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Martino F, Petroni A, Menocal MA, Corso A, Melano R, Faccone D. New insights on mcr-1-harboring plasmids from human clinical Escherichia coli isolates. PLoS One 2024; 19:e0294820. [PMID: 38408071 PMCID: PMC10896549 DOI: 10.1371/journal.pone.0294820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/09/2023] [Indexed: 02/28/2024] Open
Abstract
Mobile colistin resistance (mcr) genes were described recently in Gram-negative bacteria including carbapenem-resistant Enterobacterales. There are ten mcr genes described in different Gram-negative bacteria, however, Escherichia coli harboring mcr-1 gene is by far the most frequent combination. In Argentina, mcr-1 gene was characterized only on plasmids belonging to IncI2 group. The aim of this work was to get new insights of mcr-1-harboring plasmids from E. coli. Eight E. coli isolates from a larger collection of 192 clinical E. coli isolates carrying the mcr-1 gene were sequenced using next generation technologies. Three isolates belonged to ST131 high-risk clone, and five to single ST, ST38, ST46, ST226, ST224, and ST405. Eight diverse mcr-1-harboring plasmids were analyzed: IncI2 (1), IncX4 (3), IncHI2/2A (3) and a hybrid IncFIA/HI1A/HI1B (1) plasmid. Plasmids belonging to the IncI2 (n = 1) and IncX4 (n = 3) groups showed high similarity with previously described plasmids. Two IncHI2/HI2A plasmids, showed high identity between them, while the third, showed several differences including additional resistance genes like tet(A) and floR. One IncFIA/H1A/H1B hybrid plasmid was characterized, highly similar to pSRC27-H, a prototype plasmid lacking mcr genes. mcr-1.5 variant was found in four plasmids with three different Inc groups: IncI2, IncHI2/HI2A and the hybrid FIA/HI1A/HI1B plasmid. mcr-1.5 variant is almost exclusively described in our country and with a high frequency. In addition, six E. coli isolates carried three allelic variants codifying for CTX-M-type extended-spectrum-β-lactamases: blaCTX-M-2 (3), blaCTX-M-65 (2), and blaCTX-M-14 (1). It is the first description of mcr-1 harboring plasmids different to IncI2 group in our country. These results represents new insights about mcr-1 harboring plasmids recovered from E. coli human samples from Argentina, showing different plasmid backbones and resistance gene combinations.
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Affiliation(s)
- Florencia Martino
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires City, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires City, Argentina
| | - Alejandro Petroni
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires City, Argentina
| | - María Alejandra Menocal
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires City, Argentina
| | - Alejandra Corso
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires City, Argentina
| | - Roberto Melano
- Public Health Ontario Laboratory, Toronto, Ontario, Canadá
- University of Toronto, Toronto, Ontario, Canadá
- Pan American Health Organization, Washington, D.C., United States of America
| | - Diego Faccone
- Servicio Antimicrobianos, National Reference Laboratory in Antimicrobial Resistance (NRLAR), National Institute of Infectious Diseases (INEI), ANLIS “Dr. Carlos G. Malbrán”, Buenos Aires City, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires City, Argentina
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Wang XY, Song HW, Yi T, Shen YB, Dai CS, Sun CT, Liu DJ, Shen JZ, Wu CM, Wang Y. Dihydroartemisinin inhibits plasmid transfer in drug-resistant Escherichia coli via limiting energy supply. Zool Res 2023; 44:894-904. [PMID: 37551137 PMCID: PMC10559095 DOI: 10.24272/j.issn.2095-8137.2023.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023] Open
Abstract
Conjugative transfer of antibiotic resistance genes (ARGs) by plasmids is an important route for ARG dissemination. An increasing number of antibiotic and nonantibiotic compounds have been reported to aid the spread of ARGs, highlighting potential challenges for controlling this type of horizontal transfer. Development of conjugation inhibitors that block or delay the transfer of ARG-bearing plasmids is a promising strategy to control the propagation of antibiotic resistance. Although such inhibitors are rare, they typically exhibit relatively high toxicity and low efficacy in vivo and their mechanisms of action are inadequately understood. Here, we studied the effects of dihydroartemisinin (DHA), an artemisinin derivative used to treat malaria, on conjugation. DHA inhibited the conjugation of the IncI2 and IncX4 plasmids carrying the mobile colistin resistance gene ( mcr-1) by more than 160-fold in vitro in Escherichia coli, and more than two-fold (IncI2 plasmid) in vivo in a mouse model. It also suppressed the transfer of the IncX3 plasmid carrying the carbapenem resistance gene bla NDM-5 by more than two-fold in vitro. Detection of intracellular adenosine triphosphate (ATP) and proton motive force (PMF), in combination with transcriptomic and metabolomic analyses, revealed that DHA impaired the function of the electron transport chain (ETC) by inhibiting the tricarboxylic acid (TCA) cycle pathway, thereby disrupting PMF and limiting the availability of intracellular ATP for plasmid conjugative transfer. Furthermore, expression levels of genes related to conjugation and pilus generation were significantly down-regulated during DHA exposure, indicating that the transfer apparatus for conjugation may be inhibited. Our findings provide new insights into the control of antibiotic resistance and the potential use of DHA.
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Affiliation(s)
- Xue-Yang Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Huang-Wei Song
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Tian Yi
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Ying-Bo Shen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Chong-Shan Dai
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Cheng-Tao Sun
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - De-Jun Liu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Jian-Zhong Shen
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Cong-Ming Wu
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health Security, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, Guangdong 510642, China. E-mail:
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Genetic and phenotypic analyses of mcr-harboring extended-spectrum β-lactamase-producing Escherichia coli isolates from companion dogs and cats in Japan. Vet Microbiol 2023; 280:109695. [PMID: 36848815 DOI: 10.1016/j.vetmic.2023.109695] [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: 10/30/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023]
Abstract
The emergence of mcr plasmid-mediated colistin-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacterales among companion dogs and cats poses a risk of the animals acting as reservoirs for cross-species transmission. However, current knowledge of mcr-harboring ESBL-producing Enterobacterales in companion dogs and cats is still limited; thus, the genetic and phenotypic characteristics of the bacterial isolates and plasmids, in companion dogs and cats, remain to be elucidated. Here, we identified mcr gene-harboring ESBL-producing Escherichia coli isolates during whole-genome sequencing of ESBL-producing E. coli isolates from a dog and a cat in Osaka, Japan. Colistin-resistant MY732 isolate from a dog carried two plasmids: mcr-1.1-harboring IncI2 plasmid and blaCTX-M-14-harboring IncFIB plasmid. Conjugation assays revealed that both plasmids can be co-transferred even though the IncFIB plasmid lacked a conjugal transfer gene cassette. The other isolate MY504 from a cat harbored two bla genes and mcr-9 on the identical IncHI2 plasmid. This isolate was not resistant to colistin, which is likely to be due to deletion of the regulatory two-component QseBC system associated with the mcr-9 expression. To the best of our knowledge, this is the first report of a colistin-resistant ESBL-producing E. coli isolate harboring mcr-1 from a companion dog in Japan. Given that the mcr gene-harboring IncI2 and IncHI2 plasmids in this study shared high homology with plasmids from human or animal-derived Enterobacterales, companion dogs and cats may act as important reservoirs for cross-species transmission of the mcr gene in the community, in Japan.
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Algarni S, Han J, Gudeta DD, Khajanchi BK, Ricke SC, Kwon YM, Rhoads DD, Foley SL. In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens. Front Microbiol 2023; 13:1095128. [PMID: 36777021 PMCID: PMC9908598 DOI: 10.3389/fmicb.2022.1095128] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/22/2022] [Indexed: 01/27/2023] Open
Abstract
Introduction The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk. Methods To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences. Results and Discussion In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.
