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Liu M, Wu J, Zhao J, Xi Y, Jin Y, Yang H, Chen S, Long J, Duan G. Global epidemiology and genetic diversity of mcr-positive Klebsiella pneumoniae: A systematic review and genomic analysis. ENVIRONMENTAL RESEARCH 2024; 259:119516. [PMID: 38950813 DOI: 10.1016/j.envres.2024.119516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/03/2024]
Abstract
The rapid increase of mcr-positive Klebsiella pneumoniae (K. pneumoniae) has received considerable attention and poses a major public health concern. Here, we systematically analyzed the global distribution of mcr-positive K. pneumoniae isolates based on published articles as well as publicly available genomes. Combining strain information from 78 articles and 673 K. pneumoniae genomes, a total of 1000 mcr-positive K. pneumoniae isolates were identified. We found that mcr-positive K. pneumoniae has disseminated widely worldwide, especially in Asia, with a higher diversity of sequence types (STs). These isolates were disseminated in 57 countries and were associated with 12 different hosts. Most of the isolates were found in China and were isolated from human sources. Moreover, MLST analysis showed that ST15 and ST11 accounted for the majority of mcr-positive K. pneumoniae, which deserve sustained attention in further surveillance programs. mcr-1 and mcr-9 were the dominant mcr variants in mcr-positive K. pneumoniae. Furthermore, a Genome-wide association study (GWAS) demonstrated that mcr-1- and mcr-9-producing genomes exhibited different antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), thereby indicating a distinct evolutionary path. Notably, the phylogenetic analysis suggested that certain mcr-positive K. pneumoniae genomes from various geographical areas and hosts harbored a high degree of genetic similarities (<20 SNPs), suggesting frequent cross-region and cross-host clonal transmission. Overall, our results emphasize the significance of monitoring and exploring the transmission and evolution of mcr-positive K. pneumoniae in the context of "One health".
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Affiliation(s)
- Mengyue Liu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Wu
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaxue Zhao
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yanyan Xi
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Yuefei Jin
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Haiyan Yang
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shuaiyin Chen
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Jinzhao Long
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China.
| | - Guangcai Duan
- Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
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Wang Q, Wang W, Zhu Q, Shoaib M, Chengye W, Zhu Z, Wei X, Bai Y, Zhang J. The prevalent dynamic and genetic characterization of mcr-1 encoding multi-drug resistant Escherichia coli strains recovered from poultry in Hebei, China. J Glob Antimicrob Resist 2024:S2213-7165(24)00071-7. [PMID: 38795771 DOI: 10.1016/j.jgar.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/03/2024] [Accepted: 04/02/2024] [Indexed: 05/28/2024] Open
Abstract
OBJECTIVES Colistin is known as the last resort antibiotic to treat the infections caused by multi-drug resistant (MDR) foodborne pathogens. The emergence and widespread dissemination of plasmid-mediated colistin resistance gene mcr-1 in the E. coli incurs potential threat to public health. Here, we investigated the epidemiology, transmission dynamics, and genetic characterization of mcr-1 harboring E. coli isolates from poultry origin in Hebei province, China. METHODS A total of 297 fecal samples were collected from the two large poultry farms in Hebei province, China. The samples were processed for E. coli identification by MALDI-TOF-MS and 16S rD4A sequencing. Then, mcr-1 gene harboring E. coli strains were identified by PCR and subjected to antimicrobial susceptibility testing by broth microdilution assay. The genomic characterization of the isolates was done by whole genome sequencing using the various bioinformatics tools, and multi-locus sequence typing (MLST) was done by sequence analysis of the seven housekeeping genes. The conjugation experiment was done to check the transferability of mcr-1 along with the plasmid stability testing. RESULTS A total of six mcr-1 E. coli isolates with MIC of 4 μg/mL were identified from 297 samples (2.02%). The mcr-1 harboring E. coli were identified as MDR and belonged to ST101 (n=4) and ST410 (n=2). The genetic environment of mcr-1 presented its position on IncHI2 plasmid in four isolates and p0111 in two isolates which is rarely reported plasmid type for mcr-1. Moreover, both type of plasmids was transferable to recipient J53, and mcr-1 was flanked by three mobile elements ISApl1, Tn3, and IS26 forming a novel backbone Tn3-IS26-mcr-1- pap2-ISApl1 on p0111 plasmid. The phylogenetic analysis shared a common lineage with mcr-1 harboring isolates from the environment, human and animals which indicate its horizontal spread among the diverse sources, species, and hosts. CONCLUSION This study recommends the one health approach for future surveillance across multiple sources and bacterial species to adopt relevant measures and reduce global resistance crises.
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Affiliation(s)
- Qing Wang
- College of Veterinary Medicine, Gansu Agricultural University, No. 1 Yingmen village, Anning District, Lanzhou, 730070, Gansu Province, P.R.China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Weiwei Wang
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Qiqi Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China; College of life science and Food Engineering, Hebei University of Engineering, Handan, Hebei Province 056038, P.R.China
| | - Muhammad Shoaib
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Wang Chengye
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China; College of life science and Food Engineering, Hebei University of Engineering, Handan, Hebei Province 056038, P.R.China
| | - Zhen Zhu
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China; College of life science and Food Engineering, Hebei University of Engineering, Handan, Hebei Province 056038, P.R.China
| | - Xiaojuan Wei
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Yubin Bai
- Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China
| | - Jiyu Zhang
- College of Veterinary Medicine, Gansu Agricultural University, No. 1 Yingmen village, Anning District, Lanzhou, 730070, Gansu Province, P.R.China; Key Laboratory of New Animal Drug Project of Gansu Province, Lanzhou, Gansu Province 730050, P.R.China; Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agriculture, Lanzhou, Gansu Province 730050, P.R.China; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730050, P.R.China.
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Ali MW, Karmakar S, Utsho KS, Kabir A, Arif M, Islam MS, Rahman MT, Hassan J. First detection and characterization of mcr-1 colistin resistant E. coli from wild rat in Bangladesh. PLoS One 2024; 19:e0296109. [PMID: 38743696 PMCID: PMC11093362 DOI: 10.1371/journal.pone.0296109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 04/14/2024] [Indexed: 05/16/2024] Open
Abstract
Colistin resistance is a global concern warning for a one health approach to combat the challenge. Colistin resistant E. coli and their resistance determinants are widely distributed in the environment, and rats could be a potential source of these isolates and resistant determinants to a diverse environmental setting. This study was aimed to determine the presence of colistin resistant E. coli (CREC) in wild rats, their antimicrobial resistance (AMR) phenotypes, and genotypic analysis of mcr-1 CREC through whole genome sequencing (WGS). A total of 39 rats were examined and CREC was isolated from their fecal pellets onto MacConkey agar containing colistin sulfate (1 μg/ mL). AMR of the CREC was determined by disc diffusion and broth microdilution was employed to determine MIC to colistin sulfate. CREC were screened for mcr genes (mcr-1 to mcr-8) and phylogenetic grouping by PCR. Finally, WGS of one mcr-1 CREC was performed to explore its genetic characteristics especially resistomes and virulence determinants. 43.59% of the rats carried CREC with one (2.56%) of them carrying CREC with mcr-1 gene among the mcr genes examined. Examination of seventeen (17) isolates from the CREC positive rats (n = 17) revealed that majority of them belonging to the pathogenic phylogroup D (52.94%) and B2 (11.76%). 58.82% of the CREC were MDR on disc diffusion test. Shockingly, the mcr-1 CREC showed phenotypic resistance to 16 antimicrobials of 8 different classes and carried the ARGs in its genome. The mcr-1 gene was located on a 60 kb IncI2 plasmid. On the other hand, ARGs related to aminoglycosides, phenicols, sulfonamides, tetracyclines and trimethoprims were located on a 288 kb mega-plasmid separately. The mcr-1 CREC carried 58 virulence genes including genes related to adhesion, colonization, biofilm formation, hemolysis and immune-evasion. The isolate belonged to ST224 and closely related to E. coli from different sources including UPEC clinical isolates from human based on cgMLST analysis. The current research indicates that rats might be a possible source of CREC, and the presence of mcr-1 and other ARGs on plasmid increases the risk of ARGs spreading and endangering human health and other environmental components through this infamous pest.
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Affiliation(s)
- Md. Wohab Ali
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Susmita Karmakar
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Kishor Sosmith Utsho
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Ajran Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad Arif
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Shafiqul Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Nambiar RB, Elbediwi M, Ed-Dra A, Wu B, Yue M. Epidemiology and antimicrobial resistance of Salmonella serovars Typhimurium and 4,[5],12:i- recovered from hospitalized patients in China. Microbiol Res 2024; 282:127631. [PMID: 38330818 DOI: 10.1016/j.micres.2024.127631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
Global emergence of multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium is a continuing challenge for modern healthcare. However, the knowledge, regarding the epidemiology of salmonellosis caused by the monophasic variant S. 4,[5],12:i:- in hospitalized patients, is limited in China. To bridge this gap, we carried out a retrospective study to determine the antimicrobial resistance, trends, and risk factors of S. Typhimurium and S. 4,[5],12:i:- (n = 329) recovered from patients in Zhejiang province between 2011 and 2019. The results showed that 90.57% (298/329) of the isolates were MDR; among them, 48.94% (161/329) and 12.46% (41/329) were phenotypically resistant to cephalosporins and fluoroquinolones, respectively, which are the drugs of choice used to treat salmonellosis in clinics. Additionally, we observed a higher incidence of infections among the young population (<5 years old). Notably, the higher prevalence of ST34 (sequence type 34) isolates, especially after 2014, with MDR (57.05%, 170/298) phenotype, and incidence of ST34 isolates co-harbouring mcr-1 (mobile colistin resistance gene) and blaCTX-M-14 (β-lactamase gene) suggest an association between STs and drug resistance. Together, the increasing prevalence of MDR ST34 calls for enhanced monitoring strategies to mitigate the spread and dissemination of MDR clones of S. Typhimurium and S. 4,[5],12:i-. Our study provides improved knowledge about non-typhoid Salmonella (NTS) infections, which could help in the effective recommendation of antimicrobials in hospitalized patients.
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Affiliation(s)
- Reshma B Nambiar
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Mohammed Elbediwi
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Abdelaziz Ed-Dra
- Laboratory of Engineering and Applied Technologies, Higher School of Technology, M'ghila Campus, Sultan Moulay Slimane University, BP: 591, Beni Mellal, Morocco
| | - Beibei Wu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Min Yue
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
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5
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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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Castañeda-Barba S, Top EM, Stalder T. Plasmids, a molecular cornerstone of antimicrobial resistance in the One Health era. Nat Rev Microbiol 2024; 22:18-32. [PMID: 37430173 DOI: 10.1038/s41579-023-00926-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2023] [Indexed: 07/12/2023]
Abstract
Antimicrobial resistance (AMR) poses a substantial threat to human health. The widespread prevalence of AMR is, in part, due to the horizontal transfer of antibiotic resistance genes (ARGs), typically mediated by plasmids. Many of the plasmid-mediated resistance genes in pathogens originate from environmental, animal or human habitats. Despite evidence that plasmids mobilize ARGs between these habitats, we have a limited understanding of the ecological and evolutionary trajectories that facilitate the emergence of multidrug resistance (MDR) plasmids in clinical pathogens. One Health, a holistic framework, enables exploration of these knowledge gaps. In this Review, we provide an overview of how plasmids drive local and global AMR spread and link different habitats. We explore some of the emerging studies integrating an eco-evolutionary perspective, opening up a discussion about the factors that affect the ecology and evolution of plasmids in complex microbial communities. Specifically, we discuss how the emergence and persistence of MDR plasmids can be affected by varying selective conditions, spatial structure, environmental heterogeneity, temporal variation and coexistence with other members of the microbiome. These factors, along with others yet to be investigated, collectively determine the emergence and transfer of plasmid-mediated AMR within and between habitats at the local and global scale.
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Affiliation(s)
- Salvador Castañeda-Barba
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA.
- Institute for Modelling Collaboration and Innovation, University of Idaho, Moscow, ID, USA.
