onset of clinical disease with the outcome of infection being death in almost 100% of cases. Whilst vaccination, and the combination of vaccine and rabies immunoglobulin treatment for post-exposure administration are available, no tools have been identified that can reduce or prevent rabies virus replication once clinical disease has initiated. The search for effective antiviral molecules to treat those that have already developed clinical disease associated with rabies virus infection is considered one of the most important goals in rabies research. The current study assesses a single chain antibody molecule (ScFv) based on a monoclonal antibody that potently neutralises rabies in vitro as a potential therapeutic candidate. The recombinant ScFv was generated in Nicotiana benthamiana by transient expression, and was chemically conjugated (ScFv/RVG) to a 29 amino acid peptide, specific for nicotinic acetylcholine receptor (nAchR) binding in the CNS. This conjugated molecule was able to bind nAchR in vitro and enter neuronal cells more efficiently than ScFv. The ability of the ScFv/RVG to neutralise virus in vivo was assessed using a staggered administration where the molecule was inoculated either four hours before, two days after or four days after infection. The ScFv/RVG conjugate was evaluated in direct comparison with HRIG and a potential antiviral molecule, Favipiravir (also known as T-705) to indicate whether there was greater bioavailability of the ScFv in the brains of treated mice. The study indicated that the approach taken with the ScFv/RVG conjugate may have utility in the design and implementation of novel tools targetting rabies virus infection in the brain.
Published: 2019
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26. Wild Rats, Laboratory Rats, Pet Rats: Global Seoul Hantavirus Disease Revisited

Author: Jan Clement, Ho-Wang Lee, Marc Van Ranst, Graham Lloyd, Lorraine M. McElhinney, Jean-Marc Reynes, James W. LeDuc, Centre national de Référence (CNR) des Hantavirus [UZ Leuven, Belgium], University Hospitals Leuven [Leuven], University of Texas Medical Branch at Galveston, Public Health England [Salisbury] (PHE), Centre National de Référence Hantavirus / National Reference Center Hantavirus (CNR ), Institut Pasteur [Paris] (IP), Animal and Plant Health Agency [Addlestone, UK] (APHA), WHO Collaborating Centre for Hemorrhagic Fever with renal Syndrome [Seoul, South Korea], National Academy of Sciences of the Republic of Korea [Seoul] (NAS), Megan Golding and Lorraine McElhinney are supported by funding from Defra, the Scottish Government and the Welsh Government, through grant SV3045 and the EU Horizon 2020 research and innovation programme under grant agreement number 653316 (EVAg). James Le Duc is supported by NIH/NIAID award 5UC7AI094660-09., We are indebted to Dirk De Weerdt, UZA, Belgium, for the illustrations, and to Megan Golding, APHA, UK, for her skillful technical assistance in the preparation of this manuscript., and Institut Pasteur [Paris]
Subjects: 0301 basic medicine, Brown rat, Rodent, lcsh:QR1-502, Physiology, Review, Disease, Global Health, Communicable Diseases, Emerging, lcsh:Microbiology, hantavirus, Seoul virus (SEOV), 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Medicine, acute kidney injury (AKI), Geography, Medical, Microhematuria, Seoul virus, biology, hemorrhagic fever with renal syndrome (HFRS), Pets, 3. Good health, Laboratory rat, Infectious Diseases, Hemorrhagic Fever with Renal Syndrome, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, brown rat, medicine.medical_specialty, 030231 tropical medicine, Animals, Wild, hantavirus disease, 03 medical and health sciences, Animals, Laboratory, Virology, biology.animal, Animals, Hantavirus, pet rat, business.industry, Public health, hantavirus cardio-pulmonary syndrome (HCPS), biology.organism_classification, medicine.icd_9_cm_classification, Rats, wild rat, 030104 developmental biology, laboratory rat, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Human Pathology
Abstract: Recent reports from Europe and the USA described Seoul orthohantavirus infection in pet rats and their breeders/owners, suggesting the potential emergence of a "new" public health problem. Wild and laboratory rat-induced Seoul infections have, however, been described since the early eighties, due to the omnipresence of the rodent reservoir, the brown rat Rattus norvegicus. Recent studies showed no fundamental differences between the pathogenicity and phylogeny of pet rat-induced Seoul orthohantaviruses and their formerly described wild or laboratory rat counterparts. The paucity of diagnosed Seoul virus-induced disease in the West is in striking contrast to the thousands of cases recorded since the 1980s in the Far East, particularly in China. This review of four continents (Asia, Europe, America, and Africa) puts this "emerging infection" into a historical perspective, concluding there is an urgent need for greater medical awareness of Seoul virus-induced human pathology in many parts of the world Given the mostly milder and atypical clinical presentation, sometimes even with preserved normal kidney function, the importance of simple but repeated urine examination is stressed, since initial but transient proteinuria and microhematuria are rarely lacking. ispartof: VIRUSES-BASEL vol:11 issue:7 ispartof: location:Switzerland status: published
Published: 2019
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27. Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus

Author: Peter A. Durr, Bénédicte Lambrecht, Mikael Berg, Muhammad Munir, Claude P. Muller, Siba K. Samal, Claudio L. Afonso, Emmanuel Albina, Dilmara Reischak, Mia Kim Torchetti, Hualei Liu, David L. Suarez, Chantal J. Snoeck, Nicola S Lewis, Mahmoud Sabra, Gabriela V. Goujgoulova, Diego G. Diel, Kiril M. Dimitrov, Kang-Seuk Choi, Joseph T. Hicks, Zhiliang Wang, Renata Servan de Almeida, Steven Van Borm, Isabella Monne, Frank Y. K. Wong, Patricia Gil, Celia Abolnik, Patti J. Miller, Sam McCullough, Christian Grund, Ilya Chvala, Alice Fusaro, Tony M. Joannis, Helena Lage Ferreira, Ian H. Brown, Haijin Liu, Justin Bahl, S. N. Kolosov, Ismaila Shittu, François-Xavier Briand, USDA-ARS : Agricultural Research Service, University of Pretoria [South Africa], Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of Georgia [USA], Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), Ministry of Agriculture, Food and Rural Affairs, Partenaires INRAE, Federal State Budgetary Institution Federal Centre for Animal Health, South Dakota State University (SDSTATE), Australian Animal Health Laboratory (AAHL), CSIRO Health and Biosecurity [Australia], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO)-Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Universidade de São Paulo (USP), Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), National Diagnostic Science and Research Veterinary Medical Institute, Friedrich-Loeffler-Institut (FLI), National Veterinary Research Institute, United States Department of Agriculture - Animal and Plant Health Inspection Service, Sciensano [Bruxelles], Réseau International des Instituts Pasteur (RIIP), University of London, Northwest A&F University, China Animal Health and Epidemiology Center, Luxembourg Institute of Health (LIH), Lancaster University, Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil, South Valley University, University of Maryland [College Park], University of Maryland System, U.S. Department of Agriculture, ARS CRIS Project [6612-32000-072-00D], and BBSRCBiotechnology and Biological Sciences Research Council (BBSRC) [BB/R012695/1, BB/M008681/1]
Subjects: 0301 basic medicine, Future studies, International Cooperation, Newcastle disease virus (NDV), Inference, L73 - Maladies des animaux, Avian parasnyxovirus 1 (APMV-1), Databases, Genetic, Nomenclature, Data Curation, Phylogeny, Likelihood Functions, Systèmes de classification, Phylogenetic analysis, Phylogenetic tree, Microbiology and Parasitology, Classification, Microbiologie et Parasitologie, 3. Good health, Paramyxovirus aviaire, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, C30 - Documentation et information, RNA, Viral, Veterinary medicine and animal Health, Génotype, Genotype, Microbiology (medical), Consensus, 030106 microbiology, Bayesian probability, Newcastle disease virus, Guidelines as Topic, Computational biology, Biology, Microbiology, Newcastle disease, Avian paramyxovirus 1 (APMV-1), Article, 03 medical and health sciences, Variation génétique, Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Genetic diversity, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Sequence Analysis, RNA, Virus maladie de newcastle, Bayes Theorem, biology.organism_classification, 030104 developmental biology, Médecine vétérinaire et santé animal, PARAMYXOVIRUS, Phylogenetic nomenclature
Abstract: Several Avian paramyxoviruses 1 (synonymous with Newcastle disease virus or NDV, used hereafter) classification systems have been proposed for strain identification and differentiation. These systems pioneered classification efforts; however, they were based on different approaches and lacked objective criteria for the differentiation of isolates. These differences have created discrepancies among systems, rendering discussions and comparisons across studies difficult. Although a system that used objective classification criteria was proposed by Diel and co-workers in 2012, the ample worldwide circulation and constant evolution of NDV, and utilization of only some of the criteria, led to identical naming and/or incorrect assigning of new sub/genotypes. To address these issues, an international consortium of experts was convened to undertake in-depth analyses of NDV genetic diversity. This consortium generated curated, up-to-date, complete fusion gene class I and class II datasets of all known NDV for public use, performed comprehensive phylogenetic neighbor-Joining, maximum-likelihood, Bayesian and nucleotide distance analyses, and compared these inference methods. An updated NDV classification and nomenclature system that incorporates phylogenetic topology, genetic distances, branch support, and epidemiological independence was developed. This new consensus system maintains two NDV classes and existing genotypes, identifies three new class II genotypes, and reduces the number of sub-genotypes. In order to track the ancestry of viruses, a dichotomous naming system for designating sub-genotypes was introduced. In addition, a pilot dataset and sub-trees rooting guidelines for rapid preliminary genotype identification of new isolates are provided. Guidelines for sequence dataset curation and phylogenetic inference, and a detailed comparison between the updated and previous systems are included. To increase the speed of phylogenetic inference and ensure consistency between laboratories, detailed guidelines for the use of a supercomputer are also provided. The proposed unified classification system will facilitate future studies of NDV evolution and epidemiology, and comparison of results obtained across the world., Highlights • An international consortium phylogenetically studied the diversity of NDV. • Consensus objective NDV classification and nomenclature system was developed. • Optimal phylogenetic inference method with guidelines is recommended. • Curated, up-to-date, complete fusion gene datasets for public use were created. • Three new NDV genotypes were identified.
Published: 2019
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28. Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe