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Affiliation(s)
- Suad Algarni
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Jing Han
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Dereje D. Gudeta
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Bijay K. Khajanchi
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States
| | - Steven C. Ricke
- Meat Science & Animal Biologics Discovery Program and Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| | - Young Min Kwon
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Douglas D. Rhoads
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | - Steven L. Foley
- Division of Microbiology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, United States,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States,*Correspondence: Steven L. Foley, ✉
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5
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Milman O, Yelin I, Kishony R. Systematic identification of gene-altering programmed inversions across the bacterial domain. Nucleic Acids Res 2023; 51:553-573. [PMID: 36617974 PMCID: PMC9881135 DOI: 10.1093/nar/gkac1166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/22/2022] [Accepted: 01/05/2023] [Indexed: 01/10/2023] Open
Abstract
Programmed chromosomal inversions allow bacteria to generate intra-population genotypic and functional heterogeneity, a bet-hedging strategy important in changing environments. Some programmed inversions modify coding sequences, producing different alleles in several gene families, most notably in specificity-determining genes such as Type I restriction-modification systems, where systematic searches revealed cross phylum abundance. Yet, a broad, gene-independent, systematic search for gene-altering programmed inversions has been absent, and little is known about their genomic sequence attributes and prevalence across gene families. Here, identifying intra-species variation in genomes of over 35 000 species, we develop a predictive model of gene-altering inversions, revealing key attributes of their genomic sequence attributes, including gene-pseudogene size asymmetry and orientation bias. The model predicted over 11,000 gene-altering loci covering known targeted gene families, as well as novel targeted families including Type II restriction-modification systems, a protein of unknown function, and a fusion-protein containing conjugative-pilus and phage tail domains. Publicly available long-read sequencing datasets validated representatives of these newly predicted inversion-targeted gene families, confirming intra-population genetic heterogeneity. Together, these results reveal gene-altering programmed inversions as a key strategy adopted across the bacterial domain, and highlight programmed inversions that modify Type II restriction-modification systems as a possible new mechanism for maintaining intra-population heterogeneity.
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Affiliation(s)
- Oren Milman
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Idan Yelin
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Roy Kishony
- To whom correspondence should be addressed. Tel: +972 4 8293737;
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Tang B, Wang J, Zheng X, Chang J, Ma J, Wang J, Ji X, Yang H, Ding B. Antimicrobial resistance surveillance of Escherichia coli from chickens in the Qinghai Plateau of China. Front Microbiol 2022; 13:885132. [PMID: 35935206 PMCID: PMC9354467 DOI: 10.3389/fmicb.2022.885132] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/04/2022] [Indexed: 01/19/2023] Open
Abstract
Antimicrobial resistance (AMR) may lead to worldwide epidemics through human activities and natural transmission, posing a global public safety threat. Colistin resistance mediated by the mcr-1 gene is the most prevalent among animal-derived Escherichia coli, and mcr-1-carrying E. coli have been frequently detected in central-eastern China. However, animal-derived E. coli with AMR and the prevalence of mcr-1 in the Qinghai Plateau have been rarely investigated. Herein, 375 stool samples were collected from 13 poultry farms in Qinghai Province and 346 E. coli strains were isolated, of which eight carried mcr-1. The AMR rates of the E. coli strains to ampicillin, amoxicillin/clavulanic acid, and tetracycline were all above 90%, and the resistance rates to ciprofloxacin, cefotaxime, ceftiofur, and florfenicol were above 70%. Multidrug-resistant strains accounted for 95.66% of the total isolates. Twelve E. coli strains showed colistin resistance, from which a total of 46 AMR genes and 36 virulence factors were identified through whole-genome sequencing. The mcr-1 gene resided on the IncHI2, IncI2-type and IncY-type plasmids, and mcr-1 was located in the nikA-nikB-mcr-1-pap2 gene cassette (three strains) or the pap2-mcr-1-ISApl1 structure (one strain). Completed IncI2-type plasmid pMCR4D31–3 sequence (62,259 bp) revealed that it may cause the horizontal transmission of mcr-1 and may increase the risk of its spread through the food chain. Taken together, the AMR of chicken-derived E. coli in the plateau is of concern, suggesting that it is very necessary for us to strengthen the surveillance in various regions under the background of one health.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Biao Tang,
| | - Jingge Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
| | - Xue Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiang Chang
- State Key Laboratory of Microbial Metabolism, School of Agriculture and Biology, MOST-USDA Joint Research Center for Food Safety, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Juan Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xiaofeng Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baoan Ding
- College of Agriculture and Animal Husbandry, Qinghai University, Xining, China
- Baoan Ding,
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Darphorn TS, Brul S, Ter Kuile BH. Genetic editing of multi-resistance plasmids in Escherichia coli isolated from meat during transfer. Plasmid 2022; 122:102640. [PMID: 35870604 DOI: 10.1016/j.plasmid.2022.102640] [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: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022]
Abstract
Resistance plasmids mediate the rapid spread of antimicrobial resistance, which poses a threat to veterinary and human healthcare. This study addresses the question whether resistance plasmids from Escherichia coli isolated from foodstuffs always transfer unchanged to recipient E. coli cells, or that genetic editing can occur. Strains containing between one and five different plasmids were co-incubated with a standard recipient strain. Plasmids isolated from transconjugant strains were sequenced using short and long read technologies and compared to the original plasmids from the donor strains. After one hour of co-incubation only a single plasmid was transferred from donor to recipient strains. If the donor possessed several plasmids, longer co-incubation resulted in multiple plasmids being transferred. Transferred plasmids showed mutations, mostly in mobile genetic elements, in the conjugative transfer gene pilV and in genes involved in plasmid maintenance. In one transconjugant, a resistance cluster encoding tetracycline resistance was acquired by the IncI1 plasmid from the IncX1 plasmid that was also present in the donor strain, but that was not transferred. A single plasmid transferred twelve times back and forth between E. coli strains resulted in a fully conserved plasmid with no mutations, apart from repetitive rearrangements of pilV from and back to its original conformation in the donor strain. The overall outcome suggests that some genetic mutations and rearrangements can occur during plasmid transfer. The possibility of such mutations should be taken into consideration in epidemiological research aimed at attribution of resistance to specific sources.
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Affiliation(s)
- Tania S Darphorn
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Stanley Brul
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Benno H Ter Kuile
- Laboratory for Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands; Netherlands Food and Consumer Product Safety Authority, Office for Risk Assessment, Utrecht, the Netherlands.
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Allard N, Neil K, Grenier F, Rodrigue S. The Type IV Pilus of Plasmid TP114 Displays Adhesins Conferring Conjugation Specificity and Is Important for DNA Transfer in the Mouse Gut Microbiota. Microbiol Spectr 2022; 10:e0230321. [PMID: 35293798 PMCID: PMC9045228 DOI: 10.1128/spectrum.02303-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/16/2022] [Indexed: 12/02/2022] Open
Abstract
Type IV pili (T4P) are common bacterial surface appendages involved in different biological processes such as adherence, motility, competence, pathogenesis, and conjugation. In this work, we describe the T4P of TP114, an IncI2 enterobacterial conjugative plasmid recently shown to disseminate at high rates in the mouse intestinal tract. This pilus is composed of the major PilS and minor PilV pilins that are both important for conjugation in broth and in the gut microbiota but not on a solid support. The PilV-coding sequence is part of a shufflon and can bear different C-terminal domains. The shufflon is a multiple DNA inversion system containing many DNA cassettes flanked by recombination sites that are recognized by a shufflon-specific tyrosine recombinase (shufflase) promoting the recombination between DNA segments. The different PilV variants act as adhesins that can modify the affinity for different recipient bacteria. Eight PilV variants were identified in TP114, including one that has not been described in other shufflons. All PilV variants allowed conjugative transfer with different recipient Escherichia coli strains. We conclude that the T4P carried by TP114 plays a major role in mating pair stabilization in broth as well as in the gut microbiota and that the shufflon acts as a biological switch modifying the conjugative host range specificity. IMPORTANCE Conjugative plasmids are involved in horizontal gene transfer in the gut microbiota, which constitutes an important antibiotic resistance gene reservoir. However, the molecular mechanisms used by conjugative plasmids to select recipient bacteria and transfer at high rates in the mouse gut microbiota remain poorly characterized. We studied the type IV pilus carried by TP114 and demonstrated that the minor pilin PilV acts as an adhesin that can efficiently select target cells for conjugative transfer. Moreover, the pilV gene can be rapidly modified by a shufflon, hence modulating the nature of the recipient bacteria during conjugation. Our study highlights the role of mating pair stabilization for conjugation in broth as well as in the gut microbiome and explains how the host spectrum of a plasmid can be expanded simply by remodeling the PilV adhesin.
