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Brauge T, Bourdonnais E, Trigueros S, Cresson P, Debuiche S, Granier SA, Midelet G. Antimicrobial resistance and geographical distribution of Staphylococcus sp. isolated from whiting (Merlangius merlangus) and seawater in the English Channel and the North sea. Environ Pollut 2024; 345:123434. [PMID: 38290653 DOI: 10.1016/j.envpol.2024.123434] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/04/2024] [Accepted: 01/21/2024] [Indexed: 02/01/2024]
Abstract
Staphylococcus is a significant food safety hazard. The marine environment serves as a source of food for humans and is subject to various human-induced discharges, which may contain Staphylococcus strains associated with antimicrobial resistance (AMR). The aim of this study was to assess the occurrence and geographical distribution of AMR Staphylococcus isolates in seawater and whiting (Merlangius merlangus) samples collected from the English Channel and the North Sea. We isolated and identified 238 Staphylococcus strains, including 12 coagulase-positive (CoPs) and 226 coagulase-negative (CoNs) strains. All CoPs isolates exhibited resistance to at least one of the 16 antibiotics tested. Among the CoNs strains, 52% demonstrated resistance to at least one antibiotic, and 7 isolates were classified as multi-drug resistant (MDR). In these MDR strains, we identified AMR genes that confirmed the resistance phenotype, as well as other AMR genes, such as quaternary ammonium resistance. One CoNS strain carried 9 AMR genes, including both antibiotic and biocide resistance genes. By mapping the AMR phenotypes, we demonstrated that rivers had a local influence, particularly near the English coast, on the occurrence of AMR Staphylococcus. The analysis of marine environmental parameters revealed that turbidity and phosphate concentration were implicated in the occurrence of AMR Staphylococcus. Our findings underscore the crucial role of wild whiting and seawater in the dissemination of AMR Staphylococcus within the marine environment, thereby posing a risk to human health.
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Affiliation(s)
- Thomas Brauge
- French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France.
| | - Erwan Bourdonnais
- French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
| | - Sylvain Trigueros
- French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
| | - Pierre Cresson
- Ifremer, Channel/North Sea Fisheries Laboratory, Boulogne-sur-Mer, France
| | - Sabine Debuiche
- French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
| | - Sophie A Granier
- French Agency for Food, Environmental and Occupational Health & Safety, Fougères Laboratory, Fougères, France
| | - Graziella Midelet
- French Agency for Food, Environmental and Occupational Health & Safety, Laboratory for Food Safety, Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Boulogne-sur-Mer, France
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Delannoy S, Hoffer C, Youf R, Dauvergne E, Webb HE, Brauge T, Tran ML, Midelet G, Granier SA, Haenni M, Fach P, Brisabois A. High Throughput Screening of Antimicrobial Resistance Genes in Gram-Negative Seafood Bacteria. Microorganisms 2022; 10:microorganisms10061225. [PMID: 35744743 PMCID: PMC9230514 DOI: 10.3390/microorganisms10061225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 03/28/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 01/24/2023] Open
Abstract
From a global view of antimicrobial resistance over different sectors, seafood and the marine environment are often considered as potential reservoirs of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs); however, there are few studies and sparse results on this sector. This study aims to provide new data and insights regarding the content of resistance markers in various seafood samples and sources, and therefore the potential exposure to humans in a global One Health approach. An innovative high throughput qPCR screening was developed and validated in order to simultaneously investigate the presence of 41 ARGs and 33 MGEs including plasmid replicons, integrons, and insertion sequences in Gram-negative bacteria. Analysis of 268 seafood isolates from the bacterial microflora of cod (n = 24), shellfish (n = 66), flat fishes (n = 53), shrimp (n = 10), and horse mackerel (n = 115) show the occurrence of sul-1, ant(3″)-Ia, aph(3')-Ia, strA, strB, dfrA1, qnrA, and blaCTX-M-9 genes in Pseudomonas spp., Providencia spp., Klebsiella spp., Proteus spp., and Shewanella spp. isolates and the presence of MGEs in all bacterial species investigated. We found that the occurrence of MGE may be associated with the seafood type and the environmental, farming, and harvest conditions. Moreover, even if MGE were detected in half of the seafood isolates investigated, association with ARG was only identified for twelve isolates. The results corroborate the hypothesis that the incidence of antimicrobial-resistant bacteria (ARB) and ARG decreases with increasing distance from potential sources of fecal contamination. This unique and original high throughput micro-array designed for the screening of ARG and MGE in Gram-negative bacteria could be easily implementable for monitoring antimicrobial resistance gene markers in diverse contexts.
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Affiliation(s)
- Sabine Delannoy
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
- Correspondence:
| | - Corine Hoffer
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Raphaëlle Youf
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Emilie Dauvergne
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Hattie E. Webb
- Department of Animal and Food Sciences, International Center for Food Safety Excellence, Texas Tech University, Lubbock, TX 79409, USA;
| | - Thomas Brauge
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Mai-Lan Tran
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Graziella Midelet
- Bacteriology and Parasitology of Fishery and Aquaculture Products Unit, Laboratory for Food Safety, ANSES, 62200 Boulogne-sur-Mer, France; (T.B.); (G.M.)
| | - Sophie A. Granier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, ANSES, 35306 Fougères, France;
| | - Marisa Haenni
- Antimicrobial Resistance and Bacterial Virulence Unit, Lyon Laboratory, Université de Lyon, ANSES, 69364 Lyon, France;
| | - Patrick Fach
- COLiPATH Unit & Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, 94700 Maisons-Alfort, France; (C.H.); (R.Y.); (E.D.); (M.-L.T.); (P.F.)
| | - Anne Brisabois
- Strategy and Programs Department, ANSES, 94700 Maisons-Alfort, France;
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Perrin-Guyomard A, Granier SA, Slettemeås JS, Anjum M, Randall L, AbuOun M, Pauly N, Irrgang A, Hammerl JA, Kjeldgaard JS, Hammerum A, Franco A, Skarżyńska M, Kamińska E, Wasyl D, Dierikx C, Börjesson S, Geurts Y, Haenni M, Veldman K. Multicentre evaluation of a selective isolation protocol for detection of mcr-positive E. coli and Salmonella spp. in food-producing animals and meat. Lett Appl Microbiol 2022; 75:224-233. [PMID: 35388505 PMCID: PMC9544698 DOI: 10.1111/lam.13717] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 12/01/2022]
Abstract
This study was conducted to evaluate the performance of a screening protocol to detect and isolate mcr‐positive Escherichia coli and Salmonella spp. from animal caecal content and meat samples. We used a multicentre approach involving 12 laboratories from nine European countries. All participants applied the same methodology combining a multiplex PCR performed on DNA extracted from a pre‐enrichment step, followed by a selective culture step on three commercially available chromogenic agar plates. The test panel was composed of two negative samples and four samples artificially contaminated with E. coli and Salmonella spp. respectively harbouring mcr‐1 or mcr‐3 and mcr‐4 or mcr‐5 genes. PCR screening resulted in a specificity of 100% and a sensitivity of 83%. Sensitivity of each agar medium to detect mcr‐positive colistin‐resistant E. coli or Salmonella spp. strains was 86% for CHROMID® Colistin R, 75% for CHROMagarTM COL‐APSE and 70% for COLISTIGRAM. This combined method was effective to detect and isolate most of the E. coli or Salmonella spp. strains harbouring different mcr genes from food‐producing animals and food products and might thus be used as a harmonized protocol for the screening of mcr genes in food‐producing animals and food products in Europe.
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Affiliation(s)
- Agnès Perrin-Guyomard
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères Laboratory, France
| | - Sophie A Granier
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères Laboratory, France
| | | | - Muna Anjum
- Animal and Plant Health Agency, United Kingdom
| | | | | | - Natalie Pauly
- German Federal Institute for Risk Assessment, Germany
| | | | | | | | | | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Italy
| | | | | | | | - Cindy Dierikx
- National Institute for Public Health and the Environment, the Netherlands
| | - Stefan Börjesson
- National Veterinary Institute (SVA), Sweden and Public Health Agency of Sweden, Sweden
| | - Yvon Geurts
- Wageningen Bioveterinary Research, the Netherlands
| | - Marisa Haenni
- Lyon University - French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Lyon laboratory, France
| | - Kees Veldman
- Wageningen Bioveterinary Research, the Netherlands
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Dierikx C, Börjesson S, Perrin-Guyomard A, Haenni M, Norström M, Divon HH, Ilag HK, Granier SA, Hammerum A, Kjeldgaard JS, Pauly N, Randall L, Anjum MF, Smialowska A, Franco A, Veldman K, Slettemeås JS. A European multicenter evaluation study to investigate the performance on commercially available selective agar plates for the detection of carbapenemase producing Enterobacteriaceae. J Microbiol Methods 2022; 193:106418. [PMID: 35041877 DOI: 10.1016/j.mimet.2022.106418] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 12/27/2022]
Abstract
The European Food Safety Authority (EFSA) advised to prioritize monitoring carbapenemase producing Enterobacteriaceae (CPE) in food producing animals. Therefore, this study evaluated the performance of different commercially available selective agars for the detection of CPE using spiked pig caecal and turkey meat samples and the proposed EFSA cultivation protocol. Eleven laboratories from nine countries received eight samples (four caecal and four meat samples). For each matrix, three samples contained approximately 100 CFU/g CPE, and one sample lacked CPE. After overnight enrichment in buffered peptone water, broths were spread upon Brilliance™ CRE Agar (1), CHROMID® CARBA (2), CHROMagar™ mSuperCARBA™ (3), Chromatic™ CRE (4), CHROMID® OXA-48 (5) and Chromatic™ OXA-48 (6). From plates with suspected growth, one to three colonies were selected for species identification, confirmation of carbapenem resistance and detection of carbapenemase encoding genes, by methods available at participating laboratories. Of the eleven participating laboratories, seven reported species identification, susceptibility tests and genotyping on isolates from all selective agar plates. Agars 2, 4 and 5 performed best, with 100% sensitivity. For agar 3, a sensitivity of 96% was recorded, while agar 1 and 6 performed with 75% and 43% sensitivity, respectively. More background flora was noticed for turkey meat samples than pig caecal samples. Based on this limited set of samples, most commercially available agars performed adequately. The results indicate, however, that OXA-48-like and non-OXA-48-like producers perform very differently, and one should consider which CPE strains are of interest to culture when choosing agar type.