Author: Sophie A. Granier, Simon Le Hello, Arnaud Felten, Michel-Yves Mistou, Sabrina Cadel-Six, Yann Sévellec, Liljana Petrovska, Nicolas Radomski, Laboratoire de sécurité des aliments de Maisons-Alfort (LSAl), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Fougères - ANSES, Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Institut Pasteur [Paris] (IP), Animal and Plant Health Agency [Addlestone, UK] (APHA), This study was supported by the French Ministry of Agriculture, Food and Forestry and the European Union Horizon 2020 research and innovation program under grant agreement 643476 to the COMPARE project (http://www.compare-europe.eu). We are indebted to the Salmonella Network that provided the French food strains analyzed in the study. Yann Sévellec is the recipient of a doctoral fellowship (DGER-ANSES) co-financed by AgroParisTech and the French Agency for Food, Environmental and Occupational Health & Safety (ANSES)., European Project: 643476,H2020,H2020-PHC-2014-single-stage,COMPARE(2014), Laboratoire de Fougères, Bâtiment Bioagropolis, and Institut Pasteur [Paris]
Subjects: Microbiology (medical), Serotype, Veterinary medicine, reference genome ST71, lcsh:Medicine, Single-nucleotide polymorphism, Biology, Genome, poultry sector, génétique, 03 medical and health sciences, Antibiotic resistance, Immunology and Allergy, antimicrobial resistance, microbiologie, Molecular Biology, salmonella derby, 030304 developmental biology, 2. Zero hunger, Whole genome sequencing, bactérie, 0303 health sciences, Genetic diversity, General Immunology and Microbiology, 030306 microbiology, phylogenetic analysis, lcsh:R, Salmonella Derby, volaille, Europe, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Multilocus sequence typing, human infection, Flock, phage analysis
Abstract: Salmonella Derby (S. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK). Only two years later, in 2016, it was also recorded in the turkey and broiler sectors in Ireland and Spain. These S. Derby isolates were characterised as members of the multilocus sequence type (MLST) profile 71 (ST71). For the first time, we characterise by whole genome sequencing (WGS) analysis a panel of 90 S. Derby ST71 genomes to understand the routes of transmission of this emerging pathogen within the poultry/turkey food trade. Selected panel included strains isolated as early as 2010 in five leading European g countries for turkey meat production. Twenty-one of the 90 genomes were extracted from a public database&mdash, Enterobase. Five of these originated from the United States (n=3), China (n=1) and Taiwan (n=1) isolated between 1986 and 2016. A phylogenomic analysis at the core-genome level revealed the presence of three groups. The largest group contained 97.5% of the European strains and included both, turkey and human isolates that were genetically related by an average of 35 &plusmn, 15 single nucleotide polymorphism substitutions (SNPs). To illustrate the diversity, the presence of antimicrobial resistance genes and phages were characteised in 30, S. Derby ST71 genomes, including 11 belonging to this study This study revealed an emergent turkey-related S. Derby ST71 clone circulating in at least five European countries (the UK, Germany, Poland, Italy, and France) since 2010 that causes human gastroenteritis. A matter of concern is the identification of a gyrA mutation involved in resistance to quinolone, present in the Italian genomes. Interestingly, the diversity of phages seems to be related to the geographic origins. These results constitute a baseline for following the spread of this emerging pathogen and identifying appropriate monitoring and prevention measures.
Published: 2019
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29. TSEs in European goats discriminated by Western blotting into five types based on five robust molecular parameters

Author: Pirisinu, Laura, Andreoletti, Olivier, Lantier, Isabelle, Acutis, P.L., Acin, C., Goldmann, Wilfred, Sklaviadis, Theodoros, Ekateriniadou, Loukia, Fast, Christine, Papasavva-Stylianou, Penelope, Simon, S, Spiropoulos, John, Agrimi, Umberto, Jacobs, J.G., Bossers, A., van Keulen, L.J.M., Mazza, M, Nonno, Romolo, Langeveld, J.P.M., Istituto Superiore di Sanità (ISS), 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 de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Research Centre for Prion Diseases, University of Zaragoza - Universidad de Zaragoza [Zaragoza], The Roslin Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Royal (Dick) School of Veterinary Studies, University of Edinburgh, Aristotle University of Thessaloniki, Veterinary Research Institute, National Agricultural Research Foundation (NAGREF), Institute of Novel and Emerging Infectious Diseases (INNT), Friedrich-Loeffler-Institut (FLI), Veterinary Services of Cyprus, Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal and Plant Health Agency [Addlestone, UK] (APHA), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Istituto Superiore di Sanita [Rome], 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, and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: animal diseases, [SDV]Life Sciences [q-bio]
Abstract: International audience; Contrasting the knowledge about prion diseases or TSEs in sheep, only a very limited number of strain typing studies are available in goats. Two cases deriving from the zoonotic bovine BSE epidemic were however detected in goats. During 2004–2012, over 70 TSE goat brain samples were collected from seven European countries and evaluated for TSE type/strain variation. A selection of these materials was chosen for in-depth analysis based on various criteria: tissue quality, genotype, broad geographical distribution, potential type variation. Of these, 37 cases were biochemically analysed (present study) and a subset of these subjected to bioassays in seven rodent models (see parallel study of Nonno et al.). Analyses of these isolates showed that in goats different PrPSc types exist, comparable to those found in sheep such as classical scrapie, CH1641-like scrapie and Nor98/atypical scrapie. However, classical scrapie isolates could be further differentiated in two molecular subtypes based on the PK susceptibility of the N-terminus and on the molecular weight of PrPres. Importantly, the two subtypes of classical scrapie showed different geographical distribution, as one subtype was only detected in goats deriving from Italy and France. These analyses also show, that none of the field samples exhibited BSE-like features and offer a comprehensive set of robust molecular PrPres properties to exclude suspicion for the presence of BSE. These are: molecular mass of the triplet bands, presence of N-terminus epitope, glycoprofile markers, a dual population marker and the structural stability of PrP-core.This work was made possible by national support and by the following European grants: Neuroprion (FP6-FOOD-506,579), GoatBSE (FOOD-CT-2006–36,353) and GOAT-TSE-FREE (EMIDA-ERA NET). We want to memorize Jorg G Jacobs, who died in 2017. Jorg developed and performed the Triplex-WB system as well as characterized antibodies like 94B4, 12B2, 9A2, 6C2, SAF84 and L42. He also was crucial in the distinction of C-, L- and H-type BSE and in 2011 he showed elegantly the allotype composition of prion material in heterozygous sheep by the use of Endo-LysC.
Published: 2019
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30. Rodent models allow BSE discrimination of goat prions and reveal geographical differences in the biological properties of scrapie

Author: Nonno, R., Marin-Moreno, A., Espinosa, J. C., Fast, C., Keulen, L., Spiropoulos, J., Lantier, I., Andreoletti, O., Pirisinu, L., Di Bari, M. A., Aguilar-Calvo, P., Sklaviadis, T., Papasavva-Stylianou, P., Acutis, P. L., Acin, C., Alex Bossers, Jacobs, J. G., Vaccari, G., D Agostino, C., Chiappini, B., Lantier, F., Groschup, M., Agrimi, U., Torres, J. M., Langeveld, J. P. M., Istituto Superiore di Sanita [Rome], Centro de Investigacion en Sanidad Animal (INIA-CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Institute of Novel and Emerging Infectious Diseases (INNT), Friedrich-Loeffler-Institut (FLI), Wageningen BioVeterinary Research, Wageningen University and Research [Wageningen] (WUR), Animal and Plant Health Agency [Addlestone, UK] (APHA), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), 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, Aristotle University of Thessaloniki, Veterinary Services of Cyprus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Research Centre for Prion Diseases, University of Zaragoza - Universidad de Zaragoza [Zaragoza], and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: animal diseases, [SDV]Life Sciences [q-bio], nervous system diseases
Abstract: International audience; Classical scrapie (CS) is a contagious TSE of small ruminants known to circulate in Europe for centuries. More than one TSE strain is responsible for CS, still our ability to identify scrapie strains remains limited, as it has been difficult so far to reconcile data obtained in different rodent models. After the discovery of BSE in two goats, a European-broad effort was undertaken in order to understand the diversity of goat TSE strains and to discriminate BSE from them. Here, we studied goat TSEs by their relative transmission efficiency in different animal models and by the PrPSc type(s) propagated in rodents. Thus, the biological properties of TSE isolates were inferred by their specific interaction with different recipient PrP species rather than by serial passage in a single model. Goat TSE isolates from seven countries and experimental goat-BSE were inoculated in seven models: tg-mice overexpressing sheep/goat ARQ, sheep VRQ, cattle or mouse PrPs; RIII mice and bank voles. The attack rate and the survival time were combined to obtain the ‘transmission efficiency’, a parameter used to build the ‘transmission profiles’ of individual isolates across all models. Goat-BSE and Nor98 showed distinctive transmission profiles, different among them and from all other isolates. Goat-BSE was the only isolate inducing 19kDa PrPSc in all rodent models, while Nor98 was associated with 8kDa PrPSc. CS isolates showed a strong variability of transmission profiles, which was in part explained by their geographical distribution, and could be grouped into four distinct categories. CS isolates in category 1 induced the propagation solely of 21kDa PrPSc, while isolates from CS categories 2-to-4 also induced, to a different extent depending on the model, a 19kDa PrPSc type distinct from BSE. Further investigation of CNS and LRS tissues from a goat herd showed that this phenomenon reflects the selective amplification in rodents of at least two co-existing ‘sub-strain components’, 21kDa and 19kDa, whose relative amount varies with different goat tissues/isolates. Our findings show that BSE can be discriminated from a wide range of biologically and geographically diverse goat TSEs. The geographical variation observed in CS suggests the existence of distinct CS strains, as also supported by the parallel studies by Pirisinu et al. and Marin-Moreno et al. Yet, CS isolates in categories 2-to-4 were mixtures of discrete sub-strains, where it could be envisaged that competition among sub-strains play a role in defining the biological properties of individual isolates and their evolution.
Published: 2019
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31. SGI-4 in Monophasic Salmonella Typhimurium ST34 Is a Novel ICE That Enhances Resistance to Copper