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7
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Sun H, Li M, Bai Y, Sun Y, Zhu C, Xia X, Zhang H, Luo W, Zhang W, Wen Y, Bai Y, Wang L, Hu J. Preliminary view of the distribution and spread of the plasmid-mediated resistance genes in Glaesserella parasuis. J Med Microbiol 2023; 72. [PMID: 38112519 DOI: 10.1099/jmm.0.001767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Introduction. Various plasmid-mediated resistance genes have been reported in Glaesserella parasuis, but little is known about their global distribution features, evolution pattern and spread.Gap Statement. The potential mobilization mechanisms of resistance plasmids in G. parasuis have been poorly explored.Aim. The aim of the study was to investigate the prevalence and diversity of plasmid-mediated resistance genes among G. parasuis isolates, and focus on the analysis of the features of the resistance plasmids from G. parasuis.Method. The plasmids tested were sequenced using the Illumina HiSeq platform in conjunction with PCR and inverted PCR. The susceptibility of the host strains was determined by broth microdilution. The transfer of plasmids tested was conducted by electroporation. The sequence data were compared using bioinformatics tools and the data from our laboratory and the National Center for Biotechnology Information (NCBI) database.Results. Nineteen plasmids were identified from our laboratory and these resistance plasmids were functional and transferable. Moreover, we clustered five types of genetic backbones of plasmids from G. parasuis and revealed the global distribution features of the plasmid-mediated resistance genes.Conclusions. This is the first report of the coexistence of tet(H)-bearing type I plasmid and lnu(C)-bearing type II plasmid in one G. parasuis clinical isolate. In addition, this study provides the first view of the global distribution of plasmid-mediated resistance genes and classifies the plasmids in G. parasuis according to their backbone regions.
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Affiliation(s)
- Huarun Sun
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Minghui Li
- College of Animal Veterinary Medicine, Henan Agricultural University, Zhengzhou, PR China
| | - Yilin Bai
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Yawei Sun
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Chunling Zhu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Xiaojing Xia
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Huihui Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Weiyu Luo
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Wei Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Yuliang Wen
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Yueyu Bai
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Lei Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
| | - Jianhe Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, PR China
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, Zhengzhou, PR China
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8
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Chandler M, Ross K, Varani AM. The insertion sequence excision enhancer: A PrimPol-based primer invasion system for immobilizing transposon-transmitted antibiotic resistance genes. Mol Microbiol 2023; 120:658-669. [PMID: 37574851 DOI: 10.1111/mmi.15140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Evolutionary studies often identify genes that have been exchanged between different organisms and the phrase Lateral or Horizontal Gene Transfer is often used in this context. However, they rarely provide any mechanistic information concerning how these gene transfers might have occurred. With the astonishing increase in the number of sequences in public databases over the past two or three decades, identical antibiotic resistance genes have been identified in many different sequence contexts. One explanation for this would be that genes are initially transmitted by transposons which have subsequently decayed and can no longer be detected. Here, we provide an overview of a protein, IEE (Insertion Sequence Excision Enhancer) observed to facilitate high-frequency excision of IS629 from clinically important Escherichia coli O157:H7 and subsequently shown to affect a large class of bacterial insertion sequences which all transpose using the copy-out-paste-in transposition mechanism. Excision depends on both IEE and transposase indicating association with the transposition process itself. We review genetic and biochemical data and propose that IEE immobilizes genes carried by compound transposons by removing the flanking insertion sequence (IS) copies. The biochemical activities of IEE as a primase with the capacity to recognize DNA microhomologies and the observation that its effect appears restricted to IS families which use copy-out-paste-in transposition, suggests IS deletion occurs by abortive transposition involving strand switching (primer invasion) during the copy-out step. This reinforces the proposal made for understanding the widespread phenomenon loss of ISApl1 flanking mcr-1 in the compound transposon Tn6330 which we illustrate with a detailed model. This model also provides a convincing way to explain the high levels of IEE-induced precise IS excision.
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Affiliation(s)
- Mick Chandler
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Karen Ross
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, USA
| | - Alessandro M Varani
- School of Agricultural and Veterinary Sciences, Universidade Estadual Paulista, Sao Paulo, Brazil
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Ogunlana L, Kaur D, Shaw LP, Jangir P, Walsh T, Uphoff S, MacLean RC. Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings. THE ISME JOURNAL 2023; 17:2058-2069. [PMID: 37723338 PMCID: PMC10579358 DOI: 10.1038/s41396-023-01509-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
Antibiotic resistance tends to carry fitness costs, making it difficult to understand how resistance can be maintained in the absence of continual antibiotic exposure. Here we investigate this problem in the context of mcr-1, a globally disseminated gene that confers resistance to colistin, an agricultural antibiotic that is used as a last resort for the treatment of multi-drug resistant infections. Here we show that regulatory evolution has fine-tuned the expression of mcr-1, allowing E. coli to reduce the fitness cost of mcr-1 while simultaneously increasing colistin resistance. Conjugative plasmids have transferred low-cost/high-resistance mcr-1 alleles across an incredible diversity of E. coli strains, further stabilising mcr-1 at the species level. Regulatory mutations were associated with increased mcr-1 stability in pig farms following a ban on the use of colistin as a growth promoter that decreased colistin consumption by 90%. Our study shows how regulatory evolution and plasmid transfer can combine to stabilise resistance and limit the impact of reducing antibiotic consumption.
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Affiliation(s)
- Lois Ogunlana
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Divjot Kaur
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Liam P Shaw
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Pramod Jangir
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Timothy Walsh
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - R C MacLean
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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Abban MK, Ayerakwa EA, Mosi L, Isawumi A. The burden of hospital acquired infections and antimicrobial resistance. Heliyon 2023; 9:e20561. [PMID: 37818001 PMCID: PMC10560788 DOI: 10.1016/j.heliyon.2023.e20561] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/21/2023] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
The burden of Hospital care-associated infections (HCAIs) is becoming a global concern. This is compounded by the emergence of virulent and high-risk bacterial strains such as "ESKAPE" pathogens - (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species), especially within Intensive care units (ICUs) that house high-risk and immunocompromised patients. In this review, we discuss the contributions of AMR pathogens to the increasing burden of HCAIs and provide insights into AMR mechanisms, with a particular focus on last-resort antibiotics like polymyxins. We extensively discuss how structural modifications of surface-membrane lipopolysaccharides and cationic interactions influence and inform AMR, and subsequent severity of HCAIs. We highlight some bacterial phenotypic survival mechanisms against polymyxins. Lastly, we discuss the emergence of plasmid-mediated resistance as a phenomenon making mitigation of AMR difficult, especially within the ICUs. This review provides a balanced perspective on the burden of HCAIs, associated pathogens, implication of AMR and factors influencing emerging AMR mechanisms.
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Affiliation(s)
- Molly Kukua Abban
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Eunice Ampadubea Ayerakwa
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
| | - Abiola Isawumi
- West African Centre for Cell Biology of Infectious Pathogens, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, P.O. Box LG 54, Volta Road, University of Ghana, Legon, Accra, Ghana
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11
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Attalla ET, Khalil AM, Zakaria AS, Baker DJ, Mohamed NM. Genomic characterization of colistin-resistant Klebsiella pneumoniae isolated from intensive care unit patients in Egypt. Ann Clin Microbiol Antimicrob 2023; 22:82. [PMID: 37689686 PMCID: PMC10492301 DOI: 10.1186/s12941-023-00632-9] [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: 06/25/2023] [Accepted: 08/29/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Egypt has witnessed elevated incidence rates of multidrug-resistant Klebsiella pneumoniae infections in intensive care units (ICUs). The treatment of these infections is becoming more challenging whilst colistin-carbapenem-resistant K. pneumoniae is upsurging. Due to the insufficiently available data on the genomic features of colistin-resistant K. pneumoniae in Egypt, it was important to fill in the gap and explore the genomic characteristics, as well as the antimicrobial resistance, the virulence determinants, and the molecular mechanisms of colistin resistance in such a lethal pathogen. METHODS Seventeen colistin-resistant clinical K. pneumoniae isolates were collected from ICUs in Alexandria, Egypt in a 6-month period in 2020. Colistin resistance was phenotypically detected by modified rapid polymyxin Nordmann/Poirel and broth microdilution techniques. The isolates susceptibility to 20 antimicrobials was determined using Kirby-Bauer disk diffusion method. Whole genome sequencing and bioinformatic analysis were employed for exploring the virulome, resistome, and the genetic basis of colistin resistance mechanisms. RESULTS Out of the tested K. pneumoniae isolates, 82.35% were extensively drug-resistant and 17.65% were multidrug-resistant. Promising susceptibility levels towards tigecycline (88.24%) and doxycycline (52.94%) were detected. Population structure analysis revealed seven sequence types (ST) and K-types: ST383-K30, ST147-K64, ST17-K25, ST111-K63, ST11-K15, ST14-K2, and ST525-K45. Virulome analysis revealed yersiniabactin, aerobactin, and salmochelin siderophore systems in ˃ 50% of the population. Hypervirulence biomarkers, iucA (52.94%) and rmpA/A2 (5.88%) were detected. Extended-spectrum β-lactamase- and carbapenemase-producers accounted for 94.12% of the population, with blaCTX-M-15, blaNDM-5, and blaOXA-48 reaching 64.71%, 82.35%, and 82.35%, respectively. Chromosomal alterations in mgrB (82.35%) were the most prevailing colistin resistance-associated genetic change followed by deleterious mutations in ArnT (23.53%, L54H and G164S), PmrA (11.76%, G53V and D86E), PmrB (11.76%, T89P and T134P), PmrC (11.76%, S257L), PhoQ (5.88%, L322Q and Q435H), and ArnB (5.88%, G47D) along with the acquisition of mcr-1.1 by a single isolate of ST525. CONCLUSIONS In this study, we present the genotypic colistin resistance mechanisms in K. pneumoniae isolated in Egypt. More effective antibiotic stewardship protocols must be implemented by Egyptian health authorities to restrain this hazard and safeguard the future utility of colistin. This is the first characterization of a complete sequence of mcr-1.1-bearing IncHI2/IncHI2A plasmid recovered from K. pneumoniae clinical isolate belonging to the emerging high-risk clone ST525.
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Affiliation(s)
- Eriny T. Attalla
- Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, El-Khartoom Square, Azarita, Alexandria, Egypt
| | - Amal M. Khalil
- Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, El-Khartoom Square, Azarita, Alexandria, Egypt
| | - Azza S. Zakaria
- Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, El-Khartoom Square, Azarita, Alexandria, Egypt
| | | | - Nelly M. Mohamed
- Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, El-Khartoom Square, Azarita, Alexandria, Egypt
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12
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Wang Z, Jiang Z, Xu H, Jiao X, Li Q. Prevalence and molecular characterization of mcr-1-positive foodborne ST34-Salmonella isolates in China. Microbiol Res 2023; 274:127441. [PMID: 37356255 DOI: 10.1016/j.micres.2023.127441] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) and S. 4,[5],12:i:- have become the most common serovars associated with human salmonellosis worldwide. Moreover, the emergence of mcr-carrying S. Typhimurium and S. 4,[5],12:i:- with multidrug resistance (MDR) patterns has posed a threat to public health. In this study, we retrospectively screened 2009-2022 laboratory-preserved strains for the presence of mcr genes. We obtained 16 mcr-1-positive S. Typhimurium and S. 4,[5],12:i:- strains with MDR that belonged to sequence type 34 (ST34). Whole-genome sequencing analysis revealed that the mcr-1 was located on the IncI2 or IncHI2 plasmids. The ISApl1 element downstream of mcr-1 was present in all pig-derived strains. Conjugation experiments confirmed that nine mcr-1-carrying IncHI2 plasmids could not be transferred to Escherichia coli due to loss of the conjugation region. Finally, core genome single nucleotide polymorphism (cgSNP) analyses of the 16 mcr-1-carrying strains and 77 mcr-carrying ST34-Salmonella genome sequences from the NCBI and ENA databases showed that five out of eight clusters contained strains from pig and pig products, revealing pigs and pig products as key reservoirs of mcr-1-positive ST34-Salmonella strains. The transmission of mcr-carrying ST34 Salmonella strains to humans via the pig food chain is a potential cause for public health concern in controlling human salmonellosis.
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Affiliation(s)
- Zhenyu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - Zhongyi Jiang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China
| | - Haiyan Xu
- Nantong Center for Disease Control and Prevention, Nantong 226007, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China.
| | - Qiuchun Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, China.
