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Perrin-Guyomard A, Houée P, Lucas P, Felten A, Le Devendec L, Chauvin C, Kempf I. Prevalence and molecular epidemiology of mcr-mediated colistin-resistance Escherichia coli from healthy poultry in France after national plan to reduce exposure to colistin in farm. Front Microbiol 2023; 14:1254122. [PMID: 37869671 PMCID: PMC10587439 DOI: 10.3389/fmicb.2023.1254122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Within the 2007-2014 programme for the surveillance of antimicrobial resistance (AMR) in livestock in France, mcr-1 prevalence average in commensal Escherichia coli was found to be 5.9% in turkeys and 1.8% in broilers, indicating that mobile colistin resistance had spread in farm animals. In 2017, the French national Ecoantibio2 plan was established to tackle AMR in veterinary medicine, with the objective of a 50% reduction in exposure to colistin in farm animals within 5 years (from 2014-2015 to 2020). Our objective was to update data concerning the prevalence and molecular epidemiology of colistin resistance, in consideration of colistin sales in poultry production in France. Methods Antimicrobial susceptibility of commensal E. coli isolated from broilers and turkeys at slaughterhouse was determined by broth micro-dilution. The mcr genes were screened by polymerase chain reaction (PCR). Whole genome sequencing (WGS) was used to investigate the genetic diversity of colistin-resistant isolates. Transformation experiments enabled identification of the mcr-bearing plasmid replicon types. The correlation between prevalence of colistin resistance and colistin usage data was explored statistically. Results and discussion In 2020, in France, the resistance prevalence to colistin in poultry production was 3% in turkeys and 1% in broilers, showing a significant highly positive correlation with a -68% decrease of poultry exposure to colistin since 2014. Only the mcr-1 gene was detected among the colistin-resistant E. coli. More than 80% of isolates are multi-drug resistant with 40% of isolates originating from turkeys and 44% originating from broilers co-resistant to the critically important antimicrobial ciprofloxacin. Most of the strains had no clonal relationship. The mcr gene was located in different plasmid types, carrying various other AMR genes. The decrease in colistin resistance among poultry in France can be considered a positive outcome of the national action plans for reduced colistin usage.
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Affiliation(s)
| | - Paméla Houée
- Laboratoire de Fougères, ANSES, Fougères, France
| | - Pierrick Lucas
- Laboratoire de Ploufragan-Plouzané-Niort, ANSES, Ploufragan, France
| | - Arnaud Felten
- Laboratoire de Ploufragan-Plouzané-Niort, ANSES, Ploufragan, France
| | | | - Claire Chauvin
- Laboratoire de Ploufragan-Plouzané-Niort, ANSES, Ploufragan, France
| | - Isabelle Kempf
- Laboratoire de Ploufragan-Plouzané-Niort, ANSES, Ploufragan, France
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Kempf I, Le Devendec L, Lucas P, Druilhe C, Pourcher AM. Impact of mesophilic anaerobic digestion and post-treatment of digestates on the transfer of conjugative antimicrobial resistance plasmids. Waste Manag 2022; 152:1-5. [PMID: 35963201 DOI: 10.1016/j.wasman.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/20/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Manure is a major source of antimicrobial-resistant bacteria and resistance genes carried by mobile genetic elements such as plasmids. In France, the number of on-farm biogas plants has increased significantly in recent years. Our study investigated the impact of mesophilic anaerobic digestion (AD) and the post-treatment of digestates on the fate of conjugative plasmids, along with their potential transfer of antimicrobial resistance. Samples of raw manure, digestates and post-treated digestates were collected from three on-farm biogas plants. Conjugative plasmids were captured using the Escherichia coli CV601 recipient strain and media supplemented with rifampicin and kanamycin - to which the recipient strain is resistant - and tetracycline, sulfamethoxazole, gentamicin, trimethoprim, amoxicillin, cefotaxime, ciprofloxacin or colistin. Putative transconjugants were identified and characterised by disc diffusion and whole genome sequencing. The results showed that the antimicrobial resistance genes transferred from the different matrices conferred resistance to tetracyclines, sulphonamides, trimethoprim, and/or streptomycin. Transconjugants were obtained from raw manure samples but not from digestates or post-digestates, suggesting that mesophilic AD processes may produce fewer conjugative plasmids potentially able to be transferred to Enterobacterales.