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Affiliation(s)
- Nancy Allard
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Kevin Neil
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Frédéric Grenier
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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Gonzales-Escalante E, Ruggiero M, Cerdeira L, Esposito F, Fontana H, Lincopan N, Gutkind G, Di Conza J. Whole-Genome Analysis of a High-Risk Clone of Klebsiella pneumoniae ST147 Carrying Both mcr-1 and blaNDM-1 Genes in Peru. Microb Drug Resist 2021; 28:171-179. [PMID: 34698586 DOI: 10.1089/mdr.2021.0128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The increasing prevalence and dissemination of carbapenemase-producing Enterobacterales represent a serious concern for public health. We studied the genetic features of a multidrug-resistant isolate of high-risk clone ST147 Klebsiella pneumoniae coharboring mcr-1 and blaNDM-1 recovered from a human clinical urine sample in 2017 in Peru. Whole-genome sequencing and conjugation assays identified mcr-1 and blaNDM-1 genes on two different conjugative plasmids, which belong to IncI2 and IncFIB/HI1B incompatibility groups, respectively. The presence of blaCTX-M-15 (in the studied isolate, located on the chromosome) and mutations in GyrA S83I and ParC S80I were detected, as expected for ST147. In addition, other β-lactamases (blaTEM-26 and blaOXA-1) and PMQR (qnrE2 and aac(6')-Ib-cr) among several resistance determinants were identified. The coexistence not previously described of these genes in the same high-risk clone is a cause for serious concern that supports the need for implementation of genomic surveillance studies.
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Affiliation(s)
- Edgar Gonzales-Escalante
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales - CITBM, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Melina Ruggiero
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET, Buenos Aires, Argentina
| | - Louise Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Fernanda Esposito
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Herrison Fontana
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Gabriel Gutkind
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET, Buenos Aires, Argentina
| | - Jose Di Conza
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina.,CONICET, Buenos Aires, Argentina
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Beyrouthy R, Sabença C, Robin F, Poeta P, Igrejas G, Bonnet R. Successful Dissemination of Plasmid-Mediated Extended-Spectrum β-Lactamases in Enterobacterales over Humans to Wild Fauna. Microorganisms 2021; 9:microorganisms9071471. [PMID: 34361907 PMCID: PMC8305760 DOI: 10.3390/microorganisms9071471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Background: The emergence of multidrug-resistant bacteria remains poorly understood in the wild ecosystem and at the interface of habitats. Here, we explored the spread of Escherichia coli containing IncI1-ST3 plasmid encoding resistance gene cefotaximase-Munich-1 (blaCTX-M-1) in human-influenced habitats and wild fauna using a genomic approach. Methods. Multilocus sequence typing (MLST), single-nucleotide polymorphism comparison, synteny-based analysis and data mining approaches were used to analyse a dataset of genomes and circularised plasmids. Results. CTX-M-1 E. coli sequence types (STs) were preferentially associated with ecosystems. Few STs were shared by distinct habitats. IncI1-ST3-blaCTX-M-1 plasmids are disseminated among all E. coli phylogroups. The main divergences in plasmids were located in a shuffling zone including blaCTX-M-1 inserted in a conserved site. This insertion hot spot exhibited diverse positions and orientations in a zone-modulating conjugation, and the resulting synteny was associated with geographic and biological sources. Conclusions. The ecological success of IncI1-ST3-blaCTX-M-1 appears less linked to the spread of their bacterial recipients than to their ability to transfer in a broad spectrum of bacterial lineages. This feature is associated with the diversity of their shuffling conjugation region that contain blaCTX-M-1. These might be involved in the resistance to antimicrobials, but also in their spread.
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Affiliation(s)
- Racha Beyrouthy
- Institut National de la Santé et de la Recherche Médicale, (UMR1071), Institut National de la Recherche Agronomique (USC-2018), Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (R.B.); (F.R.)
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, 63000 Clermont-Ferrand, France
| | - Carolina Sabença
- MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trá-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal; (C.S.); (P.P.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
| | - Frédéric Robin
- Institut National de la Santé et de la Recherche Médicale, (UMR1071), Institut National de la Recherche Agronomique (USC-2018), Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (R.B.); (F.R.)
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, 63000 Clermont-Ferrand, France
| | - Patricia Poeta
- MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trá-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal; (C.S.); (P.P.)
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2825-168 Caparica, Portugal
| | - Giberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 2825-168 Caparica, Portugal
| | - Richard Bonnet
- Institut National de la Santé et de la Recherche Médicale, (UMR1071), Institut National de la Recherche Agronomique (USC-2018), Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (R.B.); (F.R.)
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire, 63000 Clermont-Ferrand, France
- Correspondence: ; Tel.: +33-473754920
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Interference of ISEcp1-bla CTX-M-1 with the shufflon rearrangement in IncI1 plasmids. Plasmid 2021; 116:102578. [PMID: 33964314 DOI: 10.1016/j.plasmid.2021.102578] [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] [Received: 01/29/2021] [Revised: 04/24/2021] [Accepted: 05/04/2021] [Indexed: 11/20/2022]
Abstract
IncI1 plasmids are known disseminators of the extended-spectrum cephalosporin resistance (ESC) gene blaCTX-M-1, among species of the Enterobacteriaceae family. In several IncI1 plasmids, this gene was found incorporated into the transposition unit, ISEcp1-blaCTX-M-1-orf477, interrupting a shufflon region, a hallmark of IncI1 conjugative plasmids. The shufflon diversifies pilV gene that encodes the adhesine-type protein found on the tip of the conjugative pilus. To further elucidate the shufflon rearrangement, we examined to what extent the shufflon rearrangement was affected by the transposition-unit insertion. As expected, the interrupted shufflons generated a lower number of shufflon variants and exhibited an altered segment-deletion pattern compared to the non-interrupted shufflon. Interestingly, segment-loss frequency of the interrupted shufflons was distinctive in different plasmid hosts. Finally, the analysis of the 3' end of the pilV gene revealed that shufflon rearrangement favoured segment A to complete pilV partial open reading frame regardless of the shufflon. Thereby, it could be assumed that the A-segment has greater importance during conjugation, however, this remained a hypothesis. Further exploration of shufflon rearrangement and its importance in the plasmid-recipient selection during conjugation would be beneficial as the knowledge could be applied in developing a strategy to limit IncI1 mediated antimicrobial resistance dissemination.
