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1. Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

Author: Marisa Haenni, Christophe Dagot, Olivier Chesneau, Delphine Bibbal, Jérôme Labanowski, Michèle Vialette, Damien Bouchard, Fabrice Martin-Laurent, Louisiane Calsat, Sylvie Nazaret, Fabienne Petit, Anne-Marie Pourcher, Anne Togola, Morgane Bachelot, Edward Topp, Didier Hocquet, Laboratoire de Lyon [ANSES], Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Anti-infectieux : supports moléculaires des résistances et innovations thérapeutiques (RESINFIT), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), Collection de l'Institut Pasteur (CIP), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Innovations Thérapeutiques et Résistances (InTheRes), 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), Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Université de Poitiers-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Anses ANMV (Anses ANMV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Agroécologie [Dijon], Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon, 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), Direction de l'Evaluation des Risques (DER), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Morphodynamique Continentale et Côtière (M2C), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Milieux Environnementaux, Transferts et Interactions dans les hydrosystèmes et les Sols (METIS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Optimisation des procédés en Agriculture, Agroalimentaire et Environnement (UR OPAALE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM), Agriculture and Agri-Food Canada, Saskatoon Research Centre, Agriculture and Agri-Food (AAFC), University of Western Ontario (UWO), Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), This document was prepared thanks to the collective expert assessment, carried out by the Anses expert working group ‘Antimicrobial resistance and the environment’ (ANSES opinion 2016-SA-0252), chaired by Morgane Bachelot and whose active contributors are co-authors of this publication., Togola, Anne, Institut Pasteur [Paris], AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Agriculture and Agri-Food [Ottawa] (AAFC), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), 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), Agence nationale du médicament vétérinaire (ANMV), and École Pratique des Hautes Études (EPHE)
Subjects: [SDE] Environmental Sciences, MESH: Drug Resistance, Microbial, Antibiotic resistance, MESH: One Health, 010501 environmental sciences, Wastewater, 01 natural sciences, MESH: Waste Water, 03 medical and health sciences, Rivers, MESH: Anti-Bacterial Agents, Drug Resistance, Bacterial, Animals, GE1-350, One Health, 030304 developmental biology, 0105 earth and related environmental sciences, General Environmental Science, Environmental antibiotic concentrations, 0303 health sciences, Bacteria, Aquatic environment, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, 6. Clean water, Anti-Bacterial Agents, 3. Good health, Environmental sciences, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Terrestrial environment, 13. Climate action, [SDE]Environmental Sciences, Organic waste product, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [CHIM.OTHE]Chemical Sciences/Other, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: This document was prepared thanks to the collective expert assessment, carried out by the Anses expert working group ‘Antimicrobial resistance and the environment’ (ANSES opinion 2016-SA-0252), chaired by Morgane Bachelot and whose active contributors are co-authors of this publication.; International audience; Antimicrobial resistance (AMR) is a major global public health concern, shared by a large number of human and animal health actors. Within the framework of a One Health approach, actions should be implemented in the environmental realm, as well as the human and animal realms. The Government of France commissioned a report to provide policy and decision makers with an evidential basis for recommending or taking future actions to mitigate AMR in the environment. We first examined the mechanisms that underlie the emergence and persistence of antimicrobial resistance in the environment. This report drew up an inventory of the contamination of aquatic and terrestrial environments by AMR and antibiotics, anticipating that the findings will be representative of some other high-income countries. Effluents of wastewater treatment plants were identified as the major source of contamination on French territory, with spreading of organic waste products as a more diffuse and incidental contamination of aquatic environments. A limitation of this review is the heterogeneity of available data in space and time, as well as the lack of data for certain sources.Comparing the French Measured Environmental Concentrations (MECs) with predicted no effect concentrations (PNECs), fluoroquinolones and trimethoprim were identified as representing high and medium risk of favoring the selection of resistant bacteria in treated wastewater and in the most contaminated rivers. All other antibiotic molecules analyzed (erythromycin, clarithromycin, azithromycin, tetracycline) were at low risk of resistance selection in those environments. However, the heterogeneity of the data available impairs their full exploitation. Consequently, we listed indicators to survey AMR and antibiotics in the environment and recommended the harmonization of sampling strategies and endpoints for analyses.Finally, the objectives and methods used for the present work could comprise a useful example for how national authorities of countries sharing common socio-geographic characteristics with France could seek to better understand and define the environmental dimension of AMR in their particular settings.
Published: 2022

2. Destruction of Staphylococcus aureus biofilms by combining an antibiotic with subtilisin A or calcium gluconate

Author: Aude A. Ferran, JingJing Liu, Alain Bousquet-Mélou, Jean-Yves Madec, Marisa Haenni, 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), Innovations Thérapeutiques et Résistances (InTheRes), 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), 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, [SDV]Life Sciences [q-bio], Antibiotics, Matrix (biology), medicine.disease_cause, Extracellular polymeric substances, MESH: Staphylococcus aureus, Subtilisins, Multidisciplinary, biology, Chemistry, Extracellular Polymeric Substance Matrix, Polysaccharides, Bacterial, Glycopeptides, Drug Synergism, Staphylococcal Infections, Antimicrobial, Calcium Gluconate, Anti-Bacterial Agents, Drug Combinations, Staphylococcus aureus, Medicine, Macrolides, Fluoroquinolones, Methicillin-Resistant Staphylococcus aureus, medicine.drug_class, Science, 030106 microbiology, chemistry.chemical_element, MESH: Extracellular Polymeric Substance Matrix, Microbial Sensitivity Tests, MESH: Biofilms, Calcium, beta-Lactams, Article, Microbiology, 03 medical and health sciences, Extracellular polymeric substance, medicine, Humans, Biofilm, biology.organism_classification, 030104 developmental biology, Aminoglycosides, Biofilms, Bacteria
Abstract: In S. aureus biofilms, bacteria are embedded in a matrix of extracellular polymeric substances (EPS) and are highly tolerant to antimicrobial drugs. We thus sought to identify non-antibiotic substances with broad-spectrum activity able to destroy the EPS matrix and enhance the effect of antibiotics on embedded biofilm bacteria. Among eight substances tested, subtilisin A (0.01 U/mL) and calcium gluconate (CaG, Ca2+ 1.25 mmol/L) significantly reduced the biomass of biofilms formed by at least 21/24 S. aureus isolates. Confocal laser scanning microscopy confirmed that they both eliminated nearly all the proteins and PNAG from the matrix. By contrast, antibiotics alone had nearly no effect on biofilm biomass and the selected one (oxytetracycline-OTC) could only slightly reduce biofilm bacteria. The combination of OTC with CaG or subtilisin A led to an additive reduction (average of 2 log10 CFU/mL) of embedded biofilm bacteria on the isolates susceptible to OTC (MBC 10 CFU/mL for 20–25% of the isolates. Further studies are now required to better understand the factors that cause the biofilm produced by specific isolates (20–25%) to be susceptible to the combinations.
Published: 2021

3. Selection of ESBL-producing Escherichia coli in the gut of calves experimentally fed with milk containing antibiotic residues