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Affiliation(s)
- Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France.
| | | | - Pierrick Lucas
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France
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Lucas C, Delannoy S, Schouler C, Souillard R, Le Devendec L, Lucas P, Keita A, Fach P, Puterflam J, Bougeard S, Kempf I. Description and validation of a new set of PCR markers predictive of avian pathogenic Escherichia coli virulence. Vet Microbiol 2022; 273:109530. [DOI: 10.1016/j.vetmic.2022.109530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/02/2022] [Indexed: 10/16/2022]
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Keita A, Le Devendec L, Amelot M, Puterflam J, Lucas C, Bougeard S, Delannoy S, Schouler C, Fach P, Lucas P, Souillard R, Kempf I. Efficacy of passive immunization in broiler chicks via an inactivated Escherichia coli autogenous vaccine administered to broiler breeder hens. Avian Pathol 2022; 51:445-456. [DOI: 10.1080/03079457.2022.2084362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Alassane Keita
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Laetitia Le Devendec
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Michel Amelot
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | | | - Camille Lucas
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Stéphanie Bougeard
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Sabine Delannoy
- ANSES – French Agency for Food, Environmental and Occupational Health and Safety Food Research Laboratory, Platform IdentyPath, 94700 Maisons-Alfort, France
| | | | - Patrick Fach
- ANSES – French Agency for Food, Environmental and Occupational Health and Safety Food Research Laboratory, Platform IdentyPath, 94700 Maisons-Alfort, France
| | - Pierrick Lucas
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Rozenn Souillard
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
| | - Isabelle Kempf
- Ploufragan-Plouzané-Niort Laboratory, Zoopôle les croix, 22440 Ploufragan, France
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Drider D, Boukherroub R, Le Devendec L, Belguesmia Y, Hazime N, Mourand G, Paboeuf F, Kempf I. Impact of colistin and colistin-loaded on alginate nanoparticles on pigs infected with a colistin-resistant enterotoxigenic Escherichia coli strain. Vet Microbiol 2022; 266:109359. [PMID: 35121303 DOI: 10.1016/j.vetmic.2022.109359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 01/17/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023]
Abstract
Colistin is frequently used for the control of post-weaning diarrhoea in pigs. Colistin resistance caused by plasmidic genes is a public health issue. We evaluated, in experimental animal facilities, whether free colistin or colistin-loaded on alginate nanoparticles (colistin/Alg NPs) could select a colistin-resistant Enterotoxigenic Escherichia coli. The Alg NPs were produced by a simple top-down approach through ball milling of sodium alginate polymer precursor, and colistin loading was achieved through physical adsorption. Colistin loading on Alg NPs was confirmed using various tools such Fourier transform infrared spectroscopy and dynamic light scattering measurements. Thirty-four piglets were orally inoculated or not with a mcr-1-positive, rifampicin-resistant enterotoxigenic E. coli strain, and the inoculated pigs were either treated or not during five days with commercial colistin (100,000 IU/kg) or colistin/Alg NPs (40,415 IU/kg). Clinical signs were recorded. Fecal and post-mortem samples were analyzed by culture. The result clearly indicated that colistin/Alg NPs had a slightly better therapeutic effect. Both treatments led to a transitory decrease of the total E. coli fecal population with a majority of colistin-resistant E. coli isolates during treatment, but the dominant E. coli population was found susceptible at the end of the trial. Further studies are needed to evaluate, in diverse experimental or field conditions, the therapeutic efficacy of colistin/Alg NPs for post-weaning diarrhoea.
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Affiliation(s)
- Djamel Drider
- UMR Transfrontalière BioEcoAgro1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | - Rabah Boukherroub
- Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520, IEMN, F-59000, Lille, France
| | - Laetitia Le Devendec
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Zoopole les croix, 22440, Ploufragan, France
| | - Yanath Belguesmia
- UMR Transfrontalière BioEcoAgro1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D'Opale, ICV - Institut Charles Viollette, 59000, Lille, France
| | - Noura Hazime
- UMR Transfrontalière BioEcoAgro1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D'Opale, ICV - Institut Charles Viollette, 59000, Lille, France; Univ. Lille, CNRS, Centrale Lille, Univ. Polytechnique Hauts-de-France, UMR 8520, IEMN, F-59000, Lille, France
| | - Gwenaelle Mourand
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Zoopole les croix, 22440, Ploufragan, France
| | - Frédéric Paboeuf
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Zoopole les croix, 22440, Ploufragan, France
| | - Isabelle Kempf
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Zoopole les croix, 22440, Ploufragan, France.