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12
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Yossapol M, Yamamoto M, Sugiyama M, Odoi JO, Omatsu T, Mizutani T, Ohya K, Asai T. Association between the blaCTX-M-14-harboring Escherichia coli Isolated from Weasels and Domestic Animals Reared on a University Campus. Antibiotics (Basel) 2021; 10:antibiotics10040432. [PMID: 33924433 PMCID: PMC8069031 DOI: 10.3390/antibiotics10040432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 01/06/2023] Open
Abstract
Antimicrobial-resistant (AMR) bacteria affect human and animal health worldwide. Here, CTX-M-14-producing Escherichia coli isolates were isolated from Siberian weasels (Mustela sibirica) that were captured on a veterinary campus. To clarify the source of bacteria in the weasels, we examined the domestic animals reared in seven facilities on the campus. Extended-spectrum β-lactamase (ESBL)-producing E. coli were isolated on deoxycholate hydrogen sulfide lactose agar, containing cephalexin (50 μg/mL) or cefotaxime (2 μg/mL), and were characterized with antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), replicon typing, and β-lactamase typing analyses. Next-generation sequencing of the ESBL-encoding plasmids was also performed. CTX-M-14 producers isolated from both domestic animals and weasels were classified into six clusters with seven PFGE profiles. The PFGE and antimicrobial resistance profiles were characterized by the animal facility. All CTX-M-14 plasmids belonged to the IncI1 type with a similar size (98.9–99.3 kb), except for one plasmid that was 105.5 kb in length. The unweighted pair group method with arithmetic mean (UPGMA) revealed that the CTX-M-14 plasmid in the weasel isolates might have the same origin as the CTX-M-14 plasmid in the domestic animals. Our findings shed further light on the association of antimicrobial resistance between wild and domestic animals.
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Affiliation(s)
- Montira Yossapol
- Department of Applied Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, Gifu 5011193, Japan; (M.Y.); (M.Y.); (M.S.); (J.O.O.); (K.O.)
- Bioveterinary Research Unit, Faculty of Veterinary Sciences, Mahasarakham University, Maha Sarakham 44000, Thailand
| | - Miku Yamamoto
- Department of Applied Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, Gifu 5011193, Japan; (M.Y.); (M.Y.); (M.S.); (J.O.O.); (K.O.)
| | - Michiyo Sugiyama
- Department of Applied Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, Gifu 5011193, Japan; (M.Y.); (M.Y.); (M.S.); (J.O.O.); (K.O.)
| | - Justice Opare Odoi
- Department of Applied Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, Gifu 5011193, Japan; (M.Y.); (M.Y.); (M.S.); (J.O.O.); (K.O.)
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo 1838538, Japan; (T.O.); (T.M.)
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Diseases of Animals, Tokyo University of Agriculture and Technology, Tokyo 1838538, Japan; (T.O.); (T.M.)
| | - Kenji Ohya
- Department of Applied Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, Gifu 5011193, Japan; (M.Y.); (M.Y.); (M.S.); (J.O.O.); (K.O.)
| | - Tetsuo Asai
- Department of Applied Veterinary Science, United Graduate School of Veterinary Sciences, Gifu University, Gifu 5011193, Japan; (M.Y.); (M.Y.); (M.S.); (J.O.O.); (K.O.)
- Education and Research Center for Food Animal Health, Gifu University, Gifu 5011193, Japan
- Correspondence: ; Tel.: +81-58-293-229
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13
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Li W, Li Y, Jia Y, Sun H, Zhang C, Hu G, Yuan L. Genomic characteristics of mcr-1 and bla CTX-M-type in a single multidrug-resistant Escherichia coli ST93 from chicken in China. Poult Sci 2021; 100:101074. [PMID: 33774373 PMCID: PMC8025056 DOI: 10.1016/j.psj.2021.101074] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 01/28/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
This study was undertaken to discern the transmission characteristics of mcr-1 and blaCTX-M-type in one multidrug-resistant Escherichia coli LWY24 from chicken in China. The genetic profiles of LWY24 isolate were determined by conjugation, S1-pulsed-field gel electrophoresis, southern blot hybridization, and whole genome sequencing analysis. Meanwhile, co-transfer of plasmids in LWY24 isolate was screened by dual conjugation assays. The LWY24 isolate was identified as ST93, and harbored 3 conjugative plasmids, pLWY24J-3 (blaCTX-M-55-bearing IncFⅡ), pLWY24J-mcr-1 (mcr-1-carrying IncI2), and pLWY24J-4 (non-resistance-conferring IncI1), and one nonconjugative plasmid pLWY24 (blaCTX-M-14-containing IncHI2/IncHI2A). Numerous resistance genes, insertion sequences (especially IS26), and transposons were found in the 4 plasmids, suggesting that horizontal transmission have occurred by plasmid mating, homologous recombination, and transpositions. Under the selection pressure of cefotaxime and colistin or cefotaxime alone, the mcr-1-bearing plasmid and the blaCTX-M-55-harboring plasmid could be co-transferred at a similar frequency, with 8.00 × 10−4 or 9.00 × 10−4 transconjugants per donor cell, respectively. The specific shufflon region in mcr-1-encoding plasmid could generate up to 6 diverse PilV structures, which may further accelerate the horizontal transfer of plasmid. In conclusion, the transmission characteristics of mcr-1 and blaCTX-M-type in LWY24 isolate could due to clonal spread of ST93, selective pressure of cefotaxime, IS26-mediate homologous recombination and transposition, and the specific shufflon region.
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Affiliation(s)
- Wenya Li
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yinshu Li
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Yating Jia
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Huarun Sun
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Chunhui Zhang
- College of Animal Medicine, Henan University of Animal Husbandry & Economy, Zhengzhou 450046, China
| | - Gongzheng Hu
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China
| | - Li Yuan
- College of Animal Medicine, Henan Agricultural University, Zhengzhou 450046, China.
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14
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De Ste Croix M, Holmes J, Wanford JJ, Moxon ER, Oggioni MR, Bayliss CD. Selective and non-selective bottlenecks as drivers of the evolution of hypermutable bacterial loci. Mol Microbiol 2020; 113:672-681. [PMID: 32185830 PMCID: PMC7154626 DOI: 10.1111/mmi.14453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 12/28/2022]
Abstract
Bottlenecks reduce the size of the gene pool within populations of all life forms with implications for their subsequent survival. Here, we examine the effects of bottlenecks on bacterial commensal-pathogens during transmission between, and dissemination within, hosts. By reducing genetic diversity, bottlenecks may alter individual or population-wide adaptive potential. A diverse range of hypermutable mechanisms have evolved in infectious agents that allow for rapid generation of genetic diversity in specific genomic loci as opposed to the variability arising from increased genome-wide mutation rates. These localised hypermutable mechanisms include multi-gene phase variation (PV) of outer membrane components, multi-allele PV of restriction systems and recombination-driven antigenic variation. We review selected experimental and theoretical (mathematical) models pertaining to the hypothesis that localised hypermutation (LH) compensates for fitness losses caused by bottlenecks and discuss whether bottlenecks have driven the evolution of hypermutable loci.
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Affiliation(s)
- Megan De Ste Croix
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Jonathan Holmes
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Joseph J Wanford
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - E Richard Moxon
- Department of Paediatrics, University of Oxford Medical Sciences Division, John Radcliffe Hospital, Oxford, UK
| | - Marco R Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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15
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McMillan EA, Jackson CR, Frye JG. Transferable Plasmids of Salmonella enterica Associated With Antibiotic Resistance Genes. Front Microbiol 2020; 11:562181. [PMID: 33133037 PMCID: PMC7578388 DOI: 10.3389/fmicb.2020.562181] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Salmonella enterica is a common foodborne illness in the United States and globally. An increasing number of Salmonella infections are resistant to antibiotics, and many of the genes responsible for those resistances are carried by plasmids. Plasmids are important mediators of horizontal gene exchange, which could potentially increase the spread of antibiotic resistance (AR) genes. Twenty-eight different incompatibility groups of plasmids have been described in Enterobacteriaceae. Incompatibility groups differ in their accessory gene content, replication mechanisms, and their associations with Salmonella serotypes and animal sources. Plasmids also differ in their ability to conjugate or be mobilized, essential genes, and conditions required for transfer. It is important to understand the differences in gene content and transfer mechanisms to accurately determine the impact of plasmids on the dissemination and persistence of antibiotic resistance genes. This review will cover the most common plasmid incompatibility groups present in S. enterica with a focus on the transfer mechanisms and associated antibiotic resistance genes.
