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Mondal AH, Khare K, Saxena P, Debnath P, Mukhopadhyay K, Yadav D. A Review on Colistin Resistance: An Antibiotic of Last Resort. Microorganisms 2024; 12:772. [PMID: 38674716 PMCID: PMC11051878 DOI: 10.3390/microorganisms12040772] [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: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Antibiotic resistance has emerged as a significant global public health issue, driven by the rapid adaptation of microorganisms to commonly prescribed antibiotics. Colistin, previously regarded as a last-resort antibiotic for treating infections caused by Gram-negative bacteria, is increasingly becoming resistant due to chromosomal mutations and the acquisition of resistance genes carried by plasmids, particularly the mcr genes. The mobile colistin resistance gene (mcr-1) was first discovered in E. coli from China in 2016. Since that time, studies have reported different variants of mcr genes ranging from mcr-1 to mcr-10, mainly in Enterobacteriaceae from various parts of the world, which is a major concern for public health. The co-presence of colistin-resistant genes with other antibiotic resistance determinants further complicates treatment strategies and underscores the urgent need for enhanced surveillance and antimicrobial stewardship efforts. Therefore, understanding the mechanisms driving colistin resistance and monitoring its global prevalence are essential steps in addressing the growing threat of antimicrobial resistance and preserving the efficacy of existing antibiotics. This review underscores the critical role of colistin as a last-choice antibiotic, elucidates the mechanisms of colistin resistance and the dissemination of resistant genes, explores the global prevalence of mcr genes, and evaluates the current detection methods for colistin-resistant bacteria. The objective is to shed light on these key aspects with strategies for combating the growing threat of resistance to antibiotics.
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Affiliation(s)
- Aftab Hossain Mondal
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kriti Khare
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Prachika Saxena
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Parbati Debnath
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kasturi Mukhopadhyay
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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Shahzad S, Willcox MDP, Rayamajhee B. A Review of Resistance to Polymyxins and Evolving Mobile Colistin Resistance Gene ( mcr) among Pathogens of Clinical Significance. Antibiotics (Basel) 2023; 12:1597. [PMID: 37998799 PMCID: PMC10668746 DOI: 10.3390/antibiotics12111597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023] Open
Abstract
The global rise in antibiotic resistance in bacteria poses a major challenge in treating infectious diseases. Polymyxins (e.g., polymyxin B and colistin) are last-resort antibiotics against resistant Gram-negative bacteria, but the effectiveness of polymyxins is decreasing due to widespread resistance among clinical isolates. The aim of this literature review was to decipher the evolving mechanisms of resistance to polymyxins among pathogens of clinical significance. We deciphered the molecular determinants of polymyxin resistance, including distinct intrinsic molecular pathways of resistance as well as evolutionary characteristics of mobile colistin resistance. Among clinical isolates, Acinetobacter stains represent a diversified evolution of resistance, with distinct molecular mechanisms of intrinsic resistance including naxD, lpxACD, and stkR gene deletion. On the other hand, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa are usually resistant via the PhoP-PhoQ and PmrA-PmrB pathways. Molecular evolutionary analysis of mcr genes was undertaken to show relative relatedness across the ten main lineages. Understanding the molecular determinants of resistance to polymyxins may help develop suitable and effective methods for detecting polymyxin resistance determinants and the development of novel antimicrobial molecules.