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Roman VL, Merlin C, Baron S, Larvor E, Le Devendec L, Virta MPJ, Bellanger X. Abundance and environmental host range of the SXT/R391 ICEs in aquatic environmental communities. Environ Pollut 2021; 288:117673. [PMID: 34218080 DOI: 10.1016/j.envpol.2021.117673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 06/23/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
Mobile genetic elements (MGEs) such as plasmids or integrative conjugative elements (ICEs) are widely involved in the horizontal transfer of antibiotic resistant genes (ARGs), but their environmental host-range and reservoirs remain poorly known, as mainly assessed through the analysis of culturable and clinical bacterial isolates. In this study, we used a gradual approach for determining the environmental abundance and host-range of ICEs belonging to the SXT/R391 family, otherwise well known to bring ARGs in Vibrio spp. epidemic clones and other pathogens. First, by screening a set of aquatic bacteria libraries covering 1794 strains, we found that almost 1% of the isolates hosted an SXT/R391 element, all belonging to a narrow group of non-O1/non-O139 Vibrio cholerae. However, when SXT/R391 ICEs were then quantified in various aquatic communities, they appeared to be ubiquitous and relatively abundant, from 10-6 to 10-3 ICE copies per 16 S rDNA. Finally, the molecular exploration of the SXT/R391 host-range in two river ecosystems impacted by anthropogenic activities, using the single-cell genomic approach epicPCR, revealed several new SXT/R391 hosts mostly in the Proteobacteria phylum. Some, such as the pathogen Arcobacter cryaerophilus (Campylobacteraceae), have only been encountered in discharged treated wastewaters and downstream river waters, thus revealing a likely anthropogenic origin. Others, such as the non-pathogenic bacterium Neptunomonas acidivorans (Oceanospirillaceae), were solely identified in rivers waters upstream and downstream the treated wastewaters discharge points and may intrinsically belong to the SXT/R391 environmental reservoir. This work points out that not only the ICEs of the SXT/R391 family are more abundant in the environment than anticipated, but also that a variety of unsuspected hosts may well represent a missing link in the environmental dissemination of MGEs from and to bacteria of anthropogenic origin.
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Affiliation(s)
| | | | - Sandrine Baron
- Mycoplasmology-Bacteriology and Antimicrobial Resistance Unit, Ploufragan-Plouzané-Niort Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Ploufragan, France
| | - Emeline Larvor
- Mycoplasmology-Bacteriology and Antimicrobial Resistance Unit, Ploufragan-Plouzané-Niort Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Ploufragan, France
| | - Laetitia Le Devendec
- Mycoplasmology-Bacteriology and Antimicrobial Resistance Unit, Ploufragan-Plouzané-Niort Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Ploufragan, France
| | - Marko P J Virta
- Department of Microbiology, University of Helsinki, Helsinki, Finland
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Delannoy S, Schouler C, Souillard R, Yousfi L, Le Devendec L, Lucas C, Bougeard S, Keita A, Fach P, Galliot P, Balaine L, Puterflam J, Kempf I. Diversity of Escherichia coli strains isolated from day-old broiler chicks, their environment and colibacillosis lesions in 80 flocks in France. Vet Microbiol 2020; 252:108923. [PMID: 33221068 DOI: 10.1016/j.vetmic.2020.108923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Avian colibacillosis is the most common bacterial disease affecting broilers. To better evaluate the diversity and the origin of the causative Escherichia coli strains infecting birds, we conducted a study on 80 broiler flocks. Just before the arrival of chicks on the farm, samples were collected in the farm environment (walls, feeders, air inlets, etc.) and, upon delivery, day-old chicks (DOCs) and the transport boxes were also sampled. Isolates were obtained from these samples, and from organs of chickens exhibiting typical colibacillosis symptoms. The isolates were characterized using high-throughput qPCR to detect a range of genetic markers (phylogroups, main serogroups virulence markers, etc.). A total of 967 isolates were studied, including 203 from 28 colibacillosis episodes, 484 from DOCs, 162 from transport boxes and 118 from the farm environment. These isolates yielded 416 different genetic profiles, of which 267 were detected in single isolates, and the others were observed in up to 44 isolates from nine farms. The distributions of isolates across phylogroups and the main serogroups varied with the origin of isolation. The isolates obtained from colibacillosis cases either shared a single genetic profile or were different. In a few cases, we observed the same profile for isolates obtained from DOCs and colibacillosis lesions in the same flock or different flocks. However, some flocks receiving DOCs contaminated with isolates bearing the genetic profile of colibacillosis cases identified in other flocks remained healthy. This study highlights the huge diversity among avian E. coli isolated from diseased and non diseased birds.
