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Incompatibility Group I1 (IncI1) Plasmids: Their Genetics, Biology, and Public Health Relevance. Microbiol Mol Biol Rev 2021; 85:85/2/e00031-20. [PMID: 33910982 DOI: 10.1128/mmbr.00031-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial plasmids are extrachromosomal genetic elements that often carry antimicrobial resistance (AMR) genes and genes encoding increased virulence and can be transmissible among bacteria by conjugation. One key group of plasmids is the incompatibility group I1 (IncI1) plasmids, which have been isolated from multiple Enterobacteriaceae of food animal origin and clinically ill human patients. The IncI group of plasmids were initially characterized due to their sensitivity to the filamentous bacteriophage If1. Two prototypical IncI1 plasmids, R64 and pColIb-P9, have been extensively studied, and the plasmids consist of unique regions associated with plasmid replication, plasmid stability/maintenance, transfer machinery apparatus, single-stranded DNA transfer, and antimicrobial resistance. IncI1 plasmids are somewhat unique in that they encode two types of sex pili, a thick, rigid pilus necessary for mating and a thin, flexible pilus that helps stabilize bacteria for plasmid transfer in liquid environments. A key public health concern with IncI1 plasmids is their ability to carry antimicrobial resistance genes, including those associated with critically important antimicrobials used to treat severe cases of enteric infections, including the third-generation cephalosporins. Because of the potential importance of these plasmids, this review focuses on the distribution of the plasmids, their phenotypic characteristics associated with antimicrobial resistance and virulence, and their replication, maintenance, and transfer.
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Basbas C, Byrne BA, Chigerwe M, Escobar ED, Hodzic E, Pires AFA, Pereira RV. Detection of Cephalosporin and Fluoroquinolone Resistance Genes via Novel Multiplex qPCR in Fecal Salmonella Isolates From Northern Californian Dairy Cattle, 2002-2016. Front Microbiol 2021; 12:601924. [PMID: 33658984 PMCID: PMC7917062 DOI: 10.3389/fmicb.2021.601924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/20/2021] [Indexed: 01/01/2023] Open
Abstract
The objectives of this study were to evaluate the prevalence of extended spectrum β-lactamase (ESBL) genes, AmpC-type β-lactamase (ACBL) genes, and plasmid mediated quinolone resistance (PMQR) genes in Salmonella isolated at a Veterinary Medical Teaching Hospital microbiology laboratory, examine trends in presence of these resistance genes, and to explore the correlation between phenotypic resistance and presence of specific genes. The presence of ESBL, ACBL, and PMQR genes were detected using a single, novel multiplex qPCR. Only the genes blaCMY–2 and blaTEM were detected in the 110 Salmonella isolates tested. PMQR genes were not detected in isolates screened. Of 94 third-generation cephalosporin resistant isolates, representing eight serotypes, 48% (n = 45) were positive for blaCMY–2 only and 50% (n = 47) were simultaneously positive for blaCMY–2 and blaTEM. Two third-generation cephalosporin resistant isolates were tested negative for all β-lactamase genes in our qPCR assay and likely house ESBL genes not screened for by our qPCR assay. A logistic regression model revealed that for serotype Dublin isolates (n = 38) the odds ratio for testing positive for blaTEM when compared to all other serotypes was 51.6 (95% CI: 4.01–664.03, p = 0.0029). For serotype Typhimurium (n = 9) the odds ratio for testing positive for blaTEM when compared to all other serotypes was 43.3 (95% CI: 1.76–1000, p = 0.0216). Overall, our results suggest that the prevalence of resistance to cephalosporins and fluoroquinolones due to ESBLs, ACBLs, and PMQR genes present in bovine nontyphoidal Salmonella enterica isolates has remained relatively constant in the isolates screened over a 14-year period.