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Affiliation(s)
- Elizabeth A McMillan
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
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16
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In Silico Genotyping of Escherichia coli Isolates for Extraintestinal Virulence Genes by Use of Whole-Genome Sequencing Data. J Clin Microbiol 2020; 58:JCM.01269-20. [PMID: 32669379 PMCID: PMC7512150 DOI: 10.1128/jcm.01269-20] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause in humans of urinary tract infection and bacteremia. The previously published web tool VirulenceFinder (http://cge.cbs.dtu.dk/services/VirulenceFinder/) uses whole-genome sequencing (WGS) data for in silico characterization of E. coli isolates and enables researchers and clinical health personnel to quickly extract and interpret virulence-relevant information from WGS data. In this study, 38 ExPEC-associated virulence genes were added to the existing E. coli VirulenceFinder database. In total, 14,441 alleles were downloaded. A total of 1,890 distinct alleles were added to the database after removal of redundant sequences and analysis of the remaining alleles for open reading frames (ORFs). The database now contains 139 genes-of which 44 are related to ExPEC-and 2,826 corresponding alleles. Construction of the database included validation against 27 primer pairs from previous studies, a search for serotype-specific P fimbriae papA alleles, and a BLASTn confirmation of seven genes (etsC, iucC, kpsE, neuC, sitA, tcpC, and terC) not covered by the primers. The augmented database was evaluated using (i) a panel of nine control strains and (ii) 288 human-source E. coli strains classified by PCR as ExPEC and non-ExPEC. We observed very high concordance (average, 93.4%) between PCR and WGS findings, but WGS identified more alleles. In conclusion, the addition of 38 ExPEC-associated genes and the associated alleles to the E. coli VirulenceFinder database allows for a more complete characterization of E. coli isolates based on WGS data, which has become increasingly important considering the plasticity of the E. coli genome.
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17
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Abdul Momin MHF, Liakopoulos A, Bean DC, Phee LM, Wareham DW. A novel plasmid-mediated polymyxin resistance determinant (mcr-1.8) in Escherichia coli recovered from broiler chickens in Brunei Darussalam. J Antimicrob Chemother 2020; 74:3392-3394. [PMID: 31504534 DOI: 10.1093/jac/dkz352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Muhd Haziq F Abdul Momin
- Antimicrobial Research Group, Centre for Immunobiology, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Apostolos Liakopoulos
- Department of Microbial Biotechnology and Health, Institute of Biology, University of Leiden, Leiden, The Netherlands
| | - David C Bean
- School of Applied & Biomedical Sciences, Federation University Australia, Ballarat, Australia
| | - Lynette M Phee
- Antimicrobial Research Group, Centre for Immunobiology, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Division of Infection, Barts Healthcare NHS Trust, London, UK
| | - David W Wareham
- Antimicrobial Research Group, Centre for Immunobiology, Blizard Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Division of Infection, Barts Healthcare NHS Trust, London, UK
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18
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Cisse S, Benarbia MEA, Burel A, Friedrich M, Gabinaud B, Belz É, Guilet D, Chicoteau P, Zemb O. Standardized Natural Citrus Extract dietary supplementation influences sows’ microbiota, welfare, and preweaning piglets’ performances in commercial rearing conditions. Transl Anim Sci 2020; 4:txaa059. [PMID: 32705054 PMCID: PMC7264690 DOI: 10.1093/tas/txaa059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/07/2020] [Indexed: 11/17/2022] Open
Abstract
We investigated the effect of the Standardized Natural Citrus Extract (SNCE; Nor-Spice AB, Nor-Feed SAS, France) on the microbiota of the sows and on the weight gain of their piglets. Fifty sows were randomly divided into two groups: a control group (23 sows) with a standard diet and a SNCE group (27 sows) with a standard diet supplemented with 2,500 ppm of SNCE. Supplementation occurred 10 d before and 5 d after farrowing. Fecal samples from 16 sows (8 randomly selected sows of each dietary treatment) were collected for the fecal microbiota analysis 5 d after farrowing. The supplementation of SNCE increases the amount of cultivable Lactobacillus threefold in vitro. Microbial DNA was extracted from the fecal samples for sequencing of the 16S rRNA gene. The SNCE, which affected the microbiota as a discriminant analysis, was able to separate the microbial communities of the eight sows that received SNCE from the three control sows with 21 Operational Taxonomic Units (area under the ROC curve = 96%). SNCE also reduced the interval between farrowing and the first dejection of the sow and increased their feed intake (P-value < 0.05). Furthermore, feeding the sows with SNCE improved the weight gain of the piglets in the first week of life. These results show that SNCE supplementation allows to enhance zootechnical performances of peripartum’ sows, possibly due to the modulation of the microbiota transmitted to the piglets.
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Affiliation(s)
- Sekhou Cisse
- Nor-Feed SAS, Beaucouzé, France
- FeedInTech, Beaucouzé, France
| | | | | | | | - Beatrice Gabinaud
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | | | | | | | - Olivier Zemb
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
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Lin Y, Dong X, Wu J, Rao D, Zhang L, Faraj Y, Yang K. Metadata Analysis of mcr-1-Bearing Plasmids Inspired by the Sequencing Evidence for Horizontal Transfer of Antibiotic Resistance Genes Between Polluted River and Wild Birds. Front Microbiol 2020; 11:352. [PMID: 32210943 PMCID: PMC7076156 DOI: 10.3389/fmicb.2020.00352] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 02/18/2020] [Indexed: 12/30/2022] Open
Abstract
We sequenced the whole genomes of three mcr-1-positive multidrug-resistant E. coli strains, which were previously isolated from the environment of egret habitat (polluted river) and egret feces. The results exhibit high correlation between antibiotic-resistant phenotype and genotype among the three strains. Most of the mobilized antibiotic resistance genes (ARGs) are distributed on plasmids in the forms of transposons or integrons. Multidrug-resistant (MDR) regions of high homology are detected on plasmids of different E. coli isolates. Therefore, horizontal transfer of resistance genes has facilitated the transmission of antibiotic resistance between the environmental and avian bacteria, and the transfer of ARGs have involved multiple embedded genetic levels (transposons, integrons, plasmids, and bacterial lineages). Inspired by this, systematic metadata analysis was performed for the available sequences of mcr-1-bearing plasmids. Among these plasmids, IncHI2 plasmids carry the most additional ARGs. The composition of these additional ARGs varies according to their geographical distribution. The phylogenetic reconstruction of IncI2 and IncX4 plasmids provides the evidence for their multiregional evolution. Phylogenetic analysis at the level of mobile genetic element (plasmid) provides important epidemiological information for the global dissemination of mcr-1 gene. Highly homologous mcr-1-bearing IncI2 plasmids have been isolated from different regions along the East Asian-Australasian Flyway, suggesting that migratory birds may mediate the intercontinental transportation of ARGs.