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Affiliation(s)
- Sabine Delannoy
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France
| | | | | | - Léna Yousfi
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France
| | | | | | | | | | - Patrick Fach
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France
| | | | - Loïc Balaine
- ANSES, Ploufragan-Plouzané-Niort Laboratory, France
| | | | - Isabelle Kempf
- Université Paris-Est, ANSES, Food Safety Laboratory, Platform IdentyPath, 94701, Maisons-Alfort, France.
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Baron S, Le Devendec L, Lucas P, Larvor E, Jové T, Kempf I. Characterisation of plasmids harbouring extended-spectrum cephalosporin resistance genes in Escherichia coli from French rivers. Vet Microbiol 2020; 243:108619. [PMID: 32273005 DOI: 10.1016/j.vetmic.2020.108619] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 11/19/2022]
Abstract
Antimicrobial resistance is a "One Health" issue that requires improved knowledge of the presence and abundance of resistant bacteria in the environment. Extended-spectrum cephalosporins (ESCs) are critically important antibiotics (CIAs), and resistance to these CIAs is often encoded by beta-lactamase genes borne on conjugative plasmids. We thus decided to characterise 21 plasmids of ESC-resistant Escherichia coli randomly selected from isolates previously obtained from river water collected in a rural area in western France. The plasmids encoding ESC resistance were sequenced to investigate the diversity of the genes encoding ESC resistance and their genetic context. Sequences revealed that eleven IncI1 pMLST3 plasmids carried the blaCTX-M-1 and sul2 genes, and some of them also had the tet(A), aadA5 or dfrA17 genes. The blaCTX-M-1 gene was also detected on an IncN plasmid. Five plasmids obtained from four rivers contained blaCTX-M-14, either on IncI1 or on IncFII plasmids. Two strains from two rivers contained blaCTX-M-15 on IncN pMLST7 plasmids, with qnrS1 and dfrA14 genes. One plasmid contained the blaCTX-M-55, a blaTEM-1B-like, and fosA genes. One plasmid contained the blaCMY-2 gene. The diversity of the genes and plasmids of the resistant bacteria isolated from French rivers is probably related to the various animal and human origins of the isolated bacteria.
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Affiliation(s)
- Sandrine Baron
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France
| | | | - Pierrick Lucas
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France
| | - Emeline Larvor
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, U1092, University of Limoges, Limoges, France
| | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France.
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Mourand G, Andraud M, Jouy E, Chauvin C, Le Devendec L, Paboeuf F, Kempf I. Impact of colistin administered before or after inoculation on the transmission of a mcr-1 colistin-resistant Escherichia coli strain between pigs. Vet Microbiol 2019; 230:164-170. [PMID: 30827384 DOI: 10.1016/j.vetmic.2019.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/17/2019] [Accepted: 02/03/2019] [Indexed: 11/19/2022]
Abstract
Colistin resistance associated with plasmidic resistance genes is a serious public health issue. We aimed at studying the transmission of an mcr-1 colistin- and rifampicin-resistant Escherichia coli strain between inoculated pigs and sentinels in different controlled conditions. Three groups of four pigs were bred in separated animal rooms and inoculated on Day 0 (D0). In each inoculated group, six contact pigs were introduced on D2. The first inoculated-and-contact group was left untreated. The ten pigs in the second inoculated-and-contact group received colistin (100 000 IU/kg) before inoculation or contact (D-7 to D-5), simulating prophylactic administration. Pigs in the third inoculated-and-contact group were treated just after inoculation or before transfer (D0 to D2), simulating metaphylactic administration. Faecal samples were regularly collected and segments of intestinal tracts were obtained at necropsy, on D20-D22. Samples were cultured on rifampicin-supplemented media, and PCR was used to detect the mcr-1 gene. The kinetics of infection, based on culture results, were analysed using an SIR model. The inoculated strain was detected in all inoculated and contact pigs. The SIR model showed that one infected pig could transmit the resistant bacteria to one susceptible individual in less than 3 h on average. Prophylactic administration significantly enhanced the transmission rate and resulted in more samples containing the mcr-1 resistance gene at necropsy. No effect of metaphylactic administration could be detected on the transmission rate, nor on the carriage of the resistant strain. Our study confirms that colistin should not be used in a prophylactic manner.