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Affiliation(s)
- Cindy Dierikx
- National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721, MA, Bilthoven, the Netherlands
| | - Stefan Börjesson
- National Veterinary Institute, SE-751 89 Uppsala, Sweden; Public Health Agency of Sweden, SE-171 82 Solna, Sweden
| | - Agnès Perrin-Guyomard
- French Agency for Food, Environmental and Occupational Health & Safety, Fougères Laboratory, 10B rue Claude Bourgelat, Javené CS 40608 35306 Fougères Cedex, France
| | - Marisa Haenni
- French Agency for Food, Environmental and Occupational Health & Safety - Lyon University, Lyon Laboratory, 31, avenue Tony Garnier 69394 Lyon Cedex 07, France
| | | | - Hege H Divon
- Norwegian Veterinary Institute, P.O. Box 64, 1431 Ås, Norway
| | | | - Sophie A Granier
- French Agency for Food, Environmental and Occupational Health & Safety, Fougères Laboratory, 10B rue Claude Bourgelat, Javené CS 40608 35306 Fougères Cedex, France
| | - Annette Hammerum
- Statens Serums Institut, Artillerivej 5, DK-2300 Copenhagen S, Denmark
| | - Jette Sejer Kjeldgaard
- Technical University of Denmark, DTU Fødevareinstituttet, Kemitorvet, Bygning 202, DK-2800 Kgs Lyngby, Denmark
| | - Natalie Pauly
- German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Luke Randall
- Animal and Plant Health Agency, Woodham Ln, Addlestone KT15 3NB, United Kingdom
| | - Muna F Anjum
- Animal and Plant Health Agency, Woodham Ln, Addlestone KT15 3NB, United Kingdom
| | - Aleksandra Smialowska
- National Veterinary Research Institute, 57 Partyzantów Avenue, 24-100 PUŁAWY, Poland
| | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri", via Appia Nuova, 1411 - 00178 Roma, Italy
| | - Kees Veldman
- Wageningen Bioveterinary Research, P.O. Box 65, 8200 AB Lelystad, the Netherlands
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5
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Plassard V, Gisbert P, Granier SA, Millemann Y. Surveillance of Extended-Spectrum β-Lactamase-, Cephalosporinase- and Carbapenemase-Producing Gram-Negative Bacteria in Raw Milk Filters and Healthy Dairy Cattle in Three Farms in Île-de-France, France. Front Vet Sci 2021; 8:633598. [PMID: 33644154 PMCID: PMC7902890 DOI: 10.3389/fvets.2021.633598] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to test a surveillance protocol able to detect extended-spectrum β-lactamase (ESBL)-, cephalosporinase (AmpC)- and carbapenemase (CP)-producing gram-negative bacteria in three conveniently chosen dairy farms with known prior occurrences of ESBL- and CP-producing strains. The protocol was applied monthly for a year. At each visit, 10 healthy lactating dairy cows were rectally swabbed, and raw milk filters (RMFs) were sampled in two of the three farms. Bacterial isolation was based on a first screening step with MacConkey agar supplemented with 1 mg/L cefotaxime and commercial carbapenem-supplemented media. We failed to detect CP-producing strains but showed that ESBL-Escherichia strains, found in one farm only (13 strains), were closely associated with multi-drug resistance (12 out of 13). The limited number of conveniently selected farms and the fact that RMFs could not be retrieved from one of them limit the validity of our findings. Still, our results illustrate that ESBL-status changes monthly based on fecal swabs and negative herds should be qualified as “unsuspected” as proposed by previous authors. Although surveillance of farm statuses based on RMF analysis could theoretically allow for a better sensitivity than individual swabs, we failed to illustrate it as both farms where RMFs could be retrieved were constantly negative. Determination of CP herd-level status based on RMFs and our surveillance protocol was hindered by the presence of intrinsically resistant bacteria or strains cumulating multiple non-CP resistance mechanisms which means our protocol is not specific enough for routine monitoring of CP in dairy farms.
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Affiliation(s)
| | | | - Sophie A Granier
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Fougères, France
| | - Yves Millemann
- Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France.,Laboratoire de Sécurité des Aliments de l'ANSES, Maisons-Alfort, France
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6
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Sévellec Y, Granier SA, Le Hello S, Weill FX, Guillier L, Mistou MY, Cadel-Six S. Source Attribution Study of Sporadic Salmonella Derby Cases in France. Front Microbiol 2020; 11:889. [PMID: 32477304 PMCID: PMC7240076 DOI: 10.3389/fmicb.2020.00889] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 01/31/2020] [Accepted: 04/16/2020] [Indexed: 12/20/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Derby is one of the most frequent causes of gastroenteritis in humans. In Europe, this pathogen is one of the top five most commonly reported serovars in human cases. In France, S. Derby has been among the ten most frequently isolated serovars in humans since the year 2000. The main animal hosts of this serovar are pigs and poultry, and white meat is the main source of human contamination. We have previously shown that this serovar is polyphyletic and that three distinct genetic lineages of S. Derby cohabit in France. Two of them are associated with pork and one with poultry. In this study, we conducted a source attribution study based on single nucleotide polymorphism analysis of a large collection of 440 S. Derby human and non-human isolates collected in 2014-2015, to determine the contribution of each lineage to human contamination. In France, the two lineages associated with pork strains, and corresponding to the multilocus sequence typing (MLST) profiles ST39-ST40 and ST682 were responsible for 94% of human contaminations. Interestingly, the ST40 profile is responsible for the majority of human cases (71%). An analysis of epidemiologic data and the structure of the pork sector in France allowed us to explain the spread and the sporadic pattern of human cases that occurred in the studied period.
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Affiliation(s)
- Yann Sévellec
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France
| | - Sophie A. Granier
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France
- Laboratoire de Fougères, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Fougères, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Laurent Guillier
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France
| | - Michel-Yves Mistou
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, Université PARIS-EST, Maisons-Alfort, France
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Lepuschitz S, Baron S, Larvor E, Granier SA, Pretzer C, Mach RL, Farnleitner AH, Ruppitsch W, Pleininger S, Indra A, Kirschner AKT. Phenotypic and Genotypic Antimicrobial Resistance Traits of Vibrio cholerae Non-O1/Non-O139 Isolated From a Large Austrian Lake Frequently Associated With Cases of Human Infection. Front Microbiol 2019; 10:2600. [PMID: 31781080 PMCID: PMC6857200 DOI: 10.3389/fmicb.2019.02600] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [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: 08/14/2019] [Accepted: 10/25/2019] [Indexed: 12/13/2022] Open
Abstract
Vibrio cholerae belonging to serogroups other than O1 and O139 are opportunistic pathogens which cause infections with a variety of clinical symptoms. Due to the increasing number of V. cholerae non-O1/non-O139 infections in association with recreational waters in the past two decades, they have received increasing attention in recent literature and by public health authorities. Since the treatment of choice is the administration of antibiotics, we investigated the distribution of antimicrobial resistance properties in a V. cholerae non-O1/non-O139 population in a large Austrian lake intensively used for recreation and in epidemiologically linked clinical isolates. In total, 82 environmental isolates - selected on the basis of comprehensive phylogenetic information - and nine clinical isolates were analyzed for their phenotypic antimicrobial susceptibility. The genomes of 46 environmental and eight clinical strains were screened for known genetic antimicrobial resistance traits in CARD and ResFinder databases. In general, antimicrobial susceptibility of the investigated V. cholerae population was high. The environmental strains were susceptible against most of the 16 tested antibiotics, except sulfonamides (97.5% resistant strains), streptomycin (39% resistant) and ampicillin (20.7% resistant). Clinical isolates partly showed additional resistance to amoxicillin-clavulanic acid. Genome analysis showed that crp, a regulator of multidrug efflux genes, and the bicyclomycin/multidrug efflux system of V. cholerae were present in all isolates. Nine isolates additionally carried variants of bla CARB-7 and bla CARB-9, determinants of beta-lactam resistance and six isolates carried catB9, a determinant of phenicol resistance. Three isolates had both bla CARB-7 and catB9. In 27 isolates, five out of six subfamilies of the MATE-family were present. For all isolates no genes conferring resistance to aminoglycosides, macrolides and sulfonamides were detected. The apparent lack of either known antimicrobial resistance traits or mobile genetic elements indicates that in cholera non-epidemic regions of the world, V. cholerae non-O1/non-O139 play a minor role as a reservoir of resistance in the environment. The discrepancies between the phenotypic and genome-based antimicrobial resistance assessment show that for V. cholerae non-O1/non-O139, resistance databases are currently inappropriate for an assessment of antimicrobial resistance. Continuous collection of both data over time may solve such discrepancies between genotype and phenotype in the future.
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Affiliation(s)
- Sarah Lepuschitz
- Austrian Agency for Health and Food Safety (AGES), Institute for Medical Microbiology and Hygiene, Vienna, Austria.,Research Division of Biochemical Technology, Institute of Chemical, Environmental and BioScience Engineering, Technische Universität Wien, Vienna, Austria
| | - Sandrine Baron
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Emeline Larvor
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Sophie A Granier
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougeres Laboratory, Fougeres, France
| | - Carina Pretzer
- Institute for Hygiene and Applied Immunology - Water Microbiology, Medical University Vienna, Vienna, Austria
| | - Robert L Mach
- Research Division of Biochemical Technology, Institute of Chemical, Environmental and BioScience Engineering, Technische Universität Wien, Vienna, Austria
| | - Andreas H Farnleitner
- Research Division of Biochemical Technology, Institute of Chemical, Environmental and BioScience Engineering, Technische Universität Wien, Vienna, Austria.,Division Water Quality and Health, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Sonja Pleininger
- Austrian Agency for Health and Food Safety (AGES), Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Alexander Indra
- Austrian Agency for Health and Food Safety (AGES), Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Alexander K T Kirschner
- Institute for Hygiene and Applied Immunology - Water Microbiology, Medical University Vienna, Vienna, Austria.,Division Water Quality and Health, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Interuniversity Cooperation Centre for Water and Health, Vienna, Austria
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8
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Mesbah Zekar F, Granier SA, Touati A, Millemann Y. Occurrence of Third-Generation Cephalosporins-Resistant Klebsiella pneumoniae in Fresh Fruits and Vegetables Purchased at Markets in Algeria. Microb Drug Resist 2019; 26:353-359. [PMID: 31603740 DOI: 10.1089/mdr.2019.0249] [Citation(s) in RCA: 11] [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: 02/06/2023] Open
Abstract
This study aimed to characterize third-generation cephalosporin (3GC)-resistant Klebsiella pneumoniae isolated from fresh fruits and vegetables purchased at Bejaia city, Algeria. K. pneumoniae isolates were identified by MALDI-TOF. Susceptibility to antibiotics was tested by the disk diffusion method. Whole genome sequencing (WGS) was carried out to determine sequence type (ST), plasmid incompatibility group (Inc.), and acquired antimicrobial resistance gene presence. A total of 13 3GC-resistant K. pneumoniae strains were isolated. WGS identified blaCTX-M-15 in 11 extended-spectrum-beta-lactamases (ESBL)-K. pneumoniae and blaDHA-1 in 2 AmpC-K. pneumoniae. The aac(6')lb-cr gene was identified in 8 out of 13 isolates. Multilocus sequence typing (MLST) evidenced five different STs, namely ST14, ST45, ST219, ST236, and ST882. MDR K. pneumoniae contaminated fresh fruits and vegetables, often eaten raw and inappropriately washed, may represent an underestimated public health threat. This study highlights that hygiene measures during harvesting and retail process are of utmost importance to limit further ESBL/AmpC spread to the consumer households.
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Affiliation(s)
- Ferielle Mesbah Zekar
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria.,Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université PARIS-EST, Maisons-Alfort, France
| | - Sophie A Granier
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université PARIS-EST, Maisons-Alfort, France.,Laboratoire de Fougères, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Fougères, France
| | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algeria
| | - Yves Millemann
- Laboratoire de Sécurité des Aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université PARIS-EST, Maisons-Alfort, France.,Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, France
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9
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Hawkey J, Le Hello S, Doublet B, Granier SA, Hendriksen RS, Fricke WF, Ceyssens PJ, Gomart C, Billman-Jacobe H, Holt KE, Weill FX. Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. Microb Genom 2019; 5. [PMID: 31107206 PMCID: PMC6700661 DOI: 10.1099/mgen.0.000269] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S.enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S.enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylogeographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions, which appear to have hampered previous attempts to trace the clone’s evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials. This article contains data hosted by Microreact.