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13
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Lu X, Zhang P, Du P, Zhang X, Wang J, Yang Y, Sun H, Wang Z, Cui S, Li R, Bai L. Prevalence and Genomic Characteristics of mcr-Positive Escherichia coli Strains Isolated from Humans, Pigs, and Foods in China. Microbiol Spectr 2023; 11:e0456922. [PMID: 37042751 PMCID: PMC10269804 DOI: 10.1128/spectrum.04569-22] [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: 11/10/2022] [Accepted: 03/16/2023] [Indexed: 04/13/2023] Open
Abstract
Colistin is one of the last-resort antibiotics for treating infections caused by multidrug-resistant (MDR) Gram-negative bacteria. However, mcr genes conferring resistance to colistin have been widely identified, which is considered a global threat to public health. Here, we investigated the prevalence and characteristics of mcr-harboring Escherichia coli strains isolated from humans, animals, and foods in China by PCR, antimicrobial susceptibility testing, conjugation experiments, molecular typing, genome sequencing, and bioinformatics analysis. In total, 135 mcr-1-harboring E. coli isolates were acquired from 847 samples, and 6 isolates carried mcr-3. Among them, 131 isolates were MDR bacteria. Sixty-five resistance genes conferring resistance to multiple antimicrobials were identified in 135 isolates. The diverse pulsed-field gel electrophoresis (PFGE) patterns and sequence types (STs) of mcr-1-carrying isolates demonstrated that clonal dissemination was not the dominant mode of mcr-1 transmission. Seven types of plasmids were able to carry mcr-1 in this study, including IncI2, IncX4, IncHI2, p0111, IncY, and two hybrid plasmids. The genetic structures carrying mcr-1 of 60 isolates were successfully transferred into the recipient, including 25 IncI2 plasmids, 23 IncX4 plasmids, and an IncHI2 plasmid. mcr-1-pap2 was the dominant mcr-1-bearing structure, followed by ISApl1-mcr-1-pap2-ISApl1 (Tn6330) and ISApl1-mcr-1-pap2, among 7 mcr-1-bearing structures of 135 isolates. In conclusion, IncI2, IncX4, and IncHI2 plasmids were the major vectors spreading mcr-1 from different geographical locations and sources. The prevalence of Tn6330 may accelerate the transmission of mcr-1. Continuous surveillance of mcr-1 and variants in bacteria is vital for evaluating the public health risk posed by mcr genes. IMPORTANCE The spread of polymyxin-resistant Enterobacteriaceae poses a significant threat to public health and challenges the therapeutic options for treating infections on a global level. In this study, mcr-1-bearing ST10 E. coli was isolated from pigs, pork, and humans simultaneously, which demonstrated that ST10 E. coli was an important vehicle for the spread of mcr-1 among animals, foods, and humans. The high prevalence of mcr-1-positive E. coli strains in pigs and pork and the horizontal transmission of mcr-1-bearing plasmids in diverse E. coli strains suggest that pigs and pork are important sources of mcr-1-positive strains in humans and pose a potential threat to public health. Additional research on the prevalence and characteristics of mcr-1-positive E. coli is still required to facilitate early warning to improve polymyxin management in hospitals.
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Affiliation(s)
- Xiaoyu Lu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Pei Zhang
- 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, China
- Center for Disease Control and Prevention of Henan Province, Zhengzhou, China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, China
| | - Xiuli Zhang
- Center for Disease Control and Prevention of Henan Province, Zhengzhou, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yingying Yang
- Department of Neurology, Gaotang County People's Hospital, Gaotang, Shandong, China
| | - Honghu Sun
- Chengdu Institute for Food and Drug Control, Chengdu, 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, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shenghui Cui
- Department of Food Science, National Institutes for Food and Drug Control, Beijing, China
| | - 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, China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, 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, China
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Talat A, Miranda C, Poeta P, Khan AU. Farm to table: colistin resistance hitchhiking through food. Arch Microbiol 2023; 205:167. [PMID: 37014461 DOI: 10.1007/s00203-023-03476-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.
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Affiliation(s)
- Absar Talat
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Carla Miranda
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Department of Sciences, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal
- Toxicology Research Unit (TOXRUN), IUCS, CESPU, CRL, Gandra, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD)UTAD, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Asad U Khan
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Wang D, Zou H, Zhao L, Li Q, Meng M, Li X, Berglund B. High prevalence of Escherichia coli co-harboring conjugative plasmids with colistin- and carbapenem resistance genes in a wastewater treatment plant in China. Int J Hyg Environ Health 2023; 250:114159. [PMID: 36989999 DOI: 10.1016/j.ijheh.2023.114159] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Emergence and dissemination of resistance to last-resort antibiotics such as carbapenem and colistin is a growing, global health concern. Wastewater treatment plants (WWTPs) link human activities and the environment, can act as reservoirs and sources for emerging antibiotic resistance, and likely play a large role in antibiotic resistance transmission. The aim of this study was to investigate occurrence and characteristics of colistin- and carbapenem-resistant Escherichia coli (CCREC) in wastewater and sludge samples collected over a one-year period from different functional areas of an urban WWTP in Jinan city, Shandong, China. A total of 8 CCREC were isolated from 168 samples with selective agar and PCR, corresponding to high prevalence of 4.8%, co-harboring carbapenem resistance genes (blaNDM) and colistin resistance gene (mcr-1) and subsequently whole-genome sequenced. Additionally, all isolates were multidrug-resistant by antimicrobial susceptibility testing and carried a variety of antibiotic resistance genes. Two isolates carrying virulence genes associated with avian pathogenic E. coli were identified, one belonging to the high-risk clone O101:H9-ST167. Southern blotting was used to characterize CCREC isolates and plasmids carrying blaNDM-genes or mcr-1 could be transferred to a recipient strain E. coli J53 by in vitro conjugation assays. Resistance to other antibiotic classes were sporadically co-transferred to the transconjugant. Transposition of and mcr-1-carrying element from a transferable IncHI2-plasmid was observed among two CCREC clones isolated within 4 days of each other. The occurrence of multidrug-resistant CCREC capable of transferring their antibiotic resistance genotypes via conjugative plasmids is alarming. WWTPs bring bacteria from different sources together, providing opportunities for horizontal exchange of DNA among compatible hosts. Further dissemination of the colistin-, carbapenem-, or both colistin- and carbapenem resistant E. coli could lead to a serious threat to public health.
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Affiliation(s)
- Di Wang
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiyun Zou
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Ling Zhao
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Qi Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Min Meng
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuewen Li
- Department of Environment and Health, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
| | - Björn Berglund
- Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden
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Ali MW, Utsho KS, Karmakar S, Hoque MN, Rahman MT, Hassan J. First report on the molecular characteristics of mcr-1 colistin resistant E. coli isolated from retail broiler meat in Bangladesh. Int J Food Microbiol 2023; 388:110065. [PMID: 36610233 DOI: 10.1016/j.ijfoodmicro.2022.110065] [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: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022]
Abstract
Poultry meat is considered as a potential source of colistin resistant Escherichia coli (CREC). This study aimed to determine the prevalence and characteristics of CREC in broiler meat and ascertain their possible zoonotic potential(s). Broiler meat (n = 104) comprising 26 of each of the thigh, breast, liver, and proventriculus-gizzard was purchased from the retail outlets, Bangladesh. CREC was isolated from the meat samples on MacConkey agar plates containing colistin sulfate followed by PCR confirmation, mcr subtyping (mcr-1 to mcr-5), phylogenetic grouping and detailed molecular characterization through whole genome sequencing (WGS). Antimicrobial resistance of the CREC isolates were evaluated by disc diffusion method and MIC (minimum inhibitory concentration) of colistin sulfate was determined by broth microdilution. The investigation revealed 58 (55.77 %) of 104 samples as positive for CREC, and 53 (91.38 %) of CREC isolates carried mcr-1 gene with no other mcr subtypes evident. Most of the CREC belonged to commensal E. coli (66.04 %) with some pathogenic phylotypes (33.96 %) based on dichotomous decision tree. All the mcr-1 CREC isolates were multidrug-resistant (MDR) and had MICs of 4-8 μg/mL colistin sulfate. WGS of a commensal MDR mcr-1 CREC strain 1ChBEc2mcr revealed as a potential human pathogen belonging to ST162 that harbored 60 virulence factors associated genes (VFGs). The mcr-1 gene in 1ChBEc2mcr genome was located on a plasmid (p1ChBEc2mcr) and showed nucleotide similarities (>95 %) to another plasmid reported from human E. coli in Bangladesh. Beyond mcr-1 gene, this plasmid (p1ChBEc2mcr) also harbored genes related to aminoglycoside, beta-lactams, macrolides, and tetracycline resistance. Presence of similar mcr-1 carrying plasmids in broiler and human CREC denotes a threat of possibly human to avian (broiler) or vice-versa transfer of mcr-1 CREC through close contact as prevailing in the retail outlets of Bangladesh.
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Affiliation(s)
- Md Wohab Ali
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Kishor Sosmith Utsho
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Susmita Karmakar
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Nazmul Hoque
- Department of Gynecology, Obstetrics & Reproductive Health, Faculty of Veterinary Medicine & Animal Science, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Md Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Jayedul Hassan
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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17
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Identification of mcr-1 Genes and Characterization of Resistance Mechanisms to Colistin in Escherichia coli Isolates from Colombian Hospitals. Antibiotics (Basel) 2023; 12:antibiotics12030488. [PMID: 36978355 PMCID: PMC10044228 DOI: 10.3390/antibiotics12030488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/22/2023] [Accepted: 02/25/2023] [Indexed: 03/05/2023] Open
Abstract
We report the presence of the mcr-1 gene among 880 Escherichia coli clinical isolates collected in 13 hospitals from 12 Colombian cities between 2016 and 2019. Seven (0.8%) isolates were colistin resistant (MIC ≥ 4 µg/mL). These colistin-resistant isolates were screened for the presence of the mcr-1 gene; five carried the gene. These five isolates were subjected to whole genome sequencing (WGS) to identify additional resistomes and their ST. In addition, antimicrobial susceptibility testing revealed that all E. coli isolates carrying mcr-1 were susceptible to third generation-cephalosporin and carbapenems, except one, which carried an extended-spectrum β-lactamase (CTX-M-55), along with the fosfomycin resistance encoding gene, fosA. WGS indicated that these isolates belonged to four distinct sequence types (ST58, ST46, ST393, and a newly described ST14315) and to phylogroups B1, A, and D. In this geographic region, the spread of mcr-1 in E. coli is low and has not been inserted into high-risk clones such as ST131, which has been present in the country longer.
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Intracellular Transposition of Mobile Genetic Elements Associated with the Colistin Resistance Gene mcr-1. Microbiol Spectr 2023; 11:e0327822. [PMID: 36511714 PMCID: PMC9927407 DOI: 10.1128/spectrum.03278-22] [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] [Indexed: 12/15/2022] Open
Abstract
Mobile colistin resistance (mcr) genes are often located on conjugative plasmids, where their association with insertion sequences enables intercellular and intracellular dissemination throughout bacterial replicons and populations. Multiple mcr genes have been discovered in every habitable continent, in many bacterial species, on both plasmids and integrated into the chromosome. Previously, we showed the intercellular transfer of mcr-1 on an IncI1 plasmid, pMCR-E2899, between strains of Escherichia coli. Characterizing the intracellular dynamics of mcr-1 transposition and recombination would further our understanding of how these important genes move through bacterial populations and whether interventions can be put in place to stop their spread. In this study, we aimed to characterize transfer events from the mcr-1-containing transposon Tn7511 (ISApl1-mcr-1-pap2-ISApl1), located on plasmid pMCR-E2899, using the pBACpAK entrapment vector. Following the transformation of pBACpAK into our DH5α-Azir/pMCR-E2899 transconjugant, we captured ISApl1 in pBACpAK multiple times and, for the first time, observed the ISApl1-mediated transfer of the mcr-1 transposon (Tn7511) into the chromosome of E. coli DH5α. Whole-genome sequencing allowed us to determine consensus insertion sites of ISApl1 and Tn7511 in this strain, and comparison of these sites allowed us to explain the transposition events observed. These observations reveal the consequences of ISApl1 transposition within and between multiple replicons of the same cell and show mcr-1 transposition within the cell as part of the novel transposon Tn7511. IMPORTANCE By analyzing the intracellular transfer of clinically relevant transposons, we can understand the dissemination and evolution of drug resistance conferring mobile genetic elements (MGEs) once a plasmid enters a cell following conjugation. This knowledge will help further our understanding of how these important genes move through bacterial populations. Utilizing the pBACpAK entrapment vector has allowed us to determine the mobility of the novel mcr-1-containing transposon Tn7511.