Author: Marisa Haenni, Véronique Métayer, Alain Bousquet-Mélou, Véronique Dupouy, Nathalie Arpaillange, Jean-Yves Madec, Jessica Wucher, Béatrice B. Roques, Innovations Thérapeutiques et Résistances (InTheRes), 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), 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), and Plan EcoAntibio 2012-2017
Subjects: Male, Veterinary medicine, Antibiotic residues, MESH: Drug Resistance, Microbial, medicine.drug_class, [SDV]Life Sciences [q-bio], Antibiotics, Esbl production, Cefquinome, Calves, Biology, medicine.disease_cause, Antimicrobial resistance, Microbiology, beta-Lactamases, 03 medical and health sciences, Feces, Antibiotic resistance, Enterobacterales, medicine, Escherichia coli, Animals, Escherichia coli Infections, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, General Veterinary, 030306 microbiology, MESH: cefquinome, Age Factors, Genetic Variation, General Medicine, biochemical phenomena, metabolism, and nutrition, Antimicrobial, MESH: Cultured Milk Products, Animal Feed, Bacterial Load, Anti-Bacterial Agents, Cephalosporins, Gastrointestinal Microbiome, Milk, ESBL, Female, Cattle, MESH: Dairy Products, Dairy farms, medicine.drug
Abstract: International audience; In the bovine sector, the spread of Enterobacterales producing extended-spectrum and AmpC β-lactamases (ESBL/AmpC) mostly concerns veal calves, and the use of waste milk containing antibiotic residues has been recurrently incriminated. In this study, calves were experimentally fed with milk containing either 2,000 μg/L or 20,000 μg/L of the critically important antibiotic cefquinome. The total counts of enterobacterales and ESBL-producing E. coli were monitored using non-selective and selective media. Our data highlighted the important combination of two main factors (cefquinome exposure and initial ESBL colonization level) in the ESBL selection and amplification process in the gut of calves. Results also proved the dose-independent effect of cefquinome administration on the selection and amplification of ESBL-producing E. coli. Finally, the blaCTX-M-1/IncI1 ST3 plasmid was systematically recovered after cefquinome exposure, highlighting its epidemic success. Altogether, this work is one of the rare experimental studies providing quantitative information on the impact of waste milk containing antimicrobials on the ESBL load in calves' microbiota, and the first one using cefquinome. These data emphasise the need for global guidelines on the use of waste milk on dairy farms in order to decrease the antimicrobial resistance burden in this sector.
Published: 2021

4. Characterization of cultivable airborne bacteria and their antimicrobial resistance pattern in French milking parlour

Author: Jean-Yves Madec, Véronique Métayer, Marisa Haenni, Charlotte Valat, Janick Rocher, Frédéric Laurent, Antoine Drapeau, Sandrine Bayle, Laboratoire des Sciences des Risques (LSR), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), 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), Saint-Christol (SAINT-CHRISTOL), Institut National de la Recherche Agronomique (INRA), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes, 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), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)
Subjects: Veterinary medicine, medicine.drug_class, Antibiotic resistance, Health, Toxicology and Mutagenesis, Antibiotics, Indoor bioaerosol, 010501 environmental sciences, Opportunist pathogen, medicine.disease_cause, 01 natural sciences, Milking parlour, Milking, [SPI]Engineering Sciences [physics], medicine, Environmental Chemistry, 0105 earth and related environmental sciences, biology, Pathogenic bacteria, General Medicine, Bovine, Acinetobacter, biology.organism_classification, Pollution, Aerococcus, Airborne, Particulate matter, Bacteria
Abstract: International audience; The main goal of this preliminary study was to quantify airborne particles and characterize the dominant cultivable bacterial species as well as some Gram-positive species, and their antibiotic resistance pattern, from environmental samples taken inside and outside of a dairy milking parlour. Sampling was performed over 2 days, in different seasons. The small viable particulate matter < 10 μm (bioaerosols) and cultivable bacteria reached their highest concentrations in the milking parlour. The majority of airborne bacteria in the milking parlour belonged to the genera Staphylococcus (41.9%) and Bacillus (20.9%). A total of 32 different bacterial species of Staphylococcus, Aerococcus, Bacillus, Pseudomonas, Serratia and Acinetobacter were identified. Many of these bacteria may be opportunistic pathogens, causing disease in humans or animals. We found low levels of acquired resistance to the antibiotics commonly used in human or animal infections caused by these opportunistic bacteria. More specifically, resistance to tetracyclines (13.4%), penicillin G (13.4%) and macrolides (7.5%) was identified in Staphylococcus sp. as was a methicillin-resistant S. hominis and resistance to spiramycin (n = 1), lincomycin (n = 1) and streptomycin (n = 2) in Aerococcus sp. An assessment of the occupational risk run by dairy farmers for contracting infections after long- or short-term exposure to micro-organisms requires further studies on the concentration of opportunistic pathogenic bacteria in dairy farm environments.
Published: 2021

5. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales

Author: Pierre Bogaerts, Marisa Haenni, Elodie Couvé-Deacon, Rémy A. Bonnin, Jean-Yves Madec, Olivier Barraud, Lauraine Gauthier, Nicolas Fortineau, Philippe Glaser, Gaelle Cuzon, Laurent Dortet, Agnès B Jousset, Delphine Girlich, Thierry Naas, Youri Glupczynski, Team Resist [Le Kremlin-Bicêtre], Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, French National Reference Center for Antibiotic Resistance: Carbapenemase producing Enterobacteriaceae [Le Kremlin-Bicêtre], Ecologie et Evolution de la Résistance aux Antibiotiques / Ecology and Evolution of Antibiotics Resistance (EERA), Institut Pasteur [Paris]-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Bacteriology-Hygiene unit [Le Kremlin-Bicêtre], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), CHU UCL Namur, 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), Anti-infectieux : supports moléculaires des résistances et innovations thérapeutiques (RESINFIT), CHU Limoges-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Génomique, Environnement, Immunité, Santé, Thérapeutique (GEIST), Université de Limoges (UNILIM)-Université de Limoges (UNILIM), This work was partially funded by the University Paris-Sud, France. LD, TN and RAB are members of the Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LERMIT) supported by a grant from the French National Research Agency (ANR-10-LABX-33) and by the Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) DesInMBL [ANR-14-JAMR-002]., We want to thanks Pasteur International Bioressources Networking (PibNet, Paris, France) for providing whole genome sequencing facilities. We would like to thank the Transposon Registry for transposon nomenclature (https://transposon.lstmed.ac.uk/tn-registry). We thank INTEGRALL database for integron and gene cassette nomenclatures., ANR-10-LABX-0033,LERMIT,Research Laboratory on Drugs and Therapeutic Innovation(2010), ANR-14-JAMR-0002,DesInMBL,Structure-guided design of pan inhibitors of metallo-ß-lactamases(2014), Université Paris-Sud - Paris 11 (UP11)-Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Centre National de la Recherche Scientifique (CNRS), 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), UCL - (MGD) Laboratoire de biologie clinique, UCL - SSS/IREC/MONT - Pôle Mont Godinne, Institut Pasteur [Paris] (IP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Sud Orsay-Centre National de la Recherche Scientifique (CNRS), Bodescot, Myriam, Research Laboratory on Drugs and Therapeutic Innovation - - LERMIT2010 - ANR-10-LABX-0033 - LABX - VALID, and programmation conjointe européenne sur la résistance antimicrobienne - Structure-guided design of pan inhibitors of metallo-ß-lactamases - - DesInMBL2014 - ANR-14-JAMR-0002 - JPI AMR - VALID
Subjects: DNA, Bacterial, 0301 basic medicine, clone (Java method), Lineage (genetic), Science, 030106 microbiology, Antimicrobial resistance, beta-Lactamases, Article, 03 medical and health sciences, Plasmid, Bacterial Proteins, Belgium, Recombinase, polycyclic compounds, Animals, Humans, Clinical microbiology, Proteus mirabilis, Gene, Genetics, Multidisciplinary, biology, Phylogenetic tree, integumentary system, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Chromosomes, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, 030104 developmental biology, Composite transposon, Genes, Bacterial, DNA Transposable Elements, bacteria, Medicine, France, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Plasmids
Abstract: In Enterobacterales, the most common carbapenemases are Ambler’s class A (KPC-like), class B (NDM-, VIM- or IMP-like) or class D (OXA-48-like) enzymes. This study describes the characterization of twenty-four OXA-23 or OXA-58 producing-Proteus mirabilis isolates recovered from human and veterinary samples from France and Belgium. Twenty-two P. mirabilis isolates producing either OXA-23 (n = 21) or OXA-58 (n = 1), collected between 2013 and 2018, as well as 2 reference strains isolated in 1996 and 2015 were fully sequenced. Phylogenetic analysis revealed that 22 of the 24 isolates, including the isolate from 1996, belonged to a single lineage that has disseminated in humans and animals over a long period of time. The blaOXA-23 gene was located on the chromosome and was part of a composite transposon, Tn6703, bracketed by two copies of IS15∆II. Sequencing using Pacbio long read technology of OXA-23-producing P. mirabilis VAC allowed the assembly of a 55.5-kb structure encompassing the blaOXA-23 gene in that isolate. By contrast to the blaOXA-23 genes, the blaOXA-58 gene of P. mirabilis CNR20130297 was identified on a 6-kb plasmid. The acquisition of the blaOXA-58 gene on this plasmid involved XerC-XerD recombinases. Our results suggest that a major clone of OXA-23-producing P. mirabilis is circulating in France and Belgium since 1996.
Published: 2020

