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Chaalal N, Touati A, Bakour S, Aissa MA, Sotto A, Lavigne JP, Pantel A. Spread of OXA-48 and NDM-1-Producing Klebsiella pneumoniae ST48 and ST101 in Chicken Meat in Western Algeria. Microb Drug Resist 2020; 27:492-500. [PMID: 32208064 DOI: 10.1089/mdr.2019.0419] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aim: We investigated the prevalence of carbapenemase-producing Enterobacteriaceae (CPE) in chicken meat in Western Algeria in 2017. Results: From February to July 2017, samples of chicken meat from three poultry farms in Western Algeria were screened for the presence of CPE. Strains were characterized with regard to antibiotic resistance, β-lactamase content, Plasmid-mediated quinolone resistance, sulfonamide resistance genes, clonality (repetitive sequence-based profiles and multilocus sequence typing) and virulence traits. Of 181 samples analyzed, 29 (16.0%) carbapenemase-producing Klebsiella pneumoniae were detected. Twenty-three OXA-48-producers (79.3%) and six (20.7%) New Delhi metallo (NDM)-1-producers were observed. Clonality analysis showed three distinct lineages and clonal expansions of the OXA-48-producing K. pneumoniae ST48 and the NDM-1-producing K. pneumoniae ST101. These isolates harbored fimH, ureA, mrkD, entB, uge, and wabG. Neither capsular serotype genes nor hypermucoviscous phenotype were detected. Plasmid analysis confirmed that all these isolates harbored the transferable IncL and IncFIIK plasmids. Conclusions: This study reports the spread of OXA-48 and NDM-1-producing K. pneumoniae ST48 and ST101 in chicken meat in Western Algeria and demonstrates that food represents a reservoir of the carbapenemases encoding genes.
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Affiliation(s)
- Nadia Chaalal
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria.,Laboratory of Microbiology, National Institute of Veterinarian Sciences, Tiaret, Algeria.,Department of Microbiology and Hospital Hygiene, VBMI, INSERM U1047, CHU Nîmes, University of Montpellier, Nîmes, France
| | - Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algeria
| | - Sofiane Bakour
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Mohamed Amine Aissa
- Laboratory of Microbiology, National Institute of Veterinarian Sciences, Tiaret, Algeria
| | - Albert Sotto
- Department of Infectious Diseases, VBMI, INSERM U1047, CHU Nîmes, University of Montpellier, Nîmes, France
| | - Jean-Philippe Lavigne
- Department of Microbiology and Hospital Hygiene, VBMI, INSERM U1047, CHU Nîmes, University of Montpellier, Nîmes, France
| | - Alix Pantel
- Department of Microbiology and Hospital Hygiene, VBMI, INSERM U1047, CHU Nîmes, University of Montpellier, Nîmes, France
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52
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Baron S, Le Devendec L, Lucas P, Larvor E, Jové T, Kempf I. Characterisation of plasmids harbouring extended-spectrum cephalosporin resistance genes in Escherichia coli from French rivers. Vet Microbiol 2020; 243:108619. [PMID: 32273005 DOI: 10.1016/j.vetmic.2020.108619] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/21/2020] [Accepted: 02/21/2020] [Indexed: 11/19/2022]
Abstract
Antimicrobial resistance is a "One Health" issue that requires improved knowledge of the presence and abundance of resistant bacteria in the environment. Extended-spectrum cephalosporins (ESCs) are critically important antibiotics (CIAs), and resistance to these CIAs is often encoded by beta-lactamase genes borne on conjugative plasmids. We thus decided to characterise 21 plasmids of ESC-resistant Escherichia coli randomly selected from isolates previously obtained from river water collected in a rural area in western France. The plasmids encoding ESC resistance were sequenced to investigate the diversity of the genes encoding ESC resistance and their genetic context. Sequences revealed that eleven IncI1 pMLST3 plasmids carried the blaCTX-M-1 and sul2 genes, and some of them also had the tet(A), aadA5 or dfrA17 genes. The blaCTX-M-1 gene was also detected on an IncN plasmid. Five plasmids obtained from four rivers contained blaCTX-M-14, either on IncI1 or on IncFII plasmids. Two strains from two rivers contained blaCTX-M-15 on IncN pMLST7 plasmids, with qnrS1 and dfrA14 genes. One plasmid contained the blaCTX-M-55, a blaTEM-1B-like, and fosA genes. One plasmid contained the blaCMY-2 gene. The diversity of the genes and plasmids of the resistant bacteria isolated from French rivers is probably related to the various animal and human origins of the isolated bacteria.