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Affiliation(s)
- Jane Hawkey
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
| | - Benoît Doublet
- ISP, Institut National de la Recherche Agronomique, Université François Rabelais de Tours, UMR 1282, Nouzilly, France
| | - Sophie A Granier
- Laboratoire de sécurité des aliments, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université PARIS-EST, 94701 Maisons-Alfort, France.,Laboratoire de Fougères, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), 35306 Fougères, France
| | - Rene S Hendriksen
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - W Florian Fricke
- Department of Microbiome Research and Applied Bioinformatics, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Camille Gomart
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
| | - Helen Billman-Jacobe
- Asia-Pacific Centre for Animal Health, Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kathryn E Holt
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella , World Health Organization Collaborative Centre for the Typing and Antibiotic Resistance of Salmonella , Institut Pasteur, 75015 Paris, France
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10
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Sévellec Y, Felten A, Radomski N, Granier SA, Le Hello S, Petrovska L, Mistou MY, Cadel-Six S. Genetic Diversity of Salmonella Derby from the Poultry Sector in Europe. Pathogens 2019; 8:E46. [PMID: 30987404 PMCID: PMC6630433 DOI: 10.3390/pathogens8020046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/15/2019] [Accepted: 03/22/2019] [Indexed: 12/12/2022] Open
Abstract
Salmonella Derby (S. Derby) is emerging in Europe as a predominant serovar in fattening turkey flocks. This serovar was recorded as being predominant in the turkey sector in 2014 in the United Kingdom (UK). Only two years later, in 2016, it was also recorded in the turkey and broiler sectors in Ireland and Spain. These S. Derby isolates were characterised as members of the multilocus sequence type (MLST) profile 71 (ST71). For the first time, we characterise by whole genome sequencing (WGS) analysis a panel of 90 S. Derby ST71 genomes to understand the routes of transmission of this emerging pathogen within the poultry/turkey food trade. Selected panel included strains isolated as early as 2010 in five leading European g countries for turkey meat production. Twenty-one of the 90 genomes were extracted from a public database-Enterobase. Five of these originated from the United States (n=3), China (n=1) and Taiwan (n=1) isolated between 1986 and 2016. A phylogenomic analysis at the core-genome level revealed the presence of three groups. The largest group contained 97.5% of the European strains and included both, turkey and human isolates that were genetically related by an average of 35 ± 15 single nucleotide polymorphism substitutions (SNPs). To illustrate the diversity, the presence of antimicrobial resistance genes and phages were characteised in 30, S. Derby ST71 genomes, including 11 belonging to this study This study revealed an emergent turkey-related S. Derby ST71 clone circulating in at least five European countries (the UK, Germany, Poland, Italy, and France) since 2010 that causes human gastroenteritis. A matter of concern is the identification of a gyrA mutation involved in resistance to quinolone, present in the Italian genomes. Interestingly, the diversity of phages seems to be related to the geographic origins. These results constitute a baseline for following the spread of this emerging pathogen and identifying appropriate monitoring and prevention measures.
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Affiliation(s)
- Yann Sévellec
- Laboratory for Food Safety, Université PARIS-EST, ANSES, F-94701 Maisons-Alfort, France.
| | - Arnaud Felten
- Laboratory for Food Safety, Université PARIS-EST, ANSES, F-94701 Maisons-Alfort, France.
| | - Nicolas Radomski
- Laboratory for Food Safety, Université PARIS-EST, ANSES, F-94701 Maisons-Alfort, France.
| | - Sophie A Granier
- Laboratory for Food Safety, Université PARIS-EST, ANSES, F-94701 Maisons-Alfort, France.
| | - Simon Le Hello
- Institut Pasteur, Centre National de Référence des Salmonella, Unité des Bactéries Pathogènes Entériques, 75015 Paris, France.
| | | | - Michel-Yves Mistou
- Laboratory for Food Safety, Université PARIS-EST, ANSES, F-94701 Maisons-Alfort, France.
| | - Sabrina Cadel-Six
- Laboratory for Food Safety, Université PARIS-EST, ANSES, F-94701 Maisons-Alfort, France.
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11
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Rebelo AR, Bortolaia V, Kjeldgaard JS, Pedersen SK, Leekitcharoenphon P, Hansen IM, Guerra B, Malorny B, Borowiak M, Hammerl JA, Battisti A, Franco A, Alba P, Perrin-Guyomard A, Granier SA, De Frutos Escobar C, Malhotra-Kumar S, Villa L, Carattoli A, Hendriksen RS. Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes. ACTA ACUST UNITED AC 2019; 23. [PMID: 29439754 PMCID: PMC5824125 DOI: 10.2807/1560-7917.es.2018.23.6.17-00672] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [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] [Indexed: 02/05/2023]
Abstract
Background and aimPlasmid-mediated colistin resistance mechanisms have been identified worldwide in the past years. A multiplex polymerase chain reaction (PCR) protocol for detection of all currently known transferable colistin resistance genes (mcr-1 to mcr-5, and variants) in Enterobacteriaceae was developed for surveillance or research purposes. Methods: We designed four new primer pairs to amplify mcr-1, mcr-2, mcr-3 and mcr-4 gene products and used the originally described primers for mcr-5 to obtain a stepwise separation of ca 200 bp between amplicons. The primer pairs and amplification conditions allow for single or multiple detection of all currently described mcr genes and their variants present in Enterobacteriaceae. The protocol was validated testing 49 European Escherichia coli and Salmonella isolates of animal origin. Results: Multiplex PCR results in bovine and porcine isolates from Spain, Germany, France and Italy showed full concordance with whole genome sequence data. The method was able to detect mcr-1, mcr-3 and mcr-4 as singletons or in different combinations as they were present in the test isolates. One new mcr-4 variant, mcr-4.3, was also identified. Conclusions: This method allows rapid identification of mcr-positive bacteria and overcomes the challenges of phenotypic detection of colistin resistance. The multiplex PCR should be particularly interesting in settings or laboratories with limited resources for performing genetic analysis as it provides information on the mechanism of colistin resistance without requiring genome sequencing.
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Affiliation(s)
- Ana Rita Rebelo
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Valeria Bortolaia
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Jette S Kjeldgaard
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Susanne K Pedersen
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | - Inge M Hansen
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
| | | | | | - Maria Borowiak
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Antonio Battisti
- National Reference Laboratory for antimicrobial resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | - Alessia Franco
- National Reference Laboratory for antimicrobial resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | - Patricia Alba
- National Reference Laboratory for antimicrobial resistance, Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Rome, Italy
| | | | - Sophie A Granier
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | | | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Rene S Hendriksen
- National Food Institute, Technical University of Denmark, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Kongens Lyngby, Denmark
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12
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Sévellec Y, Granier SA, Radomski N, Felten A, Le Hello S, Feurer C, Mistou MY, Cadel-Six S. Complete Genome Sequence of Salmonella enterica subsp. enterica Serotype Derby, Associated with the Pork Sector in France. Microbiol Resour Announc 2018; 7:e01027-18. [PMID: 30533663 PMCID: PMC6256686 DOI: 10.1128/mra.01027-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/02/2018] [Indexed: 11/20/2022] Open
Abstract
In the European Union, Salmonella enterica subsp. enterica serovar Derby is the most abundant serotype isolated from pork. Recent studies have shown that this serotype is polyphyletic. However, one main genomic lineage, characterized by sequence type 40 (ST40), the presence of the Salmonella pathogenicity island 23, and showing resistance to streptomycin, sulphonamides, and tetracycline (STR-SSS-TET), is pork associated. Here, we describe the complete genome sequence of a strain from this lineage isolated in France.
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Affiliation(s)
- Yann Sévellec
- Université Paris-Est, Marne-la-Vallée, France
- ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Sophie A. Granier
- Université Paris-Est, Marne-la-Vallée, France
- ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Nicolas Radomski
- Université Paris-Est, Marne-la-Vallée, France
- ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Arnaud Felten
- Université Paris-Est, Marne-la-Vallée, France
- ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Simon Le Hello
- Institut Pasteur, Centre National de Référence des Salmonella, Unité des Bactéries Pathogènes Entériques, Paris, France
| | - Carole Feurer
- French Institute for the Pig and Pork Industry (IFIP), Le Rheu, France
| | - Michel-Yves Mistou
- Université Paris-Est, Marne-la-Vallée, France
- ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Université Paris-Est, Marne-la-Vallée, France
- ANSES, Laboratory for Food Safety, Maisons-Alfort, France
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13
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Glasset B, Herbin S, Granier SA, Cavalié L, Lafeuille E, Guérin C, Ruimy R, Casagrande-Magne F, Levast M, Chautemps N, Decousser JW, Belotti L, Pelloux I, Robert J, Brisabois A, Ramarao N. Bacillus cereus, a serious cause of nosocomial infections: Epidemiologic and genetic survey. PLoS One 2018; 13:e0194346. [PMID: 29791442 PMCID: PMC5966241 DOI: 10.1371/journal.pone.0194346] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/01/2018] [Indexed: 11/19/2022] Open
Abstract
Bacillus cereus is the 2nd most frequent bacterial agent responsible for food-borne outbreaks in France and the 3rd in Europe. In addition, local and systemic infections have been reported, mainly describing individual cases or single hospital setting. The real incidence of such infection is unknown and information on genetic and phenotypic characteristics of the incriminated strains is generally scarce. We performed an extensive study of B. cereus strains isolated from patients and hospital environments from nine hospitals during a 5-year study, giving an overview of the consequences, sources and pathogenic patterns of B. cereus clinical infections. We demonstrated the occurrence of several hospital-cross-contaminations. Identical B. cereus strains were recovered from different patients and hospital environments for up to 2 years. We also clearly revealed the occurrence of inter hospital contaminations by the same strain. These cases represent the first documented events of nosocomial epidemy by B. cereus responsible for intra and inter hospitals contaminations. Indeed, contamination of different patients with the same strain of B. cereus was so far never shown. In addition, we propose a scheme for the characterization of B. cereus based on biochemical properties and genetic identification and highlight that main genetic signatures may carry a high pathogenic potential. Moreover, the characterization of antibiotic resistance shows an acquired resistance phenotype for rifampicin. This may provide indication to adjust the antibiotic treatment and care of patients.
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Affiliation(s)
- Benjamin Glasset
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabine Herbin
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | - Sophie A. Granier
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | - Laurent Cavalié
- CHU Toulouse, Service de Bactériologie-Hygiène, IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Emilie Lafeuille
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
- Laboratoire de Bactériologie-Hygiène, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, APHP, Paris, France
| | - Cyprien Guérin
- MaiAGE, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Raymond Ruimy
- CHU Nice, Laboratoire de bactériologie, Nice, France
| | | | - Marion Levast
- Hôpital de Chambéry, Laboratoire de Biologie Médicale, Chambéry, France
| | | | - Jean-Winoc Decousser
- Hôpitaux Universitaires Paris-Sud Antoine Béclère, Laboratoire Hygiène, Clamart, France
| | - Laure Belotti
- CHU Strasbourg, Laboratoire d’hygiène hospitalière, Strasbourg, France
| | | | - Jerôme Robert
- Sorbonne Universités, UPMC Univ Paris 06, Inserm, U1135, Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
- Laboratoire de Bactériologie-Hygiène, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, APHP, Paris, France
| | - Anne Brisabois
- Université Paris-Est, Anses, Laboratory for Food Safety, Maisons-Alfort, France
| | - Nalini Ramarao
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
- * E-mail:
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14
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Briet A, Helsens N, Delannoy S, Debuiche S, Brisabois A, Midelet G, Granier SA. NDM-1-producing Vibrio parahaemolyticus isolated from imported seafood. J Antimicrob Chemother 2018; 73:2578-2579. [DOI: 10.1093/jac/dky200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Arnaud Briet
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
| | - Nicolas Helsens
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
| | - Sabine Delannoy
- Université Paris-Est, Anses, Laboratory for food safety, F-94700 Maisons-Alfort, France
| | - Sabine Debuiche
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
| | - Anne Brisabois
- Anses, Laboratory for food safety, F-62200 Boulogne-sur-Mer, France
- Université Paris-Est, Anses, Laboratory for food safety, F-94700 Maisons-Alfort, France
| | | | - Sophie A Granier
- Université Paris-Est, Anses, Laboratory for food safety, F-94700 Maisons-Alfort, France
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15
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Sévellec Y, Vignaud ML, Granier SA, Lailler R, Feurer C, Le Hello S, Mistou MY, Cadel-Six S. Polyphyletic Nature of Salmonella enterica Serotype Derby and Lineage-Specific Host-Association Revealed by Genome-Wide Analysis. Front Microbiol 2018; 9:891. [PMID: 29867804 PMCID: PMC5966662 DOI: 10.3389/fmicb.2018.00891] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 02/02/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022] Open
Abstract
In France, Salmonella Derby is one of the most prevalent serotypes in pork and poultry meat. Since 2006, it has ranked among the 10 most frequent Salmonella serotypes isolated in humans. In previous publications, Salmonella Derby isolates have been characterized by pulsed field gel electrophoresis (PFGE) and antimicrobial resistance (AMR) profiles revealing the existence of different pulsotypes and AMR phenotypic groups. However, these results suffer from the low discriminatory power of these typing methods. In the present study, we built a collection of 140 strains of S. Derby collected in France from 2014 to 2015 representative of the pork and poultry food sectors. The whole collection was characterized using whole genome sequencing (WGS), providing a significant contribution to the knowledge of this underrepresented serotype, with few genomes available in public databases. The genetic diversity of the S. Derby strains was analyzed by single-nucleotide polymorphism (SNP). We also investigated AMR by both genome and phenotype, the main Salmonella pathogenicity island (SPI) and the fimH gene sequences. Our results show that this S. Derby collection is spread across four different lineages genetically distant by an average of 15k SNPs. These lineages correspond to four multilocus sequence typing (MLST) types (ST39, ST40, ST71, and ST682), which were found to be associated with specific animal hosts: pork and poultry. While the ST71 and ST682 strains are pansusceptible, ST40 isolates are characterized by the multidrug resistant profile STR-SSS-TET. Considering virulence determinants, only ST39 and ST40 present the SPI-23, which has previously been associated with pork enterocyte invasion. Furthermore, the pork ST682 isolates were found to carry mutations in the fimH sequence that could participate in the host tropism of this group. Our phylogenetic analysis demonstrates the polyphyletic nature of the Salmonella serotype Derby and provides an opportunity to identify genetic factors associated with host adaptation and markers for the monitoring of these different lineages within the corresponding animal sectors. The recognition of these four lineages is of primary importance for epidemiological surveillance throughout the food production chains and constitutes the first step toward refining monitoring and preventing dispersal of this pathogen.
