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Brilhante M, Perreten V, Donà V. Multidrug resistance and multivirulence plasmids in enterotoxigenic and hybrid Shiga toxin-producing/enterotoxigenic Escherichia coli isolated from diarrheic pigs in Switzerland. Vet J 2018; 244:60-68. [PMID: 30825896 DOI: 10.1016/j.tvjl.2018.12.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 01/08/2023]
Abstract
Enterovirulent Escherichia coli infections cause significant losses in the pig industry. However, information about the structures of the virulence and multidrug resistance (MDR) plasmids harboured by these strains is sparse. In this study, we used whole-genome sequencing with PacBio and Illumina platforms to analyse the molecular features of the multidrug-resistant enterotoxigenic E. coli (ETEC) strain 14OD0056 and the multidrug-resistant hybrid Shiga toxin-producing/enterotoxigenic E. coli (STEC/ETEC) strain 15OD0495 isolated from diarrheic pigs in Switzerland. Strain 14OD0056 possessed three virulence plasmids similar to others previously found in ETEC strains, while 15OD0495 harboured a 119-kb multivirulence IncFII/IncX1 hybrid STEC/ETEC plasmid (p15ODTXV) that co-carried virulence genes of both ETEC and STEC pathotypes, confirming the key role of plasmids in the emergence of hybrid pathotypes. All resistance genes of 14OD0056 that conferred resistance to ampicillin (blaTEM-1b), gentamicin (aac(3)-IIa), kanamycin (aph(3')-Ia), sulfonamide (sul1 and sul2), streptomycin (aph(3″)-Ib, aph(6)-Id), tetracycline (tet(B)) and trimethoprim (dfrA1) were identified on a single 207-kb conjugative MDR plasmid of incompatibility group (Inc) IncHI1/IncFIA (p14ODMR). Strain 15OD0495 carried two antimicrobial resistance plasmids (p15ODAR and p15ODMR). The 99-kb IncI1 plasmid p15ODAR harboured only aminoglycoside resistance genes (aac(3)-IIa, aph(3″)-Ib, aph(6)-Id, aph(4)-Ia), whilst the 49-kb IncN MDR plasmid p15ODMR carried genes conferring resistance to ampicillin (blaTEM-1b), sulfonamide (sul2), streptomycin (aph(6)-Id), tetracycline (tet(A)) and trimethoprim (dfrA14). Filter mating assays showed that p14ODMR, p15ODMR and p15ODAR were conjugative at room temperature and 37°C. The co-localization of multiple resistance genes on MDR conjugative plasmids such as p14ODMR and p15ODMR poses the risk of simultaneous selection of several resistance traits during empirical treatment. Thus, preventive strategies and targeted therapy following antibiotic susceptibility testing should be encouraged to avoid further dissemination of such plasmids.
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Affiliation(s)
- M Brilhante
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - V Perreten
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - V Donà
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Touzain F, Le Devendec L, de Boisséson C, Baron S, Jouy E, Perrin-Guyomard A, Blanchard Y, Kempf I. Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers. PLoS One 2018; 13:e0188768. [PMID: 29360838 PMCID: PMC5779644 DOI: 10.1371/journal.pone.0188768] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/13/2017] [Indexed: 12/24/2022] Open
Abstract
Resistance to extended-spectrum cephalosporins (ESC) is a global health issue. The aim of this study was to analyze and compare plasmids coding for resistance to ESC isolated from 16 avian commensal and 17 avian pathogenic Escherichia coli (APEC) strains obtained respectively at slaughterhouse or from diseased broilers in 2010-2012. Plasmid DNA was used to transform E. coli DH5alpha, and the resistances of the transformants were determined. The sequences of the ESC-resistance plasmids prepared from transformants were obtained by Illumina (33 plasmids) or PacBio (1 plasmid). Results showed that 29 of these plasmids contained the blaCTX-M-1 gene and belonged to the IncI1/ST3 type, with 27 and 20 of them carrying the sul2 or tet(A) genes respectively. Despite their diverse origins, several plasmids showed very high percentages of identity. None of the blaCTX-M-1-containing plasmid contained APEC virulence genes, although some of them were detected in the parental strains. Three plasmids had the blaCMY-2 gene, but no other resistance gene. They belonged to IncB/O/K/Z-like or IncFIA/FIB replicon types. The blaCMY-2 IncFIA/FIB plasmid was obtained from a strain isolated from a diseased broiler and also containing a blaCTX-M-1 IncI1/ST3 plasmid. Importantly APEC virulence genes (sitA-D, iucA-D, iutA, hlyF, ompT, etsA-C, iss, iroB-E, iroN, cvaA-C and cvi) were detected on the blaCMY-2 plasmid. In conclusion, our results show the dominance and high similarity of blaCTX-M-1 IncI1/ST3 plasmids, and the worrying presence of APEC virulence genes on a blaCMY-2 plasmid.