Author: Priscilla Branchu, Oliver J. Charity, Matt Bawn, Gaetan Thilliez, Timothy J. Dallman, Liljana Petrovska, Robert A. Kingsley, Quadram Institute Bioscience, Gastrointestinal Bacteria Reference Unit, National Infection Service, Public Health England, Animal and Plant Health Agency [Addlestone, UK] (APHA), School of Biological Sciences [Aberdeen], University of Aberdeen, and RK was supported by research grants BB/N007964/1 and BB/M025489/1, and by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project(s) BBS/E/F/000PR10348 and BBS/E/F/000PR10349. OC was supported by a BBSRC DTP studentship (BB/M011216/1)
Subjects: Microbiology (medical), Salmonella, monophasic, integrative conjugative element, SGI-4, copper resistance, Population, lcsh:QR1-502, Multicopper oxidase, medicine.disease_cause, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Genomic island, medicine, Food and Nutrition, education, Gene, 030304 developmental biology, Original Research, 0303 health sciences, education.field_of_study, biology, 030306 microbiology, Chemistry, Periplasmic space, biology.organism_classification, Oxygen tension, Salmonella enterica, Alimentation et Nutrition, Efflux, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: A multi drug resistant (MDR) Salmonella enterica 4,[5],12:i-of sequence type 34 (monophasic S. Typhimurium ST34) is a current pandemic clone associated with livestock and numerous outbreaks in the human population. A large genomic island, termed SGI-4, is present in the monophasic Typhimurium ST34 clade and absent from other S. Typhimurium strains. SGI-4 consists of 78 open reading frames including sil and pco genes previously implicated in resistance to copper and silver, and multiple genes predicted to be involved in mobilisation and transfer by conjugation. SGI-4 was excised from the chromosome, circularised and transferred to recipient strains of S. Typhimurium at a frequency influenced by stress and induced by mitomycin C and oxygen tension. The presence of SGI-4 was associated with increased resistance to copper, particularly but not exclusively under anaerobic conditions. The presence of silCBA genes, predicted to encode an RND family efflux pump that transports copper from the periplasm to the external milieu, was sufficient to impart the observed enhanced resistance to copper. The presence of silCBA genes resulted in the absence of copper-dependent induction of a multicopper oxidase system encoded by pco genes, also present on SGI-4, suggesting that the system effectively limits the copper availability in the periplasm. The presence of silCBA genes did not affect SodCI-dependent macrophage survival.
Published: 2019
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32. Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally

Author: Theocharis Tsoleridis, Joseph G. Chappell, Okechukwu Onianwa, Denise A. Marston, Anthony R. Fooks, Elodie Monchatre-Leroy, Gérald Umhang, Marcel A. Müller, Jan F. Drexler, Christian Drosten, Rachael E. Tarlinton, Charles P. McClure, Edward C. Holmes, Jonathan K. Ball, School of Life Sciences, University of Nottingham, UK (UON), Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal and Plant Health Agency [Addlestone, UK] (APHA), Laboratoire de la rage et de la faune sauvage de Nancy (LRFSN), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Schools of Biosciences and Veterinary Medicine and Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, and The University of Sydney
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], viruses, lcsh:QR1-502, coronavirus, alphacoronavirus, COVID-19, rodents, evolution, recombination, ancestry, Coronavirus, Genome, Alphacoronavirus, lcsh:Microbiology, Monophyly, Phylogeny, Recombination, Genetic, biology, Phylogenetic tree, Arvicolinae, virus diseases, respiratory system, Europe, Bank vole, Infectious Diseases, Phylogenetic Pattern, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Rabbits, Coronavirus Infections, Asia, Field vole, 030106 microbiology, Rodentia, Genome, Viral, Article, Evolution, Molecular, 03 medical and health sciences, Virology, Animals, Whole genome sequencing, Genetic Variation, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, Rats, respiratory tract diseases, 030104 developmental biology, Evolutionary biology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Murinae
Abstract: International audience; The recent discovery of novel alphacoronaviruses (alpha-CoVs) in European and Asian rodents revealed that rodent coronaviruses (CoVs) sampled worldwide formed a discrete phylogenetic group within this genus. To determine the evolutionary history of rodent CoVs in more detail, particularly the relative frequencies of virus-host co-divergence and cross-species transmission, we recovered longer fragments of CoV genomes from previously discovered European rodent alpha-CoVs using a combination of PCR and high-throughput sequencing. Accordingly, the full genome sequence was retrieved from the UK rat coronavirus, along with partial genome sequences from the UK field vole and Poland-resident bank vole CoVs, and a short conserved ORF1b fragment from the French rabbit CoV. Genome and phylogenetic analysis showed that despite their diverse geographic origins, all rodent alpha-CoVs formed a single monophyletic group and shared similar features, such as the same gene constellations, a recombinant beta-CoV spike gene, and similar core transcriptional regulatory sequences (TRS). These data suggest that all rodent alpha CoVs sampled so far originate from a single common ancestor, and that there has likely been a long-term association between alpha CoVs and rodents. Despite this likely antiquity, the phylogenetic pattern of the alpha-CoVs was also suggestive of relatively frequent host-jumping among the different rodent species.
Published: 2019
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33. Accurate phylogenetic relationships among Mycobacterium bovis strains circulating in France based on whole genome sequencing and single nucleotide polymorphism analysis

Author: Hauer, Amandine, michelet, Lorraine, Cochard, Thierry, BRANGER, Maxime, Nunez, Javier, Boschiroli, Maria-Laura, Biet, Franck, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Animal and Plant Health Agency [Addlestone, UK] (APHA), and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: Microbiology (medical), [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, evolution, SNP, phylogenetic, bovine tuberculosis, Microbiology, Mycobacterium bovis, WGS
Abstract: International audience; In recent years the diversity of the French Mycobacterium bovis population responsible for bovine tuberculosis (bTB) outbreaks since 1970 has been described in detail. To further understand bTB evolution in France, we used single nucleotide polymorphisms (SNPs) based on whole genome sequence versus classical genotyping methods in order to identify accurate phylogenetic relationships between M. bovis strains. Whole genome sequencing was carried out on a selection of 87 strains which reflect the French M. bovis population’s genetic diversity. Sequences were compared to the M. bovis reference genome AF2122/97. Comparison among the 87 genomes revealed 9,170 sites where at least one strain shows a SNP with respect to the reference genome; 1,172 are intergenic and 7,998 in coding sequences, of which 2,880 are synonymous and 5,118 non-synonymous. SNP-based phylogenetic analysis using these 9,170 SNP is congruent with the cluster defined by spoligotyping and multilocus variable number of tandem repeat analysis typing. In addition, some SNPs were identified as specific to genotypic groups. These findings suggest new SNP targets that can be used for the development of high-resolving methods for genotyping as well as for studying M. bovis evolution and transmission patterns. The detection of non-synonymous SNPs on virulence genes enabled us to distinguish different clusters. Our results seem to indicate that genetically differentiated clusters could also display distinctive phenotypic traits.
Published: 2019
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34. Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005–2010

Author: Alison E. Mather, Thomas R. Connor, Antonia A. Lettini, Liljana Petrovska, Mary C. Bagnall, Manal AbuOun, Julian Parkhill, John Wain, Priscilla Branchu, Robert A. Kingsley, Simon R. Harris, Gordon Dougan, Andrew J. Page, Robert Davies, Katie L. Hopkins, Anthony Underwood, Animal and Plant Health Agency [Addlestone, UK] (APHA), The Wellcome Trust Sanger Institute [Cambridge], Institute for Food Research, Public Health England [London], and Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe)
Subjects: 0301 basic medicine, Salmonella, Epidemiology, [SDV]Life Sciences [q-bio], Prophages, séquençage du génome complet, lcsh:Medicine, heavy metal resistance, medicine.disease_cause, molecular epidemiology, analyse phylogénomique, Disease Outbreaks, Genomic island, Drug Resistance, Multiple, Bacterial, Genotype, MDR, bacteria, Phylogeny, Genetics, Microevolution, Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 3. Good health, Anti-Bacterial Agents, Bacterial Typing Techniques, Infectious Diseases, Italy, Epidemiological Monitoring, Salmonella Infections, Salmonella Typhimurium, monophasic, microévolution, Microbiology (medical), United Kingdom, antimicrobial resistance, microevolution, Genomic Islands, 030106 microbiology, Biology, Microbiology, lcsh:Infectious and parasitic diseases, Clonal Evolution, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, medicine, Humans, lcsh:RC109-216, Prophage, Molecular epidemiology, Research, lcsh:R, Genetic Variation, Gene Expression Regulation, Bacterial, Clone Cells, 030104 developmental biology, Composite transposon, DNA Transposable Elements, Flagellin
Abstract: Microevolution resulted in considerable genotypic variation., Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. To determine microevolution associated with monophasic Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing and phylogenomic analysis of isolates from the United Kingdom and Italy during 2005–2012. These isolates formed a single clade distinct from recent monophasic epidemic clones previously described from North America and Spain. The UK monophasic epidemic clones showed a novel genomic island encoding resistance to heavy metals and a composite transposon encoding antimicrobial drug resistance genes not present in other Salmonella Typhimurium isolates, which may have contributed to epidemiologic success. A remarkable amount of genotypic variation accumulated during clonal expansion that occurred during the epidemic, including multiple independent acquisitions of a novel prophage carrying the sopE gene and multiple deletion events affecting the phase II flagellin locus. This high level of microevolution may affect antigenicity, pathogenicity, and transmission.
Published: 2016
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35. Characterising Farms by the Movement of Animals through Them