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Affiliation(s)
- Shakeel Shahzad
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
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Schumann A, Cohn AR, Gaballa A, Wiedmann M. Escherichia coli B-Strains Are Intrinsically Resistant to Colistin and Not Suitable for Characterization and Identification of mcr Genes. Microbiol Spectr 2023; 11:e0089423. [PMID: 37199645 PMCID: PMC10269513 DOI: 10.1128/spectrum.00894-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/24/2023] [Indexed: 05/19/2023] Open
Abstract
Antimicrobial resistance is an increasing threat to human and animal health. Due to the rise of multi-, extensive, and pandrug resistance, last resort antibiotics, such as colistin, are extremely important in human medicine. While the distribution of colistin resistance genes can be tracked through sequencing methods, phenotypic characterization of putative antimicrobial resistance (AMR) genes is still important to confirm the phenotype conferred by different genes. While heterologous expression of AMR genes (e.g., in Escherichia coli) is a common approach, so far, no standard methods for heterologous expression and characterization of mcr genes exist. E. coli B-strains, designed for optimum protein expression, are frequently utilized. Here, we report that four E. coli B-strains are intrinsically resistant to colistin (MIC 8-16 μg/mL). The three tested B-strains that encode T7 RNA polymerase show growth defects when transformed with empty or mcr-expressing pET17b plasmids and grown in the presence of IPTG; K-12 or B-strains without T7 RNA polymerase do not show these growth defects. E. coli SHuffle T7 express carrying empty pET17b also skips wells in colistin MIC assays in the presence of IPTG. These phenotypes could explain why B-strains were erroneously reported as colistin susceptible. Analysis of existing genome data identified one nonsynonymous change in each pmrA and pmrB in all four E. coli B-strains; the E121K change in PmrB has previously been linked to intrinsic colistin resistance. We conclude that E. coli B-strains are not appropriate heterologous expression hosts for identification and characterization of mcr genes. IMPORTANCE Given the rise in multidrug, extensive drug, and pandrug resistance in bacteria and the increasing use of colistin to treat human infections, occurrence of mcr genes threatens human health, and characterization of these resistance genes becomes more important. We show that three commonly used heterologous expression strains are intrinsically resistant to colistin. This is important because these strains have previously been used to characterize and identify new mobile colistin resistance (mcr) genes. We also show that expression plasmids (i.e., pET17b) without inserts cause cell viability defects when carried by B-strains with T7 RNA polymerase and grown in the presence of IPTG. Our findings are important as they will facilitate improved selection of heterologous strains and plasmid combinations for characterizing AMR genes, which will be particularly important with a shift to Culture-independent diagnostic tests where bacterial isolates become increasingly less available for characterization.
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Affiliation(s)
- Anna Schumann
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Biomedical and Biological Sciences, Cornell University, Ithaca, New York, USA
| | - Alexa R. Cohn
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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Gaballa A, Wiedmann M, Carroll LM. More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases. Front Cell Infect Microbiol 2023; 13:1060519. [PMID: 37360531 PMCID: PMC10285318 DOI: 10.3389/fcimb.2023.1060519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.
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Affiliation(s)
- Ahmed Gaballa
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | - Laura M. Carroll
- Department of Clinical Microbiology, SciLifeLab, Umeå University, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
- Integrated Science Lab, Umeå University, Umeå, Sweden
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Mmatli M, Mbelle NM, Osei Sekyere J. Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update. Front Cell Infect Microbiol 2022; 12:941358. [PMID: 36093193 PMCID: PMC9462459 DOI: 10.3389/fcimb.2022.941358] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022] Open
Abstract
Background Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane. Results and discussion Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI2 conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins. Conclusion The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
- Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
- *Correspondence: John Osei Sekyere, ;
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Fortini D, Owczarek S, Dionisi AM, Lucarelli C, Arena S, Carattoli A, Villa L, García-Fernández A. Colistin Resistance Mechanisms in Human Salmonella enterica Strains Isolated by the National Surveillance Enter-Net Italia (2016–2018). Antibiotics (Basel) 2022; 11:antibiotics11010102. [PMID: 35052978 PMCID: PMC8772777 DOI: 10.3390/antibiotics11010102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Background: A collection of human-epidemiologically unrelated S. enterica strains collected over a 3-year period (2016 to 2018) in Italy by the national surveillance Enter-Net Italia was analysed. Methods: Antimicrobial susceptibility tests, including the determination of minimal inhibitory concentrations (MICs) for colistin, were performed. Colistin resistant strains were analysed by PCR to detect mobile colistin resistance (mcr) genes. In mcr-negative S. enterica serovar Enteritidis strains, chromosomal mutations potentially involved in colistin resistance were identified by a genomic approach. Results: The prevalence of colistin-resistant S. enterica strains was 7.7%, the majority (87.5%) were S. Enteritidis. mcr genes were identified only in one strain, a S. Typhimurium monophasic variant, positive for both mcr-1.1 and mcr-5.1 genes in an IncHI2 ST4 plasmid. Several chromosomal mutations were identified in the colistin-resistant mcr-negative S. Enteritidis strains in proteins involved in lipopolysaccharide and outer membrane synthesis and modification (RfbN, LolB, ZraR) and in a component of a multidrug efflux pump (MdsC). These mutated proteins were defined as possible candidates for colistin resistance in mcr-negative S. Enteritidis of our collection. Conclusions: The colistin national surveillance in Salmonella spp. in humans, implemented with genomic-based surveillance, permitted to monitor colistin resistance, determining the prevalence of mcr determinants and the study of new candidate mechanisms for colistin resistance.