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19
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Chotinantakul K, Chusri P, Okada S. Detection and characterization of ESBL-producing Escherichia coli and additional co-existence with mcr genes from river water in northern Thailand. PeerJ 2022; 10:e14408. [PMID: 36405029 PMCID: PMC9671034 DOI: 10.7717/peerj.14408] [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: 07/25/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022] Open
Abstract
Background Extended-spectrum β-lactamase producing Escherichia coli (ESBL-producing E. coli) have emerged, causing human and animal infections worldwide. This study was conducted to investigate the prevalence and molecular genetic features of ESBL-producing and multidrug-resistant (MDR) E. coli in river water. Methods A total of 172 E. coli samples were collected from the Kok River and Kham River in Chiang Rai, Thailand, during a 10-month period (2020-2021). Results We detected 45.3% of E. coli to be MDR. The prevalence of ESBL-producers was 22%. Among those ESBL-producing strains, CTX-M-15 (44.7%) was predominantly found, followed by CTX-M-55 (26.3%), CTX-M-14 (18.4%), and CTX-M-27 (10.5%). The bla TEM-1 and bla TEM-116 genes were found to be co-harbored with the bla CTX-M genes. Mobile elements, i.e., ISEcp1 and Tn3, were observed. Twelve plasmid replicons were found, predominantly being IncF (76.3%) and IncFIB (52.6%). Whole genome sequencing of ten selected isolates revealed the co-existence of ESBL with mcr genes in two ESBL-producing E. coli. A wide diversity of MLST classifications was observed. An mcr-1.1-pap2 gene cassette was found to disrupt the PUF2806 domain-containing gene, while an mcr-3.4 contig on another isolate contained the nimC/nimA-mcr-3.4-dgkA core segment. Discussion In conclusion, our data provides compelling evidence of MDR and ESBL-producing E. coli, co-existing with mcr genes in river water in northern Thailand, which may be disseminated into other environments and so cause increased risks to public health.
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Affiliation(s)
| | | | - Seiji Okada
- Division of Hematopoiesis, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Kumamoto, Japan,Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Kumamoto, Japan
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20
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Chiu S, Hancock AM, Schofner BW, Sniezek KJ, Soto-Echevarria N, Leon G, Sivaloganathan DM, Wan X, Brynildsen MP. Causes of polymyxin treatment failure and new derivatives to fill the gap. J Antibiot (Tokyo) 2022; 75:593-609. [PMID: 36123537 DOI: 10.1038/s41429-022-00561-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022]
Abstract
Polymyxins are a class of antibiotics that were discovered in 1947 from programs searching for compounds effective in the treatment of Gram-negative infections. Produced by the Gram-positive bacterium Paenibacillus polymyxa and composed of a cyclic peptide chain with a peptide-fatty acyl tail, polymyxins exert bactericidal effects through membrane disruption. Currently, polymyxin B and colistin (polymyxin E) have been developed for clinical use, where they are reserved as "last-line" therapies for multidrug-resistant (MDR) infections. Unfortunately, the incidences of strains resistant to polymyxins have been increasing globally, and polymyxin heteroresistance has been gaining appreciation as an important clinical challenge. These phenomena, along with bacterial tolerance to this antibiotic class, constitute important contributors to polymyxin treatment failure. Here, we review polymyxins and their mechanism of action, summarize the current understanding of how polymyxin treatment fails, and discuss how the next generation of polymyxins holds promise to invigorate this antibiotic class.
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Affiliation(s)
- Selena Chiu
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Anna M Hancock
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Bob W Schofner
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Katherine J Sniezek
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Gabrielle Leon
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | | | - Xuanqing Wan
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Mark P Brynildsen
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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21
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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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22
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Malaka De Silva P, Stenhouse GE, Blackwell GA, Bengtsson RJ, Jenkins C, Hall JPJ, Baker KS. A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella. Proc Biol Sci 2022; 289:20220581. [PMID: 35919999 PMCID: PMC9346365 DOI: 10.1098/rspb.2022.0581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation efficiencies for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid-associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.
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Affiliation(s)
- P. Malaka De Silva
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - George E. Stenhouse
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Grace A. Blackwell
- EMBL-EBI, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB101SA, UK,Department of Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB101SA, UK
| | - Rebecca J. Bengtsson
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Claire Jenkins
- Gastro and Food Safety (One Health) Division, UK Health Security Agency (UKHSA), Colindale, London, UK
| | - James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kate S. Baker
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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Molecular Characterization of pBOq-IncQ and pBOq-95LK Plasmids of Escherichia coli BOq 01, a New Isolated Strain from Poultry Farming, Involved in Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10081509. [PMID: 35893567 PMCID: PMC9331969 DOI: 10.3390/microorganisms10081509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022] Open
Abstract
The increase in antimicrobial resistance has raised questions about how to use these drugs safely, especially in veterinary medicine, animal nutrition, and agriculture. Escherichia coli is an important human and animal pathogen that frequently contains plasmids carrying antibiotic resistance genes. Extra chromosomal elements are required for various functions or conditions in microorganisms. Several phage-like plasmids have been identified, which are important in antibiotic resistance. In this work, the molecular characterization of the pBOq-IncQ (4.5 kb) and pBOq-95LK (95 kb) plasmids found in the E. coli strain BOq 01, a multidrug resistant bacteria isolated from a poultry farm, are considered. Plasmid pBOq-IncQ belongs to the incQ incompatibility plasmid family and is involved in sulfonamide resistance. Plasmid pBOq-95LK is a lytic phage-like plasmid that is involved in the lysis of the E. coli BOq 01 strain and carries a bleomycin resistance gene and a strain cured of this plasmid shows bleomycin sensitivity. Induction of the lytic cycle indicates that this phage-like plasmid is an active phage. This type of plasmid has been reported to acquire genes such as mcr-1, which codes for colistin resistance and bacterial persistence and is a significant public health threat. A genome comparison, a pangenomic and phylogenomic analysis with other phage-like plasmids reported in the literature were performed to understand better the evolution of this kind of plasmid in bacteria and its potential importance in antibiotic resistance.
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24
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Hamame A, Davoust B, Cherak Z, Rolain JM, Diene SM. Mobile Colistin Resistance ( mcr) Genes in Cats and Dogs and Their Zoonotic Transmission Risks. Pathogens 2022; 11:pathogens11060698. [PMID: 35745552 PMCID: PMC9230929 DOI: 10.3390/pathogens11060698] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Pets, especially cats and dogs, represent a great potential for zoonotic transmission, leading to major health problems. The purpose of this systematic review was to present the latest developments concerning colistin resistance through mcr genes in pets. The current study also highlights the health risks of the transmission of colistin resistance between pets and humans. Methods: We conducted a systematic review on mcr-positive bacteria in pets and studies reporting their zoonotic transmission to humans. Bibliographic research queries were performed on the following databases: Google Scholar, PubMed, Scopus, Microsoft Academic, and Web of Science. Articles of interest were selected using the PRISMA guideline principles. Results: The analyzed articles from the investigated databases described the presence of mcr gene variants in pets including mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-8, mcr-9, and mcr-10. Among these articles, four studies reported potential zoonotic transmission of mcr genes between pets and humans. The epidemiological analysis revealed that dogs and cats can be colonized by mcr genes that are beginning to spread in different countries worldwide. Overall, reported articles on this subject highlight the high risk of zoonotic transmission of colistin resistance genes between pets and their owners. Conclusions: This review demonstrated the spread of mcr genes in pets and their transmission to humans, indicating the need for further measures to control this significant threat to public health. Therefore, we suggest here some strategies against this threat such as avoiding zoonotic transmission.
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Affiliation(s)
- Afaf Hamame
- Faculté de Pharmacie, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille University, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;
| | - Bernard Davoust
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;
| | - Zineb Cherak
- Faculté des Sciences de la Nature et de la Vie, Université Batna-2, Route de Constantine, Fésdis, Batna 05078, Algeria;
| | - Jean-Marc Rolain
- Faculté de Pharmacie, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille University, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;
- Correspondence: (J.-M.R.); (S.M.D.); Tel.: +33-4-9183-5649 (S.M.D.)
| | - Seydina M. Diene
- Faculté de Pharmacie, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille University, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;
- IHU-Méditerranée Infection, 19-21 Boulevard Jean Moulin, CEDEX 05, 13385 Marseille, France;
- Correspondence: (J.-M.R.); (S.M.D.); Tel.: +33-4-9183-5649 (S.M.D.)
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25
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Epidemiological Prevalence of Phenotypical Resistances and Mobilised Colistin Resistance in Avian Commensal and Pathogenic E. coli from Denmark, France, The Netherlands, and the UK. Antibiotics (Basel) 2022; 11:antibiotics11050631. [PMID: 35625275 PMCID: PMC9137498 DOI: 10.3390/antibiotics11050631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 01/10/2023] Open
Abstract
Colistin has been used for the treatment of non-invasive gastrointestinal infections caused by avian pathogenic E. coli (APEC). The discovery of mobilised colistin resistance (mcr) in E. coli has instigated a One Health approach to minimise colistin use and the spread of resistance. The aim of this study was to compare colistin susceptibility of APECs (collected from Denmark n = 25 and France n = 39) versus commensal E. coli (collected from the Netherlands n = 51 and the UK n = 60), alongside genetic (mcr-1−5) and phenotypic resistance against six other antimicrobial classes (aminoglycosides, cephalosporins, fluoroquinolones, penicillins, sulphonamides/trimethoprim, tetracyclines). Minimum inhibitory concentration (MIC) values were determined using a broth microdilution method (EUCAST guidelines), and phenotypic resistance was determined using disk diffusion. Colistin MIC values of APEC were significantly lower than those for commensals by 1 dilution (p < 0.0001, Anderson-Darling test), and differences in distributions were observed between countries. No isolate carried mcr-1−5. Three phenotypically resistant isolates were identified in 2/62 APEC and 1/111 commensal isolates. Gentamicin or gentamicin−ceftriaxone co-resistance was observed in two of these isolates. This study showed a low prevalence of phenotypic colistin resistance, with no apparent difference in colistin resistance between commensal E. coli strains and APEC strains.
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26
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Li P, Zhan LI, Wang H, Gao W, Gao L, Lv S, Zhang X, Zhu G, Yan Y. First Identification and Limited Dissemination of mcr-1 Colistin Resistance in Salmonella Isolates from Jiaxing. J Food Prot 2022; 85:213-219. [PMID: 34648627 DOI: 10.4315/jfp-21-069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 10/09/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Salmonella, a major foodborne pathogen, causes severe gastrointestinal disease in people and animals worldwide. Plasmid-borne mcr-1, which confers colistin resistance in Salmonella, has significant epidemiological interest for public health safety. Here, we report the first evidence of mcr-1-mediated colistin resistance in one multidrug-resistant strain, 16062, from 355 Salmonella isolates collected for Jiaxing foodborne pathogen monitoring in Zhejiang Province from 2015 to 2019. In addition to colistin, 16062 displayed multidrug resistance to various antimicrobials (β-lactams, quinolone, sulfonamide, florfenicol, ampicillin, streptomycin, nalidixic acid, aminoglycoside, and trimethoprim-sulfamethoxazole). The mcr-1-carrying IncX4 plasmid (p16062-MCR) in this study shares a conserved structure with other mcr-IncX4 plasmids. We found that other antimicrobial-resistance genes (aac(6')-Ib-cr, aadA1, aadA2, aph(3')-Ia, oqxA, oqxB, sul1, and cmlA1) are located on p16062-cmlA, an atypical IncHI2 plasmid, in isolate 16062. This is the first identification of transferable colistin resistance in a foodborne Salmonella isolate collected in Jiaxing City, the 5-year monitoring of which revealed limited dissemination. By determining the genetic features of the plasmid vehicle, the characteristics of transferable mcr genes circulating in isolates from Jiaxing are now clearer. HIGHLIGHTS
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Affiliation(s)
- Ping Li
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - L I Zhan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Wenjie Gao
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Lei Gao
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Shencong Lv
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Xiaofei Zhang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Guoying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
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27
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He Z, Yang Y, Li W, Ma X, Zhang C, Zhang J, Sun B, Ding T, Tian GB. Comparative genomic analyses of Polymyxin-resistant Enterobacteriaceae strains from China. BMC Genomics 2022; 23:88. [PMID: 35100991 PMCID: PMC8805313 DOI: 10.1186/s12864-022-08301-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Background Mobile colistin resistance like gene (mcr-like gene) is a new type of polymyxin resistance gene that can be horizontally transferred in the Enterobacteriaceae. This has brought great challenges to the treatment of multidrug-resistant Escherichia coli and K. pneumoniae. Results K. pneumoniae 16BU137 and E. coli 17MR471 were isolated from the bus and subway handrails in Guangzhou, China. K. pneumoniae 19PDR22 and KP20191015 were isolated from patients with urinary tract infection and severe pneumonia in Anhui, China. Sequence analysis indicated that the mcr-1.1 gene was present on the chromosome of E. coli 17MR471, and the gene was in the gene cassette containing pap2 and two copies of ISApl1.The mcr-1.1 was found in the putative IncX4 type plasmid p16BU137_mcr-1.1 of K. pneumoniae 16BU137, but ISApl1 was not found in its flanking sequence. Mcr-8 variants were found in the putative IncFIB/ IncFII plasmid pKP20191015_mcr-8 of K. pneumoniae KP20191015 and flanked by ISEcl1 and ISKpn26. Conclusion This study provides timely information on Enterobacteriaceae bacteria carrying mcr-like genes, and provides a reference for studying the spread of mcr-1 in China and globally. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08301-5.