6. Trends in antimicrobial resistance among Escherichia coli from defined infections in humans and animals

Author: Jean-Yves Madec, Clémence Bourély, Nathalie Jarrige, Jocelyne Caillon, Claire Chauvin, Géraldine Cazeau, Thomas Coeffic, Marisa Haenni, Eric Jouy, Agnès Leblond, S. Thibaut, École Nationale des Services Vétérinaires (ENSV), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MedQual network, Centre hospitalier universitaire de Nantes (CHU Nantes), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Unité Epidémiologie, Santé et Bien-être (EPISABE), Laboratoire de Ploufragan-Plouzané-Niort [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), and Unité Antibiorésistance et Virulence Bactériennes
Subjects: 0301 basic medicine, Microbiology (medical), Veterinary medicine, Food-producing animals, Swine, medicine.drug_class, MESH: Dog Diseases, [SDV]Life Sciences [q-bio], 030106 microbiology, Cephalosporin, Antibiotics, Microbial Sensitivity Tests, Drug resistance, Cat Diseases, medicine.disease_cause, Poultry, 03 medical and health sciences, Dogs, Antibiotic resistance, Antibiogram, MESH: Anti-Bacterial Agents, Drug Resistance, Bacterial, medicine, Escherichia coli, Animals, Humans, Pharmacology (medical), Dog Diseases, Escherichia coli Infections, MESH: Escherichia coli Infections, Pharmacology, MESH: Microbial Sensitivity Tests, biology, Resistance (ecology), medicine.diagnostic_test, MESH: Cat Diseases, biology.organism_classification, Anti-Bacterial Agents, 3. Good health, 030104 developmental biology, Infectious Diseases, Cats, Antibiotic use, Cattle, Bacteria
Abstract: Objectives To characterize and compare resistance trends in clinical Escherichia coli isolates from humans, food-producing animals (poultry, cattle and swine) and pets (dogs and cats). Methods Antibiogram results collected between January 2014 and December 2017 by MedQual [the French surveillance network for antimicrobial resistance (AMR) in bacteria isolated from the community] and RESAPATH (the French surveillance network for AMR in bacteria from diseased animals) were analysed, focusing on resistance to antibiotics of common interest to human and veterinary medicine. Resistance dynamics were investigated using generalized additive models. Results In total, 743 637 antibiograms from humans, 48 170 from food-producing animals and 7750 from pets were analysed. For each antibiotic investigated, the resistance proportions of isolates collected from humans were of the same order of magnitude as those from food-producing animals or pets. However, resistance trends in humans differed from those observed in pets and food-producing animals over the period studied. For example, resistance to third-generation cephalosporins and fluoroquinolones was almost always below 10% for both humans and animals. However, in contrast to the notable decreases in resistance observed in both food-producing animals and pets, resistance in humans decreased only slightly. Conclusions Despite several potential biases in the data, the resistance trends remain meaningful. The strength of the parallel is based on similar data collection in humans and animals and on a similar statistical methodology. Resistance dynamics seemed specific to each species, reflecting different antibiotic-use practices. These results advocate applying the efforts already being made to reduce antibiotic use to all sectors and all species, both in human and veterinary medicine.
Published: 2020

7. Scarless Removal of Large Resistance Island AbaR Results in Antibiotic Susceptibility and Increased Natural Transformability in Acinetobacter baumannii

Author: Anne-Sophie, Godeux, Elin, Svedholm, Agnese, Lupo, Marisa, Haenni, Samuel, Venner, Maria-Halima, Laaberki, Xavier, Charpentier, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), 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), 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), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Ecologie quantitative et évolutive des communautés, Département écologie évolutive [LBBE], 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)-Université Claude Bernard Lyon 1 (UCBL), and 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 Biométrie et Biologie Evolutive - UMR 5558 (LBBE)
Subjects: Acinetobacter baumannii, Islands, Genomic Islands, Drug Resistance, Multiple, Bacterial, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents
Abstract: International audience; With a great diversity in gene composition, including multiple putative antibiotic resistance genes, AbaR islands are potential contributors to multidrug resistance in Acinetobacter baumannii. However, the effective contribution of AbaR to antibiotic resistance and bacterial physiology remains elusive. To address this, we sought to accurately remove AbaR islands and restore the integrity of their insertion site. To this end, we devised a versatile scarless genome editing strategy. We performed this genetic modification in two recent A. baumannii clinical strains: the strain AB5075 and the nosocomial strain AYE, which carry AbaR11 and AbaR1 islands of 19.7 kbp and 86.2 kbp, respectively. Antibiotic susceptibilities were then compared between the parental strains and their AbaR-cured derivatives. As anticipated by the predicted function of the open reading frame (ORF) of this island, the antibiotic resistance profiles were identical between the wild type and the AbaR11-cured AB5075 strains. In contrast, AbaR1 carries 25 ORFs, with predicted resistance to several classes of antibiotics, and the AYE AbaR1-cured derivative showed restored susceptibility to multiple classes of antibiotics. Moreover, curing of AbaRs restored high levels of natural transformability. Indeed, most AbaR islands are inserted into the comM gene involved in natural transformation. Our data indicate that AbaR insertion effectively inactivates comM and that the restored comM is functional. Curing of AbaR consistently resulted in highly transformable and therefore easily genetically tractable strains. Emendation of AbaR provides insight into the functional consequences of AbaR acquisition.
Published: 2020