Author: Slingsby, A., Paterson, A., Rigby, M., Grace, K., Nguyen, P., Perin, C., Turkay, C., Aljasem, D., City University London, Animal and Plant Health Agency [Addlestone, UK] (APHA), University of Victoria [Canada] (UVIC), and Perin, Charles
Subjects: QA75, Visualization application domains, Human-centered computing, education, SF, Geographic visualization, [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC], [INFO.INFO-HC] Computer Science [cs]/Human-Computer Interaction [cs.HC], Visualization design and evaluation methods, Visualization
Abstract: International audience; We describe a pilot study that arose from a workshop of domain and visualisation experts, and present preliminary work in which we begin to visually characterise holdings (farms) by the movement of cattle through them. This ongoing study suggests that this is a useful approach for helping DEFRA understand risk of disease spread.
Published: 2018

36. VetBioNet - Veterinary Biocontained facility Network for excellence in animal infectious disease research and experimentation: services and opportunities provided to the avian immunology research community

Author: Trapp, Sascha, DALGAARD, Tina, Vervelde, Lonneke, Stevens, Mark, Stockhofe, Norbert, Groschup, Martin, Simmons, Hugh, Millar, Kate, Rosati, Andrea, Entrican, Gary, Blanco, Esther, Waters, Ryan, Fentener Van Vlissingen, Martje, Lantier, Frédéric, VetBioNet Consortium, ., Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Department of Animal Science, Aarhus University [Aarhus], The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Wageningen University and Research Centre (WUR), Institute of Novel and Emerging Infectious Diseases (INNT), Friedrich-Loeffler-Institut (FLI), Animal and Plant Health Agency [Addlestone, UK] (APHA), University of Nottingham, UK (UON), European Association for Animal Production (EAAP), Moredun Research Institute [Penicuik, UK] (MRI), Centro de Investigacion en Sanidad Animal (INIA-CISA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Pirbright Institute, Erasmus University Rotterdam, Avian Immunology Research Group., and Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT)
Subjects: [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.IMM]Life Sciences [q-bio]/Immunology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018

37. Developing a framework of minimum standards for the risk assessment of alien species

Author: Tim Adriaens, Franz Essl, Sarah Brunel, Wolfgang Rabitsch, Stefan Schindler, Helen E. Roy, Wojciech Solarz, Merike Linnamagi, Wolfgang Nentwig, Melanie Josefsson, Gordon H. Copp, Teodora Trichkova, Jodey Peyton, Belinda Gallardo, Riccardo Scalera, Etienne Branquart, Karsten Schönrogge, Ana Nieto, Alain Roques, Bram D'hondt, Alan J. A. Stewart, Jan Pergl, Johan van Valkenburg, Olaf Booy, Sven Bacher, Piero Genovesi, Angeliki F. Martinou, Marianne Kettunen, Hannah Dean, Frances E. Lucy, Sonia Vanderhoeven, Niall Moore, Marc Kenis, Paul Stebbing, Argyro Zenetos, Natural Environment Research Council (NERC), Environment Agency Austria, Species Survival Commission, Partenaires INRAE, University of Sussex, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute for Environmental Protection and Research (ISPRA), University of Vienna [Vienna], Research Institute for Nature and Forest (INBO), Department of Biology [Fribourg], University of Freiburg [Freiburg], Department of Botany and Zoology, Stellenbosch University, Animal and Plant Health Agency [Addlestone, UK] (APHA), Newcastle University [Newcastle], Belgian Biodiversity Platform, Belgian Science Policy Office, European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes (EPPO), Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Bournemouth University [Poole] (BU), Flemish Authority, Agency for Nature and Forests, Swedish Environmental Protection Agency, CABI Europe Switzerland, Finnish Environment Institute (SYKE), Ministry of Environment, Institute of Technology Department of Environmental Science, RAF Akrotiri, Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), International Union for Conservation of Nature, Institute of Botany, Czech Academy of Sciences [Prague] (CAS), Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Institute of Nature Conservation, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences (BAS), Netherlands Food and Consumer Product Safety Authority (NVWA), Institute of Marine Biological Resources and Inland Waters, Hellenic Center for Marine Research (HCMR), and Directorate-General for the Environment [ENV.B.2/ETU/2013/0026]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], biological invasions, European union, 01 natural sciences, Ecosystem services, invasive species, International Plant Protection Convention, uitheemse soorten, risicoanalyse, exotenbeleid, media_common, Convention on Biological Diversity, invasive alien species, Invasive species (management), B003-ecology, species directed nature management, Ecology, Environmental resource management, risk assessment, prioritization, Checklist, exoten, Risk assessment, socio-economic impacts, Invasive species (species diversity), management, risicobeoordeling, standaarden, Legislation, Context (language use), legislation, 010603 evolutionary biology, Ecology and Environment, consensus methods, media_common.cataloged_instance, 14. Life underwater, non native species, biodiversity policy, biodiversity impacts, business.industry, 010604 marine biology & hydrobiology, Prevention, Invasive species (damage management), 15. Life on land, 13. Climate action, business
Abstract: International audience; 1. Biological invasions are a threat to biodiversity, society and the economy. There is an urgent need to provide evidence- based assessments of the risks posed by invasive alien species (IAS) to prioritize action. Risk assessments underpin IAS policies in many ways: informing legislation; providing justification of restrictions in trade or consumer activities; prioritizing surveillance and rapid response. There are benefits to ensuring consistency in content of IAS risk assessments globally, and this can be achieved by providing a framework of minimum standards as a checklist for quality assurance. 2. From a review of existing risk assessment protocols, and with reference to the requirements of the EU Regulation on IAS (1143/2014) and international agreements including the World Trade Organisation, Convention on Biological Diversity and International Plant Protection Convention, coupled with consensus methods, we identified and agreed upon 14 minimum standards (attributes) a riskassessment scheme should include. 3. The agreed minimum standards were as follows: (1) basic species description; (2) likelihood of invasion; (3) distribution, spread and impacts; (4) assessment of introduction pathways; (5) assessment of impacts on biodiversity and ecosystems; (6) Assessment of impact on ecosystem services; (7) assessment of socio-economic impacts; (8) consideration of status (threatened or protected) of species or habitat under threat; (9) assessment of effects of future climate change; (10) completion possible even when there is a lack of information; (11) documents information sources; (12) provides a summary in a consistent and interpretable form; (13) -includes uncertainty; (14) includes quality assurance. In deriving these minimum standards, gaps in knowledge required for completing risk assessments and the scope of existing risk assessment protocols were revealed, most notably in relation to assessing benefits, socio-economic impacts and impacts on ecosystem services but also inclusion of consideration of climate change. 4. Policy implications. We provide a checklist of components that should be within invasive alien species risk assessments and recommendations to develop risk assessments to meet these proposed minimum standards. Although inspired by implementation of the European Union Regulation on invasive alien species, and as such developed specifically within a European context, the derived framework and minimum standards could be applied globally.
Published: 2018
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38. Prevalence of tick-borne viruses in Ixodes ricinus assessed by high-throughput real-time pcr

Author: Rene Bødker, Karin Ullman, Jan Chirico, Mathilde Gondard, Conny van Solt-Smits, Kirstine Klitgaard, Lorraine Michelet, Seta Jahfari, Fimme J. van der Wal, Patrick Fach, Sara Moutailler, Anthony R. Fooks, Sabine Delannoy, Anna Aspán, Athinna Nisavanh, Elodie Devillers, Aline de Koeijer, Bernd Hoffmann, Hein Sprong, Karen L. Mansfield, 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 Dozulé, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Institut National de la Recherche Agronomique (INRA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Natl Vet Inst SVA, Institute of Diagnostic Virology, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Wageningen University and Research Centre (WUR), Laboratory for Zoonoses and Environmental Microbiology, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Animal and Plant Health Agency [Addlestone, UK] (APHA), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), CoVetLab grant (ANSES), Animal Health Department grant from INRA, CoVetLab grant (SVA), CoVetLab grant (WBVR), CoVetLab grant (DTU), CoVetLab grant (APHA), ANIHWA Grant Arbonet, ANSES, 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), and Technical University of Denmark [Lyngby] (DTU)
Subjects: 0301 basic medicine, Epidemiology, [SDV]Life Sciences [q-bio], Microfluidics, molecular epidemiology, law.invention, tick borne viruses, Tick borne, law, Prevalence, Screening method, Immunology and Allergy, Polymerase chain reaction, biology, Bacteriologie, General Medicine, Bacteriology, Host Pathogen Interaction & Diagnostics, 3. Good health, Europe, Infectious Diseases, Real-time polymerase chain reaction, Viruses, surveillance, europe, Microbiology (medical), Ixodes ricinus, Bioinformatica & Diermodellen, Real-Time Polymerase Chain Reaction, Virus, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Bio-informatics & Animal models, parasitic diseases, Animals, Epidemiology, Bio-informatics & Animal models, Host Pathogen Interaction & Diagnostics, Epidemiologie, Ixodes, General Immunology and Microbiology, Molecular epidemiology, Bacteriology, biology.organism_classification, Virology, Host Pathogen Interactie & Diagnostiek, High-Throughput Screening Assays, 030104 developmental biology, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, WIAS, microfluidic analysis, Arthropod Vector
Abstract: International audience; Ticks are one of the principal arthropod vectors of human and animal infectious diseases. Whereas the prevalence of tick-borne encephalitis virus in ticks in Europe is well studied, there is less information available on the prevalence of the other tick-borne viruses (TBVs) existing worldwide. The aim of this study was to improve the epidemiological survey tools of TBVs by the development of an efficient high-throughput test to screen a wide range of viruses in ticks. In this study, we developed a new high-throughput virus-detection assay based on parallel real-time PCRs on a microfluidic system, and used it to perform a large scale epidemiological survey screening for the presence of 21 TBVs in 18 135 nymphs of Ixodes ricinus collected from five European countries. This extensive investigation has (i) evaluated the prevalence of four viruses present in the collected ticks, (ii) allowed the identification of viruses in regions where they were previously undetected. In conclusion, we have demonstrated the capabilities of this new screening method that allows the detection of numerous TBVs in a large number of ticks. This tool represents a powerful and rapid system for TBVs surveillance in Europe and could be easily customized to assess viral emergence.
Published: 2018
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39. Scientific Reports