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Affiliation(s)
- Daniela Fortini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Slawomir Owczarek
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Anna Maria Dionisi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Claudia Lucarelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Sergio Arena
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Alessandra Carattoli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy;
| | | | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Aurora García-Fernández
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
- Correspondence:
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Stosic MS, Leangapichart T, Lunha K, Jiwakanon J, Angkititrakul S, Järhult JD, Magnusson U, Sunde M. Novel mcr-3.40 variant co-located with mcr-2.3 and blaCTX-M-63 on an IncHI1B/IncFIB plasmid found in Klebsiella pneumoniae from a healthy carrier in Thailand. J Antimicrob Chemother 2021; 76:2218-2220. [PMID: 34015105 PMCID: PMC8283730 DOI: 10.1093/jac/dkab147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/17/2021] [Indexed: 01/06/2023] Open
Affiliation(s)
- Milan S Stosic
- Section for Food Safety and Animal Health Research, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Thongpan Leangapichart
- Section for Food Safety and Animal Health Research, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Kamonwan Lunha
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jatesada Jiwakanon
- Research Group for Animal Health Technology, Khon Kaen University, Khon Kaen, Thailand
| | | | - Josef D Järhult
- Zoonosis Science Centre, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Ulf Magnusson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marianne Sunde
- Section for Food Safety and Animal Health Research, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
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Ingle DJ, Ambrose RL, Baines SL, Duchene S, Gonçalves da Silva A, Lee DYJ, Jones M, Valcanis M, Taiaroa G, Ballard SA, Kirk MD, Howden BP, Pearson JS, Williamson DA. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia. Nat Commun 2021; 12:4786. [PMID: 34373455 PMCID: PMC8352879 DOI: 10.1038/s41467-021-25073-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
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Affiliation(s)
- Danielle J Ingle
- Research School of Population Health, Australian National University, Canberra, ACT, Australia.
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Rebecca L Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Darren Y J Lee
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miriam Jones
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martyn D Kirk
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia.
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Mobilized colistin resistance (mcr) genes from 1 to 10: a comprehensive review. Mol Biol Rep 2021; 48:2897-2907. [PMID: 33839987 DOI: 10.1007/s11033-021-06307-y] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/19/2021] [Indexed: 01/17/2023]
Abstract
At the present time, the polymyxin antibiotic colistin is considered a last-line treatment option for severe human infections caused by multi-drug and carbapenem-resistant Gram-negative bacteria. Lately, the vast spread of colistin resistance among bacteria has got great attention worldwide due to its significant role as the last refuge in treating diseases caused by the resistant infectious agents. Therefore, the discovery of plasmid-mediated mobile colistin resistance (mcr) genes raised global public health concerns as they can spread by horizontal transfer and have chances of global dissemination. To date, ten slightly different variants of the mcr-1 gene (mcr-1 to mcr-10) have been identified in different bacteria isolated from animals, foods, farms, humans, and the environment. Therefore, the issue of mcr spread is growing and worsening day after day. In this backdrop, the current article presents an overview of mcr variants, their spread, and the resistance mechanisms they confer. Hence, this paper will advance our knowledge about colistin resistance while supporting the efforts toward better stewardship and proper usage of antimicrobials.