8. Persistence and Diffusion of mecC-Positive CC130 MRSA Isolates in Dairy Farms in Meurthe-et-Moselle County (France)

Author: Jacques Bietrix, Camille Kolenda, Anaïs Sapin, Marisa Haenni, Jean-Yves Madec, Michèle Bes, Céline Dupieux, Jason Tasse, Fréderic Laurent, Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Clinique vétérinaire de l'arche, Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL), Université de Lyon, 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), Centre National de Reference des Staphylocoques, Institut des Sciences Pharmaceutiques et Biologiques (ISPB), Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon
Subjects: Microbiology (medical), Veterinary medicine, Staphylococcus aureus, lcsh:QR1-502, Biology, medicine.disease_cause, Microbiology, lcsh:Microbiology, Persistence (computer science), Milking, Agar plate, 03 medical and health sciences, methicillin resistance, Multiplex polymerase chain reaction, medicine, Dairy cattle, Original Research, 030304 developmental biology, carriage, 0303 health sciences, milk, 030306 microbiology, mecC, SCCmec, dairy cow, biochemical phenomena, metabolism, and nutrition, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Carriage
Abstract: Background: Methicillin resistance in Staphylococcus aureus (MRSA) is classically conferred by the acquisition of the mecA gene encoding an additional penicillin binding protein with low affinity for beta-lactams. A mecA variant, named mecC, was described in 2011. MRSA isolates harboring mecC of both animal and human origin have since been collected in different European countries. In France, animal cases were reported in 4 dairy farms between 2008 and 2013 in the Meurthe-et-Moselle county, all located in a 30 km perimeter, suggesting a possible dissemination of mecC-positive MRSA strains. We performed a prospective study to evaluate the local epidemiology of such strains in terms of (i) dissemination among animals, humans and in the environment, and (ii) persistence in Meurthe-et-Moselle dairy cattle farms. Methods: The 4 French dairy farms with previous reports of mecC-positive MRSA strains and 14 farms in the same perimeter were included in this study. In each farm, nasal swabs, rectal swabs and milk samples were collected from 10 randomly selected cows, as well as nasal samples from family pets, volunteer farmers and veterinarians. One farm (E0), in which mecC-MRSA isolates were detected, was selected to study more deeply the dissemination of mecC-positive strains within the farm. After pre-enrichment of swabs and milk, they were subcultured on MSSA/MRSA chromogenic selective agar plates. S. aureus colonies were tested with a multiplex PCR to detect the mecA and mecC genes. The mecC-positive strains were characterized using DNA microarray. Results: mecC-positive strains were recovered in four farms, corresponding to the ones with previous reports of mecC-positive MRSA strains, and originated only from dairy cow samples. The screening in the E0 farm showed that 22% of the dairy cows carried mecC-positive MRSA. Three strains were also isolated from the environmental samples. All mecC-positive strains belonged to the clonal complex CC130 and harbored the same spa-type t1736. Conclusion: This study found that mecC-positive MRSA isolates are able to persist within the same farms for several years after being introduced in this setting and are able to widely disseminate but only among dairy cows suggesting that milking machines might be a key player.
Published: 2019

9. Antimicrobial resistance of Pasteurella multocida isolated from diseased food-producing animals and pets

Author: Clémence Bourély, Géraldine Cazeau, Eric Jouy, Marisa Haenni, Jean-Yves Madec, Nathalie Jarrige, Agnès Leblond, Emilie Gay, Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), École Nationale des Services Vétérinaires (ENSV), Université Bretagne Loire (COMUE) (UBL), and Unité Antibiorésistance et Virulence Bactériennes
Subjects: Florfenicol, Veterinary medicine, Livestock, Meat, Pasteurella multocida, [SDV]Life Sciences [q-bio], Pasteurella Infections, Microbial Sensitivity Tests, Drug resistance, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, Dogs, Antibiotic resistance, Drug Resistance, Multiple, Bacterial, Enrofloxacin, medicine, Animals, Pasteurella, Respiratory Tract Infections, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Antiinfective agent, General Veterinary, biology, 030306 microbiology, business.industry, Pets, General Medicine, biology.organism_classification, Anti-Bacterial Agents, 3. Good health, chemistry, Cattle, France, Rabbits, business, medicine.drug
Abstract: Surveillance of Pasteurella multocida resistance in food-producing animals is essential to guide the first-line treatment of respiratory diseases and to limit economic losses. Since Pasteurella are the most common bacteria isolated from dog and cat bites, this surveillance is also needed to guide treatment in humans in case of bites. The aim of this study was to characterize the phenotypic resistance of P. multocida strains isolated from respiratory infections in animals, including both food-producing animals and pets. Data collected between 2012 and 2017 by the French national surveillance network for antimicrobial resistance referred to as RESAPATH were analyzed. The proportions of resistance to antimicrobials of relevance in veterinary and human medicines were estimated for each animal species. For cattle, resistance trends over the period were investigated using non-linear analysis applied to time-series. In total, 5356 P. multocida isolates were analyzed. Proportions of resistance of P. multocida were almost all below 20% over the period, and, more precisely, all resistance proportions were below 10% for rabbits, sheep and dogs. The highest resistance proportions to enrofloxacin were identified for cattle (4.5%) and dogs (5.2%). Despite its frequent use in livestock, resistance to florfenicol was less than 1% in P. multocida strains, regardless of the animal species considered. Time series analyses revealed continuous increases in resistance to tetracycline, tilmicosin, flumequine and fluoroquinolones in P. multocida strains isolated from cattle. These trends contrast with the decrease in use of antibiotics in cattle in France and with the decrease in resistance observed in E. coli isolated from diseased cattle.
Published: 2019

10. Evolution of the Population Structure of Staphylococcus pseudintermedius in France

Author: Marine Bergot, Patricia Martins-Simoes, Hélène Kilian, Pierre Châtre, Kate A. Worthing, Jacqueline M. Norris, Jean-Yves Madec, Frédéric Laurent, Marisa Haenni, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Centre National de Reference des Staphylocoques, Université de Lyon, 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), Sydney School of Veterinary Science, Faculty of Science, The University of Sydney -The University of Sydney, The Peter Doherty Institute for Infection and Immunity [Melbourne], University of Melbourne-The Royal Melbourne Hospital, and Santé Publique France
Subjects: 0301 basic medicine, Microbiology (medical), ST496, Staphylococcus pseudintermedius, Lineage (genetic), Population, lcsh:QR1-502, Clone (cell biology), Drug resistance, Biology, Microbiology, ST258, lcsh:Microbiology, 03 medical and health sciences, Genotype, education, Pathogen, Genetics, education.field_of_study, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, dog, Multilocus sequence typing, MRSP, MLST
Abstract: International audience; Staphylococcus pseudintermedius is a colonizer as well as an important pathogen of dogs where it is responsible for skin, ear and post-operative infections. The emergence of methicillin-resistant S. pseudintermedius (MRSP) in the early 2000s, which were additionally resistant to most veterinary-licensed antibiotics, drew specific attention to these pathogens due to the limitations created in veterinary therapeutic options. Multiple studies showed that the sequence type (ST)71 was the most frequently identified clone in Europe. A few years ago, several publications have suggested a decline of the ST71 clone and the emergence of the ST258 lineage in Northern Europe. In this study, we show that ST71 is also decreasing over time in France and that the non-ST71 population is highly heterogeneous. Globally, the non-ST71 clones are more susceptible to antibiotics, which might be good news for veterinarians. Two other lineages, ST258 and ST496, seem to be successful in France. These isolates, as well as representatives of the ST71 clone, underwent whole-genome sequence. This study shows that the ST71 and ST496 clusters are highly homogenous while the ST258 cluster is more diverse. Each ST possesses a specific pattern of resistance and virulence genes. The reasons for the apparent and simultaneous success of the ST258 and ST496 clones remain unclear. But the emergence of the ST496 clone will require monitoring given its multi-resistant genotype and threat to canine health.
Published: 2018

11. Are animals a source of Stenotrophomonas maltophilia in human infections? Contributions of a nationwide molecular study

