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Sismova P, Sukkar I, Kolidentsev N, Palkovicova J, Chytilova I, Bardon J, Dolejska M, Nesporova K. Plasmid-mediated colistin resistance from fresh meat and slaughtered animals in the Czech Republic: nation-wide surveillance 2020-2021. Microbiol Spectr 2023; 11:e0060923. [PMID: 37698419 PMCID: PMC10580956 DOI: 10.1128/spectrum.00609-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/11/2023] [Indexed: 09/13/2023] Open
Abstract
The aim of this study was to determine the occurrence of plasmid-mediated colistin resistance in domestic and imported meat and slaughter animals in the Czech Republic during 2020-2021 by using selective cultivation and direct PCR testing. A total of 111 colistin-resistant Escherichia coli isolates with mcr-1 gene were obtained from 65 (9.9%, n = 659) samples and subjected to whole-genome sequencing. Isolates with mcr were frequently found in fresh meat from domestic production (14.2%) as well as from import (28.8%). The mcr-1-positive E. coli isolates predominantly originated from meat samples (16.6%), mainly poultry (27.1%), and only minor part of the isolates came from the cecum (1.7%). In contrast to selective cultivation, 205 (31.1%) samples of whole-community DNA were positive for at least one mcr variant, and other genes besides mcr-1 were detected. Analysis of whole-genome data of sequenced E. coli isolates revealed diverse sequence types (STs) including pathogenic lineages and dominance of ST1011 (15.6%) and ST162 (12.8%). Most isolates showed multidrug-resistant profile, and 9% of isolates produced clinically important beta-lactamases. The mcr-1 gene was predominantly located on one of three conjugative plasmids of IncX4 (83.5%), IncI2 (7.3%), and IncHI2 (7.3%) groups. Seventy-two percent isolates of several STs carried ColV plasmids. The study revealed high prevalence of mcr genes in fresh meat of slaughter animals. Our results confirmed previous assumptions that the livestock, especially poultry production, is an important source of colistin-resistant E. coli with the potential of transfer to humans via the food chain. IMPORTANCE We present the first data on nation-wide surveillance of plasmid-mediated colistin resistance in the Czech Republic. High occurrence of plasmid-mediated colistin resistance was found in meat samples, especially in poultry from both domestic production and import, while the presence of mcr genes was lower in the gut of slaughter animals. In contrast to culture-based approach, testing of whole-community DNA showed higher prevalence of mcr and presence of various mcr variants. Our results support the importance of combining cultivation methods with direct culture-independent techniques and highlight the need for harmonized surveillance of plasmid-mediated colistin resistance. Our study confirmed the importance of livestock as a major reservoir of plasmid-mediated colistin resistance and pointed out the risks of poultry meat for the transmission of mcr genes toward humans. We identified several mcr-associated prevalent STs, especially ST1011, which should be monitored further as they represent zoonotic bacteria circulating between different environments.
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Affiliation(s)
- Petra Sismova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Iva Sukkar
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Nikita Kolidentsev
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Jana Palkovicova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
| | | | - Jan Bardon
- Department of Microbiology, Faculty of Medicine and Dentistry Palacky University Olomouc, Olomouc, Czech Republic
- State Veterinary Institute Olomouc, Olomouc, Czech Republic
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, University Hospital Brno, Brno, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Kristina Nesporova
- Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic
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Brouwer MSM, Zandbergen Van Essen A, Kant A, Rapallini M, Harders F, Bossers A, Wullings B, Wit B, Veldman KT. Implementation of WGS analysis of ESBL-producing Escherichia coli within EU AMR monitoring in livestock and meat. J Antimicrob Chemother 2023:7185845. [PMID: 37248737 DOI: 10.1093/jac/dkad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND As WGS comes of age, changes in EU legislation implemented in 2021 allow its usage for systematic monitoring of ESBL-producing Escherichia coli from livestock and meat, replacing phenotypic testing. Presently, phenotypic testing correlates well with antimicrobial resistance predicted from WGS data. WGS has added value in the wealth of additional information that is present in the data. OBJECTIVES In this study we have detected the resistance phenotypes for a panel of antimicrobials while also analysing the molecular epidemiology of ESBL-producing E. coli. METHODS Susceptibility testing was performed with broth microdilution of selectively isolated E. coli. Short-read WGS was performed in parallel and phenotypes predicted based on the sequence data, which was also used to determine the phylogeny of the isolates. RESULTS The phenotypically determined resistance and the predicted resistance correlated 90%-100% for the different antimicrobial classes. Furthermore, clonal relationships were detected amongst ESBL-producing E. coli within livestock sectors and the meat produced by this sector. CONCLUSIONS Further implementation of WGS analysis of ESBL/AmpC-producing E. coli within the AMR monitoring programme of EU member states and global surveillance programmes will contribute to determining the attribution of livestock in the prevalence of ESBL/AmpC-encoding E. coli in humans.
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Affiliation(s)
- Michael S M Brouwer
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Alieda Zandbergen Van Essen
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Arie Kant
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Michel Rapallini
- Department of Bacteriology, Molecular Biology and AMR, Wageningen Food Safety Research part of Wageningen University and Research, Akkermaalsbos 2, Wageningen, The Netherlands
| | - Frank Harders
- Department of Bioinformatics, Epidemiology and Animal Models, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Alex Bossers
- Department of Bioinformatics, Epidemiology and Animal Models, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
| | - Bart Wullings
- Department of Bacteriology, Molecular Biology and AMR, Wageningen Food Safety Research part of Wageningen University and Research, Akkermaalsbos 2, Wageningen, The Netherlands
| | - Ben Wit
- Department of Food Safety, Netherlands Food and Consumer Product Safety Authority (NVWA), Catharijnesingel 59, Utrecht, The Netherlands
| | - Kees T Veldman
- Department of Bacteriology, Host Pathogen Interactions and Diagnostics Development, Wageningen Bioveterinary Research part of Wageningen University and Research, Edelhertweg 39, Lelystad, The Netherlands
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Fajt VR, Lubbers BV. Application and Interpretation of Antimicrobial Susceptibility Testing. Vet Clin North Am Food Anim Pract 2023; 39:115-128. [PMID: 36731992 DOI: 10.1016/j.cvfa.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial susceptibility testing (AST) is an important component of antimicrobial stewardship. This article discusses how AST methods and breakpoints are developed, describes when AST may or may not be useful in clinical practice, and discusses how to interpret AST results from bacterial isolates from cattle, sheep, and goats. Discussion of when AST is not appropriate or when veterinarians should have low confidence in AST results is also included. Applicability of genomic testing for antimicrobial susceptibility is briefly addressed.
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Affiliation(s)
- Virginia R Fajt
- Veterinary Physiology and Pharmacology, Texas A&M University, 4466 TAMU, College Station, TX 77843, USA.
| | - Brian V Lubbers
- Food Animal Therapeutics - Outreach, Kansas State University, P203 Mosier Hall, Manhattan, KS 66506, USA
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SVEPM 2021 — research sharing and networking in times of pandemic: the online Annual Conference of the Society for Veterinary Epidemiology and Preventive Medicine. Prev Vet Med 2022; 202:105611. [DOI: 10.1016/j.prevetmed.2022.105611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/10/2022] [Accepted: 03/14/2022] [Indexed: 11/19/2022]
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