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Prevalence of mobile colistin resistance (mcr) genes in extended-spectrum β-lactamase-producing Escherichia coli isolated from retail raw foods in Nha Trang, Vietnam. Int J Food Microbiol 2021; 346:109164. [PMID: 33813365 DOI: 10.1016/j.ijfoodmicro.2021.109164] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022]
Abstract
The aim of the study was to assess the presence of genes in ESBL-producing E. coli (ESBL-Ec) isolated from retail raw food in Nha Trang, Vietnam. A total of 452 food samples comprising chicken (n = 116), pork (n = 112), fish (n = 112) and shrimp (n = 112) collected between 2015 and 2017 were examined for the prevalence of ESBL-Ec. ESBL-Ec were detected in 46.0% (208/452) of retail food samples, particularly in 66.4% (77/116), 55.4% (62/112), 42.0% (47/112) 19.6% (22/112) of chicken, pork, fish and shrimp, respectively. Sixty-five out of the 208 (31.3%) ESBL-Ec isolates were positive for mcr genes including mcr-1, mcr-3 and both mcr-1 and mcr-3 genes in 56/208 (26.9%), 1/208 (0.5%) and 8/208 (3.9%) isolates, respectively. Particularly, there was higher prevalence of mcr-1 in ESBL-Ec isolates from chicken (53.2%, 41/77) in comparison to shrimp (22.7%, 5/22), pork (11.3%, 7/62) and fish (6.4%, 3/47). mcr-3 gene was detected in co-existence with mcr-1 in ESBL-Ec isolates from shrimp (9.1%, 2/22), pork (8.1%, 5/62) and fish (2.1%, 1/47) but not chicken. The 65 mcr-positive ESBL-Ec (mcr-ESBL-Ec) were colistin-resistant with the MICs of 4-8 μg/mL. All mcr-3 gene-positive isolates belonged to group A, whereas phylogenetic group distribution of isolates harboring only mcr-1 was B1 (44.6%), A (28.6%) and D (26.8%). PFGE analysis showed diverse genotypes, although some isolates demonstrated nearly clonal relationships. S1-PFGE and Southern hybridization illustrated that the mcr-1 and mcr-3 genes were located either on chromosomes or on plasmids. However, the types of mcr genes were harbored on different plasmids with varied sizes of 30-390 kb. Besides, the ESBL genes of CTX-M-1 or CTX-M-9 were also detected to be located on plasmids. Noteworthy, co-location of CTX-M-1 with mcr-1 or mcr-3 genes on the same plasmid was identified. The conjugation experiment indicated that the mcr-1 or mcr-3 was horizontally transferable. All mcr-ESBL-Ec isolates were multidrug resistance (resistance to ≥3 antimicrobial classes). Moreover, β-Lactamase-encoding genes of the CTX-M-1 (78.5%), CTX-M-9 (21.5%), TEM (61.5%) groups were found in mcr-ESBL-Ec. The astA gene was detected in 27 (41.5%) mcr-ESBL-Ec isolates demonstrating their potential virulence. In conclusion, mcr-1 and mcr-3 genes existed individually or concurrently in ESBL-Ec isolates recovered from retail raw food in Nha Trang city, which might further complicate the antimicrobial-resistant situation in Vietnam, and is a possible health risk for human.
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11
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Ortega-Paredes D, de Janon S, Villavicencio F, Ruales KJ, De La Torre K, Villacís JE, Wagenaar JA, Matheu J, Bravo-Vallejo C, Fernández-Moreira E, Vinueza-Burgos C. Broiler Farms and Carcasses Are an Important Reservoir of Multi-Drug Resistant Escherichia coli in Ecuador. Front Vet Sci 2020; 7:547843. [PMID: 33324692 PMCID: PMC7724036 DOI: 10.3389/fvets.2020.547843] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/29/2020] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major health threat for public and animal health in the twenty-first century. In Ecuador, antibiotics have been used by the poultry industry for decades resulting in the presence of multi-drug resistant (MDR) bacteria in the poultry meat production chain, with the consequent risk for public health. This study evaluated the prevalence of ESBL/AmpC and mcr genes in third-generation cephalosporin-resistant Escherichia coli (3GC-R E. coli) isolated from broiler farms (animal component), broiler carcasses (food component), and human enteritis (human component) in Quito-Ecuador. Samples were collected weekly from November 2017 to November 2018. For the animal, food, and human components, 133, 335, and 302 samples were analyzed, respectively. Profiles of antimicrobial resistance were analyzed by an automated microdilution system. Resistance genes were studied by PCR and Sanger sequencing. From all samples, 122 (91.7%), 258 (77%), and 146 (48.3%) samples were positive for 3GC-R E. coli in the animal, food, and human components, respectively. Most of the isolates (472/526, 89.7%) presented MDR phenotypes. The ESBL blaCTX-M-55, blaCTX-M-3, blaCTX-M-15, blaCTX-M-65, blaCTX-M-27, and blaCTX-M-14 were the most prevalent ESBL genes while blaCMY-2 was the only AmpC detected gene. The mcr-1 gene was found in 20 (16.4%), 26 (10.1%), and 3 (2.1%) of isolates from animal, food, and human components, respectively. The implication of poultry products in the prevalence of ESBL/AmpC and mcr genes in 3GC-R must be considered in the surveillance of antimicrobial resistance.