Author: Jean-Yves Madec, Marine Desroches, Estelle Jumas-Bilak, Jean-Winoc Decousser, Brigitte Lamy, Camille Corlouer, Mélanie Darty, Aurélie Jayol, Marisa Haenni, Karine Maillard, Laboratory of Bacteriology and Infection Control, Department of Microbiology, Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital-Henri Mondor University Hospital-Assistance Publique-Hôpitaux de Paris, Henri Mondor University Hospital-Henri Mondor University Hospital, INSERM European Unit [Fribourg, Switzerland], Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Emerging Antibiotic Resistance Unit [Fribourg, Suisse], Medical and Molecular Microbiology [Fribourg, Suisse], Faculty of Science and Medicine [Fribourg, Suisse], University of Fribourg-University of Fribourg-Faculty of Science and Medicine [Fribourg, Suisse], University of Fribourg-University of Fribourg, 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), Next-Generation Sequencing Platform [Créteil] (Génomiques), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), LABÉO, Pôle d’analyses et de recherche de Normandie (LABÉO), Departement de Bacteriologie, Hôpital Archet 2 [Nice] (CHU), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Hydrosciences Montpellier (HSM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), CHU Montpellier, Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), Dynamic Microbiology - EA 7380 (DYNAMIC), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université Paris-Est (UPE)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Université Nice Sophia Antipolis (... - 2019) (UNS), Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and École nationale vétérinaire d'Alfort (ENVA)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)
Subjects: 0301 basic medicine, Microbiology (medical), medicine.medical_specialty, Stenotrophomonas maltophilia, 030106 microbiology, Respiratory Tract Diseases, Microbial Sensitivity Tests, 03 medical and health sciences, Medical microbiology, medicine, Animals, Humans, Horses, Phylogeny, ComputingMilieux_MISCELLANEOUS, Disease Reservoirs, Genetics, Cross Infection, biology, Phylogenetic tree, Respiratory tract infections, General Medicine, biology.organism_classification, 3. Good health, Housekeeping gene, Anti-Bacterial Agents, Ciprofloxacin, 030104 developmental biology, Infectious Diseases, Phenotype, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Multilocus sequence typing, Gram-Negative Bacterial Infections, Bacteria, medicine.drug, Multilocus Sequence Typing
Abstract: Stenotrophomonas maltophilia (Sm) is an archetypal environmental opportunistic bacterium responsible for health care-associated infections. The role of animals in human Sm infections is unknown. This study aims to reveal the genetic and phylogenetic relationships between pathogenic strains of Sm, both animal and human, and identify a putative role for animals as a reservoir in human infection. We phenotypically and genotypically characterized 61 Sm strains responsible for animal infections (mainly respiratory tract infections in horses) from a French nationwide veterinary laboratory network. We tested antimicrobial susceptibility and performed MLST and genogrouping using the concatenation of the seven housekeeping genes from the original MLST scheme. Excluding the eight untypeable strains owing to the lack of gene amplification, only 10 out of the 53 strains yielded a known ST (ST5, ST39, ST162, ST8, ST27, ST126, ST131). The genogroup distribution highlighted not only genogroups (genogroups 5 and 9) comprised exclusively of animal strains but also genogroups shared by human and animal strains. Interestingly, these shared genogroups were primarily groups 2 and 6, which have previously been identified as the two most frequent genogroups among human-pathogenic Sm strains, especially among respiratory pathogens. The antimicrobial susceptibility testing underlined the presence of acquired resistance: 18.8 and 7.5% of the tested isolates were resistant to the sulfonamide-trimethoprim combination and ciprofloxacin, respectively. Animal strains of Sm shared phylogenetic traits with some of the most successful human strains. The exact relationships between the human and animal strains, and the genetic support of these common traits, need to be determined.
Published: 2018

12. Epidemic spread of Escherichia coli ST744 isolates carrying mcr-3 and blaCTX-M-55 in cattle in France

Author: Jean-Yves Madec, Racha Beyrouthy, Marisa Haenni, Pierre Châtre, Agnese Lupo, Richard Bonnet, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Faculty of Public Health [Tripoli, Liban] (FSP III), Lebanese University [Beirut], Laboratoire de Lyon, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, AFSSA, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), 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), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Agency for Food, Environmental and Occupational Health and Safety (ANSES), ANR-14-ANWA-0006,PRAHAD,Prevalence and optimised detection of resistance to antibiotics vital for animal and human health(2014), European Project: 323209,EC:FP7:HEALTH,FP7-JPROG-2012-RTD,JPIAMR(2012), Faculty of Public Health [Lebanese University] (FSP III), Lebanese University [Beirut] (LU), Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA), Animal Health and Welfare (ANIHWA) ERA-Net project (France) [ANR-14-ANWA-0006-04], and Joint Programming Initiative on Antimicrobial Resistance (JPI-EC-AMR) project Trans-Comp-ESC-R (France) [JPIAMR2016-077]
Subjects: 0301 basic medicine, Microbiology (medical), Genotype, 030106 microbiology, Cattle Diseases, Transferases (Other Substituted Phosphate Groups), Microbial Sensitivity Tests, Biology, medicine.disease_cause, beta-Lactamases, MESH: Genotype, 03 medical and health sciences, MESH: Anti-Bacterial Agents, Epidemic spread, Drug Resistance, Bacterial, medicine, Escherichia coli, MESH: Cattle Diseases, Animals, Pharmacology (medical), Epidemics, Escherichia coli Infections, ComputingMilieux_MISCELLANEOUS, Pharmacology, Colistin, MESH: Escherichia coli, Escherichia coli Proteins, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Research Letters, 3. Good health, Anti-Bacterial Agents, MESH: France, Infectious Diseases, Cattle, Topography, Medical, MESH: Transferases (Other Substituted Phosphate Groups), France
Abstract: International audience; No abstract available
Published: 2017

13. Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in water sources in Lebanon

Author: Marisa Haenni, Monzer Hamze, Mohamad Diab, Estelle Saras, Richard Bonnet, Jean-Yves Madec, Université Libanaise, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), French Agency for Food, Environmental and Occupational Health Safety (ANSES), Lebanese University, Azm & Saade Social Foundation, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, AFSSA, Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Unité Antibiorésistance et Virulence Bactériennes (AVB), Laboratoire de Lyon [ANSES], and 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)
Subjects: MESH: Water Wells, 0301 basic medicine, Veterinary medicine, Water Wells, medicine.medical_treatment, [SDV]Life Sciences [q-bio], MESH: Klebsiella pneumoniae, Water source, MESH: beta-Lactamases, Drug resistance, carbapenemase, Drug Resistance, Multiple, Bacterial, MESH: Animals, MESH: Bacterial Proteins, well, 2. Zero hunger, Antiinfective agent, MESH: Escherichia coli, General Medicine, Contamination, Enterobacteriaceae, 6. Clean water, Bacterial Typing Techniques, 3. Good health, Klebsiella pneumoniae, MESH: Multilocus Sequence Typing, lebanon, Public Health, Estuaries, Water Microbiology, MESH: Public Health, MESH: Estuaries, DNA, Bacterial, 030106 microbiology, water, MESH: Carbapenem-Resistant Enterobacteriaceae, Biology, Microbiology, beta-Lactamases, MESH: Bacterial Typing Techniques, estuary, MESH: Enterobacteriaceae, MESH: Natural Springs, 03 medical and health sciences, Antibiotic resistance, Bacterial Proteins, Escherichia coli, medicine, Animals, Humans, MESH: Lebanon, spring water, MESH: Humans, General Veterinary, Natural Springs, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Drug Resistance, Multiple, Bacterial, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, MESH: DNA, Bacterial, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Water Microbiology, Multiple drug resistance, Carbapenem-Resistant Enterobacteriaceae, 030104 developmental biology, ESBL, Beta-lactamase, Multilocus Sequence Typing
Abstract: International audience; Extended-spectrum beta-lactamases (ESBLs) have been recurrently reported in both human and veterinary medicine, and carbapenemases have also emerged in these two sectors. Such resistance phenotypes were increasingly reported in the environment, which both receives and further disseminates multidrug-resistant (MDR) bacteria. Here, we report the high contamination of water samples (68.2%; 15/22) collected in estuaries in Lebanon. From these 15 contaminated sites, a total of 21 ESBL-producing (mostly harbouring the bla(CTX-M-15) gene) and four carbapenemase-producing (two bla(OXA-48) and two bla(OXA-244)) Enterobacteriaceae were recovered. ESBL contamination was also identified in water samples collected from rural wells and spring water, although at a lower frequency. Indeed, 1.9% (3/155) and 6.1% (7/115) of the wells and springs were contaminated, respectively, and all identified isolates were CTX-M-15-producing E. coli. Interestingly, sequence types (STs) previously associated both with animal and human reservoirs were detected (ST38, ST10 and ST131), suggesting a complex source of contamination. This situation is alarming since water drawn from wells or springs is directly intended for human consumption in Lebanon without any further treatment. Moreover, even though water from estuaries is not intended for human consumption, it is used to water animals and irrigate crops. Consequently, water contamination by ESBLs and carbapenemases in Lebanon is potentially a major risk to public health. Part of this work was presented at the 7th Symposium on Antimicrobial Resistance in Animals and the Environment (ARAE).
Published: 2017