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Affiliation(s)
- Zhien He
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Yongqiang Yang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Xiaoling Ma
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China
| | - Changfeng Zhang
- Clinical Laboratory of the First Affiliated Hospital, Anhui University of Chinese Medicine, Hefei, 230031, Anhui, China
| | - Jingxiang Zhang
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital, University of Science and Technology of China, Hefei, China.
| | - Tao Ding
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China. .,Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China. .,Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China. .,Xizang Minzu University School of Medicine, Xianyang, China.
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28
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Ricker N, Chalmers G, Whalen E, Allen HK, Meinersmann RJ. Genomic Changes within a Subset of IncI2 Plasmids Associated with Dissemination of mcr-1 Genes and Other Important Antimicrobial Resistance Determinants. Antibiotics (Basel) 2022; 11:antibiotics11020181. [PMID: 35203784 PMCID: PMC8868234 DOI: 10.3390/antibiotics11020181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/01/2023] Open
Abstract
IncI2 plasmids appear to have only recently become associated with resistance genes; however, their tendency to carry resistance to the antibiotics of last resort and their widespread distribution increase their relative importance. In this study, we describe lineages within this plasmid family that have an increased likelihood of acquisition of antimicrobial resistance genes. Globally distributed mcr-1-carrying IncI2 plasmids were found to cluster with other IncI2 plasmids carrying extended-spectrum beta-lactamase genes, and separately from the non-resistant IncI2 plasmids. In addition, insertion sequence (IS) elements with no direct association with the acquired resistance genes also clustered with the resistance plasmids in the phylogenetic tree. In recognition of the biased sequencing of resistant plasmids globally, the analysis was also performed on resistant and non-resistant IncI2 plasmids sequenced in the USA through government surveillance efforts that do not rely on antibiotic selection. This analysis confirmed a distinct clustering associated with both resistance and mobile elements and identified possible genomic changes in core genes that correlate with increased acquisition of foreign DNA. This work highlights a potential genetic mechanism for increased uptake of foreign DNA within this prevalent family of plasmids.
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Affiliation(s)
- Nicole Ricker
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA 50010, USA
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: (N.R.); (R.J.M.)
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Elli Whalen
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA 50010, USA
| | - Heather K. Allen
- Food Safety and Enteric Pathogens Research Unit, ARS-USDA National Animal Disease Center, Ames, IA 50010, USA
| | - Richard J. Meinersmann
- National Poultry Research Center, USDA Agricultural Research Service, PMSP-RU, Athens, GA 30605, USA
- Correspondence: (N.R.); (R.J.M.)
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Vázquez X, García V, Fernández J, Bances M, de Toro M, Ladero V, Rodicio R, Rodicio MR. Colistin Resistance in Monophasic Isolates of Salmonella enterica ST34 Collected From Meat-Derived Products in Spain, With or Without CMY-2 Co-production. Front Microbiol 2022; 12:735364. [PMID: 35069462 PMCID: PMC8770973 DOI: 10.3389/fmicb.2021.735364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/17/2021] [Indexed: 12/02/2022] Open
Abstract
Colistin is a last-resort antibiotic in fighting severe infections caused by multidrug resistant Gram negative pathogens in hospitals. Zoonotic bacteria acquire colistin resistance in animal reservoirs and mediate its spread along the food chain. This is the case of non-typhoid serovars of Salmonella enterica. Colistin-resistant S. enterica in foods represents a threat to human health. Here, we assessed the prevalence of colistin-resistance in food-borne isolates of S. enterica (2014–2019; Asturias, Spain), and established the genetic basis and transferability of this resistance. Five out of 231 isolates tested (2.2%) were resistant to colistin. Four of them, belonging to the European monophasic ST34 clone of S. Typhimurium, were characterized in the present study. They were collected from pork or pork and beef meat-derived products, either in 2015 (three isolates) or 2019 (one isolate). Molecular typing with XbaI-PFGE and plasmid profiling revealed distinct patterns for each isolate, even though two of the 2015 isolates derived from the same sample. The MICs of colistin ranged from 8 to 16 mg/L. All isolates carried the mcr-1.1 gene located on conjugative plasmids of the incompatibility groups IncX4 (2015 isolates) or IncHI2 (2019 isolate). Apart from colistin resistance, the four isolates carried chromosomal genes conferring resistance to ampicillin, streptomycin, sulfonamides and tetracycline [blaTEM–1, strA-strB, sul2, and tet(B)] and heavy metals, including copper and silver (silESRCFBAGP and pcoGE1ABCDRSE2), arsenic (arsRSD2A2BCA1D1) ± mercury (merEDACPTR), which are characteristically associated with the European ST34 monophasic clone. The 2019 isolate was also resistant to other antibiotics, comprising third generation cephalosporins and cephamycins. The latter phenotype was conferred by the blaCMY–2 gene located on an IncI1-I(α)-ST2 plasmid. Results in the present study identified meat-derived products as a reservoir of a highly successful clone harboring transferable plasmids which confer resistance to colistin and other clinically important antibiotics. An important reduction in the number of food-borne S. enterica detected during the period of the study, together with the low frequency of colistin resistance, underlines the success of One Health initiatives, such as those implemented at the UE, to control zoonotic bacteria along the food chain and to halt the spread of antimicrobial resistance.
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Affiliation(s)
- Xenia Vázquez
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
| | - Javier Fernández
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Margarita Bances
- Laboratorio de Salud Pública (LSP), Consejería de Sanidad del Principado de Asturias, Oviedo, Spain
| | - María de Toro
- Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - Víctor Ladero
- Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain.,Grupo de Microbiología Molecular, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Rosaura Rodicio
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain
| | - M Rosario Rodicio
- Área de Microbiología, Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain.,Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
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OUP accepted manuscript. FEMS Microbiol Lett 2022; 369:6528371. [DOI: 10.1093/femsle/fnac016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
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Zhang S, Abbas M, Rehman MU, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Gao Q, Tian B, Cheng A. Updates on the global dissemination of colistin-resistant Escherichia coli: An emerging threat to public health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149280. [PMID: 34364270 DOI: 10.1016/j.scitotenv.2021.149280] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Colistin drug resistance is an emerging public health threat worldwide. The adaptability, existence and spread of colistin drug resistance in multiple reservoirs and ecological environmental settings is significantly increasing the rate of occurrence of multidrug resistant (MDR) bacteria such as Escherichia coli (E. coli). Here, we summarized the reports regarding molecular and biological characterization of mobile colistin resistance gene (mcr)-positive E. coli (MCRPEC), originating from diverse reservoirs, including but not limited to humans, environment, waste water treatment plants, wild, pets, and food producing animals. The MCRPEC revealed the abundance of clinically important resistance genes, which are responsible for MDR profile. A number of plasmid replicon types such as IncI2, IncX4, IncP, IncX, and IncFII with a predominance of IncI2 were facilitating the spread of colistin resistance. This study concludes the distribution of multiple sequence types of E. coli carrying mcr gene variants, which are possible threat to "One Health" perspective. In addition, we have briefly explained the newly known mechanisms of colistin resistance i.e. plasmid-encoded resistance determinant as well as presented the chromosomally-encoded resistance mechanisms. The transposition of ISApl1 into the chromosome and existence of intact Tn6330 are important for transmission and stability for mcr gene. Further, genetic environment of co-localized mcr gene with carbapenem-resistance or extended-spectrum β-lactamases genes has also been elaborated, which is limiting human beings to choose last resort antibiotics. Finally, environmental health and safety control measures along with spread mechanisms of mcr genes are discussed to avoid further propagation and environmental hazards of colistin resistance.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Muhammad Abbas
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Livestock and Dairy Development Department Lahore, Punjab 54000, Pakistan
| | - Mujeeb Ur Rehman
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Disease Investigation Laboratory, Livestock & Dairy Development Department, Zhob 85200, Balochistan, Pakistan
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China.
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Zhang Y, Kuang X, Liu J, Sun RY, Li XP, Sun J, Liao XP, Liu YH, Yu Y. Identification of the Plasmid-Mediated Colistin Resistance Gene mcr-1 in Escherichia coli Isolates From Migratory Birds in Guangdong, China. Front Microbiol 2021; 12:755233. [PMID: 34745062 PMCID: PMC8567052 DOI: 10.3389/fmicb.2021.755233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 09/23/2021] [Indexed: 01/10/2023] Open
Abstract
We determined the prevalence and transmission characteristics of mcr-1-positive Escherichia coli (MCRPEC) isolates from migratory birds Anser indicus in Guangdong, China. We identified 22 MCRPEC from 303 A. indicus fecal samples (7.3%) in Guangzhou, Zhaoqing, and Futian. The mcr-1 gene coexisted with 24 other types of antibiotic resistance genes (ARG), and 11 ARGs were highly prevalent at levels >50%. The MCRPEC displayed a diversity of sequence types (ST), and 19 distinct STs were identified with ST10, ST1146, and ST1147 as the most prevalent. In addition, these MCRPEC from birds were closely related phylogenetically to those from other sources in China. Whole-genome sequencing analysis demonstrated that mcr-1 was located on IncX4 (n=9, 40.9%), IncI2 (n=5, 22.7%) and IncP (n=1, 4.5%) plasmids and the latter shared an identical plasmid backbone with other sources. These results highlight the significance of migratory birds in the transmission of antibiotic resistance and provide powerful evidence that migratory birds are potential transmitters of antibiotic resistance.
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Affiliation(s)
- Yan Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xu Kuang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Juan Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ruan-Yang Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xing-Ping Li
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Jian Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiao-Ping Liao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ya-Hong Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Liu Z, Liu Y, Xi W, Liu S, Liu J, Mu H, Chen B, He H, Fan Y, Ma W, Zhang W, Fu M, Wang J, Song X. Genetic Features of Plasmid- and Chromosome-Mediated mcr-1 in Escherichia coli Isolates From Animal Organs With Lesions. Front Microbiol 2021; 12:707332. [PMID: 34456890 PMCID: PMC8386294 DOI: 10.3389/fmicb.2021.707332] [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: 05/09/2021] [Accepted: 07/08/2021] [Indexed: 11/22/2022] Open
Abstract
The genomic context of the mcr-1 gene in Escherichia coli from animal feces has been widely reported. However, less is known about the mcr-1-carrying plasmid characteristics and other functional regions of Escherichia coli isolates from animal organs with lesions. The present study investigated the antimicrobial resistance, population structure, and genetic features of mcr-1-positive Escherichia coli strains isolated from animal organs with lesions. The antimicrobial susceptibility testing indicated that 24 mcr-1-positive Escherichia coli isolates were resistant to at least three or all antimicrobial categories. MLST analysis suggested that the dominant clone complexes (CC) were mainly CC156, CC448, and CC10. In addition, ST10596, a newly discovered sequence type in swine, failed to be classified. Meanwhile, the mcr-1 gene located on the different plasmids was successfully transferred to the recipients, and whole-genome sequencing indicated the mcr-1 gene was embedded in mcr-1-pap2 cassette but not flanked by ISApl1. The mcr-1 gene is located on the chromosome and embedded in Tn6330. Furthermore, NDM-5 was found on the IncX3-type plasmid of J-8. The virB6 and traI gene of type IV secretion system (T4SS) were truncated by IS2 and IS100 and located on the IncX4- and the IncHI2/HI2A/N-type plasmids, respectively. The multidrug-resistant (MDR) region of IncHI2/HI2A/N-type plasmids contained two class 1 integrons (In0, In640) and four composite transposons (Tn4352, Tn6010, cn_4692_IS26, cn_6354_IS26). Overall, 24 mcr-1-positive Escherichia coli isolates in our study showed MDR, or even extensively drug resistant (XDR), and exhibited population diversity. The T4SS gene truncation by the insertion sequence may affect the efficiency of plasmid conjugative transfer. Furthermore, the class 1 integrons and composite transposons in the MDR region of IncHI2/HI2A/n-type plasmid contributed to the multireplicon plasmid formation, the acquisition, and transfer of antimicrobial resistance genes (ARGs).