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Affiliation(s)
- David Ortega-Paredes
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
| | - Sofía de Janon
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
| | - Fernando Villavicencio
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - Katherine Jaramillo Ruales
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador
| | - Kenny De La Torre
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - José E Villacís
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos, Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Quito, Ecuador.,Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Jaap A Wagenaar
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Jorge Matheu
- Department of Food Safety and Zoonoses, World Health Organization, Geneva, Switzerland
| | - Camila Bravo-Vallejo
- Hospital General del Sur Quito-Instituto Ecuatoriano de Seguridad Social (IESS), Quito, Ecuador
| | | | - Christian Vinueza-Burgos
- Unidad de Investigación de Enfermedades Transmitidas por Alimentos y Resistencia a los Antimicrobianos (UNIETAR), Facultad de Medicina Veterinaria y Zootecnia, Universidad Central del Ecuador, Quito, Ecuador
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12
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IS Kpn40-Mediated Mobilization of the Colistin Resistance Gene mcr-3.11 in Escherichia coli. Antimicrob Agents Chemother 2020; 64:AAC.00851-20. [PMID: 32660996 DOI: 10.1128/aac.00851-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/26/2020] [Indexed: 11/20/2022] Open
Abstract
The mobile colistin resistance gene mcr-3 has globally disseminated since it was first reported in 2017 in Escherichia coli In vitro mobilization assays in this study demonstrate the functionality of the composite transposon structure ISKpn40-mcr-3.11-dgkA-ISKpn40 in wild-type and recA - E. coli strains. These transpositions generated 4-bp duplications at the target sites. This is the first report demonstrating the mobility of the mcr-3.11 gene by transposition.
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13
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Li R, Zhang P, Yang X, Wang Z, Fanning S, Wang J, Du P, Bai L. Identification of a novel hybrid plasmid coproducing MCR-1 and MCR-3 variant from an Escherichia coli strain. J Antimicrob Chemother 2020; 74:1517-1520. [PMID: 30793748 DOI: 10.1093/jac/dkz058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To characterize the genome of an Escherichia coli harbouring both mcr-1 and mcr-3.19 on a hybrid plasmid and the underlying transmission mechanisms. METHODS Broth microdilution was used to perform antimicrobial susceptibility testing. Conjugation assays and S1-PFGE were used to assess the transferability of mcr genes. Resistance genotypes and genetic contexts were investigated, based on WGS data from the Illumina and MinION platforms. Inverse PCR was performed to test the mcr-3.19-bearing circular intermediate. Bioinformatic tools were used to further characterize the hybrid plasmid. RESULTS E. coli CP53 was identified as harbouring both mcr-1 and mcr-3.19 on a 231 859 bp hybrid plasmid pCP53-mcr1_3 containing IncFIA, IncHI1A, IncHI1B and IncN replicons. The genetic structures of mcr-1 and mcr-3.19 were similar to those reported in other mcr-1 and mcr-3.19-bearing plasmids, which suggested that recombination between mcr-bearing plasmids had been mediated by ISs. However, the MDR plasmid pCP53-mcr1_3 cannot transfer via conjugation. Furthermore, another three plasmids were identified in the isolate, two of which encoded resistance genes. In640 duplication between two MDR plasmids was observed. An MDR-region recombination existed in E. coli CP53. A core structure consisting of mcr-3-dgkA existed in mcr-3-bearing plasmids reported, to date. Circular intermediates were observed for mcr-1 and mcr-3.19 regions. CONCLUSIONS A novel mcr-3.19 was identified along with mcr-1 contained in a hybrid plasmid. This finding suggested that evolution of mcr genes among various plasmids was being driven by mobile elements. Molecular surveillance of mcr gene co-occurrence warrants further investigation to evaluate the public health risk.