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Affiliation(s)
- Yann Sévellec
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Marie-Léone Vignaud
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Sophie A. Granier
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Renaud Lailler
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Carole Feurer
- French Institute for Pig and Pork Industry, Le Rheu, France
| | - Simon Le Hello
- Centre National de Référence des Salmonella, Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Michel-Yves Mistou
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
| | - Sabrina Cadel-Six
- Université PARIS-EST, Agence Nationale de Sécurité Sanitaire de L’Alimentation, de L’Environnement et du Travail (ANSES), Laboratory for Food Safety, Maisons-Alfort, France
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16
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Webb HE, Brichta-Harhay DM, Brashears MM, Nightingale KK, Arthur TM, Bosilevac JM, Kalchayanand N, Schmidt JW, Wang R, Granier SA, Brown TR, Edrington TS, Shackelford SD, Wheeler TL, Loneragan GH. Salmonella in Peripheral Lymph Nodes of Healthy Cattle at Slaughter. Front Microbiol 2017; 8:2214. [PMID: 29170662 PMCID: PMC5684184 DOI: 10.3389/fmicb.2017.02214] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 06/26/2017] [Accepted: 10/27/2017] [Indexed: 11/13/2022] Open
Abstract
To more fully characterize the burden of Salmonella enterica in bovine peripheral lymph nodes (PLN), PLN (n = 5,450) were collected from healthy cattle at slaughter in 12 commercial abattoirs that slaughtered feedlot-fattened (FF) cattle exclusively (n = 7), cattle removed (or culled) from breeding herds (n = 3), or both FF and cull cattle (n = 2). Qualitative and quantitative methods were used to estimate prevalence and concentration of Salmonella in PLN. Isolates were subjected to a variety of phenotypic, serological, and molecular assays. Overall, Salmonella prevalence in PLN from FF and cull cattle was 7.1 and 1.8%. However, burden varied by season in that observed prevalence in PLN collected in cooler or warmer seasons was 2.4 and 8.2%, respectively. Prevalence in PLN from cull cattle in the southwest region of the US was 2.1 and 1.1% for cool and warm seasons, respectively; however, prevalence in FF PLN was far greater in that it was 6.5 and 31.1%, respectively. Salmonella was recovered from 289 (5.6%) PLN and 2.9% (n = 160) of all PLN tested had quantifiable concentrations that varied from 1.6 to 4.9 log10 colony forming units/PLN. The most common serotypes isolated from PLN were Montevideo (26.9%), Lille (14.9%), Cerro (13.0%), Anatum (12.8%), and Dublin (6.9%). In all, 376 unique isolates were collected from the 289 Salmonella-positive PLN. Antimicrobial susceptibility testing revealed the majority (80.6%) of these isolates were pansusceptible; however, 10.7% of isolates were found to be resistant to two or more antimicrobial classes. We were able to document an observed increased in prevalence of Salmonella in PLN during the warmer season, particularly in FF cattle from the southwest region of the US. The mechanisms underlying the observed association between season, region, and production source have yet to be elucidated. Nevertheless, these findings increase our understanding of the sources of contamination of beef products and shed light on transmission dynamics that may be useful in targeting these sources.
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Affiliation(s)
- Hattie E Webb
- International Center for Food Industry Excellence, Texas Tech University, Lubbock, TX, United States
| | - Dayna M Brichta-Harhay
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Mindy M Brashears
- International Center for Food Industry Excellence, Texas Tech University, Lubbock, TX, United States
| | - Kendra K Nightingale
- International Center for Food Industry Excellence, Texas Tech University, Lubbock, TX, United States
| | - Terrance M Arthur
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Joseph M Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Norasak Kalchayanand
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - John W Schmidt
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Rong Wang
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Sophie A Granier
- Laboratory for Food Safety, ANSES, Université Paris-Est, Maisons-Alfort, France
| | | | | | - Steven D Shackelford
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Tommy L Wheeler
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE, United States
| | - Guy H Loneragan
- International Center for Food Industry Excellence, Texas Tech University, Lubbock, TX, United States
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Webb HE, Angulo FJ, Granier SA, Scott HM, Loneragan GH. Illustrative examples of probable transfer of resistance determinants from food animals to humans: Streptothricins, glycopeptides, and colistin. F1000Res 2017; 6:1805. [PMID: 29188021 PMCID: PMC5686510 DOI: 10.12688/f1000research.12777.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2017] [Indexed: 12/24/2022] Open
Abstract
Use, overuse, and misuse of antimicrobials contributes to selection and dissemination of bacterial resistance determinants that may be transferred to humans and constitute a global public health concern. Because of the continued emergence and expansion of antimicrobial resistance, combined with the lack of novel antimicrobial agents, efforts are underway to preserve the efficacy of current available life-saving antimicrobials in humans. As a result, uses of medically important antimicrobials in food animal production have generated debate and led to calls to reduce both antimicrobial use and the need for use. This manuscript, commissioned by the World Health Organization (WHO) to help inform the development of the WHO guidelines on the use of medically important antimicrobials in food animals, includes three illustrations of antimicrobial use in food animal production that has contributed to the selection-and subsequent transfer-of resistance determinants from food animals to humans. Herein, antimicrobial use and the epidemiology of bacterial resistance are described for streptothricins, glycopeptides, and colistin. Taken together, these historical and current narratives reinforce the need for actions that will preserve the efficacy of antimicrobials.
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Affiliation(s)
- Hattie E. Webb
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Frederick J. Angulo
- Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Sophie A. Granier
- Laboratory for Food Safety, Anses, Université Paris-Est, Maisons-Alfort, F-94701, France
| | - H. Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Guy H. Loneragan
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, 79409, USA
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Baron S, Larvor E, Chevalier S, Jouy E, Kempf I, Granier SA, Lesne J. Antimicrobial Susceptibility among Urban Wastewater and Wild Shellfish Isolates of Non-O1/Non-O139 Vibrio cholerae from La Rance Estuary (Brittany, France). Front Microbiol 2017; 8:1637. [PMID: 28955305 PMCID: PMC5601046 DOI: 10.3389/fmicb.2017.01637] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 06/01/2017] [Accepted: 08/11/2017] [Indexed: 12/26/2022] Open
Abstract
The early 2000s marked the end of the Golden age of the antibiotics and the beginning of the awareness on the potential threat to human health due to the dissemination of antimicrobial resistance. As a base-line study, we investigated the antimicrobial susceptibility of 99 strains of non-O1/non-O139 Vibrio cholerae isolated from wastewater and shellfish in 2000/2001 within La Rance estuary (Brittany, France). All isolates were susceptible to amoxicillin-clavulanic acid, cefotaxime, imipenem, chloramphenicol, nalidixic acid, ciprofloxacin, norfloxacin, amikacin, gentamicin, tetracycline, doxycycline, trimethoprim-sulfamethoxazole, and erythromycin. The only resistances were to streptomycin, sulfonamides and ampicillin: 54.6% of the isolates had acquired resistance to at least one antimicrobial agent among them and only six isolates from cockles were multidrug resistant. On the basis of the distribution of a limited selection of resistance associated genes, our study shows that V. cholerae can constitute an environmental reservoir for these genes. However, none of our isolates harbored integron. This result casts doubt on the capacity of non-O1/non-O139 V. cholerae to acquire resistance-associated genes in such context, and on its potential role of indicator of the dissemination of antimicrobial resistance in the aquatic environment.
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Affiliation(s)
- Sandrine Baron
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Emeline Larvor
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Séverine Chevalier
- Bretagne-Loire UniversityRennes, France.,Ecole des Hautes Etudes en Santé Publique, Laboratoire d'Etude et de Recherche en Environnement et Santé, Institut de Recherche en Santé, Environnement et Travail, UMR 1085Rennes, France
| | - Eric Jouy
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Isabelle Kempf
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France.,Bretagne-Loire UniversityRennes, France
| | - Sophie A Granier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Paris-Est UniversityMaisons-Alfort, France
| | - Jean Lesne
- Bretagne-Loire UniversityRennes, France.,Ecole des Hautes Etudes en Santé Publique, Laboratoire d'Etude et de Recherche en Environnement et Santé, Institut de Recherche en Santé, Environnement et Travail, UMR 1085Rennes, France
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19
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Mesbah Zekar F, Granier SA, Marault M, Yaici L, Gassilloud B, Manceau C, Touati A, Millemann Y. From Farms to Markets: Gram-Negative Bacteria Resistant to Third-Generation Cephalosporins in Fruits and Vegetables in a Region of North Africa. Front Microbiol 2017; 8:1569. [PMID: 28883810 PMCID: PMC5573783 DOI: 10.3389/fmicb.2017.01569] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
The role of food in human exposure to antimicrobial-resistant bacteria is a growing food safety issue. The contribution of fruits and vegetables eaten raw to this exposure is still unclear. The evaluation of contamination levels of fruits, vegetables and the agricultural environment by third-generation cephalosporin (3GC)-resistant Gram-negative bacteria was performed by analyzing 491 samples of fruits and vegetables collected from 5 markets and 7 farms in Bejaia area, north-eastern Mediterranean coast of Algeria. Ninety soil samples and 45 irrigation water samples were also sampled in farms in order to assess them as potential inoculum sources. All samples were investigated at the same time on ceftazidime-containing selective media for 3GC-resistant Gram-negative bacteria detection and on Hektoen media, for Salmonella spp. presence. The bacteria isolated (n = 30) from fruits and vegetables, soil and irrigation water collected in the farms were almost all non-fermenting bacterial species (Stenotrophomonas, Acinetobacter, Pseudomonas, Ochrobactrum) except one strain of Enterobacter cloacae and two strains of Citrobacter murliniae, isolated on one cucumber and two tomato samples in the same farm. Greater diversity in bacterial species and antimicrobial resistance profiles was observed at markets: Enterobacteriaceae (n = 41) were as strongly represented as non-fermenting bacteria (n = 37). Among Enterobacteriaceae, E. cloacae (n = 21), and Klebsiella pneumoniae (n = 13) were the most common isolates. Most of the K. pneumoniae isolates were extended-spectrum beta-lactamase (ESBL) producers (n = 11). No Salmonella spp. was recovered in any sample. This study showed that fruits and vegetables including those which may be eaten up raw constitute a reservoir of 3GC-resistant Gram-negative bacteria and multi-drug resistant-bacteria in general that can be transferred to humans through food. The general public should be informed of this hazard for health in order to encourage good domestic hygiene practices. In addition, further investigation is needed throughout the production chain to enrol professionals in actions to reduce this contamination.