Author: Al Dahouk, Sascha, Köhler, Stephan, Occhialini, Alessandra, Jiménez de Bagüés, María Pilar, Hammerl, Jens Andre, Eisenberg, Tobias, Vergnaud, Gilles, Cloeckaert, Axel, Zygmunt, Michel, Whatmore, Adrian, Melzer, Falk, Drees, Kevin, Foster, Jeffrey, Wattam, Alice, Scholz, Holger, Department of Biological Safety, Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Institut de Recherche en Infectiologie de Montpellier (IRIM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Unidad de Producción y Sanidad Animal, Centro de Investigación y Tecnología Agroalimentaria, Instituto Agroalimentario de Aragón, University of Zaragoza - Universidad de Zaragoza [Zaragoza], Landesbetrieb Hessisches Landeslabor, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), German National Reference Laboratory for Animal Brucellosis, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Northern Arizona University [Flagstaff], Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre d’études d’Agents Pathogènes et Biotechologies pour la Santé (CPBS), Université Paris Sud (Paris 11), Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Paris-Saclay, Animal and Plant Health Agency (APHA), Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire (UNH), Biocomplexity Institute of Virginia Tech [Blacksburg], Virginia Tech [Blacksburg], Bundeswehr Institute of Microbiology, Federal funds from National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services HHSN272201400027C, Spanish grant INIA-RTA2013-00065-C02-01, Federal Institute for Risk Assessment, Germany 1329-485, Food and Rural Affairs at German Federal Institute SE0314 SE0316, Department of Environment, Federal Ministry of Food and Agriculture 47-003 1322-503 1322-619, Hessian Ministry of Environment, Climate Change, Agriculture and Consumer Protection, French DGA (Direction Generale de l'Armement) via the MicroType project ANR-14-ASMA-0002-02, European Defence Agency (EDA), Université de Montpellier (UM), UR Infectiologie animale et Santé publique (UR IASP), Bundeswehr Institute of Microbiology, Department of Bacteriology, Munich, Germany, RWTH Aachen University, Centro de Investigacion y Tecnologia Agroalimentaria de Aragon (CITA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Animal and Plant Health Agency [Addlestone, UK] (APHA), Friedrich-Loeffler-Institut (FLI), German Center for Infection Research, Partnersite Munich (DZIF), Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: phylogénétique, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], analysis resource, murine models, Tanzania, Mice, Germany, phénotypage, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Transmisión de enfermedades, Phylogeny, Mice, Inbred BALB C, amphibians, monocyte-derived macrophages, lipopolysaccharide, comparative sequence, mammifère, genetic diversity, Brucelosis, Biological Evolution, Brucellaceae, bacterial bioinformatics database, melitensis 16m, vole microtus-arvalis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Liver, Flagella, Host-Pathogen Interactions, Anura, Autre (Sciences du Vivant), [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], Biotechnologies, macrophage, Anfibios, brucella spp, Article, Cell Line, Genetic Heterogeneity, Bacterial Proteins, death, Animals, mammals, analyse moléculaire, Mamíferos, Macrophages, amphibien, Gene Expression Regulation, Bacterial, Brucella, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, infection, Producción y sanidad animal, Animals, Zoo, souche bactérienne, Gram-Negative Bacterial Infections, Spleen, Multilocus Sequence Typing
Abstract: Scientific reports 7, 44420 (2017). doi:10.1038/srep44420, Published by Nature Publishing Group, London
Published: 2017
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40. Experimental infection of cattle with Mycobacterium tuberculosis isolates shows the attenuation of the human tubercle bacillus for cattle

Author: Kevin Rue-Albrecht, Pierre Sarradin, Bernardo Villarreal-Ramos, Martin Vordermeier, Ronan Shaughnessy, Florence Carreras, Francisco J. Salguero, Kerri M. Malone, Adam O. Whelan, Stephen V. Gordon, Abraham Aseffa, Stefan Berg, Gobena Ameni, Bhagwati Khatri, Sébastien Holbert, Nathalie Winter, Alicia Smyth, Animal and Plant Health Agency [Addlestone, UK] (APHA), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), University of Surrey (UNIS), School of Veterinary Medicine, University of California, School of Agriculture and Food Science, University College Dublin [Dublin] (UCD), Aklilu Lemma Institute of Pathobiology, Addis Ababa University (AAU), Armauer Hansen Research Institute (AHRI), Plateforme d'Infectiologie Expérimentale (PFIE), Institut National de la Recherche Agronomique (INRA), University College Dublin (UCD), School of Biomolecular and Biomedical Sciences, EC H2020 program grant number 643381 (TBVAC2020), Trust grant number 075833/A/04/Z under their 'Animal health in the developing world' initiative, Science Foundation Ireland Investigator Award 08/IN.1/B2038, European Project: 228394,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2008-1,NADIR(2009), Gordon, Stephen V, University of California (UC), and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: 0301 basic medicine, bovin, infection expérimentale, lcsh:Medicine, Bacillus, souche pathogène atténuée, lcsh:Science, Human tubercle bacillus, 0303 health sciences, Mycobacterium bovis, Multidisciplinary, biology, Microbiology and Parasitology, Microbiologie et Parasitologie, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Mycobacterium tuberculosis complex, Biomarker (medicine), Veterinary medicine and animal Health, Female, biomarqueur, Tuberculosis, 030106 microbiology, Article, Microbiology, Mycobacterium tuberculosis, 03 medical and health sciences, medicine, Animals, Humans, 030304 developmental biology, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, 030306 microbiology, lcsh:R, Genetic variants, biology.organism_classification, medicine.disease, Virology, 030104 developmental biology, Médecine vétérinaire et santé animal, lcsh:Q, Cattle, RNA-seq, pathologie humaine, Tuberculosis, Bovine, Bacteria, Biomarkers
Abstract: The Mycobacterium tuberculosis complex (MTBC) is the collective term given to the group of bacteria that cause tuberculosis (TB) in mammals. It has been reported that M. tuberculosis H37Rv, a standard reference MTBC strain, is attenuated in cattle compared to Mycobacterium bovis. However, as M. tuberculosis H37Rv was isolated in the early 1930s, and genetic variants are known to exist, we sought to revisit this question of attenuation of M. tuberculosis for cattle by performing a bovine experimental infection with a recent M. tuberculosis isolate. Here we report infection of cattle using M. bovis AF2122/97, M. tuberculosis H37Rv, and M. tuberculosis BTB1558, the latter isolated in 2008 during a TB surveillance project in Ethiopian cattle. We show that both M. tuberculosis strains caused reduced gross pathology and histopathology in cattle compared to M. bovis. Using M. tuberculosis H37Rv and M. bovis AF2122/97 as the extremes in terms of infection outcome, we used RNA-Seq analysis to explore differences in the peripheral response to infection as a route to identify biomarkers of progressive disease in contrast to a more quiescent, latent infection. Our work shows the attenuation of M. tuberculosis strains for cattle, and emphasizes the potential of the bovine model as a ‘One Health’ approach to inform human TB biomarker development and post-exposure vaccine development.
Published: 2017
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41. Tick-pathogen interactions and vector competence: Identification of molecular drivers for tick-borne diseases