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Affiliation(s)
- Yufei Lin
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Xiaohong Dong
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Jiao Wu
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Dawei Rao
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Lihua Zhang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Yousef Faraj
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Kun Yang
- Department of Pharmaceutical and Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, China
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20
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Loayza-Villa F, Salinas L, Tijet N, Villavicencio F, Tamayo R, Salas S, Rivera R, Villacis J, Satan C, Ushiña L, Muñoz O, Zurita J, Melano R, Reyes J, Trueba GA. Diverse Escherichia coli lineages from domestic animals carrying colistin resistance gene mcr-1 in an Ecuadorian household. J Glob Antimicrob Resist 2019; 22:63-67. [PMID: 31841712 DOI: 10.1016/j.jgar.2019.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVE The aim of this study was to detect potential animal reservoirs of Escherichia coli carrying the mcr-1 gene in an Ecuadorian household. METHODS The mobile colistin-resistance gene, mcr-1, was first detected in Ecuador in a commensal E. coli isolate from a boy. A cross-sectional study was performed to detect the possible source of colistin-resistant E. coli in the boy's household. Faecal swabs and soil faecal samples were collected from companion animals. Samples were plated on selective media to isolate colistin-resistant E. coli and isolates were submitted to PCR detection of mcr-1, pulsed field gel electrophoresis (PFGE), and multi-locus sequences typing (MLST). Moreover, the genomes of all the isolates were sequenced. RESULTS Three different colistin-resistant E. coli sequence types (ST3941, 1630 and 2170), corresponding to three PFGE patterns, were obtained from a chicken and two dogs; these isolates were different from the human isolate (ST609). By whole-genome sequencing, the mcr-1.1 gene was found on IncI2 plasmids with very high nucleotide identity. CONCLUSIONS Our results indicate a polyclonal dissemination of mcr-1.1 in the environment surrounding the first MCR-producing E. coli strain reported in Ecuador. Our findings support the idea of lateral dissemination of mcr-1.1 gene between unrelated E. coli isolates.
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Affiliation(s)
| | - Liseth Salinas
- Universidad San Franscisco de Quito, Av. Diego de Robles y Pampite, Quito, Ecuador
| | | | - Fernando Villavicencio
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador
| | - Rafael Tamayo
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador
| | - Stephanie Salas
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador
| | - Ruth Rivera
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador
| | - Jose Villacis
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador; Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Carolina Satan
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador
| | - Liliana Ushiña
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador
| | - Olga Muñoz
- Instituto Nacional de Investigación en Salud Pública 'Dr. Leopoldo Izquieta Perez', Quito, Ecuador
| | - Jeannette Zurita
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Roberto Melano
- Public Health Ontario, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Jorge Reyes
- Universidad Central del Ecuador, Facultad de Ciencias Químicas, Ciudadela Universitaria - Avenida América, Quito, Ecuador
| | - Gabriel A Trueba
- Universidad San Franscisco de Quito, Av. Diego de Robles y Pampite, Quito, Ecuador
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21
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Meinersmann RJ. The biology of IncI2 plasmids shown by whole-plasmid multi-locus sequence typing. Plasmid 2019; 106:102444. [PMID: 31629716 DOI: 10.1016/j.plasmid.2019.102444] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/24/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
Abstract
IncI2 type plasmids are medium-sized (~55-80 kb) conjugative plasmids that have been found carrying important antimicrobial resistance genes but have also been frequently found as cryptic plasmids. The DNA sequences for 147 fully sequenced IncI2 plasmids were studied by a whole-plasmid multi-locus sequence typing (wpMLST) scheme. A total of 171 loci were identified of which 52 were considered core (carried by greater than 95% of the plasmids). Most of the plasmids carrying the antimicrobial gene mcr-1 were in a distinct clade while most of the antimicrobial gene free plasmids were more distantly related. However, the host strains of bacteria were disparate for both groups of plasmids, showing that conjugal transfer of IncI2 plasmid is frequent. The mcr-1 gene was likely to have been introduced into IncI2 plasmids multiple times. It was also observed that the genes for conjugation showed significant linkage disequilibrium despite substantial diversity for most of those genes. Genes associated with biofilm formation were also among the core genes. The core genes can be considered the cohesive unit that defines the IncI2 plasmid group. Given the role conjugation can play in biofilm formation, it was concluded that conjugation is an active survival strategy for IncI2 plasmids. The IncI2 plasmid will have selective advantage when the plasmid-bearing bacteria are introduced to a new animal host that carries potential conjugal mates.
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Affiliation(s)
- Richard J Meinersmann
- U.S. National Poultry Research Center, USDA Agricultural Research Service, 950 College Station Road, Athens, GA 30605, USA.
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22
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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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23
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Xiaoliang W, Huiming H, Chunlei C, Beiwen Z. Genomic characterisation of a colistin-resistant Klebsiella pneumoniae ST11 strain co-producing KPC-2, FloR, CTX-M-55, SHV-12, FosA and RmtB causing a lethal infection. J Glob Antimicrob Resist 2019; 19:78-80. [PMID: 31493525 DOI: 10.1016/j.jgar.2019.08.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/28/2019] [Accepted: 08/24/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES The aim of this study was to characterise the genomic and phenotypic characteristics of a colistin-resistant Klebsiella pneumoniae isolate causing a lethal infection that was phenotypically resistant to carbapenems and colistin. METHODS Whole-genome sequencing was performed on an Illumina HiSeq 2500 platform. Genome annotation was performed by the Rapid Annotation using Subsystem Technology (RAST) server. Antimicrobial resistance genes and plasmid replicons were identified using ResFinder 2.1 and PlasmidFinder 1.3, respectively. The isolate was further characterised by plasmid analysis using S1-PFGE and Southern blot hybridisation with a digoxigenin-labelled probe specific for blaKPC. RESULTS: The genome of K. pneumoniae LSK16 consists of a 6.02-Mbp chromosome and one plasmid. Multilocus sequence typing (MLST) identified the isolate as ST11, a close variant of the international pandemic clone ST258. The isolate was found to harbour blaKPC-2, blaSHV-12, blaCTX-M-55, floR and rmtB genes. Of note, a novel fosfomycin resistance glutathione transferase variant was confirmed by PCR and sequencing, with 98.6% (136/138) identity to fosA. Moreover, amino acid substitutions in PmrB (R256G) and PhoQ (D150G) were identified in LSK16, confirming the polymyxin/colistin resistance, although the isolate was negative for mcr genes. Southern blotting and plasmid analysis revealed that the blaKPC-2 gene was harboured on a non-conjugative IncR plasmid (˜165kb). CONCLUSION Here we identified a colistin-resistant K. pneumoniae ST11 strain co-producing KPC-2, FloR, CTX-M-55, SHV-12 and RmtB causing a lethal infection. This study provides new genomic insights into the diversity of K. pneumoniae ST11 prevalent in Zhejiang Province, China.
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Affiliation(s)
- Wu Xiaoliang
- Intensive Care Unit, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Han Huiming
- Medical College of Beihua University, Jilin, China
| | - Chen Chunlei
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zheng Beiwen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
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24
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Schmid M, Frei D, Patrignani A, Schlapbach R, Frey JE, Remus-Emsermann MNP, Ahrens CH. Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats. Nucleic Acids Res 2019; 46:8953-8965. [PMID: 30137508 PMCID: PMC6158609 DOI: 10.1093/nar/gky726] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/15/2018] [Indexed: 12/16/2022] Open
Abstract
Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length, which contained several genes that may confer fitness advantages to the strain. Its complex genome, which also included a variable shufflon region, could not be de novo assembled with long reads produced by Pacific Biosciences’ technology, but required very long reads from Oxford Nanopore Technologies. Importantly, a repeat analysis, whose results we release for over 9600 prokaryotes, indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this ‘dark matter’ for de novo genome assembly of prokaryotes. Several of these ‘dark matter’ genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assembly algorithms capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.