14. Complete sequences of qnrD-carrying plasmids in Proteus spp. collected from French animals

Author: Marisa Haenni, Eliette Schultz, Estelle Saras, Agnese Lupo, Jean-Yves Madec, Axel Cloeckaert, Sylvie Baucheron, Benoît Doublet, Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), Unité Antibiorésistance et Virulence Bactériennes, Laboratoire de Lyon, 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), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), ANSES and INRA (French National Institute for Agricultural Research), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Laboratoire de Lyon [ANSES], and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: 0301 basic medicine, Microbiology (medical), Sequence analysis, 030106 microbiology, Immunology, education, Drug resistance, Microbial Sensitivity Tests, fluoroquinolone, Microbiology, Genome, 03 medical and health sciences, Chromosome Walking, Plasmid, Bacterial Proteins, resistance gene, plasmid, Drug Resistance, Bacterial, Primer walking, Immunology and Allergy, Animals, Humans, animal, health care economics and organizations, Genetics, biology, Sequence Analysis, DNA, biology.organism_classification, gène de résistance, Proteus, 030104 developmental biology, proteus, plasmide, bacteria, Proteus Infections, salmonella enterica, Genome, Bacterial, enterobacteria, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Fluoroquinolones, Plasmids, enterobacteriaceae
Abstract: International audience; Complete sequences of [i]qnr[/i]D-carrying plasmids in [i]Proteus[/i] spp. collected from French animals
Published: 2017

15. Impact of food animal trade on the spread of mcr-1-mediated colistin resistance, Tunisia, July 2015

Author: Olfa Bouallegue, Wejdene Mansour, Wahib Mehri, Noureddine Boujaâfar, Marisa Haenni, Raoudha Grami, Jean-Yves Madec, Hôpital Universitaire Sahloul (CHU Sahloul), 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), Institut Supérieur des Sciences Appliquées et de Technologie de Mahdia, Commissariat Régional au Développement Agricole, Ministère de l'agriculture, and European Project: 291815,EC:FP7:KBBE,FP7-ERANET-2011-RTD,ANIHWA(2012)
Subjects: 0301 basic medicine, Veterinary medicine, animal structures, Meat, Tunisia, Genotype, Epidemiology, Food animal, 030106 microbiology, Microbial Sensitivity Tests, Biology, beta-Lactamases, Colistin resistance, 03 medical and health sciences, Virology, Drug Resistance, Bacterial, medicine, Escherichia coli, Prevalence, Animals, Humans, Escherichia coli Infections, business.industry, Colistin, Public Health, Environmental and Occupational Health, Commerce, Food sample, Poultry farming, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Food Microbiology, MCR-1, France, business, Peptides, Chickens, medicine.drug, Plasmids
Abstract: We report a high prevalence of MCR-1 and CTX-M-1-producing Escherichia coli in three Tunisian chicken farms. Chickens were imported from France or derived from French imported chicks. The same IncHI2-type plasmid reported to carry those genes in cattle in France and in a food sample in Portugal was found in Tunisian chickens of French origin. This suggests a significant impact of food animal trade on the spread of mcr-1-mediated colistin resistance in Europe.
Published: 2016

16. mecC-positive MRSA in horses

Author: Frédéric Laurent, Michèle Bes, Jean-Yves Madec, Véronique Métayer, Marisa Haenni, Pierre Châtre, Céline Dupieux, Karine Maillard, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Pathogénie des Staphylocoques – Staphylococcal Pathogenesis (StaPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Centre National de Reference des Staphylocoques, Université de Lyon, Laboratoire Frank Duncombe, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), Methicillin-Resistant Staphylococcus aureus, Male, Genotype, Microbial Sensitivity Tests, Biology, medicine.disease_cause, Staphylococcal infections, Microbiology, 03 medical and health sciences, Molecular typing, medicine, Prevalence, Animals, Pharmacology (medical), Horses, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Pharmacology, 0303 health sciences, 030306 microbiology, Bacterial, Staphylococcal Infections, medicine.disease, Microarray Analysis, Methicillin-resistant Staphylococcus aureus, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Anti-Bacterial Agents, Molecular Typing, Infectious Diseases, Genes, Genes, Bacterial, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, France
Abstract: International audience
Published: 2015

17. Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation

Author: Sophie Payot, Shaynoor Dramsi, Sarah Chuzeville, Jean-Yves Madec, Marisa Haenni, Dynamique des Génomes et Adaptation Microbienne (DynAMic), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie des Bactéries pathogènes à Gram-positif, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Pathogenèse de Helicobacter, Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris]
Subjects: [SDV]Life Sciences [q-bio], Immunoblotting, GBS, medicine.disease_cause, Microbiology, Streptococcus agalactiae, Antigen I/II, Antigen, medicine, Adhesins, Bacterial, Antigens, Bacterial, biology, Streptococcus, Reverse Transcriptase Polymerase Chain Reaction, Biofilm, ICE, Streptococcus gordonii, Fibrinogen binding, Genetic Variation, Fibrinogen, biology.organism_classification, Streptococcus mutans, 3. Good health, Bacterial adhesin, Interspersed Repetitive Sequences, Infectious Diseases, Biofilms, Adhesion, human activities
Abstract: International audience; Streptococcus agalactiae (i.e. Group B streptococcus, GBS) is a major human and animal pathogen. Genes encoding putative surface proteins and in particular an antigen 1/II have been identified on Integrative and Conjugative Elements (ICEs) found in GBS. Antigens I/II are multimodal adhesins promoting colonization of the oral cavity by streptococci such as Streptococcus gordonii and Streptococcus mu tans. The prevalence and diversity of antigens I/II in GBS were studied by a bioinformatic analysis. It revealed that antigens I/II, which are acquired by horizontal transfer via ICEs, exhibit diversity and are widespread in GBS, in particular in the serotype Ia/ST23 invasive strains. This study aimed at characterizing the impact on GBS biology of proteins encoded by a previously characterized ICE of S. agalactiae (ICE_515-tRNA(Lys)). The production and surface exposition of the antigen I/II encoded by this ICE was examined using RT-PCR and immunoblotting experiments. Surface proteins of ICE_515_tRNA(Lys) were found to contribute to GBS biofilm formation and to fibrinogen binding. Contribution of antigen I/II encoded by SAL 2056 to biofilm formation was also demonstrated. These results highlight the potential for ICEs to spread microbial adhesins between species.
Published: 2015