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Affiliation(s)
- Ferielle Mesbah Zekar
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de BejaiaBejaia, Algeria.,Laboratory for Food Safety, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université Paris-EstMaisons-Alfort, France
| | - Sophie A Granier
- Laboratory for Food Safety, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université Paris-EstMaisons-Alfort, France
| | - Muriel Marault
- Laboratory for Food Safety, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université Paris-EstMaisons-Alfort, France
| | - Lydia Yaici
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de BejaiaBejaia, Algeria
| | - Benoit Gassilloud
- Nancy Laboratory for Hydrology, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES)Nancy, France
| | - Charles Manceau
- Angers Laboratory for Plant Health, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES)Angers, France
| | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, Faculté des Sciences de la Nature et de la Vie, Université de BejaiaBejaia, Algeria
| | - Yves Millemann
- Laboratory for Food Safety, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail (ANSES), Université Paris-EstMaisons-Alfort, France.,Ecole Nationale Vétérinaire d'Alfort, Université Paris-EstMaisons-Alfort, France
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20
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Baron S, Granier SA, Larvor E, Jouy E, Cineux M, Wilhelm A, Gassilloud B, Le Bouquin S, Kempf I, Chauvin C. Aeromonas Diversity and Antimicrobial Susceptibility in Freshwater-An Attempt to Set Generic Epidemiological Cut-Off Values. Front Microbiol 2017; 8:503. [PMID: 28400760 PMCID: PMC5368242 DOI: 10.3389/fmicb.2017.00503] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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: 10/21/2016] [Accepted: 03/10/2017] [Indexed: 12/22/2022] Open
Abstract
The importance of the role of environment in the dissemination of antimicrobial resistant bacteria is now well recognized. Thus, bacterial indicators to monitor the phenomena are required. The Aeromonas genus is autochthonous in the aquatic environment and easy to detect in any water type, such as freshwater, or wastewater. These microorganisms are also causing infections in humans and animals (including fish). Furthermore, as Aeromonas spp. is able to acquire antimicrobial resistance mechanisms, it is candidate for indicator bacteria to follow antimicrobial resistance dissemination in aquatic environments. Unfortunately, to date, interpretation criteria for Aeromonas spp. for antimicrobial susceptibility tests are scarce in the literature. No epidemiological cut-off values for Aeromonas are currently available at EUCAST to interpret Minimum Inhibitory Concentrations (MIC). The only interpretation criteria available are clinical breakpoints from CLSI that are adapted from Enterobacteriaceae. Based on the results of MIC distributions obtained for a collection of environmental isolates of Aeromonas, this study aimed at proposing tentative epidemiological cut-off values (COWT) for Aeromonas spp. assessing whether the genus is an acceptable level of definition. Thus, 233 isolates collected from 16 rivers were identified at species level using Maldi-Tof (Bruker). Eleven different species were identified, the most abundant were A. bestiarum (n = 54), A. salmonicida (n = 45), A. sobria (n = 41), and A. eucrenophila (n = 37). 96-well micro-plates containing different concentrations of 15 antimicrobials, namely cefotaxime, ceftazidime, chloramphenicol, colistin, enrofloxacin, erythromycin, florfenicol, flumequine, gentamicin, nalidixic acid, oxolinic acid, streptomycin, temocillin, tetracycline, and trimethoprim-sulfamethoxazole, were prepared. The broth micro-dilution method was used to determine the antimicrobial susceptibility of each isolate. The estimation of COWT values was satisfactory obtained at genus level for all antimicrobials except cefotaxime and erythromycin. This first step is an invitation for other research teams to increase the amount of antimicrobial resistance data collected. Then, robustness of our proposed provisional generic epidemiological cut-off values could be assessed by testing antimicrobial susceptibility of various Aeromonas collections.
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Affiliation(s)
- Sandrine Baron
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France; Bretagne-Loire UniversityRennes, France
| | - Sophie A Granier
- Laboratory for Food Safety, French Agency for Food, Environmental and Occupational Health and Safety (Anses), Paris-Est University Maisons-Alfort, France
| | - Emeline Larvor
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France; Bretagne-Loire UniversityRennes, France
| | - Eric Jouy
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France; Bretagne-Loire UniversityRennes, France
| | - Maelan Cineux
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France; Bretagne-Loire UniversityRennes, France
| | - Amandine Wilhelm
- Laboratory for Hydrology, French Agency for Food, Environmental and Occupational Health and Safety (Anses) Nancy, France
| | - Benoit Gassilloud
- Laboratory for Hydrology, French Agency for Food, Environmental and Occupational Health and Safety (Anses) Nancy, France
| | - Sophie Le Bouquin
- Bretagne-Loire UniversityRennes, France; Epidemiology and Welfare in Poultry and Rabbit Farming, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France
| | - Isabelle Kempf
- Mycoplasmology-Bacteriology Unit, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France; Bretagne-Loire UniversityRennes, France
| | - Claire Chauvin
- Bretagne-Loire UniversityRennes, France; Epidemiology and Welfare in Pigs, Ploufragan-Plouzané Laboratory, French Agency for Food, Environmental and Occupational Health and Safety (Anses)Ploufragan, France
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Webb HE, Bugarel M, den Bakker HC, Nightingale KK, Granier SA, Scott HM, Loneragan GH. Carbapenem-Resistant Bacteria Recovered from Faeces of Dairy Cattle in the High Plains Region of the USA. PLoS One 2016; 11:e0147363. [PMID: 26824353 PMCID: PMC4732617 DOI: 10.1371/journal.pone.0147363] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/04/2016] [Indexed: 01/25/2023] Open
Abstract
Objective A study was conducted to recover carbapenem-resistant bacteria from the faeces of dairy cattle and identify the underlying genetic mechanisms associated with reduced phenotypic susceptibility to carbapenems. Methods One hundred and fifty-nine faecal samples from dairy cattle were screened for carbapenem-resistant bacteria. Phenotypic screening was conducted on two media containing ertapenem. The isolates from the screening step were characterised via disk diffusion, Modified Hodge, and Carba NP assays. Carbapenem-resistant bacteria and carbapenemase-producing isolates were subjected to Gram staining and biochemical testing to include Gram-negative bacilli. Whole genome sequencing was performed on bacteria that exhibited either a carbapenemase-producing phenotype or were not susceptible to ertapenem and were presumptively Enterobacteriaceae. Results Of 323 isolates collected from the screening media, 28 were selected for WGS; 21 of which were based on a carbapenemase-producing phenotype and 7 were presumptively Enterobacteriaceae and not susceptible to ertapenem. Based on analysis of WGS data, isolates included: 3 Escherichia coli harbouring blaCMY-2 and truncated ompF genes; 8 Aeromonas harbouring blacphA-like genes; 1 Acinetobacter baumannii harbouring a novel blaOXA gene (blaOXA-497); and 6 Pseudomonas with conserved domains of various carbapenemase-producing genes. Conclusions Carbapenem resistant bacteria appear to be rare in cattle. Nonetheless, carbapenem-resistant bacteria were detected across various genera and were found to harbour a variety of mechanisms conferring reduced susceptibility. The development and dissemination of carbapenem-resistant bacteria in livestock would have grave implications for therapeutic treatment options in human medicine; thus, continued monitoring of carbapenem susceptibility among enteric bacteria of livestock is warranted.
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Affiliation(s)
- Hattie E. Webb
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Marie Bugarel
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Henk C. den Bakker
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Kendra K. Nightingale
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Sophie A. Granier
- Antimicrobial Resistance Unit, Laboratory for Food Safety, ANSES, Paris-Est University, Maisons-Alfort Cedex, France
| | - H. Morgan Scott
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Guy H. Loneragan
- International Center for Food Industry Excellence, Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, United States of America
- * E-mail:
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Elgroud R, Granier SA, Marault M, Kerouanton A, Lezzar A, Bouzitouna-Bentchouala C, Brisabois A, Millemann Y. Contribution of Avian Salmonella enterica Isolates to Human Salmonellosis Cases in Constantine (Algeria). Biomed Res Int 2015; 2015:352029. [PMID: 26543858 PMCID: PMC4620278 DOI: 10.1155/2015/352029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/16/2015] [Accepted: 02/22/2015] [Indexed: 11/18/2022]
Abstract
An epidemiological investigation was carried out on one hundred Salmonella isolates from broiler farms, slaughterhouses, and human patients in the Constantine region of Algeria, in order to explore the contribution of avian strains to human salmonellosis cases in this region over the same period of time. The isolates were characterized by phenotypic as well as genotypic methods. A large variety of antimicrobial resistance profiles was found among human isolates, while only seven profiles were found among avian isolates. Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR), Insertion Sequence 200-PCR (IS200-PCR), and Pulsed Field Gel Electrophoresis (PFGE) resulted in the allocation of the isolates to 16, 20, and 34 different profiles, respectively. The 3 genotyping methods led to complementary results by underlining the clonality of some serovars with the diffusion and persistence of a single clone in the Constantine area as well as stressing the polymorphism present in isolates belonging to other serovars, indicating the diversity of potential reservoirs of nontyphoidal Salmonella. Altogether, our results seem to indicate that nontyphoidal avian Salmonella may play an important role in human salmonellosis in the Constantine region.
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Affiliation(s)
- Rachid Elgroud
- Laboratory of Health Management and Animal Production, Veterinary Sciences Department, Constantine Mentouri University, Constantine, Algeria ; Alfort National Veterinary School, Paris-Est University, 94704 Maisons-Alfort Cedex, France
| | - Sophie A Granier
- Antimicrobial Resistance Unit, Maisons-Alfort Laboratory for Food Safety, ANSES, Paris-Est University, 94701 Maisons-Alfort Cedex, France
| | - Muriel Marault
- Antimicrobial Resistance Unit, Maisons-Alfort Laboratory for Food Safety, ANSES, Paris-Est University, 94701 Maisons-Alfort Cedex, France
| | - Annaëlle Kerouanton
- Hygiene and Quality of Poultry and Pig Products Unit, Anses Ploufragan Laboratory, European University of Brittany, 22440 Ploufragan, France
| | - Abdesslem Lezzar
- Service de Microbiologie-Bactériologie, C.H.U. Ibn Badis, Constantine, Algeria
| | | | - Anne Brisabois
- Antimicrobial Resistance Unit, Maisons-Alfort Laboratory for Food Safety, ANSES, Paris-Est University, 94701 Maisons-Alfort Cedex, France
| | - Yves Millemann
- Alfort National Veterinary School, Paris-Est University, 94704 Maisons-Alfort Cedex, France ; Antimicrobial Resistance Unit, Maisons-Alfort Laboratory for Food Safety, ANSES, Paris-Est University, 94701 Maisons-Alfort Cedex, France
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Kempf I, Jouy E, Granier SA, Chauvin C, Sanders P, Salvat G, Madec JY. Comment on "impact of antibiotic use in the swine industry", by Mary D. Barton [Curr. Opin. Microbiol. 19 (June 2014) 9-15]. Curr Opin Microbiol 2015; 26:137-8. [PMID: 26165457 DOI: 10.1016/j.mib.2015.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Isabelle Kempf
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Européenne de Bretagne, 35000 Rennes, France.