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Affiliation(s)
- Michael Schmid
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Andrea Patrignani
- Functional Genomics Center Zurich, University of Zurich & ETH Zurich, Zurich CH-8057, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich & ETH Zurich, Zurich CH-8057, Switzerland
| | - Jürg E Frey
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland
| | - Mitja N P Remus-Emsermann
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.,Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8140, New Zealand
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil CH-8820, Switzerland.,SIB Swiss Institute of Bioinformatics, Wädenswil CH-8820, Switzerland
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25
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Kikuchi K, Lee K, Ueno H, Tomari K, Kobori S, Kaetsu A, Matsui M, Suzuki S, Sekizuka T, Kuroda M, Miyazaki M, Ohnishi M. Enterohaemorrhagic Escherichia coli O121:H19 acquired an extended-spectrum β-lactamase gene during the development of an outbreak in two nurseries. Microb Genom 2019; 5. [PMID: 31215859 PMCID: PMC6700663 DOI: 10.1099/mgen.0.000278] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Enterohaemorrhagic Escherichia coli (EHEC) is an important human pathogen worldwide. Although serotype O157 is currently the most dominant and important EHEC strain, serotypes O26, O111, O91, O103 and O121 are also recognized as serious pathogens that affect public health. EHEC outbreaks often occur in nurseries and elderly care facilities. In 2012, a nursery outbreak of EHEC O121 occurred during which the bacterium acquired a plasmid-borne extended-spectrum β-lactamase (ESBL) gene. ESBL-producing E. coli O86 was concurrently isolated from one of the EHEC patients. Therefore, we investigated the isolates by whole-genome sequence (WGS) analysis to elucidate the transmission dynamics of the EHEC strains and the ESBL plasmid. According to WGS-based phylogeny, all 17 EHEC O121 isolates were clonal, while E. coli O86 was genetically distant from the EHEC O121 isolates. The complete sequence of an ESBL plasmid encoding the CTX-M-55 β-lactamase was determined using S1-PFGE bands, and subsequent mapping of the WGS reads confirmed that the plasmid sequences from EHEC O121 and E. coli O86 were identical. Furthermore, conjugation experiments showed that the plasmid was capable of conjugative transfer. These results support the hypothesis that EHEC O121 acquired an ESBL-producing plasmid from E. coli O86 during the outbreak. This report demonstrates the importance of implementing preventive measures during EHEC outbreaks to control both secondary infection and the spread of antimicrobial resistance factors.
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Affiliation(s)
- Koji Kikuchi
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Kenichi Lee
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroyuki Ueno
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Kentaro Tomari
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Sumie Kobori
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | | | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motonobu Miyazaki
- Saitama City Institute of Health Science and Research, Saitama, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
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26
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The shufflon of IncI1 plasmids is rearranged constantly during different growth conditions. Plasmid 2019; 102:51-55. [PMID: 30885787 DOI: 10.1016/j.plasmid.2019.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/12/2019] [Accepted: 03/14/2019] [Indexed: 12/20/2022]
Abstract
One of the factors that can affect conjugation of IncI1 plasmids, amongst others, is the genetic region known as the shufflon. This multiple inversion system modifies the pilus tip proteins used during conjugation, thus affecting the affinity for different recipient cells. Although recombination is known to occur in in vitro conditions, little is known about the regulation and the extent of recombination that occurs. To measure the recombination of the shufflon, we have amplified the entire shufflon region and sequenced the amplicons using nanopore long-read sequencing. This method was effective to determine the order of the segments of the shufflon and allow for the analysis of the shufflon variants that are present in a heterogeneous pool of templates. Analysis was performed over different growth phases and after addition of cefotaxime. Furthermore, analysis was performed in different E. coli host cells to determine if recombination is likely to be influenced. Recombination of the shufflon was constantly ongoing in all conditions that were measured, although no differences in the amount of different shufflon variants or the rate at which novel variants were formed could be found. As previously reported, some variants were abundant in the population while others were scarce. This leads to the conclusion that the shufflon is continuously recombining at a constant rate, or that the method used here was not sensitive enough to detect differences in this rate. For one of the plasmids, the host cell appeared to have an effect on the specific shufflon variants that were formed which were not predominant in another host, indicating that host factors may be involved. As previously reported, the pilV-A and pilV-A' ORFs are formed at higher frequencies than other pilV ORFs. These results demonstrate that the recombination that occurs within the shufflon is not random. While any regulation of the shufflon affected by these in vitro conditions could not be revealed, the method of amplifying large regions for long-read sequencing for the analysis of multiple inversion systems proved effective.
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27
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Xu L, Wang P, Cheng J, Qin S, Xie W. Characterization of a novel bla NDM-5-harboring IncFII plasmid and an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate. Infect Drug Resist 2019; 12:511-519. [PMID: 30881056 PMCID: PMC6402710 DOI: 10.2147/idr.s192998] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background and purpose The spread of the plasmid-mediated, colistin-resistance gene mcr-1 into New Delhi metallo-β-lactamase (NDM)-producing bacterial isolates can cause untreatable infections. In this study, we conducted a molecular characterization of a novel, conjugative, blaNDM-5-positive IncFII plasmid (pNDM-EC16-50) together with an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate EC16-50. Methods and results EC16-50, which belongs to the E. coli strain ST167 and phylogroup A, was identified to co-produce NDM-5 and MCR-1. S1-PFGE and Southern blotting showed that blaNDM-5 and mcr-1 genes were located oñ95 kb and ~65 kb plasmids, respectively. A conjugation assay revealed that both blaNDM-5- and mcr-1-bearing plasmids were self-transmissible. Comparative plasmid analysis suggested that blaNDM-5-harboring F2:A-:B-plasmid might have evolved from the well-reported NDM-carrying pMC-NDM-like plasmid via recombination with a locally emerged pSJ_94 plasmid, whereas the mcr-1-carrying IncI2 plasmid was similar to previously reported mcr-1-bearing plasmids in China. Conclusion and impact This study represents the first report of the NDM-5 carrying Inc-FII- but not IncX3-type plasmid in an MCR-1-producing E. coli isolate. More striking was the dissemination of mcr-1 in a successful epidemic NDM-5-producing E. coli clone ST167, which could facilitate the spread of colistin resistance in carbapenemase-producing E. coli isolates.
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Affiliation(s)
- Lijuan Xu
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Ping Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Jing Cheng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China, .,Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan 450001, China,
| | - Weihong Xie
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China,
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28
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Bardet L, Rolain JM. Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2018; 2018:3095249. [PMID: 30631384 PMCID: PMC6305056 DOI: 10.1155/2018/3095249] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/11/2018] [Indexed: 12/27/2022]
Abstract
The recent discovery of the plasmid-mediated mcr-1 gene conferring resistance to colistin is of clinical concern. The worldwide screening of this resistance mechanism among samples of different origins has highlighted the urgent need to improve the detection of colistin-resistant isolates in clinical microbiology laboratories. Currently, phenotypic methods used to detect colistin resistance are not necessarily suitable as the main characteristic of the mcr genes is the low level of resistance that they confer, close to the clinical breakpoint recommended jointly by the CLSI and EUCAST expert systems (S ≤ 2 mg/L and R > 2 mg/L). In this context, susceptibility testing recommendations for polymyxins have evolved and are becoming difficult to implement in routine laboratory work. The large number of mechanisms and genes involved in colistin resistance limits the access to rapid detection by molecular biology. It is therefore necessary to implement well-defined protocols using specific tools to detect all colistin-resistant bacteria. This review aims to summarize the current clinical microbiology diagnosis techniques and their ability to detect all colistin resistance mechanisms and describe new tools specifically developed to assess plasmid-mediated colistin resistance. Phenotyping, susceptibility testing, and genotyping methods are presented, including an update on recent studies related to the development of specific techniques.