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Affiliation(s)
- Sandrine Baron
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France
| | | | - Pierrick Lucas
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France
| | - Emeline Larvor
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, U1092, University of Limoges, Limoges, France
| | - Isabelle Kempf
- ANSES, Ploufragan-Plouzané-Niort Laboratory, 22440 Ploufragan, France.
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53
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Palmeira JD, Haenni M, Metayer V, Madec JY, Ferreira HMN. Epidemic spread of IncI1/pST113 plasmid carrying the Extended-Spectrum Beta-Lactamase (ESBL) bla CTX-M-8 gene in Escherichia coli of Brazilian cattle. Vet Microbiol 2020; 243:108629. [PMID: 32273008 DOI: 10.1016/j.vetmic.2020.108629] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
Abstract
INTRODUCTION The prevalence of Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide and the Agri-Food sector acts as a reservoir of clinically relevant ESBL genes. Our study aimed at detecting and characterizing ESBL-producing Enterobacteriaceae responsible for intestinal colonization of Brazilian bovines. MATERIAL AND METHODS ESBL-producing E. coli isolates were recovered from fecal samples of healthy cattle in Northwest Brazil. Antimicrobial susceptibility was determined by disk diffusion. Resistance and virulence genes were identified by PCR and amplicons were sequenced, clonality was assessed by PFGE and MLST, and plasmids were characterized by replicon typing, S1-PFGE and Southern blot hybridizations. Transferability of ESBL genes was assessed by conjugation assay. RESULTS A total of 40 ESBL-producing E. coli were characterized, which originated from 34/191 animals (17.8 %) and 15/22 farms (68.2 %). The blaCTX-M-8 gene was the most frequent ESBL gene (62.5 %), followed by blaSHV-2a (20.0 %), blaCTX-M-2 (10.0 %), and blaCTX-M-15 (7.5 %). The blaCTX-M-8 gene was localized on the IncI1/pST113 plasmid in multiple E. coli sequence types across unrelated animals and farms. DISCUSSION We report the first characterization and a high prevalence of ESBL-producing E. coli in the beef cattle sector in Brazil, which is mainly supported by the spread of an epidemic IncI1/pST113/blaCTX-M-8 plasmid. Since Brazil is one of the biggest beef meat exporters worldwide, the spread of this ESBL plasmid across other sectors, countries and continents should be considered with attention.
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Affiliation(s)
- Josman Dantas Palmeira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal; UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal.
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Anses Laboratoire de Lyon, France
| | - Véronique Metayer
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Anses Laboratoire de Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Anses Laboratoire de Lyon, France
| | - Helena Maria Neto Ferreira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal; UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal
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54
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Cohen E, Davidovich M, Rokney A, Valinsky L, Rahav G, Gal-Mor O. Emergence of new variants of antibiotic resistance genomic islands among multidrug-resistant Salmonella enterica in poultry. Environ Microbiol 2019; 22:413-432. [PMID: 31715658 DOI: 10.1111/1462-2920.14858] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 01/07/2023]
Abstract
Non-typhoidal Salmonella enterica (NTS) are diverse and important bacterial pathogens consisting of more than 2600 different serovars, with varying host-specificity. Here, we characterized the poultry-associated serovars in Israel, analysed their resistome and illuminated the molecular mechanisms underlying common multidrug resistance (MDR) patterns. We show that at least four serovars including Infantis, Muenchen, Newport and Virchow present a strong epidemiological association between their temporal trends in poultry and humans. Worrisomely, 60% from all of the poultry isolates tested (n = 188) were multidrug resistant, mediated by chromosomal SNPs and different mobile genetics elements. A novel streptomycin-azithromycin resistance island and previously uncharacterized versions of the mobilized Salmonella genomic island 1 (SGI1) were identified and characterized in S. Blockley and S. Kentucky isolates respectively. Moreover, we demonstrate that the acquisition of SGI1 does not impose fitness cost during growth under nutrient-limited conditions or in the context of Salmonella infection in the mouse model. Overall, our data emphasize the role of the poultry production as a pool of specific epidemic MDR strains and autonomous genetic elements, which confer resistance to heavy metals and medically relevant antibiotics. These are likely to disseminate to humans via the food chain and fuel the increasing global antibiotic resistance crisis.