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Affiliation(s)
- Gwenaëlle Mourand
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France; Université Bretagne Loire, France
| | - Mathieu Andraud
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France; Université Bretagne Loire, France
| | - Eric Jouy
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France; Université Bretagne Loire, France
| | - Claire Chauvin
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France; Université Bretagne Loire, France
| | - Laetitia Le Devendec
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France; Université Bretagne Loire, France
| | - Frederic Paboeuf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France; Université Bretagne Loire, France
| | - Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané-Niort, Ploufragan, France; Université Bretagne Loire, France.
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Lucas P, Jouy E, Le Devendec L, de Boisséson C, Perrin-Guyomard A, Jové T, Blanchard Y, Touzain F, Kempf I. Characterization of plasmids harboring blaCTX-M genes in Escherichia coli from French pigs. Vet Microbiol 2018; 224:100-106. [DOI: 10.1016/j.vetmic.2018.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/03/2018] [Accepted: 08/03/2018] [Indexed: 12/29/2022]
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Mourand G, Jouy E, Chauvin C, Le Devendec L, Paboeuf F, Kempf I. Dissemination of the mcr-1 colistin resistance gene among pigs: An experimental study. Vet Microbiol 2018; 221:122-128. [PMID: 29981697 DOI: 10.1016/j.vetmic.2018.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/01/2018] [Accepted: 06/07/2018] [Indexed: 10/14/2022]
Abstract
Colistin resistance in Enterobacteriaceae is a public health problem. The present study was designed to evaluate the dissemination of a colistin-resistant Escherichia coli strain and its resistance gene, mcr-1, between orally inoculated pigs and their contacts. A non-inoculated control group, one low-dose and one high-dose group-both including two pens of two inoculated and three contact pigs-were raised in separate rooms. After inoculation of a colistin- and rifampicin-resistant E. coli suspension (2.5 × 105 CFU/pig for the low-dose group and 2.5 × 108 CFU/pig for the high-dose group), feces from inoculated and non-inoculated contact pigs were collected and inoculated on colistin- and rifampicin-supplemented media directly or after enrichment in rifampicin-supplemented media, then the isolates were characterized. PCR was used to detect the mcr-1 gene in lysates from feces cultivated in colistin-supplemented broth and DNA prepared from feces. Results showed that the low-dose inoculum was probably insufficient to obtain durable colonization, but could lead to the temporary presence of mcr-1-positive E. coli strains. The high-dose inoculum resulted in durable colonization of both inoculated and contact animals. In all groups, the mcr-1 gene was also detected in rifampicin-susceptible strains, suggesting its transfer to several commensal strains. A comparison of detection methods showed that more positive samples were obtained with cultures in rifampicin-supplemented media and suggests that current methods to evaluate the prevalence of colistin resistance in fecal samples suffer from poor sensitivity.
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Affiliation(s)
- Gwenaelle Mourand
- ANSES, Laboratoire de Ploufragan-Plouzané, Ploufragan, France; Université Bretagne Loire, France
| | - Eric Jouy
- ANSES, Laboratoire de Ploufragan-Plouzané, Ploufragan, France; Université Bretagne Loire, France
| | - Claire Chauvin
- ANSES, Laboratoire de Ploufragan-Plouzané, Ploufragan, France; Université Bretagne Loire, France
| | - Laetitia Le Devendec
- ANSES, Laboratoire de Ploufragan-Plouzané, Ploufragan, France; Université Bretagne Loire, France
| | - Frédéric Paboeuf
- ANSES, Laboratoire de Ploufragan-Plouzané, Ploufragan, France; Université Bretagne Loire, France
| | - Isabelle Kempf
- ANSES, Laboratoire de Ploufragan-Plouzané, Ploufragan, France; Université Bretagne Loire, France.