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Affiliation(s)
- Carl Basbas
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Barbara A Byrne
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Munashe Chigerwe
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Edlin D Escobar
- Real-Time PCR Research and Diagnostics Core Facility, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Emir Hodzic
- Real-Time PCR Research and Diagnostics Core Facility, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Alda F A Pires
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Richard V Pereira
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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Dantas Palmeira J, Ferreira HMN. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production - a threat around the world. Heliyon 2020; 6:e03206. [PMID: 32042963 PMCID: PMC7002838 DOI: 10.1016/j.heliyon.2020.e03206] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/01/2019] [Accepted: 01/09/2020] [Indexed: 01/19/2023] Open
Abstract
Food producing animal is a global challenge in terms of antimicrobial resistance spread. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are relevant opportunistic pathogens that may spread in many ecological niches of the One Health approach as human, animal and environment due to intestinal selection of antimicrobial resistant commensals in food production animals. Cattle production is a relevant ecological niche for selection of commensal bacteria with antimicrobial resistance from microbiota. Enterobacteriaceae show importance in terms of circulation of resistant-bacteria and antimicrobial resistance genes via food chain creating a resistance reservoir, setting up a threat for colonization of humans and consequent health risk. ESBL-producing Enterobacteriaceae are a threat in terms of human health responsible for life threatening outbreaks and silent enteric colonization of community populations namely the elder population. Food associated colonization is a risk difficult to handle and control. In a time of globalization of food trading, population intestinal colonization is a mirror of food production and in that sense this work aims to make a picture of ESBL-producing Enterobacteriaceae in animal production for food over the world in order to make some light in this reality of selection of resistant threats in food producing animal.
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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
| | - 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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Melo LC, Haenni M, Saras E, Cerdeira L, Moura Q, Boulouis HJ, Madec JY, Lincopan N. Genomic characterisation of a multidrug-resistant TEM-52b extended-spectrum β-lactamase-positive Escherichia coli ST219 isolated from a cat in France. J Glob Antimicrob Resist 2019; 18:223-224. [PMID: 31325616 DOI: 10.1016/j.jgar.2019.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 07/05/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES TEM-52 extended-spectrum β-lactamases (ESBLs) have been detected in members of the Enterobacteriaceae isolated from human and non-human reservoirs, mainly in European countries. Here we report the first draft genome of a multidrug-resistant TEM-52b-positive Escherichia coli isolated from a companion animal in France. METHODS Whole genomic DNA from E. coli 39590 was extracted and was sequenced using an Illumina NextSeq platform. De novo genome assembly was performed using Velvet v.1.2.10 and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline v.3.2. Genomic analyses were performed through bioinformatics tools from the Center for Genomic Epidemiology. RESULTS The genome size was calculated as 5362108bp, with 5268 protein-coding sequences and a GC content of 50.5%. E. coli strain 39590 belonged to ST219, serotype O4:H34 and phylogroup E. The antimicrobial resistome consisted of genes encoding resistance to β-lactams (blaTEM-52b), aminoglycosides [aph(3″)-Ib, aph(6)-Id, aadA2, aadA24], phenicols (catA1), sulfonamides (sul1, sul2), trimethoprim (dfrA1, dfrA14), lincosamides (lnuG) and tetracycline (tetA) as well as mutations in gyrA (Ser83Leu, Asp87Asn) and parC (Ser80Ile) conferring resistance to quinolones. Virulome analysis revealed iss, astA and eilA genes, and IncQ1, IncX4, IncX1, IncFIB and IncFIC plasmid incompatibility groups were identified. CONCLUSION This draft genome can be used as a reference sequence for comparative studies using human and non-human E. coli isolates to identify genetic events that have contributed to pathogenicity and adaptation of TEM-52-producing E. coli clones at the human-animal interface as well as to elucidate dynamics of the spread of blaTEM-52 ESBL genes.
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Affiliation(s)
- Luana C Melo
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil.
| | - Marisa Haenni
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Estelle Saras
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Louise Cerdeira
- Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil
| | - Henri-Jean Boulouis
- Université Paris-Est, Ecole Nationale Vétérinaire d'Alfort, Centre Hospitalier Universitaire Vétérinaire d'Alfort (CHUVA), Maisons-Alfort, France
| | - Jean-Yves Madec
- Université de Lyon - Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, (ANSES), Lyon, France
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo, São Paulo, Brazil.
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Carattoli A, Villa L, Fortini D, García-Fernández A. Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae. Plasmid 2018; 118:102392. [PMID: 30529488 DOI: 10.1016/j.plasmid.2018.12.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 11/22/2018] [Accepted: 12/05/2018] [Indexed: 10/27/2022]
Abstract
IncI1 has become one of the most common plasmid families in contemporary Enterobacteriaceae from both human and animal sources. In clinical epidemiology, this plasmid type ranks first as the confirmed vehicle of transmission of extended spectrum beta-lactamase and plasmid AmpC genes in isolates from food-producing animals. In this review, we describe the epidemiology and evolution of IncI1 plasmids and closely related IncIγ plasmids. We highlight the emergence of epidemic plasmids circulating among different bacterial hosts in geographically distant countries, and we address the phylogeny of the IncI1 and IncIγ family based on plasmid Multilocus Sequence Typing.