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Affiliation(s)
- Emiliano Cohen
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Assaf Rokney
- Central Laboratories, Ministry of Health, Jerusalem, Israel
| | - Lea Valinsky
- Central Laboratories, Ministry of Health, Jerusalem, Israel
| | - Galia Rahav
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ohad Gal-Mor
- The Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Clinical Microbiology and Immunology, Tel Aviv University, Tel Aviv, Israel
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55
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Hassen B, Saloua B, Abbassi MS, Ruiz-Ripa L, Mama OM, Hassen A, Hammami S, Torres C. mcr-1 encoding colistin resistance in CTX-M-1/CTX-M-15- producing Escherichia coli isolates of bovine and caprine origins in Tunisia. First report of CTX-M-15-ST394/D E. coli from goats. Comp Immunol Microbiol Infect Dis 2019; 67:101366. [PMID: 31627036 DOI: 10.1016/j.cimid.2019.101366] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/25/2019] [Accepted: 09/29/2019] [Indexed: 11/19/2022]
Abstract
The objective of this study was to isolate and characterize ESBL-producing Escherichia coli (ESBL-EC) from raw bovine and caprine milk samples, as well as from bovine faeces in Tunisia. Therefore, 120 bovine faecal samples and 9 caprine raw milk samples were collected from 2 extensive dairy-cow-farms and 5 ovine farms, respectively. In addition, 94 raw bovine milk samples, from containers and holding tanks from 50 small public-markets in the North of Tunisia, were processed for the isolation of cefotaxime-resistant E. coli (CTXR). Antimicrobial susceptibility testing was carried out by disc-diffusion/broth-microdilution methods. The presence of genes encoding ESBL, as well as those encoding colistin (mcr-1 to 5 genes)- sulfonamide-, tetracycline-, gentamicin-, quinolone and chloramphenicol-resistance and class 1 integrons were tested by PCR (and sequencing in some cases). ESBL-EC isolates were further characterized by phylogrouping and MLST/PFGE typing. Eight samples (3.6%) contained ESBL-EC isolates (3/2 from raw bovine/goat milk and 3 from cattle faeces) and one isolate/sample was characterized. Four ESBL-EC isolates, all of bovine origin (3 faeces/1 milk), were resistant to colistin (MIC: 8-16 μg/ml), harboured the mcr-1 gene and carried IncP- and IncFIB-type plasmids. The 8 ESBL-EC strains had the following characteristics: a) bovine faeces: mcr-1/CTX-M-1/D-ST1642 (3 strains); b) raw milk: mcr-1/CTX-M-1/A-ST10 (1 strain); CTX-M-15/B1-ST394 (3 strains), and CTX-M-15/A-ST46 (1 strain). Most of bovine ESBL-EC isolates were multidrug-resistant (4/5). Our results showed that ESBL-EC were detected in bovine and caprine samples (CTX-M-1/CTX-M-15 producers), being some of them colistin-resistant (associated with mcr-1 gene), and they belonged to international clonal lineages.
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Affiliation(s)
- Bilel Hassen
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Benlabidi Saloua
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis 1006, Tunisia; Université de Tunis El Manar, Faculté de Médecine de Tunis, Laboratoire de résistance aux antibiotiques LR99ES09, Tunisia
| | - Laura Ruiz-Ripa
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Olouwafemi M Mama
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP 273, 8020, Soliman, Tunisia
| | - Salah Hammami
- Université de la Manouba, IRESA, École Nationale de Médecine Vétérinaire de Sidi Thabet, Sidi Thabet 2020, Sidi Thabet, Ariana, Tunisia
| | - Carmen Torres
- Departamento de Agricultura y Alimentación, Universidad de La Rioja, 26006 Logroño, Spain.
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56
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Saidani M, Messadi L, Chaouechi A, Tabib I, Saras E, Soudani A, Daaloul-Jedidi M, Mamlouk A, Ben Chehida F, Chakroun C, Madec JY, Haenni M. High Genetic Diversity of Enterobacteriaceae Clones and Plasmids Disseminating Resistance to Extended-Spectrum Cephalosporins and Colistin in Healthy Chicken in Tunisia. Microb Drug Resist 2019; 25:1507-1513. [PMID: 31329501 DOI: 10.1089/mdr.2019.0138] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enterobacteriaceae resistant to extended-spectrum cephalosporins (ESC-R) are listed as "priority pathogens" by the World Health Organization, and the Agri-food sector has regularly been pointed out as a potential source of ESC-R for humans through food consumption and animal handling. Chicken industry and chicken meat have recurrently been under specific scrutiny due to the high proportions of ESC-R reported worldwide in this sector. In Tunisia, recent studies suggested that the plasmidic AmpC blaCMY-2 gene may have emerged in chicken. We thus collected 258 cloacal swabs from five different farms and selected ESC-R isolates to determine the current ESC-R prevalence and epidemiology. All five farms were ESC-R positive with proportions ranging from 4% to 67.3%. blaCTX-M-1/IncI1/ST3 was the dominant gene/plasmid association in chicken, but several other CTX-M genes and plasmid backgrounds were shown to spread ESC-R. Surprisingly, the CMY-2 enzyme was only identified in one isolate. In addition, we also reported the sporadic presence of the mcr-1 gene carried by an IncHI2 plasmid. Our data suggest that the high diversity of Enterobacteriaceae clones and plasmids circulating in healthy chicken in Tunisia maintains a high ESC-R proportion in flocks and constitutes a major source of ESC-R determinants further disseminating in the food chain.