Author: Anna Papa, Nataliia Rudenko, Ryan O. M. Rego, Santo Caracappa, Nicholas Johnson, Marie Vancová, Ana Domingos, Alejandro Cabezas-Cruz, Christian Gortázar, Libor Grubhoffer, Maryna Golovchenko, Sarah Bonnet, Ard M. Nijhof, José de la Fuente, Katherine M. Kocan, Nieves Ayllón, Pilar Alberdi, Anthony R. Fooks, Sandra Antunes, Agustín Estrada-Peña, Karen L. Mansfield, Margarita Villar, Alessandra Torina, Ministerio de Economía y Competitividad (España), European Commission, Universidad de Castilla La Mancha, Fundação para a Ciência e a Tecnologia (Portugal), Instituto de Investigación en Recursos Cinegéticos (IREC), Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University [Stillwater] (OSU), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), 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 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), Biology Centre, Institute of Parasitology, Czech Academy of Sciences [Prague] (CAS), Faculty of ScienceˇCeské Budeˇ jovice, Czechia, University of South Bohemia, Facultad de ciencias veterinarias [Sante Fe] (FCV), Universidad Nacional del Litoral [Santa Fe] (UNL), Animal and Plant Health Agency [Addlestone, UK] (APHA), Faculty of Health and Medicine, University of Surrey (UNIS), Institute of Infection and Global Health Liverpool, University of Liverpool, Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Department of Microbiology, Medical School, University of Thessaly [Volos] (UTH), National Center of Reference for Anaplasma, Babesia, Rickettsia and Theileria, Istituto Zooprofilattico Sperimentale della Sicilia, Ministerio de Economia y Competitividad (Spain) [BFU2016-79892-P], FCT [UID/Multi/04413/2013], University of Castilla-La Mancha (UCLM), Spain, European Project: 278976, Rego, Ryan O. M., Oklahoma State University [Stillwater], 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), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Laboratoire de santé animale, sites de Maisons-Alfort et de Normandie, Universidade Nova de Lisboa (NOVA), Czech Academy of Sciences [Prague] (ASCR), and Animal and Plant Health Agency (APHA)
Subjects: 0301 basic medicine, Microbiology (medical), Anaplasma, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Immunology, Babesia, Review, Tick, Microbiology, 03 medical and health sciences, 0302 clinical medicine, Ticks, parasitic diseases, medicine, Disease Transmission, Infectious, Animals, Humans, Microbiome, Pathogen, Genetics, Tick-borne disease, biology, Transmission (medicine), Borrelia, Flavivirus, tick, flavivirus, immunology, vaccine, medicine.disease, biology.organism_classification, bacterial infections and mycoses, Virology, 3. Good health, 030104 developmental biology, Infectious Diseases, Tick-Borne Diseases, Vector (epidemiology), Host-Pathogen Interactions, Identification (biology), Arachnid Vectors, Vaccine
Abstract: Ticks and the pathogens they transmit constitute a growing burden for human and animal health worldwide. Vector competence is a component of vectorial capacity and depends on genetic determinants affecting the ability of a vector to transmit a pathogen. These determinants affect traits such as tick-host-pathogen and susceptibility to pathogen infection. Therefore, the elucidation of the mechanisms involved in tick-pathogen interactions that affect vector competence is essential for the identification of molecular drivers for tick-borne diseases. In this review, we provide a comprehensive overview of tick-pathogen molecular interactions for bacteria, viruses, and protozoa affecting human and animal health. Additionally, the impact of tick microbiome on these interactions was considered. Results show that different pathogens evolved similar strategies such as manipulation of the immune response to infect vectors and facilitate multiplication and transmission. Furthermore, some of these strategies may be used by pathogens to infect both tick and mammalian hosts. Identification of interactions that promote tick survival, spread, and pathogen transmission provides the opportunity to disrupt these interactions and lead to a reduction in tick burden and the prevalence of tick-borne diseases. Targeting some of the similar mechanisms used by the pathogens for infection and transmission by ticks may assist in development of preventative strategies against multiple tick-borne diseases., Part of the research included in this review was supported by the Ministerio de Economia y Competitividad (Spain) grant BFU2016-79892-P and the European Union (EU) Seventh Framework Programme (FP7) ANTIGONE project number 278976. SA and AD would like to acknowledge FCT for funds to GHTM - UID/Multi/04413/2013. MV was supported by the Research Plan of the University of Castilla-La Mancha (UCLM), Spain.
Published: 2017
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42. Classical scrapie transmission in ARR/ARR genotype sheep

Author: Hervé Cassard, Fabien Corbière, Alvina Huor, Séverine Lugan, Cécile Tillier, François Schelcher, Jean-Yves Douet, Naima Aron, Pierette Costes, Caroline Lacroux, Olivier Andreoletti, Hugh Simmons, 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, Animal and Plant Health Agency [Addlestone, UK] (APHA), and Ecole Nationale Vétérinaire de Toulouse (ENVT)
Subjects: 0301 basic medicine, Genotype, 040301 veterinary sciences, Prions, Sheep Diseases, Scrapie, Biology, law.invention, 0403 veterinary science, 03 medical and health sciences, Mice, law, Virology, medicine, Limited capacity, Animals, Incubation, Transmissible spongiform encephalopathy, Sheep, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.BA]Life Sciences [q-bio]/Animal biology, 04 agricultural and veterinary sciences, Classical scrapie, medicine.disease, 030104 developmental biology, Transmission (mechanics), [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology
Abstract: International audience; The ARR allele is considered to provide a very strong resistance against classical scrapie infection in sheep. In this study, we report the occurrence of clinical transmissible spongiform encephalopathy in ARR/ARR sheep, following their inoculation by the intracerebral route with a classical scrapie isolate. On first passage, the disease displayed an incomplete attack rate transmission, with incubation periods exceeding 6 years. On second passage, the obtained prion did not display better abilities to propagate than the original isolate. These transmission results contrasted with the 100 % attack rate and the short incubation periods observed in ARQ/ARQ sheep challenged with the same isolate. These data confirm that ARR/ARR sheep cannot be considered to be fully resistant to classical scrapie. However, they also support the contention that classical scrapie has a very limited capacity to transmit and adapt to ARR/ARR sheep.
Published: 2017
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43. Infectivity in bone marrow from sporadic CJD patients

Author: Huor, A., Douet, J. Y., Lacroux, C., Lugan, S., Tillier, C., Aron, N., Cassard, H., Arnold, M., Torres, J. M., Ironside, J. W., Andréoletti, O., 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, Animal and Plant Health Agency [Addlestone, UK] (APHA), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), and University of Edinburgh
Subjects: Male, Prions, animal diseases, [SDV]Life Sciences [q-bio], Mice, Transgenic, Middle Aged, Creutzfeldt-Jakob Syndrome, Prion Proteins, nervous system diseases, Disease Models, Animal, Infectivity, sCJD, mental disorders, Animals, Humans, Female, Bone marrow, Aged
Abstract: Prion infectivity was recently identified in the blood of both sporadic and variant Creutzfeldt–Jakob disease (CJD) patients. In variant CJD (vCJD), the widespread distribution of prions in peripheral tissues of both asymptomatic and symptomatic patients is likely to explain the occurrence of the observed prionaemia. However, in sporadic CJD (sCJD), prion infectivity is described to be located principally in the central nervous system. In this study, we investigated the presence of prion infectivity in bone marrow collected after death in patients affected with different sCJD agents. Bioassays in transgenic mice expressing the human prion protein revealed the presence of unexpectedly high levels of infectivity in the bone marrow from seven out of eight sCJD cases. These findings may explain the presence of blood-borne infectivity in sCJD patients. They also suggest that the distribution of prion infectivity in peripheral tissues in sCJD patients could be wider than currently believed, with potential implications for the iatrogenic transmission risk of this disease. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Published: 2017
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44. Mixing of porpoise ecotypes in South Western UK waters revealed by genetic profiling

Author: Michael C. Fontaine, Rob Deaville, Paul Jepson, Nicolas Ray, Sylvain Piry, Nicholas J. Davison, Simon J. Goodman, Olivier Thatcher, Andrew Brownlow, Fontaine lab, Sch Biol, Fac Biol Sci, University of Leeds, Groningen Inst Evolutionary Life Sci GELIFES, University of Groningen, Inst. Zool., Zoological Society of London, Dept. Zool., University of Cambridge, EnviroSPACE Laboratory, Institute for Environmental Sciences [Geneva] (ISE), University of Geneva [Switzerland]-University of Geneva [Switzerland], Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Scottish Marine Animal Stranding Scheme, SRUC Veterinary Service, Scotland's Rural College (SRUC), Animal and Plant Health Agency [Addlestone, UK] (APHA), EnviroSPACE Laboratory, Institute for Environmental Sciences, University of Geneva, SRUC, Animal and Plant Health Agency (APHA), Fontaine, Michael C., Goodman, Simon J., and Université de Genève = University of Geneva (UNIGE)-Université de Genève = University of Geneva (UNIGE)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Climate change, Phocoena, Admixture, Biology, 010603 evolutionary biology, 01 natural sciences, Molecular ecology, 03 medical and health sciences, biology.animal, ecotype specialization, 14. Life underwater, lcsh:Science, molecular ecology, dispersal, 030304 developmental biology, Isolation by distance, ddc:333.7-333.9, 0303 health sciences, Multidisciplinary, Ecotype, Ecology, Biology (Whole Organism), continuous population, Pelagic zone, Dispersal, Continuous population, biology.organism_classification, 030104 developmental biology, climate change, Ecotype specialization, Genetic structure, Microsatellite, Biological dispersal, admixture, lcsh:Q, Bay, Porpoise, Research Article
Abstract: Contact zones between ecotypes are windows for understanding how species may react to climate changes. Here, we analysed the fine-scale genetic and morphological variation in harbour porpoises (Phocoena phocoena) around the UK by genotyping 591 stranded animals at nine microsatellite loci. The data were integrated with a prior study to map at high resolution the contact zone between two previously identified ecotypes meeting in the northern Bay of Biscay. Clustering and spatial analyses revealed that UK porpoises are derived from two genetic pools with porpoises from the southwestern UK being genetically differentiated, and having larger body sizes compared to those of other UK areas. Southwestern UK porpoises showed admixed ancestry between southern and northern ecotypes with a contact zone extending from the northern Bay of Biscay to the Celtic Sea and Channel. Around the UK, ancestry blends from one genetic group to the other along a southwest--northeast axis, correlating with body size variation, consistent with previously reported morphological differences between the two ecotypes. We also detected isolation by distance among juveniles but not in adults, suggesting that stranded juveniles display reduced intergenerational dispersal. The fine-scale structure of this admixture zone raises the question of how it will respond to future climate change and provides a reference point for further study.
Published: 2017
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45. In Vitro Modeling of Nerve–Muscle Connectivity in a Compartmentalized Tissue Culture Device

