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Karpenko A, Shelenkov A, Manzeniuk I, Kulikova N, Gevorgyan A, Mikhaylova Y, Akimkin V. Whole genome analysis of multidrug-resistant Escherichia coli isolate collected from drinking water in Armenia revealed the plasmid-borne mcr-1.1-mediated colistin resistance. Microbiol Spectr 2024:e0075124. [PMID: 39166856 DOI: 10.1128/spectrum.00751-24] [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: 03/22/2024] [Accepted: 07/19/2024] [Indexed: 08/23/2024] Open
Abstract
The rate of polymyxin-resistant Enterobacteriaceae, as well as human and animal infections caused by them, is increasing worldwide, posing a high epidemiological threat since colistin represents a last-resort antibiotic to treat complicated infections. The study of environmental niches, in particular, aquatic ecosystems in terms of genome analysis of inhabiting antimicrobial-resistant (AMR) microorganisms as reservoirs of acquired resistance determinants (AMR genes), represents a specific concern from a One Health approach. Here, we present a phenotypic AMR analysis and molecular characterization of Escherichia coli isolate found in municipal drinking water after an accident in the water supply system of a residential building in Armenia in 2021. CrieF1144 E. coli isolate was resistant to ampicillin, ampicillin/sulbactam, cefuroxime, ciprofloxacin, levofloxacin, trimethoprim/sulfamethoxazole, colistin, and tigecycline, whereas whole genome sequencing (WGS) revealed blaTEM-1B, tet(A), and a combination of dfrA14 with sul1 resistance determinants, which corresponds well with phenotypic resistance above. Moreover, the multidrug-resistant isolate studied harbored mcr-1.1 gene on a conjugative 251 Kb IncHI2 plasmid, whose structure was determined using hybrid short- and long-reads assembly. CrieF1141_p1 plasmid carried all antimicrobial resistance genes revealed in the isolate and did not harbor any virulence determinants, so it could contribute to the spread of AMR genes in the bacterial population. Two copies of ISApl1 transposase-encoding element, which is likely to mediate mcr-1.1 gene mobilization, were revealed surrounding this gene in a plasmid. IMPORTANCE Evolutionary patterns of Escherichia coli show that they usually develop into highly pathogenic forms by acquiring fitness advantages such as antimicrobial resistance (AMR) and various virulence factors through horizontal gene transfer mediated by mobile elements. This has led to high prevalence of multidrug-resistant (MDR) strains, which highlights the relevancy of enhanced surveillance to monitor and prevent transmission of the MDR bacteria to human and animal populations. However, the limited number of reports regarding the whole genome sequencing (WGS) investigation of MDR E. coli strains isolated from drinking water and harboring mcr genes hampers the adoption of a comprehensive approach to address the relationship between environmental E. coli populations and human and veterinary infections. Our results highlight the relevance of analyzing the environment, especially water, as a part of the surveillance programs to understand the origins and dissemination of antimicrobial resistance within the One Health concept.
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Affiliation(s)
- Anna Karpenko
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Andrey Shelenkov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Igor Manzeniuk
- Administrative and Management Department - Directorate, Central Research Institute of Epidemiology, Moscow, Russia
| | - Nina Kulikova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
| | - Arman Gevorgyan
- Republican Veterinary and Phytosanitary Laboratory Services Center, Yerevan, Armenia
| | - Yulia Mikhaylova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, Moscow, Russia
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Li W, He Z, Di W, Xu W, Li Y, Sun B. Transposition mechanism of IS Apl1-the determinant of colistin resistance dissemination. Antimicrob Agents Chemother 2024; 68:e0123123. [PMID: 38289082 PMCID: PMC10916398 DOI: 10.1128/aac.01231-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/18/2023] [Indexed: 03/07/2024] Open
Abstract
Multidrug-resistant Enterobacteriaceae, a prominent family of gram-negative pathogenic bacteria, causes a wide range of severe diseases. Strains carrying the mobile colistin resistance (mcr-1) gene show resistance to polymyxin, the last line of defense against multidrug-resistant gram-negative bacteria. However, the transmission of mcr-1 is not well understood. In this study, genomes of mcr-1-positive strains were obtained from the NCBI database, revealing their widespread distribution in China. We also showed that ISApl1, a crucial factor in mcr-1 transmission, is capable of self-transposition. Moreover, the self-cyclization of ISApl1 is mediated by its own encoded transposase. The electrophoretic mobility shift assay experiment validated that the transposase can bind to the inverted repeats (IRs) on both ends, facilitating the cyclization of ISApl1. Through knockout or shortening of IRs at both ends of ISApl1, we demonstrated that the cyclization of ISApl1 is dependent on the sequences of the IRs at both ends. Simultaneously, altering the ATCG content of the bases at both ends of ISApl1 can impact the excision rate by modifying the binding ability between IRs and ISAPL1. Finally, we showed that heat-unstable nucleoid protein (HU) can inhibit ISApl1 transposition by binding to the IRs and preventing ISAPL1 binding and expression. In conclusion, the regulation of ISApl1-self-circling is predominantly controlled by the inverted repeat (IR) sequence and the HU protein. This molecular mechanism deepens our comprehension of mcr-1 dissemination.
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Affiliation(s)
- Wei Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhien He
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei Di
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Weifeng Xu
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yujie Li
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Baolin Sun
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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Song H, Zou S, Huang Y, Jian C, Liu W, Tian L, Gong L, Chen Z, Sun Z, Wang Y. Salmonella Typhimurium with Eight Tandem Copies of blaNDM-1 on a HI2 Plasmid. Microorganisms 2023; 12:20. [PMID: 38257847 PMCID: PMC10819877 DOI: 10.3390/microorganisms12010020] [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: 10/22/2023] [Revised: 12/09/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024] Open
Abstract
Carbapenem-resistant Salmonella has recently aroused increasing attention. In this study, a total of four sequence type 36 Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) isolates were consecutively isolated from an 11-month-old female patient with a gastrointestinal infection, of which one was sensitive to carbapenems and three were resistant to carbapenems. Via antibiotic susceptibility testing, a carbapenemases screening test, plasmid conjugation experiments, Illumina short-reads, and PacBio HiFi sequencing, we found that all four S. Typhimurium isolates contained a blaCTX-M-14-positive IncI1 plasmid. One carbapenem-sensitive S. Typhimurium isolate then obtained an IncHI2 plasmid carrying blaNDM-1 and an IncP plasmid without any resistance genes during the disease progression. The blaNDM-1 gene was located on a new 30 kb multiple drug resistance region, which is flanked by IS26 and TnAs2, respectively. In addition, the ST_F0903R isolate contained eight tandem copies of the ISCR1 unit (ISCR1-dsbD-trpF-ble-blaNDM-1-ISAba125Δ1), but an increase in MICs to carbapenems was not observed. Our work further provided evidence of the rapid spread and amplification of blaNDM-1 through plasmid. Prompting the recognition of carbapenem-resistant Enterobacterales and the initiation of appropriate infection control measures are essential to avoid the spread of these organisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (H.S.); (S.Z.); (Y.H.); (C.J.); (W.L.); (L.T.); (L.G.); (Z.C.); (Y.W.)