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Affiliation(s)
- Mariem Saidani
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie.,Institut National agronomique de Tunisie, Université de Carthage, Tunis, Tunisie
| | - Lilia Messadi
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie
| | - Amira Chaouechi
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie
| | - Ines Tabib
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon-ANSES Site de Lyon, Lyon, France
| | - Alya Soudani
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie
| | - Monia Daaloul-Jedidi
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie
| | - Aymen Mamlouk
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie
| | - Faten Ben Chehida
- Service de Microbiologie et d'Immunologie, Ecole Nationale de Médecine Vétérinaire, Université de La Manouba, Sidi Thabet, Tunisie
| | - Chahid Chakroun
- Groupement Interprofessionnel des Produits Avicoles et Cunicoles (GIPAC), Tunis, Tunisie
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon-ANSES Site de Lyon, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon-ANSES Site de Lyon, Lyon, France
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57
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Gozi KS, Froes JR, Deus Ajude LPT, da Silva CR, Baptista RS, Peiró JR, Marinho M, Mendes LCN, Nogueira MCL, Casella T. Dissemination of Multidrug-Resistant Commensal Escherichia coli in Feedlot Lambs in Southeastern Brazil. Front Microbiol 2019; 10:1394. [PMID: 31293542 PMCID: PMC6603138 DOI: 10.3389/fmicb.2019.01394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Antimicrobial resistance (AR) is a public health issue since it limits the choices to treat infections by Escherichia coli in humans and animals. In Brazil, the ovine meat market has grown in recent years, but studies about AR in sheep are still scarce. Thus, this study aims to investigate the presence of AR in E. coli isolated from lambs during feedlot. To this end, feces from 112 lambs with 2 months of age, after weaning, were collected on the first day of the animals in the feedlot (day 0), and on the last day before slaughtering (day 42). Isolates were selected in MacConkey agar supplemented with 4 mg/L of ceftiofur and identified by biochemical methods. Isolates were submitted to an antimicrobial susceptibility test by disc-diffusion and PCR to investigate genes for phylogenetic group, virulence determinants and resistance to the several antimicrobial classes tested. The genetic localization of the bla genes detected was elucidated by S1-PFGE followed by Southern blot-hybridizations. The isolates were typed by XbaI-PFGE and MLST methods. Seventy-eight E. coli were isolated from 8/112 (7.1%) animals on day 0, and from 55/112 (49.1%) animals on day 42. Since only fimH was present in almost all E. coli (97.4%) as a virulence gene, and also 88.5% belonged to phylogroups B1 or A, we consider that isolates represent intestinal commensal bacteria. The dendrogram separated the 78 non-virulent isolates in seven clusters, two of which comprised 50 E. coli belonging to ST/CC 1727/446 or ST 3994 recovered on day 42 commonly harboring the genotype bla CMY -2-aac(3)-IIa -tetA-sul1-sul2-floR-cmlA. Special attention should be given to the presence of bla CTX-M-15, a worldwide gene spread, and bla CTX-M-14, a hitherto undetected gene in Enterobacteriaceae from food-producing animals in Brazil. Importantly, E. coli lineages and plasmids carrying bla genes detected here have already been reported as sources of infection in humans either from animals, food, or the environment, which raises public health concerns. Hence, two types of commensal E. coli carrying important AR genes clearly prevailed during feedlot, but lambs are also reservoirs of bacteria carrying important AR genes such as bla CTX-M-14 and bla CTX-M-15, mostly related to antimicrobial treatment failure.