Author: Mark Rigby, Virgile Viasnoff, Juan Burrone, Andrew S. Lowe, Stephanie Hynes, Ivo Lieberam, Carolina Barcellos Machado, Victoria Gonzalez Sabater, Peter Harley, Danielle Stevenson, Perrine Pluchon, Department of Biological Sciences, Dartmouth College [Hanover], Animal and Plant Health Agency [Addlestone, UK] (APHA), Natural Environment Research Council (NERC), MRC Centre for Developmental Neurobiology, Mechanobiology Institute [Singapore] (MBI), and National University of Singapore (NUS)
Subjects: microdevice, myofibre, Biomedical Engineering, Hindbrain, Optogenetics, Biology, Article, General Biochemistry, Genetics and Molecular Biology, Neuromuscular junction, Biomaterials, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, Myocyte, motor neuron, optogenetics, Neurotransmitter, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Denervation, 0303 health sciences, Motor neuron, embryonic stem cell, Embryonic stem cell, medicine.anatomical_structure, chemistry, Neuroscience, 030217 neurology & neurosurgery
Abstract: Motor neurons project axons from the hindbrain and spinal cord to muscle, where they induce myofibre contractions through neurotransmitter release at neuromuscular junctions. Studies of neuromuscular junction formation and homeostasis have been largely confined to in vivo models. In this study we have merged three powerful tools - pluripotent stem cells, optogenetics and microfabrication – and designed an open microdevice in which motor axons grow from a neural compartment containing embryonic stem cell-derived motor neurons and astrocytes through microchannels to form functional neuromuscular junctions with contractile myofibers in a separate compartment. Optogenetic entrainment of motor neurons in this reductionist neuromuscular circuit enhanced neuromuscular junction formation more than two-fold, mirroring the activity-dependence of synapse development in vivo. We incorporated an established motor neuron disease model into our system and found that coculture of motor neurons with SOD1G93A astrocytes resulted in denervation of the central compartment and diminished myofiber contractions, a phenotype which was rescued by the Receptor Interacting Serine/Threonine Kinase 1 (RIPK1) inhibitor Necrostatin. This coculture system replicates key aspects of nerve-muscle connectivity in vivo and represents a rapid and scalable alternative to animal models of neuromuscular function and disease.
Published: 2019
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46. Mononucleated Blood Cell Populations Display Different Abilities To Transmit Prion Disease by the Transfusion Route

Author: Fabien Corbière, Claire Litaise, Hervé Cassard, Caroline Lacroux, Naima Aron, Séverine Lugan, Jean-Yves Douet, Pierrette Costes, Mark Arnold, Cécile Tillier, Hugh Simmons, Olivier Andreoletti, 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, Animal and Plant Health Agency [Addlestone, UK] (APHA), and EU FP7 provided funding to Olivier Andreoletti under grant number Priority CT2009-222887. EU FEDER/INTERREG provided funding to Olivier Andreoletti under grant number EFA282/13 TANSPRION.
Subjects: atypical scrapie, 0301 basic medicine, medicine.medical_specialty, Blood transfusion, Prions, [SDV]Life Sciences [q-bio], medicine.medical_treatment, T-Lymphocytes, Immunology, Scrapie, 030204 cardiovascular system & hematology, Biology, Microbiology, Peripheral blood mononuclear cell, Creutzfeldt-Jakob Syndrome, components, 03 medical and health sciences, Mice, 0302 clinical medicine, genotypes, Virology, medicine, Animals, creutzfeldt-jakob-disease, spongiform encephalopathy, risk, Whole blood, B-Lymphocytes, Transmissible spongiform encephalopathy, Sheep, infectivity, Macrophages, Transfusion Reaction, Transfusion medicine, Mononucleated Blood Cell, medicine.disease, 3. Good health, Disease Models, Animal, 030104 developmental biology, Leukoreduction, variant cjd, Insect Science, Leukocytes, Mononuclear
Abstract: Previous experiments carried out in a sheep scrapie model demonstrated that the transfusion of 200 μl of prion-infected whole blood has an apparent 100% efficacy for disease transmission. These experiments also indicated that, despite the apparent low infectious titer, the intravenous administration of white blood cells (WBC) resulted in efficient disease transmission. In the study presented here, using the same transmissible spongiform encephalopathy (TSE) animal model, our aim was to determine the minimal number of white blood cells and the specific abilities of mononucleated cell populations to transmit scrapie by the transfusion route. Our results confirmed that the transfusion of 100 μl, but not 10 μl, of fresh whole blood collected in asymptomatic scrapie-infected donor sheep can transmit the disease. The data also show that the intravenous administration of 10 5 WBCs is sufficient to cause scrapie in recipient sheep. Cell-sorted CD45R + (predominantly B lymphocytes), CD4 + /CD8 + (T lymphocytes), and CD14 + (monocytes/macrophages) blood cell subpopulations all were shown to contain prion infectivity by bioassays in ovine PrP transgenic mice. However, while the intravenous administration of 10 6 CD45 + or CD4 + /8 + living cells was able to transmit the disease, similar numbers of CD14 + cells failed to infect the recipients. These data support the contention that mononucleated blood cell populations display different abilities to transmit TSE by the transfusion route. They also represent an important input for the risk assessment of blood-borne prion disease transmission and for refining the target performance of leukoreduction processes that currently are applied to mitigate the transmission risk in transfusion medicine. IMPORTANCE Interindividual variant Creutzfeldt-Jakob disease (vCJD) transmission through blood and blood-derived products is considered a major public health issue in transfusion medicine. Over the last decade, TSE in sheep has emerged as a relevant model for assessing the blood-borne vCJD transmission risk. In this study, using a sheep TSE model, we characterized the ability of different peripheral blood mononucleated cell populations to infect TSE-free recipients by the transfusion route. Our results indicate that as little as 10 5 WBC and 100 μl of blood collected from asymptomatic scrapie infected animals can transmit the disease. They also demonstrate unambiguously that peripheral blood mononuclear cell subpopulations display dramatically different abilities to transmit the disease. These data represent an important input for the risk assessment of blood-borne prion disease transmission and for refining the target performance of leukoreduction processes that currently are applied to mitigate the transmission risk in transfusion medicine.
Published: 2016
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47. A heterogeneous population of motile Brucellae out of the frog pond

Author: Al-Dahouk, S., Kohler, S., Occhialini, A., Jiménez de Bagüés, María P, Hammerl, Jens A, Eisenberg, Tobias, Vergnaud, G., Cloeckaert, Axel, Zygmunt, Michel S., Whatmore, Adrian M., Melzer, Falk, Drees, K.P., Foster, J.T., Wattam, A.R., Scholz, Holger C., Department of Biological Safety, Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Centre d’études d’Agents Pathogènes et Biotechologies pour la Santé (CPBS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Landesbetrieb Hessisches Landeslabor, I2BC, Centre National de la Recherche Scientifique (CNRS), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Animal and Plant Health Agency [Addlestone, UK] (APHA), Friedrich-Loeffler-Institut (FLI), Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire (UNH), Virginia Bioinformatics Institute, Virginia Tech [Blacksburg], Bundeswehr Institute of Microbiology, ProdInra, Migration, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), and Bundeswehr Institute of Microbiology. DEU.
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Rana, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Brucella, ComputingMilieux_MISCELLANEOUS
Abstract: Session DP : Biological Protection and Environmental Hazards; International audience
Published: 2015