| | - Eric Jouy
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Européenne de Bretagne, 35000 Rennes, France
| | - Sophie A Granier
- Université Paris-Est, ANSES, Laboratoire de Sécurité des Aliments de Maisons-Alfort, Unité Caractérisation et Epidémiologie Bactérienne 23, avenue du Général de Gaulle, 94706 Maisons-Alfort Cedex, France
| | - Claire Chauvin
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Européenne de Bretagne, 35000 Rennes, France
| | | | - Gilles Salvat
- ANSES, Ploufragan Laboratory, 22440 Ploufragan, France; Université Européenne de Bretagne, 35000 Rennes, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France
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Millemann Y, Granier SA, Boulouis H, Lailler R, Belbis G. Salmonellosis due to a monophasic variant of
Salmonella
Typhimurium in a cow. Vet rec case rep 2014. [DOI: 10.1136/vetreccr-2014-000116] [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: 11/04/2022]
Affiliation(s)
- Yves Millemann
- Animal Production and Public HealthAlfort National Veterinary SchoolParis‐Est UniversityMaisons‐AlfortFrance
- Laboratory for Food SafetyANSESParis‐Est UniversityMaisons‐AlfortFrance
| | - Sophie A Granier
- Laboratory for Food SafetyANSESParis‐Est UniversityMaisons‐AlfortFrance
| | | | - Renaud Lailler
- Laboratory for Food SafetyANSESParis‐Est UniversityMaisons‐AlfortFrance
| | - Guillaume Belbis
- Animal Production and Public HealthAlfort National Veterinary SchoolParis‐Est UniversityMaisons‐AlfortFrance
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Le Hello S, Bekhit A, Granier SA, Barua H, Beutlich J, Zając M, Münch S, Sintchenko V, Bouchrif B, Fashae K, Pinsard JL, Sontag L, Fabre L, Garnier M, Guibert V, Howard P, Hendriksen RS, Christensen JP, Biswas PK, Cloeckaert A, Rabsch W, Wasyl D, Doublet B, Weill FX. The global establishment of a highly-fluoroquinolone resistant Salmonella enterica serotype Kentucky ST198 strain. Front Microbiol 2013; 4:395. [PMID: 24385975 PMCID: PMC3866546 DOI: 10.3389/fmicb.2013.00395] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [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: 10/15/2013] [Accepted: 12/03/2013] [Indexed: 11/13/2022] Open
Abstract
While the spread of Salmonella enterica serotype Kentucky resistant to ciprofloxacin across Africa and the Middle-East has been described recently, the presence of this strain in humans, food, various animal species (livestock, pets, and wildlife) and in environment is suspected in other countries of different continents. Here, we report results of an in-depth molecular epidemiological study on a global human and non-human collection of S. Kentucky (n = 70). We performed XbaI-pulsed field gel electrophoresis and multilocus sequence typing, assessed mutations in the quinolone resistance-determining regions, detected β-lactam resistance mechanisms, and screened the presence of the Salmonella genomic island 1 (SGI1). In this study, we highlight the rapid and extensive worldwide dissemination of the ciprofloxacin-resistant S. Kentucky ST198-X1-SGI1 strain since the mid-2000s in an increasingly large number of contaminated sources, including the environment. This strain has accumulated an increasing number of chromosomal and plasmid resistance determinants and has been identified in the Indian subcontinent, Southeast Asia and Europe since 2010. The second substitution at position 87 in GyrA (replacing the amino acid Asp) appeared helpful for epidemiological studies to track the origin of contamination. This global study provides evidence leading to the conclusion that high-level resistance to ciprofloxacin in S. Kentucky is a simple microbiological trait that facilitates the identification of the epidemic clone of interest, ST198-X1-SGI1. Taking this into account is essential in order to detect and monitor it easily and to take rapid measures in livestock to ensure control of this infection.
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Affiliation(s)
- Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur Paris, France
| | - Amany Bekhit
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur Paris, France ; Biochemistry Department, Faculty of Pharmacy, Minia University Minia, Egypt
| | - Sophie A Granier
- Unité Caractérisation et épidémiologie Bactérienne, Laboratoire de Sécurité des Aliments, Université Paris-Est Anses, Maisons-Alfort, France
| | - Himel Barua
- Department of Microbiology, Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University Chittagong, Bangladesh
| | - Janine Beutlich
- Unit Antimicrobial Resistance and Resistance Determinants, National Reference Laboratory for Antimicrobial Resistance, Department Biological Safety, Federal Institute for Risk Assessment Berlin, Germany
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute Puławy, Poland
| | - Sebastian Münch
- National Reference Centre for Salmonellae and other Bacterial Enteric Pathogens, Robert Koch Institute Wernigerode, Germany
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, University of Sydney, ICPMR Sydney, NSW, Australia
| | - Brahim Bouchrif
- Institut Pasteur du Maroc, Sécurité alimentaire et Environnement Casablanca, Maroc
| | - Kayode Fashae
- Department of Microbiology, University of Ibadan Ibadan, Nigeria
| | | | - Lucile Sontag
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur Paris, France
| | - Laetitia Fabre
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur Paris, France
| | - Martine Garnier
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur Paris, France
| | - Véronique Guibert
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur Paris, France
| | - Peter Howard
- Institut Pasteur du Maroc, Sécurité alimentaire et Environnement Casablanca, Maroc
| | - Rene S Hendriksen
- WHO Collaborating Center for Antimicrobial Resistance in Foodborne Pathogens and European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark Kgs. Lyngby, Denmark
| | - Jens P Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Copenhagen, Denmark
| | - Paritosh K Biswas
- Department of Microbiology, Faculty of Veterinary Medicine, Chittagong Veterinary and Animal Sciences University Chittagong, Bangladesh
| | - Axel Cloeckaert
- Institut national de la recherche agronomique, UMR1282 Infectiologie et Santé publique Nouzilly, France ; Université François Rabelais de Tours, UMR1282 Infectiologie et Santé publique Tours, France
| | - Wolfgang Rabsch
- National Reference Centre for Salmonellae and other Bacterial Enteric Pathogens, Robert Koch Institute Wernigerode, Germany
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute Puławy, Poland
| | - Benoit Doublet
- Institut national de la recherche agronomique, UMR1282 Infectiologie et Santé publique Nouzilly, France ; Université François Rabelais de Tours, UMR1282 Infectiologie et Santé publique Tours, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur Paris, France
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Kerouanton A, Rose V, Weill FX, Granier SA, Denis M. Genetic Diversity and Antimicrobial Resistance Profiles ofSalmonella entericaSerotype Derby Isolated from Pigs, Pork, and Humans in France. Foodborne Pathog Dis 2013; 10:977-84. [DOI: 10.1089/fpd.2013.1537] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Annaëlle Kerouanton
- Anses, Ploufragan/Plouzané Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
- European University of Brittany, France
| | - Valérie Rose
- Anses, Ploufragan/Plouzané Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
- European University of Brittany, France
| | - François-Xavier Weill
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Salmonella, Paris, France
| | - Sophie A. Granier
- Paris-Est University, Laboratory for Food Safety, Bacterial Characterization and Epidemiology Unit, Maisons-Alfort, France
| | - Martine Denis
- Anses, Ploufragan/Plouzané Laboratory, Hygiene and Quality of Poultry and Pig Products Unit, Ploufragan, France
- European University of Brittany, France
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Tabo DA, Diguimbaye CD, Granier SA, Moury F, Brisabois A, Elgroud R, Millemann Y. Prevalence and antimicrobial resistance of non-typhoidal Salmonella serotypes isolated from laying hens and broiler chicken farms in N'Djamena, Chad. Vet Microbiol 2013; 166:293-8. [PMID: 23810700 DOI: 10.1016/j.vetmic.2013.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [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: 03/29/2013] [Revised: 05/30/2013] [Accepted: 05/31/2013] [Indexed: 10/26/2022]
Abstract
This study aimed at updating knowledge on the prevalence and antimicrobial resistance characteristics of Salmonella isolated from poultry in the province of N'Djamena, Chad. The results collected during this study provide the first baseline data on the prevalence of contamination by Salmonella in laying hens and broiler chicken farms in N'Djamena. All samples were collected from sixteen poultry farms over two periods of six months each: from August 2010 to January 2011 and from September 2011 to February 2012. Diagnostic methods used during this study allowed to isolate eighty four Salmonella strains, belonging to twenty seven different serotypes. The most frequent serotypes were Salmonella Colindale (19%) followed by S. Minnesota (18%) S. Havana and S. Riggil (each 6%), S. Kottbus and S. Amager (4.7%), S. Idikan, Mississipi, and Muenchen (3.6%). Other serotypes were poorly represented. The majority of these serotypes were susceptible to all antibiotics tested (CLSI Standards), except some S. Colindale isolates that exhibited a decreased susceptibility to fluoroquinolones, S. Limete resistant to three antibiotics and S. Minnesota isolates resistant to five different antimicrobial classes. The different serotypes and antibiotic resistance profiles that were observed highlight the substantial diversity of Salmonella in Chad, the contribution of avian isolates to human salmonellosis and Salmonella's capacity to colonize all types of environment worldwide.
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Affiliation(s)
- Djim-adjim Tabo
- Faculté des Sciences Exactes et Appliquées (FSEA), Université de N'Djamena, Chad.
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Derra FA, Karlsmose S, Monga DP, Mache A, Svendsen CA, Félix B, Granier SA, Geyid A, Taye G, Hendriksen RS. Occurrence of Listeria spp. in Retail Meat and Dairy Products in the Area of Addis Ababa, Ethiopia. Foodborne Pathog Dis 2013; 10:577-9. [DOI: 10.1089/fpd.2012.1361] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Firehiwot Abera Derra
- Food Microbiology Section, Food Science and Nutrition Research Directorate, Ethiopian Health and Nutrition Research Institute, Addis Ababa, Ethiopia
| | - Susanne Karlsmose
- WHO Collaborating Centre for Antimicrobial Resistance in Food-borne Pathogens and EU Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kingsly Lyngby, Denmark
| | - Dharam P. Monga
- Microbiology, Immunology, and Parasitology Department, Medical Faculty, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abebe Mache
- Microbiology, Immunology, and Parasitology Department, Medical Faculty, Addis Ababa University, Addis Ababa, Ethiopia
| | - Christina Aaby Svendsen
- WHO Collaborating Centre for Antimicrobial Resistance in Food-borne Pathogens and EU Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kingsly Lyngby, Denmark
| | - Benjamin Félix
- Paris-Est University, ANSES, French Agency for Food, Environmental, and Occupational Health and Safety, Laboratory for Food Safety, European Union Reference Laboratory for Listeria monocytogenes, Maisons-Alfort, France
| | - Sophie A. Granier
- Paris-Est University, ANSES, French Agency for Food, Environmental, and Occupational Health and Safety, Laboratory for Food Safety, European Union Reference Laboratory for Listeria monocytogenes, Maisons-Alfort, France
| | - Abera Geyid
- Food Microbiology Section, Food Science and Nutrition Research Directorate, Ethiopian Health and Nutrition Research Institute, Addis Ababa, Ethiopia
| | - Girum Taye
- Food Microbiology Section, Food Science and Nutrition Research Directorate, Ethiopian Health and Nutrition Research Institute, Addis Ababa, Ethiopia
| | - Rene S. Hendriksen
- WHO Collaborating Centre for Antimicrobial Resistance in Food-borne Pathogens and EU Reference Laboratory for Antimicrobial Resistance, National Food Institute, Technical University of Denmark, Kingsly Lyngby, Denmark
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David JM, Sanders P, Bemrah N, Granier SA, Denis M, Weill FX, Guillemot D, Watier L. Attribution of the French human Salmonellosis cases to the main food-sources according to the type of surveillance data. Prev Vet Med 2013; 110:12-27. [PMID: 23453456 DOI: 10.1016/j.prevetmed.2013.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Salmonella are the most common bacterial cause of foodborne infections in France and ubiquitous pathogens present in many animal productions. Assessing the relative contribution of the different food-animal sources to the burden of human cases is a key step towards the conception, prioritization and assessment of efficient control policy measures. For this purpose, we considered a Bayesian microbial subtyping attribution approach based on a previous published model (Hald et al., 2004). It requires quality integrated data on human cases and on the contamination of their food sources, per serotype and microbial subtype, which were retrieved from the French integrated surveillance system for Salmonella. The quality of the data available for such an approach is an issue for many countries in which the surveillance system has not been designed for this purpose. In France, the sources are monitored simultaneously by an active, regulation-based surveillance system that produces representative prevalence data (as ideally required for the approach) and a passive system relying on voluntary laboratories that produces data not meeting the standards set by Hald et al. (2004) but covering a broader range of sources. These data allowed us to study the impact of data quality on the attribution results, globally and focusing on specific features of the data (number of sources and contamination indicator). The microbial subtyping attribution model was run using an adapted parameterization previously proposed (David et al., 2012). A total of 9076 domestic sporadic cases were included in the analyses as well as 9 sources among which 5 were common to the active and the passive datasets. The greatest impact on the attribution results was observed for the number of sources. Thus, especially in the absence of data on imported products, the attribution estimates presented here should be considered with caution. The results were comparable for both types of surveillance, leading to the conclusion that passive data constitute a potential cost-effective complement to active data collection, especially interesting because the former encompass a greater number of sources. The model appeared robust to the type of surveillance, and provided that some methodological aspects of the model can be enhanced, it could also serve as a risk-based guidance tool for active surveillance systems.