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Affiliation(s)
- Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
| | - Pei Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Nutrition, School of Public Health, Sun Yat-Sen University, Guangzhou, P. R. China.,Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, P. R. China
| | - Xiaorong Yang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, P. R. China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
| | - Séamus Fanning
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, P. R. China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, Shaanxi, P. R. China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, P. R. China
| | - Li Bai
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, P. R. China
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14
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Sia CM, Greig DR, Day M, Hartman H, Painset A, Doumith M, Meunier D, Jenkins C, Chattaway MA, Hopkins KL, Woodford N, Godbole G, Dallman TJ. The characterization of mobile colistin resistance ( mcr) genes among 33 000 Salmonella enterica genomes from routine public health surveillance in England. Microb Genom 2020; 6:e000331. [PMID: 32003708 PMCID: PMC7067213 DOI: 10.1099/mgen.0.000331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/05/2020] [Indexed: 12/15/2022] Open
Abstract
To establish the prevalence of mobile colistin resistance (mcr) genes amongst Salmonella enterica isolates obtained through public health surveillance in England (April 2014 to September 2017), 33 205 S. enterica genome sequences obtained from human, food, animal and environmental isolates were screened for the presence of mcr variants 1 to 8. The mcr-positive genomes were assembled, annotated and characterized according to plasmid type. Nanopore sequencing was performed on six selected isolates with putative novel plasmids, and phylogenetic analysis was used to provide an evolutionary context for the most commonly isolated clones. Fifty-two mcr-positive isolates were identified, of which 32 were positive for mcr-1, 19 for mcr-3 and 1 for mcr-5. The combination of Illumina and Nanopore sequencing identified three novel mcr-3 plasmids and one novel mcr-5 plasmid, as well as the presence of chromosomally integrated mcr-1 and mcr-3. Monophasic S. enterica serovar Typhimurium accounted for 27/52 (52 %) of the mcr-positive isolates, with the majority clustering in clades associated with travel to Southeast Asia. Isolates in these clades were associated with a specific plasmid range and an additional extended-spectrum beta-lactamase genotype. Routine whole-genome sequencing for public health surveillance provides an effective screen for novel and emerging antimicrobial determinants, including mcr. Complementary long-read technologies elucidated the genomic context of resistance determinants, offering insights into plasmid dissemination and linkage to other resistance genes.
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Affiliation(s)
| | - David R. Greig
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Martin Day
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Hassan Hartman
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Anais Painset
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Michel Doumith
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Daniele Meunier
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | | | - Katie L. Hopkins
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Neil Woodford
- National Infection Service, Public Health England, London, NW9 5EQ, UK
| | - Gauri Godbole
- National Infection Service, Public Health England, London, NW9 5EQ, UK
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15
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Hadjadj L, Baron SA, Olaitan AO, Morand S, Rolain JM. Co-occurrence of Variants of mcr-3 and mcr- 8 Genes in a Klebsiella pneumoniae Isolate From Laos. Front Microbiol 2019; 10:2720. [PMID: 31849875 PMCID: PMC6887894 DOI: 10.3389/fmicb.2019.02720] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022] Open
Abstract
Colistin is considered as a last resort antibiotic. The re-use of this antibiotic highlighted the emergence of colistin resistance mediated by chromosomal and plasmidic resistance mechanisms. Five colistin-resistant Klebsiella pneumoniae strains from Laos and Thailand were analyzed by Next Generation Sequencing (NGS) approaches to determine their colistin resistance mechanisms. Antimicrobial susceptibility testing, conjugation and transformation were performed on these strains. Moreover, whole genome sequencing (WGS) combining Illumina (MiSeq) and Oxford Nanopore technologies (MinION) was realized to obtain closed genomes and plasmids. Resistome analyses as well as location of mcr genes and its genetic environments were done in silico. All five strains had colistin MIC of 32 mg/L and were positive for mcr-3 variants including additionally positive for a mcr-8 variant gene. The novel variants were named mcr-3.21, mcr-3.26, mcr-3.28, and mcr-8.3 genes. The mcr-3 variants genes were located on plasmids IncP1, IncFII, and IncI1 type, while mcr-8.3 gene was found on an IncFII type plasmid. The genetic environment of mcr-3.21 and mcr-3.26 genes were composed of a composite transposon ISKpn40- mcr-3-dgkA- ISKpn40. Concerning mcr-8.3 gene, a similar genetic environment of mcr-8.1 gene surrounded by ISIX2 and IS903B was observed. To the best of our knowledge, this is the first description of the novel variants mcr-3.21, mcr-3.26, mcr-3.28 and mcr-8.3 genes as well as the first study on co-occurrence of mcr-3 and mcr-8 genes. Spread and evolution of mcr genes should be monitored.