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Shahzad S, Willcox MDP, Rayamajhee B. A Review of Resistance to Polymyxins and Evolving Mobile Colistin Resistance Gene ( mcr) among Pathogens of Clinical Significance. Antibiotics (Basel) 2023; 12:1597. [PMID: 37998799 PMCID: PMC10668746 DOI: 10.3390/antibiotics12111597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023] Open
Abstract
The global rise in antibiotic resistance in bacteria poses a major challenge in treating infectious diseases. Polymyxins (e.g., polymyxin B and colistin) are last-resort antibiotics against resistant Gram-negative bacteria, but the effectiveness of polymyxins is decreasing due to widespread resistance among clinical isolates. The aim of this literature review was to decipher the evolving mechanisms of resistance to polymyxins among pathogens of clinical significance. We deciphered the molecular determinants of polymyxin resistance, including distinct intrinsic molecular pathways of resistance as well as evolutionary characteristics of mobile colistin resistance. Among clinical isolates, Acinetobacter stains represent a diversified evolution of resistance, with distinct molecular mechanisms of intrinsic resistance including naxD, lpxACD, and stkR gene deletion. On the other hand, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa are usually resistant via the PhoP-PhoQ and PmrA-PmrB pathways. Molecular evolutionary analysis of mcr genes was undertaken to show relative relatedness across the ten main lineages. Understanding the molecular determinants of resistance to polymyxins may help develop suitable and effective methods for detecting polymyxin resistance determinants and the development of novel antimicrobial molecules.
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Affiliation(s)
- Shakeel Shahzad
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
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Boonyasiri A, Brinkac LM, Jauneikaite E, White RC, Greco C, Seenama C, Tangkoskul T, Nguyen K, Fouts DE, Thamlikitkul V. Characteristics and genomic epidemiology of colistin-resistant Enterobacterales from farmers, swine, and hospitalized patients in Thailand, 2014-2017. BMC Infect Dis 2023; 23:556. [PMID: 37641085 PMCID: PMC10464208 DOI: 10.1186/s12879-023-08539-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Colistin is one of the last resort therapeutic options for treating carbapenemase-producing Enterobacterales, which are resistant to a broad range of beta-lactam antibiotics. However, the increased use of colistin in clinical and livestock farming settings in Thailand and China, has led to the inevitable emergence of colistin resistance. To better understand the rise of colistin-resistant strains in each of these settings, we characterized colistin-resistant Enterobacterales isolated from farmers, swine, and hospitalized patients in Thailand. METHODS Enterobacterales were isolated from 149 stool samples or rectal swabs collected from farmers, pigs, and hospitalized patients in Thailand between November 2014-December 2017. Confirmed colistin-resistant isolates were sequenced. Genomic analyses included species identification, multilocus sequence typing, and detection of antimicrobial resistance determinants and plasmids. RESULTS The overall colistin-resistant Enterobacterales colonization rate was 26.2% (n = 39/149). The plasmid-mediated colistin-resistance gene (mcr) was detected in all 25 Escherichia coli isolates and 9 of 14 (64.3%) Klebsiella spp. isolates. Five novel mcr allelic variants were also identified: mcr-2.3, mcr-3.21, mcr-3.22, mcr-3.23, and mcr-3.24, that were only detected in E. coli and Klebsiella spp. isolates from farmed pigs. CONCLUSION Our data confirmed the presence of colistin-resistance genes in combination with extended spectrum beta-lactamase genes in bacterial isolates from farmers, swine, and patients in Thailand. Differences between the colistin-resistance mechanisms of Escherichia coli and Klebsiella pneumoniae in hospitalized patients were observed, as expected. Additionally, we identified mobile colistin-resistance mcr-1.1 genes from swine and patient isolates belonging to plasmids of the same incompatibility group. This supported the possibility that horizontal transmission of bacterial strains or plasmid-mediated colistin-resistance genes occurs between humans and swine.
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Affiliation(s)
- Adhiratha Boonyasiri
- Faculty of Medicine Siriraj Hospital, Mahidol University, Salaya, Thailand
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
| | - Lauren M Brinkac
- J. Craig Venter Institute, Rockville, MD, 20850, USA
- Noblis, Reston, VA, 20191, USA
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College, London, UK
| | | | - Chris Greco
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | | | - Kevin Nguyen
- J. Craig Venter Institute, Rockville, MD, 20850, USA
| | | | - Visanu Thamlikitkul
- Faculty of Medicine Siriraj Hospital, Mahidol University, Salaya, Thailand.
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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Hu X, Chen Y, Xu H, Qiao J, Ge H, Liu R, Zheng B. Genomic epidemiology and transmission characteristics of mcr1-positive colistin-resistant Escherichia coli strains circulating at natural environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163600. [PMID: 37086987 DOI: 10.1016/j.scitotenv.2023.163600] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
MCR-positive Escherichia coli (MCRPEC) have been reported in humans worldwide. The high prevalence of mcr-1 poses clinical and environmental risks due to its diverse genetic mechanisms. Given the vital role of animals and the environment in the spread of antibiotic resistance, a "One Health" perspective should be taken when addressing antimicrobial resistance issues. This study conducted a prospective study in six farms (located in Jiaxing City, Zhejiang province, China) in 2019. MCRPEC strains were screened from samples of different sources. The molecular epidemiological surveys and transmission potential were investigated by whole-genome sequencing and phylogenetic analysis. MCRPEC were detected in different farms with various sources. Sequence type complex 10 was dominant and distributed widely in multiple sources. Core-genome multilocus sequence type (cgMLST) analysis indicated that clonal transmission could occur within and between farms. In addition, mcr-1 genes with different locations showed different transmission tendencies. The study indicated that interspecies and cross-regional transmission of MCRPEC could occur between different sectors in farms. Further surveillance and research of non-clinical MCRPEC strains are necessary to reduce the threat of MCRPEC.
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Affiliation(s)
- Xinjun Hu
- Department of Infectious Diseases, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, China
| | - Yingying Chen
- Department of Neurosurgery, Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing 312000, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Jie Qiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Haoyu Ge
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China.
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310000, China
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Xiang Y, Liu Z, Yu G, Song Y, Li Y, Geng X, Ma L, Guo J, Tan L, Chen P. Genetic characteristic of coexisting of mcr-1 and blaNDM-5 in Escherichia coli isolates from lesion-bearing animal organs. Front Microbiol 2023; 14:1116413. [PMID: 37007493 PMCID: PMC10050402 DOI: 10.3389/fmicb.2023.1116413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/21/2023] [Indexed: 03/17/2023] Open
Abstract
The coexistence of mcr-1 and blaNDM-5 in the plasmid of Escherichia coli has been widely reported and such strains have been mainly isolated from animal and human feces. However, few reports have focused on the genetic diversity of mcr-1-carrying chromosomes and blaNDM-5-carrying plasmids in E. coli isolates from lesion-bearing animal organs. This study investigated the genetic characteristics of chromosome-mediated mcr-1 and plasmid-mediated blaNDM-5 in E. coli isolated from lesion-bearing animal organs. Nine mcr-1- and blaNDM-5-positive E. coli strains (MNPECs) showed extensive drug resistance (XDR). The predominant clonal complexes (CC) mainly belonged to CC156, CC10, and CC165 from the 56 MNEPCs (including nine strains in this study) retrieved from the literature. These strains were widely distributed in China, and originated from pig fecal samples, human stool/urine samples as well as intestinal contents of chicken. Two transconjugants harboring blaNDM-5 gene were also successfully obtained from two donors (J-8 and N-14) and this transfer increased the MIC for meropenem by 256 times. However, conjugative transfer of mcr-1 gene failed. Both J-8 and N-14 strains contained point mutations associated with quinolone resistance and more than three types of AMR genes, including the mcr-1 gene on the chromosome and the blaNDM-5 gene on the IncX3-type plasmid. The genetic structure of mcr-1 located on the chromosome was an intact Tn6330, and blaNDM-5-carrying IncX3-type plasmid was ISAb125-IS5-blaNDM-5-bleO-trpF-tat-cutA-IS26 gene cassette. Moreover, differences between chromosomes included additional partial sequence of phage integrated into host genome and the different genes associated with O-antigen synthesis.