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Affiliation(s)
- Zengyuan Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yingqiu Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wei Xi
- Qingdao Adverse Drug Reaction Monitoring Center, China Qingdao Institute for Food and Drug Control, Qingdao, China
| | - Shuangshi Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jia Liu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hailong Mu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Beibei Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hao He
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yunpeng Fan
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wuren Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Weimin Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Mingzhe Fu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xiaoping Song
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
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Anan MMG, El-Seidi EA, Mostafa MS, Rashed LA, El-Wakil DM. Detection of Plasmid-Mediated Mobile Colistin Resistance Gene ( mcr-1) in Enterobacterales Isolates from a University Hospital. Infect Drug Resist 2021; 14:3063-3070. [PMID: 34408450 PMCID: PMC8364850 DOI: 10.2147/idr.s318787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Colistin represents one of the last treatment options for infections caused by multi-drug resistant (MDR) Enterobacterales. The emergence of a plasmid-mediated mobile colistin resistance-1 (mcr-1) gene has raised serious concerns about its potential dissemination among bacteria. METHODS In this study, we evaluated the chromogenic medium, CHROMID® Colistin Resistance (COLR) agar, for the rapid detection of colistin-resistant Enterobacterales using broth microdilution (BMD) as a reference method. We also attempted to detect mcr-1, -2, -3, -4, and -5 genes, as well as the insertion sequence ISApl1 via polymerase chain reaction (PCR), followed by sequencing of mcr gene(s). RESULTS Among the 100 studied Enterobacterales isolates, 53% of them were colistin-resistant, with higher rate among Klebsiella pneumoniae (75%) as compared to Escherichia coli (44.4%). The COLR agar showed 83.2% sensitivity and 97.9% specificity for the detection of colistin resistance. Among colistin-resistant isolates, mcr-1 gene was only detected in four (7.5%) E. coli isolates. The ISApl1 was not found among mcr-1 positive isolates. Sequencing of mcr-1 gene revealed nucleotide sequence homogeneity with the wild-type mcr-1 gene in BLAST. CONCLUSION The COLR agar is a promising phenotypic method for the detection of colistin-resistant Enterobacterales. Multiplex PCR followed by sequencing can be used for mcr genes' detection and characterization.
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Affiliation(s)
- Mera Mohammed Galal Anan
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Eman Ahmed El-Seidi
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Marwa Salah Mostafa
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Laila Ahmed Rashed
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Doaa Mahdy El-Wakil
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt
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Comparative Genomic Analysis of Extended-spectrum β-lactamase and mcr-1 Positive Escherichia coli from Gut Microbiota of Healthy Singaporeans. Appl Environ Microbiol 2021; 87:e0048821. [PMID: 34347523 DOI: 10.1128/aem.00488-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and six different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analysed the genetic context of the resistance genes and found that composite transposons played important roles in the co-transfer of blaCTX-M-15/55 and qnrS1, as well as the acquisition of mcr-1. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome SNPs shared by these isolates, we identified possible clonal transmission of a MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. Importance The human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, we found that MDR E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, and are highly diverse to each other. By comparing their genomes with the ESBL-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected a MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.
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A transposon-associated CRISPR/Cas9 system specifically eliminates both chromosomal and plasmid-borne mcr-1 in Escherichia coli. Antimicrob Agents Chemother 2021; 65:e0105421. [PMID: 34339270 PMCID: PMC8448152 DOI: 10.1128/aac.01054-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The global spread of antimicrobial-resistant bacteria has been one of the most severe threats to public health. The emergence of the mcr-1 gene has posed a considerable threat to antimicrobial medication since it deactivates one last-resort antibiotic, colistin. There have been reports regarding the mobilization of the mcr-1 gene facilitated by ISApl1-formed transposon Tn6330 and mediated rapid dispersion among Enterobacteriaceae species. Here, we developed a CRISPR/Cas9 system flanked by ISApl1 in a suicide plasmid capable of exerting sequence-specific curing against the mcr-1-bearing plasmid and killing the strain with chromosome-borne mcr-1. The constructed ISApl1-carried CRISPR/Cas9 system either restored sensitivity to colistin in strains with plasmid-borne mcr-1 or directly eradicated the bacteria harboring chromosome-borne mcr-1 by introducing an exogenous CRISPR/Cas9 targeting the mcr-1 gene. This method is highly efficient in removing the mcr-1 gene from Escherichia coli, thereby resensitizing these strains to colistin. The further results demonstrated that it conferred the recipient bacteria with immunity against the acquisition of the exogenous mcr-1 containing the plasmid. The data from the current study highlighted the potential of the transposon-associated CRISPR/Cas9 system to serve as a therapeutic approach to control the dissemination of mcr-1 resistance among clinical pathogens.
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Zheng Z, Lei Y, Wang Y, Lin C, Lin J. Occurrence of mcr Positive Strains and Molecular Characteristics of Two mcr-1 Positive Salmonella typhimurium and Escherichia coli from a Chinese Women's and Children's Hospital. Infect Drug Resist 2021; 14:2925-2932. [PMID: 34349527 PMCID: PMC8327187 DOI: 10.2147/idr.s322686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/22/2021] [Indexed: 12/18/2022] Open
Abstract
Background The purpose of this study was to evaluate the prevalence of mobile colistin resistance genes (mcr) in Gram-negative bacteria and to analyze the molecular characteristics of mcr-1 positive Salmonella typhimurium strain 75 and Escherichia coli strain 107 from the Quanzhou Women’s and Children’s Hospital in China. Methods The genes mcr-1 through mcr-9 were screened via multiplex PCR. Antibiotic susceptibility was detected using a GN11 card with the VITEK-2 compact automated system. Whole genomes were sequenced using PacBio’s single molecule real-time (SMRT) technology. Results In this study, mcr-1 was detected in only four strains, with a positivity rate of 0.65% (4/616). All the four strains were resistant to more than three different kinds of antibiotics. The mcr-1 positive S. typhimurium strain 75 harbored IncHI2 plasmid, which carried mcr-1 gene, while the mcr-1 positive E. coli strain 107 contained four plasmids including one mcr-1 harboring IncHI2 plasmid, one IncFII plasmid and two IncI1-I (Alpha) plasmids. Mobile elements carrying mcr-1 in the 75_plasmid and 107_plasmid-1 were located in the IS1086(ISApl1)-IS30A(ISApl1)-mcr-1-hp and IS1086(ISApl1)-mcr-1-hp regions, respectively. Tn6010 carrying drug efflux pump genes was found in 75_plasmid, while cn_31611_IS26 carrying multi-drug resistance (MDR) genes were found in 107_plasmid-1. Conclusion This study found that mcr-1 was prevalent at a low frequency in the Quanzhou Women’s and Children’s Hospital. A similar genetic pattern of mcr-1 transmission was found in both E. coli and S. typhimurium.
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Affiliation(s)
- Zhenzhu Zheng
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Ying Lei
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Yinna Wang
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Chunli Lin
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
| | - Jiansheng Lin
- Department of Laboratory Medicine, Quanzhou Women's and Children's Hospital, Quanzhou, People's Republic of China
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Lu J, Dong N, Liu C, Zeng Y, Sun Q, Zhou H, Hu Y, Chen S, Shen Z, Zhang R. Prevalence and molecular epidemiology of mcr-1-positive Klebsiella pneumoniae in healthy adults from China. J Antimicrob Chemother 2021; 75:2485-2494. [PMID: 32516364 DOI: 10.1093/jac/dkaa210] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To investigate the nationwide prevalence of mcr-1-positive Klebsiella pneumoniae (MCRPKP) strains among healthy adults in China and identify their phenotypic and genomic characterizations. METHODS A total of 7401 rectal swab samples were collected from healthy individuals in 30 hospitals located in 30 provinces and municipalities of mainland China in 2016. Colistin-resistant bacteria were enriched in colistin-supplemented lysogeny broth. MCRPKP strains were isolated and characterized with MALDI-TOF MS, PCR analysis and antimicrobial susceptibility testing. The genomic characteristics of MCRPKP strains were determined by WGS and bioinformatics analysis. RESULTS Seven MCRPKP strains and one mcr-1-positive Klebsiella variicola strain were selectively isolated from six locales (three from Henan and one from each of Tianjin, Jiangxi, Yunnan, Gansu and Tibet). Antimicrobial susceptibility testing results indicated that all mcr-1-positive strains were susceptible to meropenem, aztreonam and ceftazidime/avibactam. WGS analysis suggested these strains belonged to seven distinct STs: ST15, ST1425, ST1462, ST273, ST307, ST391 and ST37-SLV. mcr-1 genes were carried by diverse plasmids, including IncHI2 (n = 3), IncX4 (n = 2), IncHI2/IncN (n = 1), IncFIB (n = 1) and one other plasmid type. Two ST15 strains harboured both mcr-1 and mcr-8 genes, which has not been reported before. CONCLUSIONS Our data indicated a low prevalence of mcr-1-positive Klebsiella strains (0.11%, 8/7401) in healthy individuals in mainland China and most of these strains remained susceptible to clinically important antibiotics. The prevalence and coexistence of mcr-1 and mcr-8 in K. pneumoniae may further threaten public health through either the food chain or environmental routes.
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Affiliation(s)
- Jiayue Lu
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yu Zeng
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Qiaoling Sun
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Hongwei Zhou
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yanyan Hu
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
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Abstract
The reversibility of antibiotic resistance is theoretically attractive due to the prospect of restoring the clinical potency of antibiotics. It is important to find out the factors that affect the reversibility of antibiotic resistance. Here, an mcr-1-positive multidrug-resistant (MDR) environmental Escherichia coli isolate was successively passaged under four antibiotic-free culture conditions. The relative abundances of multiple antibiotic resistance genes (ARGs) kept decreasing during the successive passages. The linear correlations between abundances of ARGs on the same MDR plasmid reflected that the decay of antibiotic resistance during the passage was mainly due to the elimination of the MDR plasmid (pMCR_W5-6). Colistin-susceptible strains were isolated at the end of the passage. The whole-genome sequencing of two susceptible isolates detected the elimination of the MDR plasmid and deletion of the mcr-1 gene. Deletions of DNA fragments from chromosome and plasmid were closely related to a variety of insertion sequences (ISs). The results of coculture of resistant and susceptible strains at different antibiotic concentrations indicated that the high fitness cost led to the poor stability of mobile ARGs. Strict control of the use of antibiotics can at least reverse the severe antibiotic resistance caused by mobile ARGs of high fitness cost. IMPORTANCE The dissemination of bacterial antibiotic resistance is a serious threat to human health. The development of new antibiotics faces both economic and technological challenges. The reversibility of antibiotic resistance has become an important issue causing wide concern due to the prospect of restoring the clinical potency of antibiotics. Our study suggests that the high mobility of ARGs of high fitness cost may just reflect their poor stability. Therefore, strict control of the use of antibiotics can at least reverse the severe antibiotic resistance caused by mobile ARGs of high fitness cost. This study brings hope for the possibility of curbing the dissemination of antibiotic resistance.
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Girardello R, Piroupo CM, Martins J, Maffucci MH, Cury AP, Franco MRG, Malta FDM, Rocha NC, Pinho JRR, Rossi F, Duarte AJDS, Setubal JC. Genomic Characterization of mcr-1.1-Producing Escherichia coli Recovered From Human Infections in São Paulo, Brazil. Front Microbiol 2021; 12:663414. [PMID: 34177843 PMCID: PMC8221240 DOI: 10.3389/fmicb.2021.663414] [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: 02/02/2021] [Accepted: 05/12/2021] [Indexed: 11/25/2022] Open
Abstract
Polymyxins are one of most important antibiotics available for multidrug-resistant Gram-negative infections. Diverse chromosomal resistance mechanisms have been described, but the polymyxin resistance phenotype is not yet completely understood. The objective of this study was to characterize colistin resistant mcr-1-producing strains isolated from human infections over one year in a hospital setting (Hospital das Clínicas, São Paulo, Brazil). We isolated 490 colistin-resistant Gram-negative rods, of which eight were mcr-1.1-positive Escherichia coli, the only species with this result, indicating a low incidence of the mcr-1 production mechanism among colistin-resistant isolates. All mcr-1.1 positive isolates showed similarly low MICs for colistin and were susceptible to most antibiotics tested. The isolates showed diversity of MLST classification. The eight mcr-1.1-positive E. coli genomes were sequenced. In seven of eight isolates the mcr-1.1 gene is located in a contig that is presumed to be a part of an IncX4 plasmid; in one isolate, it is located in a contig that is presumed to be part of an IncHI2A plasmid. Three different genomic contexts for mcr-1.1 were observed, including a genomic cassette mcr-1.1-pap2 disrupting a DUF2806 domain-containing gene in six isolates. In addition, an IS1-family transposase was found inserted next to the mcr-1.1 cassette in one isolate. An mcr-1.1-pap2 genomic cassette not disrupting any gene was identified in another isolate. Our results suggest that plasmid dissemination of hospital-resident strains took place during the study period and highlight the need for continued genomic surveillance.