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Affiliation(s)
- Linda Hadjadj
- Aix Marseille Univ, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- Aix Marseille Univ, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Abiola Olumuyiwa Olaitan
- Aix Marseille Univ, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Serge Morand
- Institut des Sciences de l'Évolution, CNRS-IRD-UM2, CC065, Université Montpellier 2, Montpellier, France
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France.,IHU Méditerranée Infection, Marseille, France.,Assistance Publique des Hôpitaux de Marseille, Marseille, France
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16
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Loss of mcr Genes Mediated by Plasmid Elimination and IS Apl1. Antimicrob Agents Chemother 2019; 63:AAC.01002-19. [PMID: 31209010 DOI: 10.1128/aac.01002-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 06/11/2019] [Indexed: 11/20/2022] Open
Abstract
We characterized the stability of a plasmid pCP53-mcr1_3 encoding mcr-1 and mcr-3.19 with and without colistin exposure during cultural passages via S1-pulsed-field gel electrophoresis (PFGE) and nanopore MinION sequencing. Both mcr-1 and mcr-3.19 were missing in certain subclones, mediated by genetic excision (ISApl1-mcr-1-pap2), and deletions of large multidrug resistance (MDR) regions confirmed by ISApl1 and plasmid elimination. Without colistin exposure, the eradication of mcr genes is feasible, while the factors influencing the elimination processes warrant further study.
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17
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Partridge SR, Di Pilato V, Doi Y, Feldgarden M, Haft DH, Klimke W, Kumar-Singh S, Liu JH, Malhotra-Kumar S, Prasad A, Rossolini GM, Schwarz S, Shen J, Walsh T, Wang Y, Xavier BB. Proposal for assignment of allele numbers for mobile colistin resistance (mcr) genes. J Antimicrob Chemother 2018; 73:2625-2630. [PMID: 30053115 PMCID: PMC6148208 DOI: 10.1093/jac/dky262] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The initial report of the mcr-1 (mobile colistin resistance) gene has led to many reports of mcr-1 variants and other mcr genes from different bacterial species originating from human, animal and environmental samples in different geographical locations. Resistance gene nomenclature is complex and unfortunately problems such as different names being used for the same gene/protein or the same name being used for different genes/proteins are not uncommon. Registries exist for some families, such as bla (β-lactamase) genes, but there is as yet no agreed nomenclature scheme for mcr genes. The National Center for Biotechnology Information (NCBI) recently took over assigning bla allele numbers from the longstanding Lahey β-lactamase website and has agreed to do the same for mcr genes. Here, we propose a nomenclature scheme that we hope will be acceptable to researchers in this area and that will reduce future confusion.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital, New South Wales, Australia
| | - Vincenzo Di Pilato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michael Feldgarden
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Daniel H Haft
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - William Klimke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology & Molecular Pathology group – Cell Biology and Histology, University of Antwerp, Antwerp, Belgium
| | - Jian-Hua Liu
- College of Veterinary Medicine, National Risk Assessment Laboratory for Antimicrobial Resistance of Microorganisms in Animals, South China Agricultural University, Guangzhou, China
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Arjun Prasad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Timothy Walsh
- Department of Medical Microbiology and Infectious Disease, Cardiff University, Cardiff, UK
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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