48. Crossing Frontiers in Tackling Pathways of Biological Invasions

Author: Petr Pyšek, Sabrina Kumschick, Philip E. Hulme, Stefan Schindler, Tim M. Blackburn, Ingolf Kühn, Alain Roques, Giuseppe Brundu, Belinda Gallardo, Shyama Pagad, René Eschen, Angeliki F. Martinou, Argyro Zenetos, Helen E. Roy, Hanno Seebens, Jonathan M. Jeschke, Riccardo Scalera, Sven Bacher, Montserrat Vilà, Franz Essl, Sarah Brunel, Ana Cristina Cardoso, Wolfgang Rabitsch, Wolfgang Nentwig, Jan Pergl, Marc Kenis, Olaf Booy, Piero Genovesi, Bella S. Galil, Sonia Vanderhoeven, Quentin Groom, Emili García-Berthou, Colette O'Flynn, Colin A. Harrower, John R. U. Wilson, David M. Richardson, Stelios Katsanevakis, Μαρτίνου, Αγγελική, Department of Botany and Zoology, Stellenbosch University, University of Vienna [Vienna], Department of Biodiversity and Nature Conservation, Environment Agency Austria, Department of Biology, Northern Arizona University [Flagstaff], University of Adelaide, Distinguished Scientist Fellowship Program, King Saud University [Riyadh] (KSU), University College of London [London] (UCL), Animal and Plant Health Agency [Addlestone, UK] (APHA), Department of Agriculture, Università degli studi di Napoli Federico II, European and Mediterranean Plant Protection Organization - Organisation Européenne et Méditerranéenne pour la Protection des Plantes (EPPO), European Commission, CABI, Delemont, Switzerland, Partenaires INRAE, CSIC, EBD, E-41080 Seville, Spain, CSIR National Institute of Oceanography [India] (NIO), Department of environmental sciences, Universitat de Girona (UdG), International Union for Conservation of Nature, Institute for Environmental Protection and Research (ISPRA), Meise Botanic Garden, Natural Environment Research Council (NERC), Bio-Protection Research Centre, Lincoln University, University of the Aegean, Centre for Agricultural and Biosciences International (CABI), German Centre for Integrative Biodiversity Research (iDiv), Department of Geobotany and Botanical Garden, Martin-Luther-Universität Halle Wittenberg (MLU), Department of Community Ecology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of Cyprus, Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), National Biodiversity Data Centre, Waterford Institute of Technology, University of Auckland [Auckland], Institute of Botany, Czech Academy of Sciences [Prague] (CAS), Charles University in Prague, Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), University of Oldenburg, Plate-forme Belge de la Biodiversité, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Hellenic Center for Marine Research (HCMR), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Institute of Biology at the Department of Biology, Chemistry and Pharmacy, Free University of Berlin (FU), Austrian Climate Research Program ('Spec-Adapt') [KR11AC0K00355], ERA-Net BiodivERsA (project WhoIsNext), Austrian Science Foundation FWF, German VW-Foundation, ERA-Net BiodivERsA (project FFII), German Research Foundation DFG [JE 288/7-1], DFG [JE 288/9-1], DST-NRF Centre of Excellence for Invasion Biology, Working for Water programme, Swiss National Science Foundation, Drakenstein Trust, Natural Environment Research Council, Department for Environment, Food, and Rural Affairs, Joint Nature Conservation Committee, Czech Academy of Sciences [RVO 67985939], Czech Science Foundation [14-36079G, P504/11/1028], Czech Academy of Sciences, and Severo Ochoa Program for Centres of Excellence in R+D+I [SEV-2012-0262]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Temporal trends, Alien species, alien species, Introduced species, Biology, 580 Plants (Botany), 010603 evolutionary biology, 01 natural sciences, temporal trends, propagule pressure, Ecology, 010604 marine biology & hydrobiology, Propagule pressure, 15. Life on land, Biological Sciences, Key features, Management, Pathway information, Impact, impact, 570 Life sciences, biology, 590 Animals (Zoology), General Agricultural and Biological Sciences, Natural Sciences, management
Abstract: International audience; Substantial progress has been made in understanding how pathways underlie and mediate biological invasions. However, key features of their role in invasions remain poorly understood, available knowledge is widely scattered, and major frontiers in research and management are insufficiently characterized. We review the state of the art, highlight recent advances, identify pitfalls and constraints, and discuss major challenges in four broad fields of pathway research and management: pathway classification, application of pathway information, management response, and management impact. We present approaches to describe and quantify pathway attributes (e.g., spatiotemporal changes, proxies of introduction effort, environmental and socioeconomic contexts) and how they interact with species traits and regional characteristics. We also provide recommendations for a research agenda with particular focus on emerging (or neglected) research questions and present new analytical tools in the context of pathway research and management.
Published: 2015
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49. ResFinder 4.0 for predictions of phenotypes from genotypes

Author: Isabelle Kempf, Frank Møller Aarestrup, Marilyn C. Roberts, Valeria Bortolaia, Guido Werner, Linda Fagelhauer, Lurdes Clemente, Mette Pinholt, Ana-Rita Rebelo, Etienne Ruppé, Joël Mossong, Rosa Lundbye Allesøe, Satu Olkkola, Vincent Cattoir, Alain Philippon, Kerstin Stingl, Minh Ngoc Nguyen, Jasmine Coppens, Jennifer K. Bender, Ole Lund, Surbhi Malhotra-Kumar, Muna F. Anjum, Alfred Ferrer Florensa, Kinga Wieczorek, Ana Amaro, Suvi Nykäsenoja, Catherine Ragimbeau, Nicholas A. Duggett, Rolf Sommer Kaas, Basil Britto Xavier, Trinad Chakraborty, Stefan Schwarz, Henrik Westh, Serge Losch, Bernd Neumann, Technical University of Denmark [Lyngby] (DTU), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, University of Washington [Seattle], Freie Universität Berlin, ARN régulateurs bactériens et médecine (BRM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), CHU Pontchaillou [Rennes], Université Paris Descartes - Faculté de Médecine (UPD5 Médecine), Université Paris Descartes - Paris 5 (UPD5), Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), Robert Koch Institute [Berlin] (RKI), German Federal Institute for Risk Assessment [Berlin] (BfR), Universiteit Antwerpen [Antwerpen], University of Copenhagen = Københavns Universitet (KU), Hvidovre Hospital, Animal and Plant Health Agency [Addlestone, UK] (APHA), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Finnish Food Authority, Partenaires INRAE, National Veterinary Research Institute [Pulawy, Pologne] (NVRI), Instituto Nacional de Investigação Agrária e Veterinária = National Institute for Agrarian and Veterinary Research [Oeiras, Portugal] (INIAV), Laboratoire National de Santé [Luxembourg] (LNS), NNF16OC0021856, Novo Nordisk Fonden, 03ZZ0815A, Bundesministerium für Bildung und Forschung, Global Surveillance of Antimicrobial Resistance, German Center of Infection Research, Zoonoses Network ‘ESBL, 01KI1313G, German Federal Ministry of Education and Research, European Project: 643476,H2020,H2020-PHC-2014-single-stage,COMPARE(2014), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Universiteit Antwerpen = University of Antwerpen [Antwerpen], and University of Copenhagen = Københavns Universitet (UCPH)
Subjects: Microbiology (medical), Genotype, [SDV]Life Sciences [q-bio], Antimicrobial susceptibility, Microbial Sensitivity Tests, Drug resistance, Computational biology, Biology, 03 medical and health sciences, Antibiotic resistance, Antibiogram, SDG 3 - Good Health and Well-being, Drug Resistance, Bacterial, medicine, Animals, Humans, AcademicSubjects/MED00740, Pharmacology (medical), Original Research, 030304 developmental biology, Pharmacology, 0303 health sciences, medicine.diagnostic_test, 030306 microbiology, Pharmacology. Therapy, Antimicrobial, Anti-Bacterial Agents, 3. Good health, Phenotype, AcademicSubjects/MED00290, Infectious Diseases, Human medicine, AcademicSubjects/MED00230
Abstract: Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.
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50. Estimating the likelihood of ESBL-producing E. coli carriage in slaughter-aged pigs following bacterial introduction onto a farm: A multiscale risk assessment

Author: Catherine McCarthy, Robin R. L. Simons, Christine Gavin, Pascal Sanders, Alexis Viel, Animal and Plant Health Agency [Addlestone, UK] (APHA), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and European Project: 773830, H2020-SFS-2017-1 ,One Health EJP(2018)
Subjects: pig, Microbiology (medical), Veterinary medicine, Epidemiology, medicine.drug_class, abattoir, Disinfectant, Population, Antibiotics, résistance aux antibiotiques, Biology, Pharmacokinetic-pharmacodynamic model, law.invention, 03 medical and health sciences, Antibiotic resistance, law, résistance aux antimicrobians, Escherichia coli, medicine, animal, porcin, antimicrobial resistance, human, microbiologie, bacteria, education, 030304 developmental biology, bactérie, 2. Zero hunger, 0303 health sciences, education.field_of_study, 030306 microbiology, microbiology, transmission, swine, modèle pharmacodynamique pharmacocinétique, Transmission model, Antimicrobial, élevage, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Transmission (mechanics), Carriage, slaughter, humain, Risk assessment, farm
Abstract: International audience; The transmission of antimicrobial resistance (AMR) between animals, their environment, food and humans is a complex issue. Previous pharmacokinetic-pharmacodynamic (PKPD) models indicate that extended-spectrum β-lactamase (ESBL) resistant bacterial populations may be self-sustaining through horizontal and vertical gene transfer, even in the absence of antimicrobial pressure. However, models focusing purely on the biochemical aspects fail to incorporate the complicated host population dynamics which occur within a farm environment. Models of disease transmission within commercial farm environments can provide further insight to the on-farm transmission dynamics of AMR between animals and their environment, as well as predict the effect of various on-farm interventions. Here, we present a risk assessment which predicts the likelihood that slaughter-aged pigs would carry resistant bacteria after a single introduction of ESBL E. coli on commercial pig farms. We incorporate outputs from a PKPD model which explores the complex host/gastrointestinal bacteria interplay after antimicrobial treatment; with an on-farm model of bacterial transmission. The risk assessment is designed to be adaptable for the simultaneous transmission of multiple bacteria and resistant strains. We predicted that after introduction onto a pig farm, ESBL E. coli bacteria are likely to persist on the farm for more than a year, leading to a high batch prevalence (39.4% slaughter pigs, 5th and 95th percentiles: 0.0–57.5) and high faecal shedding. A comparison of different farm management types suggested that all-in-all-out housing was a protective measure for both prevalence in slaughter-aged pigs and faecal shedding rates. We applied two main interventions at the farm level, an enhanced cleaning and disinfectant (C&D) protocol and isolation of pigs in sick pens for the duration of their antibiotic treatment. Both interventions were able to reduce the number of pigs shedding more than 2 log10 ESBL E. coli from 18.7% (5th and 95th percentiles: 5.9–30.4) in the baseline scenario, to 7.2% (5th and 95th percentiles: 0.0–21.5) when an enhanced C&D protocol was applied, 0.1% (5th and 95th percentiles: 0.0–0.3) when sick pens were used and 0.1% (5th and 95th percentiles: 0.0–0.3) when a combination of enhanced C&D plus sick pens was used. Both scenarios also reduced the prevalence in batches of pigs going to slaughter. This effect was largest when sick pens were used, where 75% of batches had 0% positive pigs. The results suggest that a single introductory event is sufficient to cause a substantial risk of carriage in slaughter-aged pigs. Further quantitative microbial risk assessments (QMRA) are needed to consider the onwards risk posed to later parts of the food chain.
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