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Affiliation(s)
- Alessandra Carattoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Daniela Fortini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Aurora García-Fernández
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Castellanos M, Decré D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E. Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins. Microb Genom 2018; 4. [PMID: 30080134 PMCID: PMC6202452 DOI: 10.1099/mgen.0.000203] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic history of the parental strains. Finer scale analysis of the more abundant clusters IncF and IncI1 showed that ESBL-encoding plasmids and plasmids isolated before the use of 3GCs had the same diversity and phylogenetic history, and that acquisition of ESBL-encoding genes had occurred during multiple independent events. Moreover, the blaCTX-M-15 gene, unlike other CTX-M genes, was inserted at a hot spot in a blaTEM-1-Tn2 transposon. These findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of blaCTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmids that carry a Tn2-blaTEM-1 transposon.
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Affiliation(s)
- Catherine Branger
- 1IAME, UMR1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, UFR de Medecine, 16 Rue Henri Huchard, Paris 75018, France
| | - Alice Ledda
- 2Department of Infectious Disease Epidemiology, Imperial College, London, W2 1PG, UK
| | | | - Benoît Doublet
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Stéphanie Fouteau
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - Valérie Barbe
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - David Roche
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Stéphane Cruveiller
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Claudine Médigue
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Miguel Castellanos
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Dominique Decré
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Laurence Drieux-Rouze
- 9APHP, Hôpital de la Pitié-Salpêtrière Service de Bactériologie-Hygiène, 75015, Paris, France
| | - Olivier Clermont
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Jérémy Glodt
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Olivier Tenaillon
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Axel Cloeckaert
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Guillaume Arlet
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Erick Denamur
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
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Casella T, Nogueira MCL, Saras E, Haenni M, Madec JY. High prevalence of ESBLs in retail chicken meat despite reduced use of antimicrobials in chicken production, France. Int J Food Microbiol 2017; 257:271-275. [DOI: 10.1016/j.ijfoodmicro.2017.07.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/02/2017] [Accepted: 07/05/2017] [Indexed: 11/26/2022]
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Haenni M, Châtre P, Métayer V, Bour M, Signol E, Madec JY, Gay E. Comparative prevalence and characterization of ESBL-producing Enterobacteriaceae in dominant versus subdominant enteric flora in veal calves at slaughterhouse, France. Vet Microbiol 2014; 171:321-7. [PMID: 24629776 DOI: 10.1016/j.vetmic.2014.02.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/11/2014] [Accepted: 02/14/2014] [Indexed: 11/29/2022]
Abstract
Food-producing animals have become a growing reservoir of Extended-Spectrum Beta-Lactamase (ESBL)-producing bacteria. In cattle, veal calves are exposed to high amounts of antibiotics but ESBL prevalence data are still limited compared to other food sectors such as poultry production. Based on the investigation of 491 veal calves from different slaughtering batches at 12 abattoirs, this study shows a prevalence of 29.4% of ESBL producers in the faecal flora of veal calves in France in 2012. A variety of blaCTX-M genes was found, reflecting possible diverse pathways of dissemination in cattle. Another major conclusion is the comparison of the ESBL prevalence in the dominant versus sub-dominant Escherichia coli population of the same calves (1% and 29.4%, respectively). Also, the ESBL E. coli clones in the sub-dominant flora mostly differed from the non-ESBL dominant E. coli clones of the same calves. Of note, the distribution of blaCTX-M genes and E. coli phylogroups were similar to the ones previously found in ESBL E. coli clones from diseased calves. The hypothesis that ESBL genes may distribute more abundantly in certain backgrounds of E. coli was also discussed. In all, as recently reported in the Netherlands, these results strongly suggest a recent increase in the prevalence of ESBL carriage in French veal calves, which should be considered one of the major ESBL reservoirs in food animals.
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Affiliation(s)
- Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France.