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Affiliation(s)
- Yungai Xiang
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zengyuan Liu
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China
| | - Guo Yu
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuxia Song
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Li
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xujing Geng
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liying Ma
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Junqing Guo
- Henan Institute of Modern Chinese Veterinary Medicine, Zhengzhou, Henan, China
| | - Li Tan
- Department of Reproductive Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- *Correspondence: Li Tan,
| | - Pengju Chen
- Henan Institute of Modern Chinese Veterinary Medicine, Zhengzhou, Henan, China
- Shandong Xindehui Biotechnology Company Ltd., Yuncheng, Shandong, China
- Pengju Chen,
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Amaro A, Leão C, Guerra V, Albuquerque T, Clemente L. Plasmid-Mediated Colistin Resistance Genes mcr-1 and mcr-4 in Multidrug-Resistant Escherichia coli Strains Isolated from a Healthy Pig in Portugal. Microb Drug Resist 2023; 29:78-84. [PMID: 36930202 DOI: 10.1089/mdr.2022.0228] [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: 03/18/2023] Open
Abstract
Antimicrobial resistance encoded by mobile colistin resistance (mcr) genes is a global and emergent threat. In this study, we report the occurrence of two different populations of colistin-resistant Escherichia coli harboring mcr-1 and mcr-4 variants in the intestinal microbiome of a healthy pig. Following antimicrobial susceptibility determination, the presence of mcr genes in two E. coli strains, isolated according to different selective microbiological procedures, was screened by PCR. Whole-genome sequencing confirmed that both strains were multidrug-resistant; INIAV_002EC was an AmpC producer carrying blaCMY-2, blaTEM-1B, qnrS1, mcr-1.1 genes, and INIAV_001EC carrying blaTEM-1A, tetB, and mcr-4.1 genes, along with mutations in quinolone resistance-determining regions. In addition, both strains harbored sul3, dfrA, and aadA1 determinants. Further genome analysis revealed different plasmid replicons associated with the mcr genes, IncX4 associated with mcr-1.1, and ColE10 with mcr-4.1. In addition, other replicons, including IncFIA, IncI1-Iγ, IncX1, IncY, in INIAV_002EC, and IncX1, IncI1, and p0111, in INIAV_001EC, were identified. Furthermore, both strains belonged to ST215 serotype O68:H12 and ST156 serotype O25:H28, respectively. This finding highlights the pig gut flora as a potential reservoir of mobile colistin resistance genes and reports the presence of the mcr-4.1 gene found for the first time in Portugal.
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Affiliation(s)
- Ana Amaro
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
| | - Célia Leão
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
- University of Évora, MED-Mediterranean Institute for Agriculture, Environment and Development, Évora, Portugal
| | - Vanessa Guerra
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
- Faculty of Science, University of Lisbon, Lisbon, Portugal
| | - Teresa Albuquerque
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, National Institute of Agrarian and Veterinary Research (INIAV, IP), Oeiras, Portugal
- Faculty of Veterinary Science, CIISA-Centre for Interdisciplinary Research in Animal Health, Lisbon, Portugal
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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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Yamamoto Y, Higashi A, Ikawa K, Hoang HTT, Yamaguchi T, Kawahara R, Noguchi H, Nguyen TN, Khong DT, Tran HT. Horizontal transfer of a plasmid possessing mcr-1 marked with a single nucleotide mutation between Escherichia coli isolates from community residents. BMC Res Notes 2022; 15:196. [PMID: 35659286 PMCID: PMC9166650 DOI: 10.1186/s13104-022-06079-z] [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: 02/21/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives The widespread dissemination of phenotypic colistin-resistant (COR) bacteria in the community threatens public health. The horizontal gene transfer of the mobile colistin resistance gene via plasmids is thought to be one of the main mechanisms for dissemination. However, genotypic evidence to prove this in community settings is limited. This study used genome analysis to demonstrate the direct horizontal colistin resistance gene transfer via plasmids in isolates from the community. Results A total of 19 isolates of COR Escherichia coli from stool specimens of 23 residents from seven households in the Vietnamese community were assessed in this study. The whole-genome sequence data of isolates were acquired using a combination of DNBSEQ short-reads and Nanopore long-read sequencing. Analysis of genomic data was performed using online tools such as Geneious. Analysis of the genomic information of COR E. coli isolates revealed that the isolates from two residents of different households had a similar IncP1 plasmid possessing mcr-1.1, marked with a single nucleotide mutation at the same position. The study provided direct evidence to prove that mcr was horizontally transmitted among bacteria in community residents. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06079-z.
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Affiliation(s)
- Yoshimasa Yamamoto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.
| | - Ayano Higashi
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Kanoko Ikawa
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Hoa Thi Thanh Hoang
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Takahiro Yamaguchi
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Ryuji Kawahara
- Department of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Hideki Noguchi
- Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Japan
| | - Thang Nam Nguyen
- Center for Medical and Pharmaceutical Research and Service, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Diep Thi Khong
- Center for Medical and Pharmaceutical Research and Service, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Hoa Thi Tran
- Center for Medical and Pharmaceutical Research and Service, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
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11
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Pungpian C, Angkititrakul S, Chuanchuen R. Genomic characterization of antimicrobial resistance in mcr-carrying ESBL-producing Escherichia coli from pigs and humans. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35766988 DOI: 10.1099/mic.0.001204] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome sequencing (WGS) was conducted to characterize mcr-carrying extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (n=7). These E. coli isolates originated from two pigs (TH2 and TH3) and two humans (TH8 and TH9) from Thailand, and three pigs from Lao PDR (LA1, LA2 and LA3). Four E. coli sequence types/serotypes - ST6833/H20 (TH2 and TH3), ST48/O160:H40 (TH8 and TH9), ST5708/H45 (LA1) and ST10562/O148:H30 (LA2 and LA3) - were identified. The plasmid replicon type IncF was identified in all isolates. The point mutations Ser31Thr in PmrA and His2Arg in PmrB were found concurrently in all isolates (colistin MIC=4-8 µg ml-1). LA1 contained up to five point mutations in PmrB, and the colistin MIC was not significantly different from that for the other isolates. All mcr-1.1 was located in the ISApl1-mcr-1-pap2 element, while all mcr-3.1 was located in the TnAs2-mcr-3.1-dgkA-ISKpn40 element. The mcr-3.1 and bla CTX-M-55 genes were co-localized on the same plasmid, which concurrently contained cml, qnrS1 and tmrB. The bla CTX-M-55 and mcr-3.1 genes were located on conjugative plasmids and could be transferred horizontally under selective pressure from ampicillin or colistin. In conclusion, comprehensive insights into the genomic information of ESBL-producing E. coli harbouring mcr were obtained. As mcr-carrying ESBL-producing E. coli were detected in pigs and humans, a holistic and multisectoral One Health approach is required to contain antimicrobial resistance (AMR).