18. Population structure and antimicrobial susceptibility of Pseudomonas aeruginosa from animal infections in France

Author: Jean-Yves Madec, Didier Hocquet, Xavier Bertrand, Christophe Guyeux, Cécile Ponsin, Pascal Cholley, Marisa Haenni, Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Centre Hospitalier Régional Universitaire [Besançon] (CHRU Besançon), Laboratoire Chrono-environnement - UFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Technologie de Belfort-Montbeliard (UTBM), Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), AFSSA, Centre Hospitalier Régional Universitaire [Besançon] ( CHRU Besançon ), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies ( FEMTO-ST ), Université de Technologie de Belfort-Montbeliard ( UTBM ) -Ecole Nationale Supérieure de Mécanique et des Microtechniques ( ENSMM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail [Lyon] ( ANSES Lyon ), Agence nationale de sécurité sanitaire de l’alimentation, de l’environnement et du travail (Anses), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), and Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Population, Population structure, Cattle Diseases, Antimicrobial susceptibility, Human pathogen, [INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE], Drug resistance, Biology, medicine.disease_cause, Microbiology, [INFO.INFO-IU]Computer Science [cs]/Ubiquitous Computing, [INFO.INFO-CR]Computer Science [cs]/Cryptography and Security [cs.CR], Dogs, Antibiotic resistance, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Drug Resistance, Bacterial, medicine, Animals, Pseudomonas Infections, Dog Diseases, Horses, education, Phylogeny, ComputingMilieux_MISCELLANEOUS, education.field_of_study, General Veterinary, Animal, Pseudomonas aeruginosa, General Medicine, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, veterinary(all), Anti-Bacterial Agents, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [INFO.INFO-MA]Computer Science [cs]/Multiagent Systems [cs.MA], Multilocus sequence typing, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], Cattle, Horse Diseases, France, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], Research Article, MLST
Abstract: Background Pseudomonas aeruginosa is a major human pathogen, which also affects animals. It is thought that P. aeruginosa has a non-clonal epidemic population structure, with distinct isolates found in humans, animals or the environment. However, very little is known about the structure of the P. aeruginosa population from diseased animals. Data on antimicrobial resistance are also scarce. Results Thirty-four already registered and 19 new MLST profiles were identified. Interestingly, a few clones were more prevalent, and clones associated to human outbreaks were also detected. Multidrug resistance phenotypes were overall rare. Conclusion We highlight the non clonal structure of the population and show a higher prevalence of specific clones, possibly correlating with higher pathogenicity. The low proportion of antimicrobial resistance contrasts with the high resistance rate of human isolates. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0324-x) contains supplementary material, which is available to authorized users.
Published: 2015

19. Survey of multidrug resistance integrative mobilizable elements SGI1 and PGI1 in Proteus mirabilis in humans and dogs in France, 2010-13

Author: Axel Cloeckaert, Catherine Neuwirth, Laurent Mereghetti, Benoît Doublet, Eliane Siebor, Jean-Yves Madec, Eliette Schultz, Marisa Haenni, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), INRA, ANSES, and Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT)
Subjects: Microbiology (medical), DNA, Bacterial, Salmonella, Gene Transfer, Horizontal, Genomic Islands, Genotype, Microbial Sensitivity Tests, medicine.disease_cause, Polymerase Chain Reaction, Microbiology, law.invention, Dogs, law, Genomic island, Drug Resistance, Multiple, Bacterial, medicine, Pulsed-field gel electrophoresis, Animals, Humans, Pharmacology (medical), Proteus mirabilis, Polymerase chain reaction, 2. Zero hunger, Pharmacology, biology, Genetic Variation, biology.organism_classification, 3. Good health, New Delhi metallo-beta-lactamase 1, Anti-Bacterial Agents, Electrophoresis, Gel, Pulsed-Field, Multiple drug resistance, Interspersed Repetitive Sequences, Molecular Typing, Proteus, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, biology.protein, France, Proteus Infections
Abstract: OBJECTIVES To characterize MDR genomic islands related to Salmonella genomic island 1 (SGI1) and Proteus genomic island 1 (PGI1) in Proteus mirabilis from human and animal sources in France in light of the previously reported cases. METHODS A total of 52 and 46 P. mirabilis clinical strains from human and animal sources, respectively, were studied for the period 2010-13. MDR was assessed by antimicrobial susceptibility testing, PCR detection of SGI1 and PGI1 and PCR mapping of the MDR regions. The diversity of the SGI1/PGI1-positive P. mirabilis strains was assessed by PFGE. RESULTS Twelve P. mirabilis strains (5 humans and 7 dogs) were found to harbour an MDR island related to SGI1 or PGI1. Among them, several SGI1 variants were identified in diverse P. mirabilis genetic backgrounds. The variant SGI1-V, which harbours the ESBL bla VEB-6 gene, was found in closely genetically related human and dog P. mirabilis strains. The recently described PGI1 element was also identified in human and dog strains. Finally, one strain harboured a novel SGI genomic island closely related to SGI1 and SGI2 without an insertion of the MDR region. CONCLUSION This study reports for the first time, to our knowledge, SGI1-positive and PGI1-positive P. mirabilis strains from dogs in France. The genetic diversity of the strains suggests several independent horizontal acquisitions of these MDR elements. The potential transmission of SGI1/PGI1-positive P. mirabilis strains between animals and humans is of public health concern, notably with regard to the spread of ESBL and carbapenemase genes, i.e. bla VEB-6 and bla NDM-1.
Published: 2015