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Affiliation(s)
- Raquel Girardello
- Laboratório de Microbiologia Molecular e Clínica, Programa de Pós-Graduação em Ciências da Saúde, Universidade São Francisco, Braganca Paulista, Brazil
| | - Carlos Morais Piroupo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Marcia Helena Maffucci
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula Cury
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Renata Gomes Franco
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | | - Natália Conceição Rocha
- Laboratório de Microbiologia Molecular e Clínica, Programa de Pós-Graduação em Ciências da Saúde, Universidade São Francisco, Braganca Paulista, Brazil.,Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - João Renato Rebello Pinho
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Técnicas Especiais, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Flavia Rossi
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alberto José da Silva Duarte
- Hospital das Clínicas, Divisão Laboratório Central, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Lentz SAM, Dalmolin TV, Barth AL, Martins AF. mcr-1 Gene in Latin America: How Is It Disseminated Among Humans, Animals, and the Environment? Front Public Health 2021; 9:648940. [PMID: 34026712 PMCID: PMC8139396 DOI: 10.3389/fpubh.2021.648940] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/22/2021] [Indexed: 12/29/2022] Open
Affiliation(s)
- Silvia Adriana Mayer Lentz
- Programa de Ps Graduao em Microbiologia Agrcola e Do Ambiente, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil.,Laboratrio de Microbiologia Aplicada, Instituto de Cincias Bsicas da Sade, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | | | - Afonso Lus Barth
- Laboratrio de Pesquisa em Resistncia Bacteriana (LABRESIS), Hospital de Clnicas de Porto Alegre, Porto Alegre, Brazil
| | - Andreza Francisco Martins
- Programa de Ps Graduao em Microbiologia Agrcola e Do Ambiente, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil.,Laboratrio de Microbiologia Aplicada, Instituto de Cincias Bsicas da Sade, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil.,Laboratrio de Pesquisa em Resistncia Bacteriana (LABRESIS), Hospital de Clnicas de Porto Alegre, Porto Alegre, Brazil
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Bilal H, Rehman TU, Khan MA, Hameed F, Jian ZG, Han J, Yang X. Molecular Epidemiology of mcr-1, bla KPC-2, and bla NDM-1 Harboring Clinically Isolated Escherichia coli from Pakistan. Infect Drug Resist 2021; 14:1467-1479. [PMID: 33888998 PMCID: PMC8057800 DOI: 10.2147/idr.s302687] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/11/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose The multiple-drug resistant Escherichia coli are among the deadliest pathogens causing life-threatening infections. This study was planned to determine the molecular epidemiology of mcr-1, bla KPC-2, and bla NDM-1 harboring clinically isolated E. coli from Pakistan. Methods In total, 545 strains of E. coli from clinical samples were collected from June 2018 to September 2019. All the isolates were screened for colistin-resistance, extended-spectrum-β-lactamases (ESBL), and carbapenemases through the micro-dilution method, Double-Disk-Synergy-Test (DDST), and Modified-Hodge-Test (MHT). The detection, sequence-typing, conjugal transfer, S1-PFGE, plasmid-replicon-typing, and southern-blotting for mcr, ESBL, and carbapenemase-encoding genes were performed. Findings A total of four (0.73%) colistin-resistant strains carrying alongside mcr-1 and bla CTX-M-15 genes, three of these strains also had the bla TEM-1 gene. The presence of ESBL genes was detected in 139 (25.5%) isolates harboring bla CTXM-15 (74.82%), bla TEM (34.53%), bla SHV (28.06%) and bla OXA-1 (28.78%). In 129 carbapenemase-producers, 35.83% possessed bla NDM-1, 26.67% bla KPC-2, 8.3% bla OXA-48, 25% bla VIM-1, and 20.83% bla IMP-1 genes. The sequence typing revealed that mcr-1 harboring isolates belonged to ST405, ST117, and ST156. Fifty percent of bla KPC-2 and 48.83% of bla NDM-1 were found on ST131 and ST1196, respectively. Two rare types of STs, ST7584, and ST8671 were also identified in this study. The mcr-1 gene was located on Incl2 (60-kb) plasmid. The bla KPC-2 was present on (140-kb) IncH12, (100-kb) IncN, (90-kb) Incl1, while bla NDM-1 was located on (70-kb) IncFIIK, (140-kb) IncH12, (100-kb) IncN, (60-kb) IncA/C, and (45-kb) IncFII plasmids, which were successfully trans-conjugated. Among the plasmid types, the Incl1 carrying bla KPC-2, IncH12 harboring bla KPC-2 and bla NDM-1, and IncFIIK carrying bla NDM-1 were for the first time detected in Pakistan. Conclusion The mcr-1, bla KPC-2, and bla NDM-1 genes finding in various clonal and plasmids types indicate that a substantial selection of the resistance genes had occurred in our clinical strains.
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Affiliation(s)
- Hazrat Bilal
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
| | - Tayyab Ur Rehman
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Muhammad Asif Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Fareeha Hameed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Zhang Gao Jian
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
| | - Jianxiong Han
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
| | - Xingyuan Yang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
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Genomic Insights into a Colistin-Resistant Uropathogenic Escherichia coli Strain of O23:H4-ST641 Lineage Harboring mcr-1.1 on a Conjugative IncHI2 Plasmid from Egypt. Microorganisms 2021; 9:microorganisms9040799. [PMID: 33920265 PMCID: PMC8069611 DOI: 10.3390/microorganisms9040799] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
The reintroduction of colistin, a last-resort antibiotic for multidrug-resistant pathogens, resulted in the global spread of plasmid-mediated mobile colistin resistance (mcr) genes. Our study investigated the occurrence of colistin resistance among Escherichia coli isolated from patients with urinary tract infections admitted to a teaching hospital in Egypt. Out of 67 isolates, three isolates were colistin-resistant, having a minimum inhibitory concentration of 4 µg/mL and possessing the mcr-1 gene. A double mechanism of colistin resistance was detected; production of mcr-1 along with amino acid substitution in PmrB (E123D and Y358N) and PmrA (G144S). Broth mating experiments inferred that mcr-1 was positioned on conjugative plasmids. Whole-genome sequencing of EC13049 indicated that the isolate belonged to O23:H4-ST641 lineage and to phylogroup D. The mcr-1-bearing plasmid corresponded to IncHI2 type with a notable similarity to other E. coli plasmids previously recovered from Egypt. The unbanned use of colistin in the Egyptian agriculture sector might have created a potential reservoir for the mcr-1 gene in food-producing animals that spread to humans. More proactive regulations must be implemented to prevent further dissemination of this resistance. This is the first characterization of mcr-1-carrying IncHI2:ST4 plasmid recovered from E. coli of a clinical source in Egypt.
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Li R, Du P, Zhang P, Li Y, Yang X, Wang Z, Wang J, Bai L. Comprehensive Genomic Investigation of Coevolution of mcr genes in Escherichia coli Strains via Nanopore Sequencing. GLOBAL CHALLENGES (HOBOKEN, NJ) 2021; 5:2000014. [PMID: 33728052 PMCID: PMC7933819 DOI: 10.1002/gch2.202000014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/19/2020] [Indexed: 06/12/2023]
Abstract
Horizontal gene transfer facilitates the spread of antibiotic resistance genes, which constitutes a global challenge. However, the evolutionary trajectory of the mobile colistin resistome in bacteria is largely unknown. To investigate the coevolution and fitness cost of the colistin resistance genes in wild strains, different assays to uncover the genomic dynamics of mcr-1 and mcr-3 in bacterial populations are utilized. Escherichia coli strains harboring both mcr-1 and mcr-3.1/3.5 are isolated and mcr genes are associated with diverse mobile elements. Under exposure to colistin, the mcr-1-bearing resistome is stably inherited during bacterial replication, but mcr-3 is prone to be eliminated in populations of certain strains. In the absence of colistin, the persistence rates of the mcr-1 and mcr-3-bearing subclones varies depending on the genomic background. The decay of the mcr-bearing bacterial populations can be mediated by the elimination of mcr-containing segments, large genomic deletions, and plasmid loss. Mobile elements, including plasmids and transposons, are double-edged swords in the evolution of the resistome. The findings support the idea that antibiotic overuse accounts for global spread of multidrug-resistant (MDR) bacteria. Therefore, stringent regulation of antibiotic prescription for humans and animals should be performed systematically to alleviate the threat of MDR bacteria.
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Affiliation(s)
- Ruichao Li
- Jiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesCollege of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
- Institute of Comparative MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Pengcheng Du
- Institute of Infectious DiseasesBeijing Ditan HospitalCapital Medical University, and Beijing Key Laboratory of Emerging Infectious DiseasesBeijing100015P. R. China
| | - Pei Zhang
- Key Laboratory of Food Safety Risk AssessmentNational Health Commission of the People's Republic of ChinaChina National Center for Food Safety Risk AssessmentBeijing100022P. R. China
| | - Yan Li
- Jiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesCollege of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Xiaorong Yang
- Center for Disease Control and Prevention of Sichuan ProvinceChengdu610041P. R. China
| | - Zhiqiang Wang
- Jiangsu Co‐Innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesCollege of Veterinary MedicineYangzhou UniversityYangzhou225009P. R. China
| | - Juan Wang
- College of Veterinary MedicineNorthwest A&F UniversityYangling712100P. R. China
| | - Li Bai
- Key Laboratory of Food Safety Risk AssessmentNational Health Commission of the People's Republic of ChinaChina National Center for Food Safety Risk AssessmentBeijing100022P. R. China
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Li W, Li Y, Jia Y, Sun H, Zhang C, Hu G, Yuan L. Genomic characteristics of mcr-1 and bla CTX-M-type in a single multidrug-resistant Escherichia coli ST93 from chicken in China. Poult Sci 2021; 100:101074. [PMID: 33774373 PMCID: PMC8025056 DOI: 10.1016/j.psj.2021.101074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
This study was undertaken to discern the transmission characteristics of mcr-1 and blaCTX-M-type in one multidrug-resistant Escherichia coli LWY24 from chicken in China. The genetic profiles of LWY24 isolate were determined by conjugation, S1-pulsed-field gel electrophoresis, southern blot hybridization, and whole genome sequencing analysis. Meanwhile, co-transfer of plasmids in LWY24 isolate was screened by dual conjugation assays. The LWY24 isolate was identified as ST93, and harbored 3 conjugative plasmids, pLWY24J-3 (blaCTX-M-55-bearing IncFⅡ), pLWY24J-mcr-1 (mcr-1-carrying IncI2), and pLWY24J-4 (non-resistance-conferring IncI1), and one nonconjugative plasmid pLWY24 (blaCTX-M-14-containing IncHI2/IncHI2A). Numerous resistance genes, insertion sequences (especially IS26), and transposons were found in the 4 plasmids, suggesting that horizontal transmission have occurred by plasmid mating, homologous recombination, and transpositions. Under the selection pressure of cefotaxime and colistin or cefotaxime alone, the mcr-1-bearing plasmid and the blaCTX-M-55-harboring plasmid could be co-transferred at a similar frequency, with 8.00 × 10−4 or 9.00 × 10−4 transconjugants per donor cell, respectively. The specific shufflon region in mcr-1-encoding plasmid could generate up to 6 diverse PilV structures, which may further accelerate the horizontal transfer of plasmid. In conclusion, the transmission characteristics of mcr-1 and blaCTX-M-type in LWY24 isolate could due to clonal spread of ST93, selective pressure of cefotaxime, IS26-mediate homologous recombination and transposition, and the specific shufflon region.
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Affiliation(s)
- Wenya Li
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yinshu Li
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yating Jia
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Huarun Sun
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Chunhui Zhang
- College of Animal Medicine, Henan University of Animal Husbandry & Economy, Zhengzhou 450046, China
| | - Gongzheng Hu
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Li Yuan
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China.