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Baron S, Le Devendec L, Touzain F, Jouy E, Lucas P, de Boisséson C, Larvor E, Kempf I. Longitudinal study of Escherichia coli plasmid resistance to extended-spectrum cephalosporins in free-range broilers. Vet Microbiol 2018. [PMID: 29519517 DOI: 10.1016/j.vetmic.2018.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Resistance to extended-spectrum cephalosporins (ESCs) is mostly borne by conjugative plasmids. The aim of the present study was to evaluate the characteristics and diversity of ESC resistance plasmids in Escherichia coli from different free-range broiler flocks in France, and their persistence in flocks during rearing. Two hatcheries were selected. Faecal samples from 11 flocks were collected from before their arrival on the broiler production farm up to their slaughter at the end of the rearing period. A selection of 25 E. coli isolates obtained at different times from different flocks but all harbouring an ESC resistance gene was characterised. The plasmids coding for ESC resistance were sequenced using Mi-seq Illumina technology or the ion proton system (Ion Torrent). Ten IncI1 ST12 plasmids carried the blaCMY-2 gene, and most of them had no other resistance genes. All blaCMY-2 plasmids were obtained from day-old to 7-day-old chicks from four flocks hatched at the same hatchery and sent to three different farms. Sequence comparisons showed identity percentages higher than 99%. Fifteen IncI1 ST3 plasmids were obtained from day-old to 77-day-old broilers from seven flocks on six farms. These plasmids harboured the blaCTX-M-1 gene, and most also had the tet(A) and sul2 genes, with sequence identity higher than 99%. For both types of plasmid, very high identity percentages were also obtained with published sequences of plasmids isolated from broilers in other countries or from other animal species. Thus, unlike the IncI1 ST12 blaCMY-2 plasmids, the epidemic nature of the IncI1 ST3 blaCTX-M-1 plasmids in the French poultry production makes it difficult to determine the origin of a contamination which may persist for weeks in a flock.
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Affiliation(s)
- Sandrine Baron
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France
| | - Laetitia Le Devendec
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France
| | - Fabrice Touzain
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France
| | - Eric Jouy
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France
| | - Pierrick Lucas
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France
| | - Claire de Boisséson
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France
| | - Emeline Larvor
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France
| | - Isabelle Kempf
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Bretagne Loire, France.
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Touzain F, Le Devendec L, de Boisséson C, Baron S, Jouy E, Perrin-Guyomard A, Blanchard Y, Kempf I. Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers. PLoS One 2018; 13:e0188768. [PMID: 29360838 PMCID: PMC5779644 DOI: 10.1371/journal.pone.0188768] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/13/2017] [Indexed: 12/24/2022] Open
Abstract
Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this study was to analyze and compare plasmids coding for resistance to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli (APEC) strains obtained respectively at slaughterhouse or from diseased broilers in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the resistances of the transformants were determined. The sequences of the ESC-resistance plasmids prepared from transformants were obtained by Illumina (33 plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids contained the blaCTX-M-1 gene and belonged to the IncI1/ST3 type, with 27 and 20 of them carrying the sul2 or tet(A) genes respectively. Despite their diverse origins, several plasmids showed very high percentages of identity. None of the blaCTX-M-1-containing plasmid contained APEC virulence genes, although some of them were detected in the parental strains. Three plasmids had the blaCMY-2 gene, but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB replicon types. The blaCMY-2 IncFIA/FIB plasmid was obtained from a strain isolated from a diseased broiler and also containing a blaCTX-M-1 IncI1/ST3 plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT, etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the blaCMY-2 plasmid. In conclusion, our results show the dominance and high similarity of blaCTX-M-1 IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a blaCMY-2 plasmid.