20. Assessment of Adhesins as an Indicator of Pathovar-Associated Virulence Factors in Bovine Escherichia coli

Author: Charlotte Valat, Karine Forest, Frédéric Auvray, Véronique Métayer, Thomas Méheut, Charlène Polizzi, Emilie Gay, Marisa Haenni, Eric Oswald, Jean-Yves Madec, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Université Paris-Est (UPE), Unité Epidémiologie, Centre de Physiopathologie de Toulouse-Purpan (INSERM U563 - CNRS UMR1037), Centre National de la Recherche Scientifique (CNRS)-Centre de lutte contre le cancer (CLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Institut Claudius Regaud, Centre Hospitalier Universitaire de Purpan (CHU Purpan), ProdInra, Migration, 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), and Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Institut Claudius Regaud-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de lutte contre le cancer (CLCC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Genotype, Virulence Factors, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Virulence, Cattle Diseases, medicine.disease_cause, Serogroup, Applied Microbiology and Biotechnology, Virulence factor, Microbiology, Serology, Enteritis, 03 medical and health sciences, Pathogenic Escherichia coli, Drug Resistance, Bacterial, medicine, Escherichia coli, Animals, Adhesins, Bacterial, Escherichia coli Infections, 030304 developmental biology, 0303 health sciences, Ecology, biology, 030306 microbiology, Public and Environmental Health Microbiology, Sequence Analysis, DNA, biochemical phenomena, metabolism, and nutrition, biology.organism_classification, medicine.disease, Bacterial adhesin, [SDV] Life Sciences [q-bio], Pathovar, Cattle, Food Science, Biotechnology
Abstract: The CS31A, F17, and F5 adhesins are usually targeted by serology-based methods to detect pathogenic Escherichia coli associated with calf enteritis. However, the virulence traits of the selected isolates are still poorly described. Here, from a set of 349 diarrheagenic E. coli isolates from cattle, we demonstrated a 70.8% concordance rate (Cohen's kappa, 0.599) between serology- and PCR-based approaches for the detection of adhesins under field conditions. A 79% to 82.4% correspondence between the two methods was found for fimbrial adhesins, whereas major discrepancies (33%) were observed for CS31A-type antigens. Various F17A variants were found, such as F17Ac (20K) (50%), F17Aa (FY) (18.9%), F17Ab (8.1%), and F17Ad (111K) (5.4%), including a high proportion (17.6%) of new F17A internal combinations (F17Aab, F17Aac, and F17Abc) or untypeable variants. In addition, the highest proportion of pathovar-associated virulence factor (VF) genes was observed among E. coli isolates that produced F5/F41 adhesins. A specific link between the heat-stable toxins related to the enterotoxigenic E. coli (ETEC) pathovar and adhesins was identified. STa was significantly linked to F5/F41 and EAST1 to CS31A adhesins ( P < 0.001), respectively, whereas NTEC was associated with F17 adhesin ( P = 0.001). Clustering between phylogroups according to the adhesin types was also observed. Also, few Shiga toxin-producing E. coli (STEC) or enteropathogenic E. coli (EPEC) pathovars were identified. Finally, no statistically significant difference was observed in the occurrence of extended-spectrum beta lactamase (ESBL) production according to the adhesins expressed by the isolates ( P = 0.09). Altogether, this study gives new insights into the relationship between adhesins, VF, and antimicrobial resistance in calf enteritis and supports the need for further standardization of methodologies for such approaches.
Published: 2014

21. Evaluation des risques d’émergence d’antibiorésistances liés aux modes d’utilisation des antibiotiques dans le domaine de la santé animale

Author: Jean-François Guillot, Jacqueline Bastien, Joel Bertin, Alain Bousquet‐mélou, Mireille Bruneau, Claire Chauvin, Bertrand Faroult, Denis Fric, Emilie Gay, Thierry Gidenne, Etienne Giraud, Sophie Granier, Marisa Haenni, Christophe Hugnet, Isabelle Kempf, Laurentie Michel, Arlette Laval, Michel Ledru, Jean-Yves Madec, Christine Medaille, Yves Millemann, Laurent Poirel, Herve Pouliquen, Frederic Rousseau, Yannick Rugraff, Pascal Sanders, Philippe Schmidely, Université de Tours, Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Ploufragan - Plouzané, Laboratoire d'études et de recherches en pathologie bovine et hygiène des viandes, Agence Française de Sécurité Sanitaire des Aliments (AFSSA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Unité Antibiorésistance et Virulence Bactériennes, Clinique Vétérinaire des Lavandes, Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Vebiotel - Laboratoire de Biologie Vétérinaire, École nationale vétérinaire d'Alfort (ENVA), Résistances émergentes aux antibiotiques, Institut National de la Santé et de la Recherche Médicale (INSERM), Modélisation Systémique Appliquée aux Ruminants (MoSAR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, ANSES, AFSSA, UR Infectiologie animale et Santé publique (UR IASP), Institut National de la Recherche Agronomique (INRA), Université de Tours (UT), and Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT)
Subjects: [SDV]Life Sciences [q-bio]
Published: 2014

22. Mise en évidence et caractérisation de l’îlot génomique de multi-résistance aux antibiotiques SGI1 chez Proteus mirabilis dans le réservoir humain et animal en France

Author: Eliette Schultz, Jean Yves Madec, Marisa Haenni, Axel Cloeckaert, Benoît Doublet, Laurent Mereghetti, ProdInra, Migration, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2013

23. Spread of the blaTEM-52 gene is mainly ensured by IncI1/ST36 plasmids in Escherichia coli isolated from cattle in France

Author: Estelle Saras, Jean-Yves Madec, Véronique Métayer, Benoît Doublet, Marisa Haenni, Axel Cloeckaert, Unité Antibiorésistance et Virulence Bactériennes, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Anses, and Institut National de la Recherche Agronomique (INRA)-Université de Tours
Subjects: Microbiology (medical), Gene Transfer, Horizontal, Genotype, Cattle Diseases, Microbial Sensitivity Tests, Biology, medicine.disease_cause, beta-Lactamases, Microbiology, 03 medical and health sciences, Plasmid, medicine, Escherichia coli, Animals, Pharmacology (medical), Gene, Escherichia coli Infections, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Pharmacology, 0303 health sciences, 030306 microbiology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Molecular Typing, Infectious Diseases, DNA Transposable Elements, Cattle, France, Plasmids
Abstract: International audience
Published: 2012

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23 results on '"Marisa Haenni"'

1. Environmental contamination in a high-income country (France) by antibiotics, antibiotic-resistant bacteria, and antibiotic resistance genes: Status and possible causes

2. Destruction of Staphylococcus aureus biofilms by combining an antibiotic with subtilisin A or calcium gluconate

3. Selection of ESBL-producing Escherichia coli in the gut of calves experimentally fed with milk containing antibiotic residues

4. Characterization of cultivable airborne bacteria and their antimicrobial resistance pattern in French milking parlour

5. A single Proteus mirabilis lineage from human and animal sources: a hidden reservoir of OXA-23 or OXA-58 carbapenemases in Enterobacterales

6. Trends in antimicrobial resistance among Escherichia coli from defined infections in humans and animals

7. Scarless Removal of Large Resistance Island AbaR Results in Antibiotic Susceptibility and Increased Natural Transformability in Acinetobacter baumannii

8. Persistence and Diffusion of mecC-Positive CC130 MRSA Isolates in Dairy Farms in Meurthe-et-Moselle County (France)

9. Antimicrobial resistance of Pasteurella multocida isolated from diseased food-producing animals and pets

10. Evolution of the Population Structure of Staphylococcus pseudintermedius in France

11. Are animals a source of Stenotrophomonas maltophilia in human infections? Contributions of a nationwide molecular study

12. Epidemic spread of Escherichia coli ST744 isolates carrying mcr-3 and blaCTX-M-55 in cattle in France

13. Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in water sources in Lebanon

14. Complete sequences of qnrD-carrying plasmids in Proteus spp. collected from French animals

15. Impact of food animal trade on the spread of mcr-1-mediated colistin resistance, Tunisia, July 2015

16. mecC-positive MRSA in horses

17. Antigen I/II encoded by integrative and conjugative elements of Streptococcus agalactiae and role in biofilm formation

18. Population structure and antimicrobial susceptibility of Pseudomonas aeruginosa from animal infections in France

19. Survey of multidrug resistance integrative mobilizable elements SGI1 and PGI1 in Proteus mirabilis in humans and dogs in France, 2010-13

20. Assessment of Adhesins as an Indicator of Pathovar-Associated Virulence Factors in Bovine Escherichia coli

21. Evaluation des risques d’émergence d’antibiorésistances liés aux modes d’utilisation des antibiotiques dans le domaine de la santé animale

22. Mise en évidence et caractérisation de l’îlot génomique de multi-résistance aux antibiotiques SGI1 chez Proteus mirabilis dans le réservoir humain et animal en France

23. Spread of the blaTEM-52 gene is mainly ensured by IncI1/ST36 plasmids in Escherichia coli isolated from cattle in France

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