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Affiliation(s)
- Chanika Pungpian
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sunpetch Angkititrakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Rungtip Chuanchuen
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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12
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Madu Emeka P, Ineta Badg L, Estrella E, Belgira An G, Ezzat Khal H. Investigation of Colistin and Polymyxin B on Clinical Extreme Resistant Enterobacteriaceae Isolates for Surveillance Purposes. INT J PHARMACOL 2022. [DOI: 10.3923/ijp.2022.699.713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Furlan JPR, Dos Santos LDR, Ramos MS, Gallo IFL, Moretto JAS, Stehling EG. Occurrence of clinically relevant antimicrobial resistance genes, including mcr-3 and mcr-7.1, in soil and water from a recreation club. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:819-828. [PMID: 32735122 DOI: 10.1080/09603123.2020.1799953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
We researched clinically relevant antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in environmental samples from a recreation club in Brazil. A total of 172 amplicons (105 from soil and 67 from water) of 26 ARGs (20 among the soil and water samples; four only in soil samples; two only in water samples) were detected. Nine MGEs were detected, including plasmids and class 1 integron. The absolute abundance of the mcr-3 gene ranged from 1.12 × 102 to 1.81 × 103 copies/mL-1 in water samples. The rapid spread of mcr-like genes in several sources has generated a huge concern to public health. Accordingly, understanding of antimicrobial resistance, carry out surveillance studies may contribute to tackle antimicrobial resistance. As the environmental samples were collected from a popular recreation club in Brazil, this study points out to the risk and exposure to clinically relevant ARGs, especially to mcr-3 and mcr-7.1 genes.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento De Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade De Ciências Farmacêuticas De Ribeirão Preto, Universidade De São Paulo (USP), Ribeirão Preto, Brasil
| | - Lucas David Rodrigues Dos Santos
- Departamento De Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade De Ciências Farmacêuticas De Ribeirão Preto, Universidade De São Paulo (USP), Ribeirão Preto, Brasil
| | - Micaela Santana Ramos
- Departamento De Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade De Ciências Farmacêuticas De Ribeirão Preto, Universidade De São Paulo (USP), Ribeirão Preto, Brasil
| | - Inara Fernanda Lage Gallo
- Departamento De Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade De Ciências Farmacêuticas De Ribeirão Preto, Universidade De São Paulo (USP), Ribeirão Preto, Brasil
| | - Jéssica Aparecida Silva Moretto
- Departamento De Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade De Ciências Farmacêuticas De Ribeirão Preto, Universidade De São Paulo (USP), Ribeirão Preto, Brasil
| | - Eliana Guedes Stehling
- Departamento De Análises Clínicas, Toxicológicas E Bromatológicas, Faculdade De Ciências Farmacêuticas De Ribeirão Preto, Universidade De São Paulo (USP), Ribeirão Preto, Brasil
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14
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Miguela-Villoldo P, Moreno MA, Rodríguez-Lázaro D, Gallardo A, Hernández M, Serrano T, Sáez JL, de Frutos C, Agüero M, Quesada A, Domínguez L, Ugarte-Ruiz M. Longitudinal study of the mcr-1 gene prevalence in Spanish food-producing pigs from 1998 to 2021 and its relationship with the use of polymyxins. Porcine Health Manag 2022; 8:12. [PMID: 35300732 PMCID: PMC8932235 DOI: 10.1186/s40813-022-00255-0] [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: 10/25/2021] [Accepted: 01/21/2022] [Indexed: 11/15/2022] Open
Abstract
Background Resistance to colistin was an uncommon phenomenon traditionally linked to chromosome point mutations, but since the first description of a plasmid-mediated colistin-resistance in late 2015, transmissible resistance to colistin has become a Public Health concern. Despite colistin is considered as a human last resort antibiotic, it has been commonly used in swine industry to treat post-weaning diarrhoea in piglets. However, the progressively increase of colistin resistance during the last decade led to the Spanish Medicines and Healthcare Products Agency (AEMPS) to launch a strategic and voluntary plan aimed to reduce colistin consumption in pig production. Our longitudinal study (1998–2021) aimed to evaluate the trend of colistin resistance mediated through the mcr-1 mobile gene in Spanish food-producing pig population and compare it with published polymyxin sales data in veterinary medicine to assess their possible relationships. Results The first mcr-1 positive sample was observed in 2004, as all samples from 1998 and 2002 were mcr-1 PCR-negative. We observed a progressive increase of positive samples from 2004 to 2015, when mcr-1 detection reached its maximum peak (33/50; 66%). From 2017 (27/50; 54%) to 2021 (14/81; 17%) the trend became downward, reaching percentages significantly lower than the 2015 peak (p < 0.001). The abundance of mcr-1 gene in PCR-positive samples showed a similar trend reaching the highest levels in 2015 (median: 6.6 × 104mcr-1 copies/mg of faeces), but decreased significantly from 2017 to 2019 (median 2.7 × 104, 1.2 × 103, 4.6 × 102mcr-1 copies/mg of faeces for 2017, 2018 and 2019, respectively), and stabilizing in 2021 (1.6 × 102mcr-1 copies/mg of faeces) with similar values than 2019. Conclusions Our study showed the decreasing trend of colistin resistance associated to mcr-1 gene, after a previous increase from among 2004–2015, since the European Medicines Agency and AEMPS strategies were applied in 2016 to reduce colistin use in animals, suggesting a connection between polymyxin use and colistin resistance. Thus, these plans could have been effective in mcr-1 reduction, reaching lower levels than those detected in samples collected 17 years ago, when resistance to colistin was not yet a major concern.
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Affiliation(s)
- Pedro Miguela-Villoldo
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain. .,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain.
| | - Miguel A Moreno
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - David Rodríguez-Lázaro
- Área de Microbiología, Departamento de Biotecnología y Ciencia de los Alimentos, Universidad de Burgos, Burgos, Spain
| | - Alejandro Gallardo
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Avenida de la Universidad s/n, 10003, Cáceres, Spain
| | - Marta Hernández
- Laboratorio de Biología Molecular y Microbiología, Instituto Tecnológico Agrario de Castilla y León, Valladolid, Spain
| | | | - José L Sáez
- Subdirección General de Sanidad e Higiene Animal y Trazabilidad, Ministerio de Agricultura y Pesca, Alimentación y Medio Ambiente, Madrid, Spain
| | | | | | - Alberto Quesada
- Departamento de Bioquímica, Biología Molecular y Genética, Facultad de Veterinaria, Universidad de Extremadura, Avenida de la Universidad s/n, 10003, Cáceres, Spain.,INBIO G+C, Universidad de Extremadura, Avenida de la Universidad s/n, 10003, Cáceres, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain.,Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, 28040, Madrid, Spain
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15
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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: 31] [Impact Index Per Article: 10.3] [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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16
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Co-Occurrence of blaOXA-23 in the Chromosome and Plasmid: Increased Fitness in Carbapenem-Resistant Acinetobacter baumannii. Antibiotics (Basel) 2021; 10:antibiotics10101196. [PMID: 34680777 PMCID: PMC8532878 DOI: 10.3390/antibiotics10101196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
This study aims to explore the co-occurrence of chromosomal and plasmid blaOXA-23 in carbapenem-resistant A. baumannii (CRAB) and its influence on phenotypes. A total of 11 CRAB isolates containing copies of blaOXA-23 on the chromosome and plasmid (CO), as well as 18 closely related isolates with blaOXA-23, located on either the chromosome or plasmid (SI), were selected for the determination of antibiotic susceptibility, virulence phenotype, and characteristic genomic differences. The co-occurrence of blaOXA-23 on the CRAB chromosome and plasmids did not enhance carbapenem resistance, but trimethoprim/sulfamethoxazole exhibited significantly reduced minimum inhibitory concentrations in CO. CO demonstrated a higher degree of fitness compared to SI. An increased biofilm formation ability and serum tolerance were also identified in CO, which may be associated with virulence genes, which include csuD, entE, pgaA, and plc. blaOXA-23-carrying transposons were found at different insertion sites on the chromosome. The most common site was AbaR-type genomic islands (50%). Two types of plasmids were found in CO. The co-occurrence of blaOXA-23 on the chromosome and a plasmid in CRAB had little effect on carbapenem susceptibility but was accompanied by increased fitness and virulence. Different origins and independent insertions of blaOXA-23-carrying transposons were identified in both the chromosomal and plasmid sequences.