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Affiliation(s)
- Fabrice Touzain
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Laetitia Le Devendec
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Claire de Boisséson
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Sandrine Baron
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Eric Jouy
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Agnès Perrin-Guyomard
- Université Bretagne Loire, Rennes, France
- ANSES, Fougères Laboratory, Fougères, France
| | - Yannick Blanchard
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Isabelle Kempf
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
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Delannoy S, Le Devendec L, Jouy E, Fach P, Drider D, Kempf I. Characterization of Colistin-Resistant Escherichia coli Isolated from Diseased Pigs in France. Front Microbiol 2017; 8:2278. [PMID: 29209292 PMCID: PMC5702452 DOI: 10.3389/fmicb.2017.02278] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/06/2017] [Indexed: 11/17/2022] Open
Abstract
We studied a collection of 79 colistin-resistant Escherichia coli isolates isolated from diseased pigs in France between 2009 and 2013. We determined a number of phenotypic and genetic characters using broth microdilution to characterize their antimicrobial susceptibility. We performed pulse field gel electrophoresis (PFGE) to assess their genetic diversity and assign them to phylogroups. High-throughput real-time PCR micro-array was used to screen for a selection of genetic markers of virulence, and PCR and sequencing of the main recognized resistance genes allowed us to investigate the mechanisms of colistin resistance. Results showed that isolates belonged to several phylogroups and most had a unique PFGE profile. More than 50% of the isolates were also resistant to sulfonamides, trimethoprim, tetracycline, ampicillin or chloramphenicol. The mcr-1 gene was detected in 70 out of 79 isolates and was transferred by conjugation in 33 of them, sometimes together with resistance to sulfonamides, trimethoprim, tetracycline, ampicillin, chloramphenicol, cefotaxime, or gentamicin. Mutations in the amino-acid sequences of proteins MgrB, PhoP, PhoQ, PmrB, but not PmrA, were detected in isolates with or without the mcr-1 gene. More than one-third of the isolates harbored the F18, F4, astA, hlyA, estI, estII, elt, stx2e, iha, orfA, orfB, paa, terE, ecs1763, or ureD virulence markers. In conclusion, although most isolates had a unique PFGE profile, a few particular combinations of phylogenetic groups, virulence genes and mutations in the sequenced genes involved in colistin resistance were identified on a number of occasions, suggesting the persistence of certain isolates over several years.
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Affiliation(s)
- Sabine Delannoy
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Food Safety Laboratory, Université Paris-Est, Maisons-Alfort, France
| | - Laetitia Le Devendec
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Eric Jouy
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Patrick Fach
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Food Safety Laboratory, Université Paris-Est, Maisons-Alfort, France
| | - Djamel Drider
- Institut Charles Viollette, Université de Lille, Lille, France
| | - Isabelle Kempf
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
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Le Devendec L, Mourand G, Bougeard S, Léaustic J, Jouy E, Keita A, Couet W, Rousset N, Kempf I. Impact of colistin sulfate treatment of broilers on the presence of resistant bacteria and resistance genes in stored or composted manure. Vet Microbiol 2016; 194:98-106. [DOI: 10.1016/j.vetmic.2015.11.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 11/16/2022]
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Meguenni N, Le Devendec L, Jouy E, Le Corvec M, Bounar-Kechih S, Bakour R, Kempf I. First Description of an Extended-Spectrum Cephalosporin- and Fluoroquinolone-Resistant Avian PathogenicEscherichia coliClone in Algeria. Avian Dis 2015; 59:20-3. [DOI: 10.1637/10804-022414-reg.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Kempf I, Le Roux A, Perrin-Guyomard A, Mourand G, Le Devendec L, Bougeard S, Richez P, Le Pottier G, Eterradossi N. Effect of in-feed paromomycin supplementation on antimicrobial resistance of enteric bacteria in turkeys. Vet J 2013; 198:398-403. [DOI: 10.1016/j.tvjl.2013.05.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 05/17/2013] [Accepted: 05/19/2013] [Indexed: 10/26/2022]
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Le Devendec L, Bouder A, Dheilly A, Hellard G, Kempf I. Persistence and spread of qnr, extended-spectrum beta-lactamase, and ampC resistance genes in the digestive tract of chickens. Microb Drug Resist 2010; 17:129-34. [PMID: 21190475 DOI: 10.1089/mdr.2010.0096] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The aim of this assay was to develop an experimental model of digestive colonization of chickens with bacteria harboring qnr, extended-spectrum beta-lactamase, or ampC genes. Specific pathogen-free chickens were orally inoculated with two Escherichia coli strains containing either the plasmid pMG252 bearing bla(FOX) and qnrA genes, or pMG298 bearing bla(CTX-M) and qnrB genes. Analysis of strains isolated from fecal samples showed that the two strains were able to persist for several weeks in the digestive flora of inoculated birds and could rapidly spread to noninoculated ones. However, the multi-resistant isolates were maintained as a small proportion of the overall enterobacterial population. The qnr, extended-spectrum beta-lactamase, and ampC resistance genes could be transferred, in vivo, in the absence of selective pressure, to other chicken E. coli or Klebsiella pneumoniae isolates.
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Affiliation(s)
- Laetitia Le Devendec
- Anses, Laboratoire de Ploufragan-Plouzané, Unité Mycoplasmologie Bactériologie, Ploufragan, France
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