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Affiliation(s)
- Fabrice Touzain
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Laetitia Le Devendec
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Claire de Boisséson
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Sandrine Baron
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Eric Jouy
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Agnès Perrin-Guyomard
- Université Bretagne Loire, Rennes, France
- ANSES, Fougères Laboratory, Fougères, France
| | - Yannick Blanchard
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
| | - Isabelle Kempf
- ANSES, Ploufragan Laboratory, Ploufragan, France
- Université Bretagne Loire, Rennes, France
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Knowles M, Stinson S, Lambert D, Carrillo C, Koziol A, Gauthier M, Blais B. Genomic Tools for Customized Recovery and Detection of Foodborne Shiga Toxigenic Escherichia coli. J Food Prot 2016; 79:2066-2077. [PMID: 28221970 DOI: 10.4315/0362-028x.jfp-16-220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Genomic antimicrobial resistance (AMR) prediction tools have the potential to support foodborne illness outbreak investigations through their application in the analysis of bacterial genomes from causative strains. The AMR marker profile of a strain of interest, initially identified in outbreak-associated clinical samples, may serve as the basis for customization of selective enrichment media, facilitating its recovery from samples in a food safety investigation. Different possibilities for AMR analyses include the use of comprehensive AMR gene databases such as the Comprehensive Antibiotic Resistance Database, which can be mined with in-house bioinformatics alignment tools (e.g., Antimicrobial Resistance Marker Identifier), or publicly available tools based on clinically relevant acquired AMR gene databases (e.g., ResFinder). In combination with a previously reported pipeline (SigSeekr) designed to identify specific DNA sequences associated with a particular strain for its rapid identification by PCR, it should be possible to deploy custom recovery and identification tools for the efficient detection of priority pathogens such as Shiga toxigenic Escherichia coli (STEC) outbreak strains within the time frame of an active investigation. Using a laboratory STEC strain as a model, trimethoprim resistance identified by both Antimicrobial Resistance Marker Identifier and ResFinder was used as the basis for its selective recovery against a background of commensal E. coli bacteria in ground beef samples. Enrichment in modified tryptic soy broth containing trimethoprim greatly enhanced the recovery of low numbers of model strain cells inoculated in ground beef samples, as verified by the enumeration of colonies on plating media using a strain-specific PCR method to determine the recovery efficiency for the target strain. We discuss the relative merits of different AMR marker prediction tools for this purpose and describe how such tools can be utilized to good effect in a typical outbreak investigation scenario.
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Affiliation(s)
- Michael Knowles
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Sara Stinson
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Dominic Lambert
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Catherine Carrillo
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Adam Koziol
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Martine Gauthier
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
| | - Burton Blais
- Research and Development Section, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, 960 Carling Avenue, Building 22, Central Experimental Farm, Ottawa, Ontario, Canada K1A 0C6
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Kubasova T, Cejkova D, Matiasovicova J, Sekelova Z, Polansky O, Medvecky M, Rychlik I, Juricova H. Antibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium. Genome Biol Evol 2016; 8:1661-71. [PMID: 27189997 PMCID: PMC5390554 DOI: 10.1093/gbe/evw105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2016] [Indexed: 11/13/2022] Open
Abstract
Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of four IncHI1 plasmids transferring resistance to antibiotics by two different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approximately 123 kbp and 122 genes while the total pan-genome represented approximately 600 kbp. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46% and 50% in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kbp and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host, they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic-resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.
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Affiliation(s)
- Tereza Kubasova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Darina Cejkova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | | | - Zuzana Sekelova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Ondrej Polansky
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Matej Medvecky
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Ivan Rychlik
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
| | - Helena Juricova
- Veterinary Research Institute, Hudcova 70, Brno 621 00, Czech Republic
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