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17
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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: 7] [Impact Index Per Article: 2.3] [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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18
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Kalová A, Gelbíčová T, Overballe-Petersen S, Litrup E, Karpíšková R. Characterisation of Colistin -Resistant Enterobacterales and Acinetobacter Strains Carrying mcr Genes from Asian Aquaculture Products. Antibiotics (Basel) 2021; 10:antibiotics10070838. [PMID: 34356760 PMCID: PMC8300808 DOI: 10.3390/antibiotics10070838] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/29/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Aquaculture systems are widely recognised as hotspots for horizontal gene transfer, and the need for screening for bacteria carrying antimicrobial resistance genes in aquaculture systems is becoming more important. In this study, we characterised seventeen bacterial strains (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and A. nosocomialis) resistant to colistin originating from retailed aquaculture products imported from Vietnam to the Czech Republic. The mcr-1.1 gene was found located on plasmid types IncHI2, IncI2, and IncX4, as well as on the rarely described plasmid types IncFIB-FIC and IncFIB(K), phage-like plasmid p0111, and on the chromosome of E. coli. One E. coli strain carried the mcr-3.5 gene on IncFII(pCoo) plasmid in addition to the mcr-1.1 gene located on IncHI2 plasmid. K. pneumoniae was found to carry the mcr-1.1 and mcr-8.2 genes on IncFIA(HI1) plasmid. The mcr-4.3 gene was found on similar untypeable plasmids of A. baumannii and A. nosocomialis strains, pointing to the possible interspecies transfer of plasmids carrying the mcr-4 gene. Our results highlight that some aquaculture products of Asian origin can represent an important source of variable plasmids carrying mcr genes. The results showed an involvement of phages in the incorporation of the mcr-1 gene into plasmids or the chromosome in E. coli strains from aquaculture. The detection of E. coli with the mcr-1 gene in the chromosome points to the risks associated with the stabilisation of the mcr genes in the bacterial chromosome.
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Affiliation(s)
- Alžběta Kalová
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00 Brno, Czech Republic; (T.G.); (R.K.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 602 00 Brno, Czech Republic
- Correspondence:
| | - Tereza Gelbíčová
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00 Brno, Czech Republic; (T.G.); (R.K.)
| | | | - Eva Litrup
- Statens Serum Institut, 2300 Copenhagen, Denmark; (S.O.-P.); (E.L.)
| | - Renáta Karpíšková
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, 621 00 Brno, Czech Republic; (T.G.); (R.K.)
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19
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Pérez-Garza J, Franco-Frías E, García-Heredia A, García S, Leon JS, Jaykus LA, Heredia N. The Cantaloupe Farm Environment Has a Diverse Genetic Pool of Antibiotic-Resistance and Virulence Genes. Foodborne Pathog Dis 2021; 18:469-476. [PMID: 33900863 DOI: 10.1089/fpd.2020.2900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cantaloupes contaminated with pathogens have led to many high-profile outbreaks and illnesses. Since bacterial virulence genes (VGs) can act in tandem with antibiotic-resistance and mobile genetic elements, there is a need to evaluate these gene reservoirs in fresh produce, such as cantaloupes. The goal of this study was to assess the distribution of antibiotic-resistance, virulence, and mobile genetic elements genes (MGEGs) in cantaloupe farm environments. A total of 200 samples from cantaloupe melons (n = 99), farm workers' hands (n = 66), and production water (n = 35) were collected in México. Each sample was assayed for the presence of 14 antibiotic-resistance genes, 15 VGs, and 5 MGEGs by polymerase chain reaction. Our results indicated that tetracycline (tetA and tetB) (18% of cantaloupe, 45% of hand samples) and sulfonamide (sul1) (30% of cantaloupe, 71% of hand samples) resistance genes were frequently detected. The colistin resistance gene (mcr1) was detected in 10% of cantaloupe and 23% of farm workers' hands. Among VGs, Salmonella genes invA and spiA were the most abundant. There was a significantly higher likelihood of detecting antibiotic-resistance, virulence, and MGEGs on hands compared with water samples. These results demonstrate a diverse pool of antibiotic-resistance and VGs in cantaloupe production.
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Affiliation(s)
- Janeth Pérez-Garza
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
| | - Eduardo Franco-Frías
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
| | - Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, USA
| | - Santos García
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
| | - Juan S Leon
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Lee-Ann Jaykus
- Department of Food Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Norma Heredia
- Laboratorio de Bioquímica y Genética de Microorganismos, Departamento de Microbiologia e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolas de los Garza, México
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20
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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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Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae: a Systematic Review of Current Reports. mSystems 2020; 5:5/6/e00783-20. [PMID: 33323413 PMCID: PMC7771540 DOI: 10.1128/msystems.00783-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. A systematic review of all studies published in PubMed database between 2015 to October 2020 was performed. Journal articles evaluating carbapenem and polymyxin resistance mechanisms, respectively, were included. The search identified 171 journal articles for inclusion. Different New Delhi metallo-β-lactamase (NDM) carbapenemase variants had different transcriptional and affinity responses to different carbapenems. Mutations within the Klebsiella pneumoniae carbapenemase (KPC) mobile transposon, Tn4401, affect its promoter activity and expression levels, increasing carbapenem resistance. Insertion of IS26 in ardK increased imipenemase expression 53-fold. ompCF porin downregulation (mediated by envZ and ompR mutations), micCF small RNA hyperexpression, efflux upregulation (mediated by acrA, acrR, araC, marA, soxS, ramA, etc.), and mutations in acrAB-tolC mediated clinical carbapenem resistance when coupled with β-lactamase activity in a species-specific manner but not when acting without β-lactamases. Mutations in pmrAB, phoPQ, crrAB, and mgrB affect phosphorylation of lipid A of the lipopolysaccharide through the pmrHFIJKLM (arnBCDATEF or pbgP) cluster, leading to polymyxin resistance; mgrB inactivation also affected capsule structure. Mobile and induced mcr, efflux hyperexpression and porin downregulation, and Ecr transmembrane protein also conferred polymyxin resistance and heteroresistance. Carbapenem and polymyxin resistance is thus mediated by a diverse range of genetic and transcriptional mechanisms that are easily activated in an inducing environment. The molecular understanding of these emerging mechanisms can aid in developing new therapeutics for multidrug-resistant Enterobacteriaceae isolates.