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Affiliation(s)
- J M David
- Anses, Laboratoire de Fougères, Fougères, F-35302, France
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Jouy E, Le Roux A, Kéranflec'h A, Granier SA, Laurent F, Kempf I, Brisabois A, Cariolet R, Chauvin C. Methicillin-resistant Staphylococcus aureus ST398 contamination and transmission in pigs after a low dose inoculation. Lett Appl Microbiol 2012; 54:518-23. [PMID: 22404325 DOI: 10.1111/j.1472-765x.2012.03239.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Methicillin-resistant Staphylococcus aureus (MRSA) ST398 has recently been described as a zoonotic agent. Its transmission between animals seems to be a pivotal factor in its emergence and dissemination. This experimental trial was performed to describe MRSA ST398 contamination and transmission in pigs after a low dose inoculation. METHODS AND RESULTS Twelve specific pathogen-free (SPF) pigs were randomly divided between two separate pens. Three pigs in each pen received a nasal inoculation of 2 × 10(4) colony-forming units per animal, and three naïve pigs were left in contact with them. Every 2 days and at necropsy, different samples were screened for MRSA. It was detected in nasal swabs from five inoculated and three naïve contact pigs, as early as 1 day after inoculation. MRSA was also found in environmental wipes but never in faecal samples. At necropsy, MRSA was detected in the lymph nodes of two contact pigs and in the tonsils and lymph nodes of three inoculated pigs. Twelve other SPF pigs were included as negative control in a separate room. CONCLUSION This experiment showed that inoculation of a low dose of MRSA ST398 could lead to the horizontal transmission of the bacterium between pigs, the contamination of mandibular lymph nodes and the contamination of the environment without faecal carriage. SIGNIFICANCE AND IMPACT OF THE STUDY The minimal inoculated dose via nasal route to observe transmission of MRSA ST398 between pigs is equal or lower to 2 × 10(4) colony-forming units per animal, and faecal excretion seems not to be a necessary condition for horizontal transmission.
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Affiliation(s)
- E Jouy
- Anses, Ploufragan-Plouzané Laboratory, Ploufragan, France.
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Bouzidi N, Aoun L, Zeghdoudi M, Bensouilah M, Elgroud R, Oucief I, Granier SA, Brisabois A, Desquilbet L, Millemann Y. Salmonella contamination of laying-hen flocks in two regions of Algeria. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.05.027] [Citation(s) in RCA: 15] [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: 12/01/2022]
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Le Hello S, Hendriksen RS, Doublet B, Fisher I, Nielsen EM, Whichard JM, Bouchrif B, Fashae K, Granier SA, Jourdan-Da Silva N, Cloeckaert A, Threlfall EJ, Angulo FJ, Aarestrup FM, Wain J, Weill FX. International Spread of an Epidemic Population of Salmonella enterica Serotype Kentucky ST198 Resistant to Ciprofloxacin. J Infect Dis 2011; 204:675-84. [PMID: 21813512 DOI: 10.1093/infdis/jir409] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Simon Le Hello
- Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Salmonella, World Health Organization (WHO) Collaborating Centre for Reference and Research on Salmonella, Paris, France
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Garcia-Migura L, Sunde M, Karlsmose S, Veldman K, Schroeter A, Guerra B, Granier SA, Perrin-Guyomard A, Gicquel-Bruneau M, Franco A, Englund S, Teale C, Heiska H, Clemente L, Boerlin P, Moreno MA, Daignault D, Mevius D, Hendriksen RS, Aarestrup FM. Establishing streptomycin epidemiological cut-off values for Salmonella and Escherichia coli. Microb Drug Resist 2011; 18:88-93. [PMID: 21749212 DOI: 10.1089/mdr.2011.0064] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
This study was conducted to elucidate the accuracy of the current streptomycin epidemiological cut-off value (ECOFF) for Escherichia coli and Salmonella spp. A total of 236 Salmonella enterica and 208 E. coli isolates exhibiting MICs between 4 and 32 mg/L were selected from 12 countries. Isolates were investigated by polymerase chain reaction for aadA, strA, and strB streptomycin resistance genes. Out of 236 Salmonella isolates, 32 (13.5%) yielded amplicons for aadA (n = 23), strA (n = 9), and strB (n = 11). None of the 60 Salmonella isolates exhibiting MIC 4 mg/L harbored resistance genes. Of the Salmonella isolates exhibiting MICs 8 mg/L, 16 mg/L, and 32 mg/L, 1.6%, 15%, and 39%, respectively, tested positive for one or more genes. For most monitoring programs, the streptomycin ECOFF for Salmonella is wild type (WT) ≤32 or ≤16 mg/L. A cut-off value of WT ≤32 mg/L would have misclassified 13.5% of the strains as belonging to the WT population, since this proportion of strains harbored resistance genes and exhibited MICs ≤32 mg/L. Out of 208 E. coli strains, 80 (38.5%) tested positive for aadA (n = 69), strA (n = 18), and strB (n = 31). Of the E. coli isolates exhibiting MICs of 4 mg/L, 8 mg/L, 16 mg/L, and 32 mg/L, 3.6%, 17.6%, 53%, and 82.3%, respectively, harbored any of the three genes. Based on the European Committee on Antimicrobial Susceptibility Testing guidelines (ECOFF ≤16 mg/L), 25% of the E. coli strains presenting MIC ≤16 mg/L would have been incorrectly categorized as belonging to the WT population. The authors recommend an ECOFF value of WT ≤16 mg/L for Salmonella and WT ≤8 mg/L for E. coli.
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Bugarel M, Granier SA, Weill FX, Fach P, Brisabois A. A multiplex real-time PCR assay targeting virulence and resistance genes in Salmonella enterica serotype Typhimurium. BMC Microbiol 2011; 11:151. [PMID: 21707966 PMCID: PMC3150258 DOI: 10.1186/1471-2180-11-151] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 06/27/2011] [Indexed: 12/02/2022] Open
Abstract
Background Typhimurium is the main serotype of Salmonella enterica subsp. enterica implicated in food-borne diseases worldwide. This study aimed to detect the prevalence of ten markers combined in a macro-array based on multiplex real-time PCR. We targeted characteristic determinants located on pathogenicity islands (SPI-2 to -5, virulence plasmid pSLT and Salmonella genomic island 1 (SGI1)) as well as a specific 16S-23S rRNA intergenic spacer sequence of definitive type 104 (DT104). To investigate antimicrobial resistance, the study also targeted the presence of genes involved in sulfonamide (sul1) and beta-lactam (blaTEM) resistance. Finally, the intI1 determinant encoding integrase from class 1 integron was also investigated. Results A total of 538 unrelated S. Typhimurium strains isolated between 1999 and 2009 from various sources, including food animals, food products, human and environmental samples were studied. Based on the combined presence or absence of these markers, we distinguished 34 different genotypes, including three major genotypes encountered in 75% of the studied strains, Although SPI determinants were almost always detected, SGI1, intI1, sul1 and blaTEM determinants were found 47%, 52%, 54% and 12% of the time respectively, varying according to isolation source. Low-marker patterns were most often detected in poultry sources whereas full-marker patterns were observed in pig, cattle and human sources. Conclusion The GeneDisc® assay developed in this study madeit easier to explore variability within serotype Typhimurium by analyzing ten relevant gene determinants in a large collection of strains. This real-time multiplex method constitutes a valuable tool for strains characterization on epidemiological purposes.
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Affiliation(s)
- Marie Bugarel
- French Agency for Food, Environmental and Occupational Health Safety (ANSES) Laboratory for Food Safety, Maisons-Alfort Cedex, France
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Bouzidi N, Aoun L, Dekhil M, Granier SA, Poirel L, Brisabois A, Nordmann P, Millemann Y. Co-occurrence of aminoglycoside resistance gene armA in non-Typhi Salmonella isolates producing CTX-M-15 in Algeria. J Antimicrob Chemother 2011; 66:2180-1. [PMID: 21676906 DOI: 10.1093/jac/dkr237] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Hopkins KL, Kirchner M, Guerra B, Granier SA, Lucarelli C, Porrero MC, Jakubczak A, Threlfall EJ, Mevius DJ. Multiresistant Salmonella enterica serovar 4,[5],12:i:- in Europe: a new pandemic strain? Euro Surveill 2010. [DOI: 10.2807/ese.15.22.19580-en] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A marked increase in the prevalence of S. enterica serovar 4,[5],12:i:- with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines (R-type ASSuT) has been noted in food-borne infections and in pigs/pig meat in several European countries in the last ten years. One hundred and sixteen strains of S. enterica serovar 4,[5],12:i:- from humans, pigs and pig meat isolated in England and Wales, France, Germany, Italy, Poland, Spain and the Netherlands were further subtyped by phage typing, pulsed-field gel electrophoresis and multilocus variable number tandem repeat analysis to investigate the genetic relationship among strains. PCR was performed to identify the fljB flagellar gene and the genes encoding resistance to ampicillin, streptomycin, sulphonamides and tetracyclines. Class 1 and 2 integrase genes were also sought. Results indicate that genetically related serovar 4,[5],12:i:- strains of definitive phage types DT193 and DT120 with ampicillin, streptomycin, sulphonamide and tetracycline resistance encoded by blaTEM, strA-strB, sul2 and tet(B) have emerged in several European countries, with pigs the likely reservoir of infection. Control measures are urgently needed to reduce spread of infection to humans via the food chain and thereby prevent the possible pandemic spread of serovar 4,[5],12:i:- of R-type ASSuT as occurred with S. Typhimurium DT104 during the 1990s.
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Affiliation(s)
- K L Hopkins
- Health Protection Agency Centre for Infections, London, United Kingdom
| | - M Kirchner
- Veterinary Laboratories Agency, Weybridge, United Kingdom
| | - B Guerra
- Federal Institute for Risk Assessment, Berlin, Germany
| | - S A Granier
- Agence Française de Sécurité Sanitaire des Aliments, Maisons-Alfort, France
| | | | - M C Porrero
- Health Surveillance Centre (VISAVET), University Complutense, Madrid, Spain
| | - A Jakubczak
- National Institute of Public Health, Warsaw, Poland
| | - E J Threlfall
- Health Protection Agency Centre for Infections, London, United Kingdom
| | - D. J Mevius
- Faculty of veterinary Medicine, Utrecht University, The Netherlands
- Central Veterinary Institute of Wageningen, Lelystad, The Netherlands
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Hopkins KL, Kirchner M, Guerra B, Granier SA, Lucarelli C, Porrero MC, Jakubczak A, Threlfall EJ, Mevius DJ. Multiresistant Salmonella enterica serovar 4,[5],12:i:- in Europe: a new pandemic strain? Euro Surveill 2010; 15:19580. [PMID: 20546690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
A marked increase in the prevalence of S. enterica serovar 4,[5],12:i:- with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines (R-type ASSuT) has been noted in food-borne infections and in pigs/pig meat in several European countries in the last ten years. One hundred and sixteen strains of S. enterica serovar 4,[5],12:i:- from humans, pigs and pig meat isolated in England and Wales, France, Germany, Italy, Poland, Spain and the Netherlands were further subtyped by phage typing, pulsed-field gel electrophoresis and multilocus variable number tandem repeat analysis to investigate the genetic relationship among strains. PCR was performed to identify the fljB flagellar gene and the genes encoding resistance to ampicillin, streptomycin, sulphonamides and tetracyclines. Class 1 and 2 integrase genes were also sought. Results indicate that genetically related serovar 4,[5],12:i:- strains of definitive phage types DT193 and DT120 with ampicillin, streptomycin, sulphonamide and tetracycline resistance encoded by blaTEM, strA-strB, sul2 and tet(B) have emerged in several European countries, with pigs the likely reservoir of infection. Control measures are urgently needed to reduce spread of infection to humans via the food chain and thereby prevent the possible pandemic spread of serovar 4,[5],12:i:- of R-type ASSuT as occurred with S. Typhimurium DT104 during the 1990s.