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Affiliation(s)
- Katia Suemi Gozi
- Centro de Investigação e Microrganismos, FAMERP, São José do Rio Preto, Brazil
| | | | | | | | | | - Juliana Regina Peiró
- Faculdade de Medicina Veterinária, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Marcia Marinho
- Faculdade de Medicina Veterinária, São Paulo State University (UNESP), Araçatuba, Brazil
| | | | | | - Tiago Casella
- Centro de Investigação e Microrganismos, FAMERP, São José do Rio Preto, Brazil
- Hospital de Base, São José do Rio Preto, Brazil
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Collineau L, Boerlin P, Carson CA, Chapman B, Fazil A, Hetman B, McEwen SA, Parmley EJ, Reid-Smith RJ, Taboada EN, Smith BA. Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges. Front Microbiol 2019; 10:1107. [PMID: 31231317 PMCID: PMC6558386 DOI: 10.3389/fmicb.2019.01107] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/01/2019] [Indexed: 12/20/2022] Open
Abstract
Whole-genome sequencing (WGS) will soon replace traditional phenotypic methods for routine testing of foodborne antimicrobial resistance (AMR). WGS is expected to improve AMR surveillance by providing a greater understanding of the transmission of resistant bacteria and AMR genes throughout the food chain, and therefore support risk assessment activities. At this stage, it is unclear how WGS data can be integrated into quantitative microbial risk assessment (QMRA) models and whether their integration will impact final risk estimates or the assessment of risk mitigation measures. This review explores opportunities and challenges of integrating WGS data into QMRA models that follow the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR. We describe how WGS offers an opportunity to enhance the next-generation of foodborne AMR QMRA modeling. Instead of considering all hazard strains as equally likely to cause disease, WGS data can improve hazard identification by focusing on those strains of highest public health relevance. WGS results can be used to stratify hazards into strains with similar genetic profiles that are expected to behave similarly, e.g., in terms of growth, survival, virulence or response to antimicrobial treatment. The QMRA input distributions can be tailored to each strain accordingly, making it possible to capture the variability in the strains of interest while decreasing the uncertainty in the model. WGS also allows for a more meaningful approach to explore genetic similarity among bacterial populations found at successive stages of the food chain, improving the estimation of the probability and magnitude of exposure to AMR hazards at point of consumption. WGS therefore has the potential to substantially improve the utility of foodborne AMR QMRA models. However, some degree of uncertainty remains in relation to the thresholds of genetic similarity to be used, as well as the degree of correlation between genotypic and phenotypic profiles. The latter could be improved using a functional approach based on prediction of microbial behavior from a combination of 'omics' techniques (e.g., transcriptomics, proteomics and metabolomics). We strongly recommend that methodologies to incorporate WGS data in risk assessment be included in any future revision of the Codex Alimentarius Guidelines for Risk Analysis of Foodborne AMR.
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Affiliation(s)
- Lucie Collineau
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Patrick Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Carolee A. Carson
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Brennan Chapman
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Aamir Fazil
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
| | - Benjamin Hetman
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Scott A. McEwen
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - E. Jane Parmley
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
| | - Richard J. Reid-Smith
- Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Eduardo N. Taboada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Ben A. Smith
- Public Health Risk Sciences Division, National Microbiology Laboratory, Public Health Agency of Canada, Guelph, ON, Canada
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Abstract
Antibiotic resistance reservoirs within food-producing animals are thought to be a risk to animal and human health. This study describes the minimum natural resistome of pig faeces as the bacteria are under no direct antibiotic selective pressure. The faecal resistome of 257 different genes comprised 56 core and 201 accessory resistance genes. The genes present at the highest relative abundances across all samples were tetW, tetQ, tet44, tet37, tet40, mefA, aadE, ant(9)-1, ermB and cfxA2. This study characterized the baseline resistome, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures. The microbiome hierarchical analysis resulted in a cluster tree with a highly similar pattern to that of the accessory resistome cluster tree. Functional capacity profiling identified genes associated with horizontal gene transfer. We identified a statistically significant positive correlation between the total antibiotic resistome and suggested indicator genes, which agree with using these genes as indicators of the total resistomes. The correlation between total resistome and total microbiome in this study was positive and statistically significant. Therefore, the microbiome composition influenced the resistome composition. This study identified a core and accessory resistome present in a cohort of healthy pigs, in the same conditions without antibiotics. It highlights the presence of antibiotic resistance in the absence of antibiotic selective pressure and the variability between animals even under the same housing, food and living conditions. Antibiotic resistance will remain in the healthy pig gut even when antibiotics are not used. Therefore, the risk of antibiotic resistance transfer from animal faeces to human pathogens or the environment will remain in the absence of antibiotics.
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Affiliation(s)
- Aoife Joyce
- 1 Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Sinead Murphy
- 1 Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Fiona Walsh
- 1 Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
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Bacanlı M, Başaran N. Importance of antibiotic residues in animal food. Food Chem Toxicol 2019; 125:462-466. [DOI: 10.1016/j.fct.2019.01.033] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/25/2023]
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