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Lin Y, Yang L, Lu L, Wang K, Li J, Li P, Liu Y, Liu X, Li P, Song H. Genomic features of an Escherichia coli ST156 strain harboring chromosome-located mcr-1 and plasmid-mediated blaNDM-5. INFECTION GENETICS AND EVOLUTION 2020; 85:104499. [DOI: 10.1016/j.meegid.2020.104499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/07/2020] [Accepted: 08/05/2020] [Indexed: 11/25/2022]
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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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Emergence of mcr-3 carrying Escherichia coli in Diseased Pigs in South Korea. Microorganisms 2020; 8:microorganisms8101538. [PMID: 33036214 PMCID: PMC7650651 DOI: 10.3390/microorganisms8101538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/03/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022] Open
Abstract
We examined the prevalence and molecular characteristics of mcr-3 carrying colistin-resistant Escherichia coli among cattle, pig, and chicken isolates in South Korea. Among a total of 185 colistin-resistant E. coli isolates determined in this study (47 from cattle, 90 from pigs, and 48 from chicken), PCR amplification detected mcr-3 genes in 17 isolates predominantly from diseased pigs. The mcr-3 genes were characterized as mcr-3.1 in 15 isolates and mcr-3.5 in 2 isolates. The mcr-3 gene was transferred to the E. coli J53 recipient strain from more than 50% of the mcr-3-carrying isolates. The mcr-3.1 and mcr-3.5 genes were identified predominantly in IncHI2 and IncP plasmids, respectively. Multi-locus sequence typing analysis revealed eight previously reported sequence types (ST), including ST1, ST10, and ST42. We identified isolates with similar pulsed-field gel electrophoresis patterns from diseased pigs in three farms. Besides, the isolates carried various virulence factors and demonstrated resistance to multiple antimicrobials, including β-lactams and quinolones. Further, the mcr-3.5 encodes three amino acid substitutions compared with mcr-3.1. To the best of our knowledge, this is the first report of pathogenic E. coli carrying mcr-3.5 in South Korea, which implies that mcr-3 variants may have already been widely spread in the pig industry.
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Li R, Zhang P, Yang X, Wang Z, Fanning S, Wang J, Du P, Bai L. Identification of a novel hybrid plasmid coproducing MCR-1 and MCR-3 variant from an Escherichia coli strain. J Antimicrob Chemother 2020; 74:1517-1520. [PMID: 30793748 DOI: 10.1093/jac/dkz058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To characterize the genome of an Escherichia coli harbouring both mcr-1 and mcr-3.19 on a hybrid plasmid and the underlying transmission mechanisms. METHODS Broth microdilution was used to perform antimicrobial susceptibility testing. Conjugation assays and S1-PFGE were used to assess the transferability of mcr genes. Resistance genotypes and genetic contexts were investigated, based on WGS data from the Illumina and MinION platforms. Inverse PCR was performed to test the mcr-3.19-bearing circular intermediate. Bioinformatic tools were used to further characterize the hybrid plasmid. RESULTS E. coli CP53 was identified as harbouring both mcr-1 and mcr-3.19 on a 231 859 bp hybrid plasmid pCP53-mcr1_3 containing IncFIA, IncHI1A, IncHI1B and IncN replicons. The genetic structures of mcr-1 and mcr-3.19 were similar to those reported in other mcr-1 and mcr-3.19-bearing plasmids, which suggested that recombination between mcr-bearing plasmids had been mediated by ISs. However, the MDR plasmid pCP53-mcr1_3 cannot transfer via conjugation. Furthermore, another three plasmids were identified in the isolate, two of which encoded resistance genes. In640 duplication between two MDR plasmids was observed. An MDR-region recombination existed in E. coli CP53. A core structure consisting of mcr-3-dgkA existed in mcr-3-bearing plasmids reported, to date. Circular intermediates were observed for mcr-1 and mcr-3.19 regions. CONCLUSIONS A novel mcr-3.19 was identified along with mcr-1 contained in a hybrid plasmid. This finding suggested that evolution of mcr genes among various plasmids was being driven by mobile elements. Molecular surveillance of mcr gene co-occurrence warrants further investigation to evaluate the public health risk.
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Affiliation(s)
- Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
| | - Pei Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Nutrition, School of Public Health, Sun Yat-Sen University, Guangzhou, P. R. China.,Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, P. R. China
| | - Xiaorong Yang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, P. R. China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, P. R. China
| | - Séamus Fanning
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, P. R. China.,UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, No. 22 Xinong Road, Yangling 712100, Shaanxi, P. R. China
| | - Pengcheng Du
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, P. R. China
| | - Li Bai
- Key Laboratory of Food Safety Risk Assessment, National Health Commission of the People's Republic of China, China National Center for Food Safety Risk Assessment, Beijing, P. R. China
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Dos Santos LDR, Furlan JPR, Ramos MS, Gallo IFL, de Freitas LVP, Stehling EG. Co-occurrence of mcr-1, mcr-3, mcr-7 and clinically relevant antimicrobial resistance genes in environmental and fecal samples. Arch Microbiol 2020; 202:1795-1800. [PMID: 32382766 DOI: 10.1007/s00203-020-01890-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/22/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022]
Abstract
Multidrug-resistant bacteria harboring different antimicrobial resistance genes (ARGs) have been detected worldwide. The association of plasmid-mediated colistin resistance genes (mcr-like) and other ARGs in bacteria isolated from animals is a huge concern worldwide. Therefore, this study aimed to investigate the presence of mcr-like genes and clinically relevant ARGs as well as plasmids in samples from a zoo. Fecal and environmental (soil and water) samples were collected from a zoo and the DNA of cultivable aerobic bacteria was extracted. ARGs were screened by PCR and the plasmids were detected using the PCR-based replicon typing method. A total of 74 amplicons from 27 ARGs [mcr-1, mcr-3, mcr-7.1, blaCTX-M-Gp1, blaCTX-M-Gp2, blaCTX-M-Gp9, blaVEB, blaPER, blaCMY, tetA, tetB, tetC, aadA, aac(6')-Ib, aph(3')-Ia, ant(2'')-Ia, qnrA, qnrB, qnrS, oqxA, oqxB, sul1, sul2, sul3, cmlA, mefAE, ermB] and 21 amplicons from eight plasmid families (IncY, ColE-like, IncFrepB, IncFIA, IncFIB, IncHI1, IncFIC, IncP) were detected. These findings reinforce that the zoo acts as a reservoir of clinically relevant ARGs, including mcr-like, and call attention to the monitoring studies in the zoo. Therefore, to the best of our knowledge, this is the first report of the world of mcr-1, mcr-3 and mcr-7.1 in environmental samples from the zoo.
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Affiliation(s)
- Lucas David Rodrigues Dos Santos
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, 14040-903, Brasil
| | - João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, 14040-903, Brasil
| | - Micaela Santana Ramos
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, 14040-903, Brasil
| | - Inara Fernanda Lage Gallo
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, 14040-903, Brasil
| | | | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto-Universidade de São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, 14040-903, Brasil.
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Kananizadeh P, Oshiro S, Watanabe S, Iwata S, Kuwahara-Arai K, Shimojima M, Ogawa M, Tada T, Kirikae T. Emergence of carbapenem-resistant and colistin-susceptible Enterobacter cloacae complex co-harboring bla IMP-1 and mcr-9 in Japan. BMC Infect Dis 2020; 20:282. [PMID: 32299378 PMCID: PMC7161257 DOI: 10.1186/s12879-020-05021-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
Background The spread of Enterobacteriaceae producing both carbapenemases and Mcr, encoded by plasmid-mediated colistin resistance genes, has become a serious public health problem worldwide. This study describes three clinical isolates of Enterobacter cloacae complex co-harboring blaIMP-1 and mcr-9 that were resistant to carbapenem but susceptible to colistin. Methods Thirty-two clinical isolates of E. cloacae complex non-susceptible to carbapenems were obtained from patients at 14 hospitals in Japan. Their minimum inhibitory concentrations (MICs) were determined by broth microdilution methods and E-tests. Their entire genomes were sequenced by MiSeq and MinION methods. Multilocus sequence types were determined and a phylogenetic tree constructed by single nucleotide polymorphism (SNP) alignment of whole genome sequencing data. Results All 32 isolates showed MICs of ≥2 μg/ml for imipenem and/or meropenem. Whole-genome analysis revealed that all these isolates harbored blaIMP-1, with three also harboring mcr-9. These three isolates showed low MICs of 0.125 μg/ml for colistin. In two of these isolates, blaIMP-1 and mcr-9 were present on two separate plasmids, of sizes 62 kb and 280/290 kb, respectively. These two isolates did not possess a qseBC gene encoding a two-component system, which is thought to regulate the expression of mcr-9. In the third isolate, however, both blaIMP-1 and mcr-9 were present on the chromosome. Conclusion The mcr-9 is silently distributed among carbapenem-resistant E. cloacae complex isolates, of which are emerging in hospitals in Japan. To our knowledge, this is the first report of isolates of E. cloacae complex harboring both blaIMP-1 and mcr-9 in Japan.