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Affiliation(s)
- K L Hopkins
- Health Protection Agency Centre for Infections, London, United Kingdom.
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Elgroud R, Zerdoumi F, Benazzouz M, Bouzitouna-Bentchouala C, Granier SA, Frémy S, Brisabois A, Dufour B, Millemann Y. Characteristics of Salmonella contamination of broilers and slaughterhouses in the region of Constantine (Algeria). Zoonoses Public Health 2008; 56:84-93. [PMID: 18705656 DOI: 10.1111/j.1863-2378.2008.01164.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The present study provides the first data about the prevalence of Salmonella contamination of broilers and slaughterhouses in the region of Constantine, Algeria. The serotypes and anti-microbial resistance phenotypes of the isolates were determined, and risk factors contributing to the contamination were evaluated. A total of 2490 samples, 1800 originating from 30 broiler farms and 690 from 15 slaughterhouses, were taken during two periods: March 2005-June 2006 and September 2006-March 2007. Salmonella contamination concerned 37% of the broiler farms and 53% of the slaughterhouses. Among the 55 isolates recovered, 10 different serotypes were identified. The most frequently recovered serotypes in both slaughterhouses and breeder farms were S. Hadar (36%, n = 20), S. Virchow (16%, n = 9), S. Infantis (10.9%, n = 6), S. Albany (11%, n = 6) and S. Carnac (7%, n = 4). Isolates belonging to S. Heidelberg (2%, n = 1) and S. Rissen (2%, n = 1) were found only in farms, while those belonging to S. Typhimurium (9%, n = 5), S. Enteritidis (4%, n = 2) and S. Montevideo (2%, n = 1) were recovered only from slaughterhouses. Thirty-nine isolates (80%) were resistant to at least one anti-microbial and 51% were multi-resistant, i.e. resistant to two or more anti-microbial molecules. About 58% (n = 32) were resistant to streptomycin, 36% (n = 20) to tetracyclines, 27% (n = 15) to nalidixic acid, 13% (n = 7) to ofloxacin and one isolate to enrofloxacin. Finally, seven distinct anti-microbial resistance profiles were identified. In parallel, four risk factors were found to be significantly associated with Salmonella contamination. Together with the huge spread of Salmonella in the broiler production chain in Constantine, Algeria, these risk factors highlight the hazards of the broiler channels, particularly linked to poor technical and hygiene practices.
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Affiliation(s)
- R Elgroud
- Laboratoire de pathologie animale, développement des élevages et surveillance de la chaîne alimentaire, Département des sciences vétérinaires, Université Mentouri de Constantine, W: Constantine, Algeria
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Egorova S, Timinouni M, Demartin M, Granier SA, Whichard JM, Sangal V, Fabre L, Delauné A, Pardos M, Millemann Y, Espié E, Achtman M, Grimont PAD, Weill FX. Ceftriaxone-resistant salmonella enterica serotype Newport, France. Emerg Infect Dis 2008; 14:954-7. [PMID: 18507913 PMCID: PMC2600296 DOI: 10.3201/eid1406.071168] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The multidrug-resistant (MDR) Salmonella enterica serotype Newport strain that produces CMY-2 beta-lactamase (Newport MDR-AmpC) was the source of sporadic cases and outbreaks in humans in France during 2000-2005. Because this strain was not detected in food animals, it was most likely introduced into France through imported food products.
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Granier SA, Leflon-Guibout V, Goldstein FW, Nicolas-Chanoine MH. New Klebsiella oxytoca beta-lactamase genes bla(OXY-3) and bla(OXY-4) and a third genetic group of K oxytoca based on bla(OXY-3). Antimicrob Agents Chemother 2003; 47:2922-8. [PMID: 12936995 PMCID: PMC182611 DOI: 10.1128/aac.47.9.2922-2928.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The two genetic groups (oxy-1 and oxy-2) previously identified in the Klebsiella oxytoca taxon are recognizable by four independent molecular markers: (i). ERIC-1R profiles, (ii). 16S ribosomal DNA (rDNA) signature sequences, (iii). singular nucleotides in a defined fragment of the rpoB gene, and (iv) the type of the strain's bla(OXY) gene (i.e., bla(OXY-1) or bla(OXY-2)). K. oxytoca strains SG266 and SG271 could not be classified into these genetic groups based on their ERIC-1R profile and bla(OXY) gene sequence. With regard to the gene identity percentages between the bla(OXY-1) and bla(OXY-2) gene groups (86.8% +/- 0.4%) and within a bla(OXY) gene group (>99%), it was concluded that the bla(OXY) gene of strain SG271 was representative of a new bla(OXY) gene group (bla(OXY-3)), since the mean identity percentages between it and the two bla(OXY) gene groups were 85.5% +/- 0.2% and 84.4% +/- 0.4%, respectively. Since the corresponding percentages were 95.0% +/- 0.4% and 86.2% +/- 0.3% for strain SG266, it was impossible to classify its bla(OXY) gene, which was therefore named bla(OXY-4). The 16S rDNA signature sequences of the two strains could be determined only after cloning experiments. The SG266 clones displayed the same signature sequence as that of the genetic group oxy-1, whereas the SG271 clones displayed three different 16S rDNA signature sequences that also differed from those of the two genetic groups. Singular nucleotides were found within the rpoB sequence of the two strains, allowing for their distinction from the two genetic groups. All of these results, combined with those previously obtained by the ERIC-1R PCR method, indicate that strain SG271 is representative of a new K. oxytoca genetic group (oxy-3), whereas strain SG266 could not be classified.
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Affiliation(s)
- Sophie A Granier
- Service de Microbiologie-Hygiène, Hôpital Ambroise Paré, Boulogne-Billancourt, Paris, France
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Granier SA, Plaisance L, Leflon-Guibout V, Lagier E, Morand S, Goldstein FW, Nicolas-Chanoine MH. Recognition of two genetic groups in the Klebsiella oxytoca taxon on the basis of chromosomal beta-lactamase and housekeeping gene sequences as well as ERIC-1 R PCR typing. Int J Syst Evol Microbiol 2003; 53:661-668. [PMID: 12807183 DOI: 10.1099/ijs.0.02408-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whilst searching for a molecular method to identify the different species of Raoultella and Klebsiella oxytoca, it was observed that the OXY-1 and OXY-2 beta-lactamase-producing K. oxytoca isolates displayed two distinguishable enterobacterial repetitive intergenic consensus (ERIC)-1R profiles. It was hypothesized that the two groups of chromosomal beta-lactamases might correspond to two groups of strains in the K. oxytoca taxon. To confirm this hypothesis, clinical isolates and reference strains of K. oxytoca were studied by determination of the sequence of their bla(OXY) genes, and of a partial fragment of their 16S rRNA (387 bp) and rpoB (512 bp) genes. The sequence data were phylogenetically analysed by using the parsimony method. Four clinical isolates possessed a bla(OXY-1) gene and nine possessed a bla(OXY-2) gene. The mean percentage of rpoB and 16S rRNA gene identity was > 99% within each group of strains, whereas it was 96.56 +/- 0.24% for rpoB genes and 97.80 +/- 0.22% for 16S rRNA genes between the group of strains harbouring the bla(OXY-1) gene and the group harbouring the bla(OXY-2) gene. The phylogenetic tree resulting from combined analysis of the 16S rRNA and rpoB datasets showed that the K. oxytoca isolates were monophyletic and separated into two clades; these clades included strains with either the bla(OXY-1) gene or the bla(OXY-2) gene. This result was supported with high bootstrap values of 97 and 99%, respectively. Moreover, the two groups of strains displayed distinct ERIC-1R profiles, with bands characteristic of each profile. Thus, the chromosomal bla(OXY) gene sequence is able to delineate not only two groups of beta-lactamases in K. oxytoca, but also two clades in the K. oxytoca taxon, in a manner similar to the sequence of housekeeping genes. These results suggest that K. oxytoca should be divided into two genetic groups, group OXY-1 represented by K. oxytoca strain SL781 (=CIP 104963) and group OXY-2 by K. oxytoca strain SL91l (= CIP 106098).
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Affiliation(s)
- Sophie A Granier
- Laboratoire de Microbiologie Médicale, Fondation Hôpital Saint-Joseph, Paris, France
- Service de Microbiologie-Hygiène, Hôpital Ambroise Paré AP-HP, Université Versailles-Saint-Quentin-en-Yvelines-UFR Médicale Paris-Ile-de-France-Ouest, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France
| | - Laetitia Plaisance
- Centre de Biologie et d'Ecologie Tropicale et Méditerranéenne, UMR 5555, Université de Perpignan, France
| | - Véronique Leflon-Guibout
- Service de Microbiologie-Hygiène, Hôpital Ambroise Paré AP-HP, Université Versailles-Saint-Quentin-en-Yvelines-UFR Médicale Paris-Ile-de-France-Ouest, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France
| | - Evelyne Lagier
- Service de Microbiologie, Centre Hospitalier du Pays d'Aix, Aix en Provence, France
| | - Serge Morand
- Centre de Biologie et d'Ecologie Tropicale et Méditerranéenne, UMR 5555, Université de Perpignan, France
| | - Fred W Goldstein
- Laboratoire de Microbiologie Médicale, Fondation Hôpital Saint-Joseph, Paris, France
| | - Marie-Hélène Nicolas-Chanoine
- Service de Microbiologie-Hygiène, Hôpital Ambroise Paré AP-HP, Université Versailles-Saint-Quentin-en-Yvelines-UFR Médicale Paris-Ile-de-France-Ouest, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France
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Granier SA, Leflon-Guibout V, Goldstein FW, Nicolas-Chanoine MH. Enterobacterial repetitive intergenic consensus 1R PCR assay for detection of Raoultella sp. isolates among strains identified as Klebsiella oxytoca in the clinical laboratory. J Clin Microbiol 2003; 41:1740-2. [PMID: 12682174 PMCID: PMC153902 DOI: 10.1128/jcm.41.4.1740-1742.2003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The enterobacterial repetitive intergenic consensus 1R PCR method, which provided recognizable profiles for reference strains of the three species of Raoultella and the two genetic groups of Klebsiella oxytoca, was applied to 19 clinical isolates identified as K. oxytoca. By this method, as confirmed by species-specific gene sequencing, two Raoultella ornithinolytica and two unclassifiable K. oxytoca isolates were identified.
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Affiliation(s)
- Sophie A Granier
- Service de Microbiologie-Hygiène, Hôpital Ambroise Paré AP-HP, Boulogne, France
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Granier SA, Nicolas-Chanoine MH, Nguyen Van JC, Leflon-Guibout V, Kitzis MD, Goldstein FW. False susceptibility of Klebsiella oxytoca to some extended-spectrum cephalosporins. J Antimicrob Chemother 2002; 50:303-4. [PMID: 12161419 DOI: 10.1093/jac/dkf123] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Granier SA, Leflon-Guibout V, Nicolas-Chanoine MH, Bush K, Goldstein FW. The extended-spectrum K1 beta-lactamase from Klebsiella oxytoca SC 10,436 is a member of the bla(OXY-2) family of chromosomal Klebsiella enzymes. Antimicrob Agents Chemother 2002; 46:2056-7. [PMID: 12019142 PMCID: PMC127276 DOI: 10.1128/aac.46.6.2056-2057.2002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Granier SA, Nguyen Van JC, Kitzis MD, Goldstein FW, Leflon-Guibout V, Nicolas-Chanoine MH. First description of a TEM-30 (IRT-2)-producing Klebsiella oxytoca isolate. Antimicrob Agents Chemother 2002; 46:1158-9. [PMID: 11897614 PMCID: PMC127080 DOI: 10.1128/aac.46.4.1158-1159.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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