| | - Pierre Châtre
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France
| | - Véronique Métayer
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France
| | - Maxime Bour
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France
| | - Elodie Signol
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France
| | - Emilie Gay
- Unité Epidémiologie, ANSES Site de Lyon, 31 avenue Tony Garnier, 69364 Lyon, France
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Doublet B, Praud K, Nguyen-Ho-Bao T, Argudin MA, Bertrand S, Butaye P, Cloeckaert A. Extended-spectrum -lactamase- and AmpC -lactamase-producing D-tartrate-positive Salmonella enterica serovar Paratyphi B from broilers and human patients in Belgium, 2008-10. J Antimicrob Chemother 2013; 69:1257-64. [DOI: 10.1093/jac/dkt504] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Hordijk J, Wagenaar JA, Kant A, van Essen-Zandbergen A, Dierikx C, Veldman K, Wit B, Mevius D. Cross-sectional study on prevalence and molecular characteristics of plasmid mediated ESBL/AmpC-producing Escherichia coli isolated from veal calves at slaughter. PLoS One 2013; 8:e65681. [PMID: 23724148 PMCID: PMC3665799 DOI: 10.1371/journal.pone.0065681] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/25/2013] [Indexed: 11/18/2022] Open
Abstract
Objectives The presence of ESBL/AmpC-producing E. coli in cattle has been reported previously, however information on veal calves is limited. This study describes the prevalence and molecular characteristics of E. coli with non-wild type susceptibility to cefotaxime in veal calves at slaughter. Methods Faecal samples from 100 herds, 10 individual animals per herd, were screened for E. coli with non-wild type susceptibility for cefotaxime. Molecular characterization of ESBL/AmpC genes and plasmids was performed on one isolate per herd by microarray, PCR and sequence analysis. Results 66% of the herds were positive for E. coli with non-wild type susceptibility for cefotaxime. Within-herd prevalence varied from zero to 90%. 83% of E. coli producing ESBL/AmpC carried blaCTX-M genes, of which blaCTX-M-1, blaCTX-M-14 and blaCTX-M-15 were most prevalent. The dominant plasmids were IncI1 and IncF-type plasmids. Conclusions A relatively high prevalence of various blaCTX-M producing E. coli was found in veal calves at slaughter. The genes were mainly located on IncI1 and IncF plasmids.
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Affiliation(s)
- Joost Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Coupland P, Chandra T, Quail M, Reik W, Swerdlow H. Direct sequencing of small genomes on the Pacific Biosciences RS without library preparation. Biotechniques 2013; 53:365-72. [PMID: 23227987 DOI: 10.2144/000113962] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/12/2012] [Indexed: 01/25/2023] Open
Abstract
We have developed a sequencing method on the Pacific Biosciences RS sequencer (the PacBio) for small DNA molecules that avoids the need for a standard library preparation. To date this approach has been applied toward sequencing single-stranded and double-stranded viral genomes, bacterial plasmids, plasmid vector models for DNA-modification analysis, and linear DNA fragments covering an entire bacterial genome. Using direct sequencing it is possible to generate sequence data from as little as 1 ng of DNA, offering a significant advantage over current protocols which typically require 400-500 ng of sheared DNA for the library preparation.
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Extended-spectrum cephalosporin-resistant Gram-negative organisms in livestock: an emerging problem for human health? Drug Resist Updat 2013; 16:22-45. [PMID: 23395305 DOI: 10.1016/j.drup.2012.12.001] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 12/22/2012] [Indexed: 12/18/2022]
Abstract
Escherichia coli, Salmonella spp. and Acinetobacter spp. are important human pathogens. Serious infections due to these organisms are usually treated with extended-spectrum cephalosporins (ESCs). However, in the past two decades we have faced a rapid increasing of infections and colonization caused by ESC-resistant (ESC-R) isolates due to production of extended-spectrum-β-lactamases (ESBLs), plasmid-mediated AmpCs (pAmpCs) and/or carbapenemase enzymes. This situation limits drastically our therapeutic armamentarium and puts under peril the human health. Animals are considered as potential reservoirs of multidrug-resistant (MDR) Gram-negative organisms. The massive and indiscriminate use of antibiotics in veterinary medicine has contributed to the selection of ESC-R E. coli, ESC-R Salmonella spp. and, to less extent, MDR Acinetobacter spp. among animals, food, and environment. This complex scenario is responsible for the expansion of these MDR organisms which may have life-threatening clinical significance. Nowadays, the prevalence of food-producing animals carrying ESC-R E. coli and ESC-R Salmonella (especially those producing CTX-M-type ESBLs and the CMY-2 pAmpC) has reached worryingly high values. More recently, the appearance of carbapenem-resistant isolates (i.e., VIM-1-producing Enterobacteriaceae and NDM-1 or OXA-23-producing Acinetobacter spp.) in livestock has even drawn greater concerns. In this review, we describe the aspects related to the spread of the above MDR organisms among pigs, cattle, and poultry, focusing on epidemiology, molecular mechanisms of resistance, impact of antibiotic use, and strategies to contain the overall problem. The link and the impact of ESC-R organisms of livestock origin for the human scenario are also discussed.
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