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Affiliation(s)
- Pegah Kananizadeh
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Satoshi Oshiro
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shin Watanabe
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shu Iwata
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Kyoko Kuwahara-Arai
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | | | - Miho Ogawa
- BML, Inc Department of Microbiology, Kawagoe, Saitama, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
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High Prevalence of Colistin-Resistant Escherichia coli with Chromosomally Carried mcr-1 in Healthy Residents in Vietnam. mSphere 2020; 5:5/2/e00117-20. [PMID: 32132160 PMCID: PMC7056805 DOI: 10.1128/msphere.00117-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Elucidation of the mechanism of the wide dissemination of colistin-resistant bacteria in communities of developing countries is an urgent public health issue. In this study, we investigated the genetic background of the colistin resistance gene mcr in E. coli isolates from the fecal microbiota of healthy human residents living in a community in Vietnam with a high prevalence of colistin-resistant E. coli. Our study revealed for the first time, a surprisingly high percentage (36.8%) of colistin-resistant E. coli carrying chromosomal mcr-1, the emergence of which may have occurred recently, in the fecal microbiota of the community residents. The mcr-1 transposon on the chromosome may develop into a more stable genotype by the loss of insertion sequences (ISs). Our results are valuable in understanding the mechanism underlying the increasing prevalence of colistin-resistant bacteria within a community. The wide distribution of colistin-resistant bacteria in developing countries has become a common phenomenon. To understand the mechanisms underlying their distribution, we studied the mcr genetic background of colistin-resistant Escherichia coli isolates from the fecal microbiota of healthy human residents from a community in Vietnam with a high prevalence of colistin-resistant E. coli with mcr. Fifty-seven colistin-resistant isolates were obtained from 98 residents; one isolate was collected from each individual and analyzed for mcr. We found that 36.8% of the isolates carried chromosomal mcr-1. Further, 63.2% and 1.8% of the isolates carried mcr-1 on the plasmid and the plasmid/chromosome, respectively. Whole-genome sequencing of genetically unrelated isolates showed that the majority (6 of 7) of the isolates had the chromosomal mcr-1 in a complete ancestral mcr-1 transposon Tn6330, ISApl1-mcr-1-PAP2-ISApl1, which was inserted at various positions on the chromosomes. In addition, the majority (87.5%) of Tn6330 of mcr-1-carrying plasmids (n = 8) lacked both upstream and downstream ISApl1 transposons. The results obtained in this study indicate that plasmid-to-chromosomal transfer of mcr-1 may have occurred recently in the fecal microbiota of the residents. Additionally, Tn6330 on the chromosome may lose ISApl1 from the transposon during multiplication to gain a more stable mcr-1 state on the chromosome. Stabilization of resistance by the chromosomal incorporation of mcr-1 would be an additional challenge in combating the dissemination of resistant bacteria. IMPORTANCE Elucidation of the mechanism of the wide dissemination of colistin-resistant bacteria in communities of developing countries is an urgent public health issue. In this study, we investigated the genetic background of the colistin resistance gene mcr in E. coli isolates from the fecal microbiota of healthy human residents living in a community in Vietnam with a high prevalence of colistin-resistant E. coli. Our study revealed for the first time, a surprisingly high percentage (36.8%) of colistin-resistant E. coli carrying chromosomal mcr-1, the emergence of which may have occurred recently, in the fecal microbiota of the community residents. The mcr-1 transposon on the chromosome may develop into a more stable genotype by the loss of insertion sequences (ISs). Our results are valuable in understanding the mechanism underlying the increasing prevalence of colistin-resistant bacteria within a community.
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Li XP, Sun RY, Song JQ, Fang LX, Zhang RM, Lian XL, Liao XP, Liu YH, Lin J, Sun J. Within-host heterogeneity and flexibility of mcr-1 transmission in chicken gut. Int J Antimicrob Agents 2019; 55:105806. [PMID: 31533074 DOI: 10.1016/j.ijantimicag.2019.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/27/2019] [Accepted: 09/11/2019] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To characterize the colistin-resistant bacterial population in the gut and assess diversity of mcr-1 transmission within a single individual. METHODS Large numbers of isolates (>100 colonies/chicken cecum sample) were collected from nine randomly selected mcr-1-positive chickens in China and used for comprehensive microbiological, molecular and comparative genomics analyses. RESULTS Of 1273 colonies, 968 were mcr-1 positive (962 Escherichia coli, two Escherichia fergusonii, two Klebsiella pneumoniae and two Klebsiella quasipneumoniae). One to six colistin-resistant species and three to 10 E. coli pulsed-field gel electrophoresis (PFGE) clusters could be identified from each sample. Whole-genome sequencing (WGS) analysis of the representative E. coli strains revealed three to nine sequence types observed in a single chicken host. The mcr-1 genes are located in either chromosomes or plasmids of different types, including IncI2 (n=30), IncHI2 (n=14), IncX4 (n=4), p0111(n=2) and IncHI1(n=1). Strikingly, in single cecum samples, one to five Inc type plasmids harbouring mcr-1 could be identified. Great diversity was also observed for the same IncI2 plasmid within a single chicken host. In addition, up to eight genetic contexts of the mcr-1 gene occurred within a single chicken. CONCLUSIONS There is extensive heterogeneity and flexibility of mcr-1 transmission in chicken gut due to bacterial species differences, distant clonal relatedness of isolates, many types and variations of mcr-positive plasmids, and the flexible genetic context of the mcr-1 gene. These compelling findings indicate that the gut is a 'melting pot' for active horizontal transfer of the mcr-1 gene.
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Affiliation(s)
- Xing-Ping Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China; Department of Animal Science, The University of Tennessee, Knoxville, TN, USA
| | - Ruan-Yang Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
| | - Jia-Qi Song
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
| | - Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
| | - Xin-Lei Lian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China
| | - Jun Lin
- Department of Animal Science, The University of Tennessee, Knoxville, TN, USA.
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, P. R. China; College of Veterinary Medicine, South China Agricultural University, Guangzhou, P. R. China.