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Xu Y, Liu L, Zhang H, Feng Y. Co-production of Tet(X) and MCR-1, two resistance enzymes by a single plasmid. Environ Microbiol 2021; 23:7445-7464. [PMID: 33559156 DOI: 10.1111/1462-2920.15425] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/04/2021] [Indexed: 12/17/2022]
Abstract
Tigecycline and colistin are few of 'last-resort' antibiotic defences used in anti-infection therapies against carbapenem-resistant bacterial pathogens. The successive emergence of plasmid-borne tet(X) tigecycline resistance mechanism and mobile colistin resistance (mcr) determinant, renders them clinically useless. Here, we report that co-carriage of tet(X6) and mcr-1 gives co-resistance to both classes of antibiotics by a single plasmid in Escherichia coli. Tet(X6), the new tigecycline resistance enzyme is functionally defined. Both Tet(X6) and MCR-1 robustly interfere accumulation of antibiotic-induced reactive oxygen species (ROS). Unlike that mcr-1 exerts fitness cost in E. coli, tet(X6) does not. In the tet(X6)-positive strain that co-harbors mcr-1, tigecycline resistance is independently of colistin resistance caused by MCR-1-mediated lipid A remodelling, and vice versa. In general consistency with that of MCR-1, Tet(X6) leads to the failure of tigecycline treatment in the infection model of G. mellonella. Taken together, the co-production of Tet(X) and MCR-1 appears as a major clinic/public health concern.
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Affiliation(s)
- Yongchang Xu
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Lizhang Liu
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China.,College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
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Gao Y, Xia L, Pan R, Xuan H, Guo H, Song Q, Wei J, Shao D, Liu K, Li Z, Qiu Y, Ma Z, Li B. Identification of mcr-1 and a novel chloramphenicol resistance gene catT on an integrative and conjugative element in an Actinobacillus strain of swine origin. Vet Microbiol 2021; 254:108983. [PMID: 33486327 DOI: 10.1016/j.vetmic.2021.108983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 01/05/2021] [Indexed: 11/27/2022]
Abstract
The aim of this study was to characterize a mcr-1-carrying integrative and conjugative element (ICE) in a novel Pasteurellaceae-like bacteria of swine origin. The mcr-1-positive GY-402 strain, recovered from a pig fecal sample, was subjected to whole genome sequencing with the combination of Illumina Hiseq and MinION platforms. Genome-based taxonomy revealed that strain GY-402 exhibited highest ANI value (84.89 %) to Actinobacillus succinogenes, which suggested that it represented a novel Actinobacillus species. Sequence analysis revealed that mcr-1 was clustered with eight other resistance genes in the MDR region of a novel ICE element, named ICEAsp1. Inverse PCR and mating assays showed that ICEAsp1 is active and transferrable. In addition, six circular forms mediated by four ISApl1 elements were detected with different inverse PCR sets, indicating that flexible composite transposons could be formed by pairwise combinations of multiple IS copies. Cloning experiment and phylogenetic analysis revealed that the novel Cat protein, designated CatT, belongs to type-A family and confers resistance to chloramphenicol. In conclusion, this is, to the best of our knowledge, the first report of mcr-1 gene on ICE structure and also in Pasteurellaceae bacteria. The diverse composite transposons mediated by multicopy IS elements may facilitate the dissemination of different resistance genes.
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Affiliation(s)
- Yun Gao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; College of Veterinary Medicine, Xinjiang Agricultural University, Urmuqi, 830052, China
| | - Lining Xia
- College of Veterinary Medicine, Xinjiang Agricultural University, Urmuqi, 830052, China
| | - Ruyi Pan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Huiyong Xuan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; College of Veterinary Medicine, Xinjiang Agricultural University, Urmuqi, 830052, China
| | - Hongdou Guo
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Qiangqiang Song
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China; College of Veterinary Medicine, Xinjiang Agricultural University, Urmuqi, 830052, China
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Donghua Shao
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Zongjie Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Beibei Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
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48
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Shafiq M, Huang J, Shah JM, Ali I, Rahman SU, Wang L. Characterization and resistant determinants linked to mobile elements of ESBL-producing and mcr-1-positive Escherichia coli recovered from the chicken origin. Microb Pathog 2021; 150:104722. [PMID: 33421607 DOI: 10.1016/j.micpath.2020.104722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/22/2020] [Accepted: 12/27/2020] [Indexed: 01/13/2023]
Abstract
The spread of antimicrobial resistance (AMR) in Escherichia coli is a complex process linked with various mobile genetic elements (MGEs) like plasmids, transposons, and integrons. This study aimed to determine the co-occurrence of ESBL and mcr-1 and their physical linkage with MGEs in E. coli. E. coli strains of chicken origin were obtained from different commercial farms of eastern China from 2010 to 2011. Antimicrobial sensitivity testing, identification of different antibiotic-resistant genes (ARGs), and prevalence and evidence involvement of integrons, ISEcp1, ISCR1, and ISApl1, were determined. A multiplex PCR was used to detect virulence genes and the phylogenetic clustering of isolates. Conjugation experiments, plasmid replicon typing were performed to know the transferability of ARGs and MGEs. A total of 83.33% of isolates were found to be multidrug-resistant (MDR). The incidence rate of blaCTX-M, blaSHV,blaTEM, and mcr-1 was found to be 30%, 10.95%, 8.09%, and 36.66%, respectively. The most prevalent combination was noticed for mcr-1 and blaCTX-M 73%, whereas the most prominent blaCTX-M alleles found, were blaCTX-M-55 46%, followed by blaCTX-M-14 31%, and blaCTX-M-15 13%. The frequency of ISEcp1, ISCR1, ISApl1, and int1 was 27.77%, 53.70%, 51.85%, and 70.37% respectively. Most β-lactamases, especially blaCTX-M, blaSHV, and blaTEM, were associated with ISEcp1, ISCR1, and Integron 1, whereas the ISAPl1-mcr-1 segment was observed in mcr-1-positive E. coli isolates. Phylogrouping revealed that group A was the most predominant phylotype, whereas the common virulence genes detected in these isolates were EHEC, EAEC, and EPEC. Conjugation assay also indicated that multiple genetic elements were involved; common plasmids identified were FIB 61.11%, followed by IncHI2 48.14%, and FrepB 33.33%. Propagation of such MDR strains carrying multiple resistance elements among the bacterial population is a threat of worry.
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Affiliation(s)
- Muhammad Shafiq
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinhu Huang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jan Mohammad Shah
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ilyas Ali
- College of Animal Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sadeeq Ur Rahman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, KP, Pakistan
| | - Liping Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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49
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Shen C, Zhong LL, Ma F, El-Sayed Ahmed MAEG, Doi Y, Zhang G, Liu Y, Huang S, Li HY, Zhang L, Liao K, Xia Y, Dai M, Yan B, Tian GB. Genomic patterns and characterizations of chromosomally-encoded mcr-1 in Escherichia coli populations. Gut Pathog 2020; 12:55. [PMID: 33292487 PMCID: PMC7700713 DOI: 10.1186/s13099-020-00393-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/17/2020] [Indexed: 01/20/2023] Open
Abstract
The emergence and transmission of the mobile colistin resistance gene (mcr-1) threatened the extensive use of polymyxin antimicrobials. Accumulated evidence showed that the banning of colistin additive in livestock feed efficiently reduce mcr-1 prevalence, not only in animals but also in humans and environments. However, our previous study has revealed that a small proportion of Escherichia coli could continually carry chromosomally-encoded mcr-1. The chromosomally-encoded events, indicated the existence of stabilized heritage of mcr-1 and revealed a potential threat in the antimicrobial stewardship interventions, are yet to be investigated. In this study, we systematically investigated the genetic basis of chromosomally-encoded mcr-1 in prevalence and potential mechanisms of lineage, plasmid, insertion sequence, and phage. Our results demonstrated that the emergence of chromosomally-encoded mcr-1 could originate from multiple mechanisms, but mainly derived through the recombination of ISApl1/Tn6330. We reported a specific transmission mechanism, which is a phage-like region without lysogenic components, could associate with the emergence and stabilization of chromosomally-encoded mcr-1. These results highlighted the potential origin and risks of chromosomally-encoded mcr-1, which could be a heritable repository and thrive again when confronted with new selective pressures. To the best of our knowledge, this is the first study to systematically reveal the genomic basis of chromosomally-encoded mcr-1, and report a specific transmission pattern involved in phage-like region. Overall, we demonstrate the origin mechanisms and risks of chromosomally-encoded mcr-1. It highlights the need of public attention on chromosome-encoded mcr-1 to prevent from its reemergence.
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Affiliation(s)
- Cong Shen
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Lan-Lan Zhong
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Furong Ma
- Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Mohamed Abd El-Gawad El-Sayed Ahmed
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
- Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology (MUST), Cairo, Egypt
| | - Yohei Doi
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Guili Zhang
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Yang Liu
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China
| | - Songyin Huang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hong-Yu Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liyan Zhang
- Department of Clinical Laboratory, Guangdong Provincial People's Hospital/Guangdong Academy of Medical Sciences, Guangzhou, 510080, Guangdong, China
| | - Kang Liao
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China
| | - Yong Xia
- Department of Clinical Laboratory Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Min Dai
- School of Laboratory Medicine, Chengdu Medical College, Chengdu, 610500, China
| | - Bin Yan
- Department of Neonatal Surgery, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, 510080, China.
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, 510080, China.
- School of Medicine, Xizang Minzu University, Xianyang, 712082, Shaanxi, China.
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50
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Savin M, Bierbaum G, Blau K, Parcina M, Sib E, Smalla K, Schmithausen R, Heinemann C, Hammerl JA, Kreyenschmidt J. Colistin-Resistant Enterobacteriaceae Isolated From Process Waters and Wastewater From German Poultry and Pig Slaughterhouses. Front Microbiol 2020; 11:575391. [PMID: 33193188 PMCID: PMC7661462 DOI: 10.3389/fmicb.2020.575391] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Due to the high prevalence of colistin-resistant Enterobacteriaceae in poultry and pigs, process waters and wastewater from slaughterhouses were considered as a hotspot for isolates carrying plasmid-encoded, mobilizable colistin resistances (mcr genes). Thus, questions on the effectiveness of wastewater treatment in in-house and municipal wastewater treatment plants (WWTPs) as well as on the diversity of the prevailing isolates, plasmid types, and their transmissibility arise. Process waters and wastewater accruing in the delivery and unclean areas of two poultry and two pig slaughterhouses were screened for the presence of target colistin-resistant bacteria (i.e., Escherichia coli, Klebsiella spp., Enterobacter cloacae complex). In-house and municipal WWTPs (mWWTPs) including receiving waterbodies were investigated as well. Samples taken in the poultry slaughterhouses yielded the highest occurrence of target colistin-resistant Enterobacteriaceae (40.2%, 33/82), followed by mWWTPs (25.0%, 9/36) and pig slaughterhouses (14.9%, 10/67). Recovered isolates exhibited various resistance patterns. The resistance rates using epidemiological cut-off values were higher in comparison to those obtained with clinical breakpoints. Noteworthy, MCR-1-producing Klebsiella pneumoniae and E. coli were detected in scalding waters and preflooders of mWWTPs. A total of 70.8% (46/65) of E. coli and 20.6% (7/34) of K. pneumoniae isolates carried mcr-1 on a variety of transferable plasmids with incompatibility groups IncI1, IncHI2, IncX4, IncF, and IncI2 ranging between 30 and 360 kb. The analyzed isolates carrying mcr-1 on transferable plasmids (n = 53) exhibited a broad diversity, as they were assigned to 25 different XbaI profiles. Interestingly, in the majority of colistin-resistant mcr-negative E. coli and K. pneumoniae isolates non-synonymous polymorphisms in pmrAB were detected. Our findings demonstrated high occurrence of colistin-resistant E. coli and K. pneumoniae carrying mcr-1 on transferrable plasmids in poultry and pig slaughterhouses and indicate their dissemination into surface water.
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Affiliation(s)
- Mykhailo Savin
- Institute of Animal Sciences, University of Bonn, Bonn, Germany.,Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, Bonn, Germany
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Khald Blau
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Marijo Parcina
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Esther Sib
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, Bonn, Germany
| | - Kornelia Smalla
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Ricarda Schmithausen
- Institute for Hygiene and Public Health, Medical Faculty, University of Bonn, Bonn, Germany
| | | | - Jens A Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, Bonn, Germany.,Department of Fresh Produce Logistics, Hochschule Geisenheim University, Geisenheim, Germany
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