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30
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Zając M, Sztromwasser P, Bortolaia V, Leekitcharoenphon P, Cavaco LM, Ziȩtek-Barszcz A, Hendriksen RS, Wasyl D. Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011-2016. Front Microbiol 2019; 10:1753. [PMID: 31440216 PMCID: PMC6694793 DOI: 10.3389/fmicb.2019.01753] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/15/2019] [Indexed: 11/23/2022] Open
Abstract
The emergence of plasmid-mediated colistin resistance (mcr genes) threatens the effectiveness of polymyxins, which are last-resort drugs to treat infections by multidrug- and carbapenem-resistant Gram-negative bacteria. Based on the occurrence of colistin resistance the aims of the study were to determine possible resistance mechanisms and then characterize the mcr-positive Escherichia coli. The research used material from the Polish national and EU harmonized antimicrobial resistance (AMR) monitoring programs. A total of 5,878 commensal E. coli from fecal samples of turkeys, chickens, pigs, and cattle collected in 2011-2016 were screened by minimum inhibitory concentration (MIC) determination for the presence of resistance to colistin (R) defined as R > 2 mg/L. Strains with MIC = 2 mg/L isolated in 2014-2016 were also included. A total of 128 isolates were obtained, and most (66.3%) had colistin MIC of 2 mg/L. PCR revealed mcr-1 in 80 (62.5%) isolates recovered from 61 turkeys, 11 broilers, 2 laying hens, 1 pig, and 1 bovine. No other mcr-type genes (including mcr-2 to -5) were detected. Whole-genome sequencing (WGS) of the mcr-1-positive isolates showed high diversity in the multi-locus sequence types (MLST) of E. coli, plasmid replicons, and AMR and virulence genes. Generally mcr-1.1 was detected on the same contig as the IncX4 (76.3%) and IncHI2 (6.3%) replicons. One isolate harbored mcr-1.1 on the chromosome. Various extended-spectrum beta-lactamase (bla SHV-12, bla CTX-M-1, bla CTX-M-15, bla TEM-30, bla TEM-52, and bla TEM-135) and quinolone resistance genes (qnrS1, qnrB19, and chromosomal gyrA, parC, and parE mutations) were present in the mcr-1.1-positive E. coli. A total of 49 sequence types (ST) were identified, ST354, ST359, ST48, and ST617 predominating. One isolate, identified as ST189, belonged to atypical enteropathogenic E. coli. Our findings show that mcr-1.1 has spread widely among production animals in Poland, particularly in turkeys and appears to be transferable mainly by IncX4 and IncHI2 plasmids spread across diverse E. coli lineages. Interestingly, most of these mcr-1-positive E. coli would remain undetected using phenotypic methods with the current epidemiological cut-off value (ECOFF). The appearance and spread of mcr-1 among various animals, but notably in turkeys, might be considered a food chain, and public health hazard.
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Affiliation(s)
- Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
| | - Paweł Sztromwasser
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
| | - Valeria Bortolaia
- Research Group for Genomic Epidemiology, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Lina M. Cavaco
- Statens Serum Institute, Copenhagen University, Copenhagen, Denmark
| | - Anna Ziȩtek-Barszcz
- Department of Epidemiology, National Veterinary Research Institute, Puławy, Poland
| | - Rene S. Hendriksen
- Research Group for Genomic Epidemiology, European Union Reference Laboratory for Antimicrobial Resistance, WHO Collaborating Centre for Antimicrobial Resistance in Foodborne Pathogens and Genomics, National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute, Puławy, Poland
- Department of Omics Analyses, National Veterinary Research Institute, Puławy, Poland
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Zhang H, Wei W, Huang M, Umar Z, Feng Y. Definition of a Family of Nonmobile Colistin Resistance (NMCR-1) Determinants Suggests Aquatic Reservoirs for MCR-4. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1900038. [PMID: 31179218 PMCID: PMC6548957 DOI: 10.1002/advs.201900038] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Polymyxins, a family of cationic antimicrobial peptides, are recognized as a last-resort clinical option used in the treatment of lethal infections with carbapenem-resistant pathogens. A growing body of mobile colistin resistance (MCR) determinants renders colistin ineffective in the clinical and human sectors, posing a challenge to human health and food security. However, the origin and reservoir of the MCR family enzymes is poorly understood. Herein, a new family of nonmobile colistin resistance (from nmcr-1 to nmcr-1.8) from the aquatic bacterium Shewanella is reported. NMCR-1 (541aa) displays 62.78% identity to MCR-4. Genetic and structural analyses reveal that NMCR-1 shares a similar catalytic mechanism and functional motifs, both of which are required for MCR action and its resultant phenotypic resistance to polymyxin. Phylogeny and domain-swapping demonstrate that NMCR-1 is a progenitor of MCR-4 rather than MCR-1/2. Additionally, the experiment of bacterial growth and viability reveals that NMCR-1 promotes fitness cost as MCR-1/4 does in the recipient Escherichia coli. In summary, the finding suggests that the aquatic bacterium Shewanella (and even its associated aquaculture) is a reservoir for MCR-4 mobile colistin resistance.
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Affiliation(s)
- Huimin Zhang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- Carl R. Woese Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Wenhui Wei
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Man Huang
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Zeeshan Umar
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youjun Feng
- Department of Pathogen Biology & Microbiology and Department of General Intensive Care Unit of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
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32
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Belaynehe KM, Shin SW, Park KY, Jang JY, Won HG, Yoon IJ, Yoo HS. Genetic Analysis of p17S-208 Plasmid Encoding the Colistin Resistance mcr-3 Gene in Escherichia coli Isolated from Swine in South Korea. Microb Drug Resist 2018; 25:457-461. [PMID: 30379604 DOI: 10.1089/mdr.2018.0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We screened, for the first time, plasmid-mediated colistin resistance mcr-3 genes among 636 Escherichia coli isolates collected from swine in South Korea. Whole-genome sequencing showed that the E. coli strain harbored the mcr-3 gene in a p17S-208 plasmid with an IncHI2-ST3 plasmid type and a size of 260,399 base pairs. The deduced amino acid sequences revealed that persistent evolution in the bacterial genome has resulted in mcr gene variants. There is a need for extensive surveillance to prevent the dissemination of colistin resistance mcr genes from animal to human.
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Affiliation(s)
- Kuastros Mekonnen Belaynehe
- 1 Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University , Seoul, Republic of Korea
| | - Seung Won Shin
- 1 Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University , Seoul, Republic of Korea
| | - Kyung Yoon Park
- 2 Research Unit, Green Cross Veterinary Products , Yongin, Republic of Korea
| | - Ji Young Jang
- 2 Research Unit, Green Cross Veterinary Products , Yongin, Republic of Korea
| | - Ho Geun Won
- 1 Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University , Seoul, Republic of Korea.,3 Chung Ang Vaccine Laboratory , Daejeon, Republic of Korea
| | - In Joong Yoon
- 3 Chung Ang Vaccine Laboratory , Daejeon, Republic of Korea
| | - Han Sang Yoo
- 1 Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University , Seoul, Republic of Korea.,4 Institute of Green Bio Science and Technology, Seoul National University , Pyeongchang, Republic of Korea
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Lv J, Mohsin M, Lei S, Srinivas S, Wiqar RT, Lin J, Feng Y. Discovery of a mcr-1-bearing plasmid in commensal colistin-resistant Escherichia coli from healthy broilers in Faisalabad, Pakistan. Virulence 2018; 9:994-999. [PMID: 29667494 PMCID: PMC6037438 DOI: 10.1080/21505594.2018.1462060] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jiali Lv
- a School of Food and Biological Engineering, Shaanxi University of Science and Technology , Xi'an , Shaanxi , China
| | - Mashkoor Mohsin
- b Institute of Microbiology, University of Agriculture , Faisalabad , Pakistan
| | - Sheng Lei
- a School of Food and Biological Engineering, Shaanxi University of Science and Technology , Xi'an , Shaanxi , China.,c Department of Medical Microbiology and Parasitology , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | | | - Raja Talish Wiqar
- b Institute of Microbiology, University of Agriculture , Faisalabad , Pakistan
| | - Jingxia Lin
- c Department of Medical Microbiology and Parasitology , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China
| | - Youjun Feng
- a School of Food and Biological Engineering, Shaanxi University of Science and Technology , Xi'an , Shaanxi , China.,c Department of Medical Microbiology and Parasitology , Zhejiang University School of Medicine , Hangzhou , Zhejiang , China.,e College of Animal Sciences, Zhejiang University , Hangzhou , Zhejiang , China
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