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Affiliation(s)
- Lucie Bardet
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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29
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Li B, Ke B, Zhao X, Guo Y, Wang W, Wang X, Zhu H. Antimicrobial Resistance Profile of mcr-1 Positive Clinical Isolates of Escherichia coli in China From 2013 to 2016. Front Microbiol 2018; 9:2514. [PMID: 30405572 PMCID: PMC6206212 DOI: 10.3389/fmicb.2018.02514] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/02/2018] [Indexed: 01/22/2023] Open
Abstract
Multidrug-resistant (MDR) Escherichia coli poses a great challenge for public health in recent decades. Polymyxins have been reconsidered as a valuable therapeutic option for the treatment of infections caused by MDR E. coli. A plasmid-encoded colistin resistance gene mcr-1 encoding phosphoethanolamine transferase has been recently described in Enterobacteriaceae. In this study, a total of 123 E. coli isolates obtained from patients with diarrheal diseases in China were used for the genetic analysis of colistin resistance in clinical isolates. Antimicrobial resistance profile of polymyxin B (PB) and 11 commonly used antimicrobial agents were determined. Among the 123 E. coli isolates, 9 isolates (7.3%) were resistant to PB and PCR screening showed that seven (5.7%) isolates carried the mcr-1 gene. A hybrid sequencing analysis using single-molecule, real-time (SMRT) sequencing and Illumina sequencing was then performed to resolve the genomes of the seven mcr-1 positive isolates. These seven isolates harbored multiple plasmids and are MDR, with six isolates carrying one mcr-1 positive plasmid and one isolate (14EC033) carrying two mcr-1 positive plasmids. These eight mcr-1 positive plasmids belonged to the IncX4, IncI2, and IncP1 types. In addition, the mcr-1 gene was the solo antibiotic resistance gene identified in the mcr-1 positive plasmids, while the rest of the antibiotic resistance genes were mostly clustered into one or two plasmids. Interestingly, one mcr-1 positive isolate (14EC047) was susceptible to PB, and we showed that the activity of MCR-1-mediated colistin resistance was not phenotypically expressed in 14EC047 host strain. Furthermore, three isolates exhibited resistance to PB but did not carry previously reported mcr-related genes. Multilocus sequence typing (MLST) showed that these mcr-1 positive E. coli isolates belonged to five different STs, and three isolates belonged to ST301 which carried multiple virulence factors related to diarrhea. Additionally, the mcr-1 positive isolates were all susceptible to imipenem (IMP), suggesting that IMP could be used to treat infection caused by mcr-1 positive E. coli isolates. Collectively, this study showed a high occurrence of mcr-1 positive plasmids in patients with diarrheal diseases of Guangzhou in China and the abolishment of the MCR-1 mediated colistin resistance in one E. coli isolate.
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Affiliation(s)
- Baiyuan Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China.,CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Bixia Ke
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, China
| | - Xuanyu Zhao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yunxue Guo
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Weiquan Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxue Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Honghui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou, China
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30
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1139] [Impact Index Per Article: 189.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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Zheng B, Yu X, Xu H, Guo L, Zhang J, Huang C, Shen P, Jiang X, Xiao Y, Li L. Complete genome sequencing and genomic characterization of two Escherichia coli strains co-producing MCR-1 and NDM-1 from bloodstream infection. Sci Rep 2017; 7:17885. [PMID: 29263349 PMCID: PMC5738369 DOI: 10.1038/s41598-017-18273-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 12/04/2017] [Indexed: 11/27/2022] Open
Abstract
We previously described the discovery of two Escherichia coli isolates (EC1002 and EC2474) co-harbouring mcr-1 and blaNDM-1 genes, which were recovered from bloodstream infection in China. More importantly, these antibiotic resistance genes were located on different plasmids and signaling the potential spread of pandrug-resistant bacteria. Here, the complete genome sequences of both isolates were determined using Pacbio RS II and Illumina HiSeq2000 systems. The genome of EC1002 consists of a 5,177,501 base pair chromosome and four circular plasmids, while the genome of EC2474 consists of a 5,013,813 base pair chromosome and three plasmids. The plasmid replicon type of pEC1002_NDM and pEC2474_NDM were identified as IncA/C2 and IncF, respectively. The genetic environment of blaNDM-1 in this study was similar to blaNDM-carrying plasmids detected in China, although the overall nucleotide identity and query coverage were variable. The plasmid replicon type of pEC1002_MCR and pEC2474_MCR were identified as IncI2 and IncHI2, respectively. Two different genetic strategies for mcr-1 gene spread were observed in this study and blaNDM-1 genes were also found transferred by two different mobile genetic elements in two plasmids. The findings of this study further support that the diversified transfer mechanisms of blaNDM-1 and mcr-1 present in Enterobacteriaceae.
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Affiliation(s)
- 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, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Yu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 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, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lihua Guo
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jing Zhang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Huang
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ping Shen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiawei Jiang
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yonghong Xiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.
| | - Lanjuan Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Zurfluh K, Nüesch-Inderbinen M, Klumpp J, Poirel L, Nordmann P, Stephan R. Key features of mcr-1-bearing plasmids from Escherichia coli isolated from humans and food. Antimicrob Resist Infect Control 2017; 6:91. [PMID: 28878890 PMCID: PMC5585931 DOI: 10.1186/s13756-017-0250-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/25/2017] [Indexed: 11/29/2022] Open
Abstract
Background Mcr-1-harboring Enterobacteriaceae are reported worldwide since their first discovery in 2015. However, a limited number of studies are available that compared full-length plasmid sequences of human and animal origins. Methods In this study, mcr-1-bearing plasmids from seven Escherichia coli isolates recovered from patients (n = 3), poultry meat (n = 2) and turkey meat (n = 2) in Switzerland were further analyzed and compared. Isolates were characterized by multilocus sequence typing (MLST). The mcr-1-bearing plasmids were transferred by transformation into reference strain E. coli DH5α and MCR-1-producing transformants were selected on LB-agar supplemented with 2 mg/L colistin. Purified plasmids were then sequenced and compared. Results MLST revealed six distinct STs, illustrating the high clonal diversity among mcr-1-positive E. coli isolates of different origins. Two different mcr-1-positive plasmids were identified from a single E. coli ST48 human isolate. All other isolates possessed a single mcr-1 harboring plasmid. Transferable IncI2 (size ca. 60–61 kb) and IncX4 (size ca. 33–35 kb) type plasmids each bearing mcr-1 were found associated with human and food isolates. None of the mcr-1-positive IncI2 and IncX4 plasmids possessed any additional resistance determinants. Surprisingly, all but one of the sequenced mcr-1-positive plasmids lacked the ISApl1 element, which is a key element mediating acquisition of mcr-1 into various plasmid backbones. Conclusions There is strong evidence that the food chain may be an important transmission route for mcr-1-bearing plasmids. Our data suggest that some “epidemic” plasmids rather than specific E. coli clones might be responsible for the spread of the mcr-1 gene along the food chain.
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Affiliation(s)
- Katrin Zurfluh
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Magdalena Nüesch-Inderbinen
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstr. 7, 8092 Zurich, Switzerland
| | - Laurent Poirel
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology Unit, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance, Medical and Molecular Microbiology Unit, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance, University of Fribourg, Fribourg, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland
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Wang Q, Sun J, Li J, Ding Y, Li XP, Lin J, Hassan B, Feng Y. Expanding landscapes of the diversified mcr-1-bearing plasmid reservoirs. MICROBIOME 2017; 5:70. [PMID: 28683827 PMCID: PMC5500976 DOI: 10.1186/s40168-017-0288-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Polymyxin is a cationic polypeptide antibiotic that can disrupt bacterial cell membrane by interacting with its lipopolysaccharide molecules and is used as a last resort drug against lethal infections by the carbapenem-resistant superbugs (like NDM-1). However, global discovery of the MCR-1 colistin resistance dramatically challenges the newly renewed interest in colistin for clinical use. METHODS The mcr-1-harboring plasmids were acquired from swine and human Escherichia coli isolated in China, from 2015 to 2016, and subjected to Illumina PacBio RSII and Hi-Seq2000 for full genome sequencing. PCR was applied to close the gap of the assembled contigs. Ori-Finder was employed to predict the replication origin (oriC) in plasmids. The phenotype of MCR-1-producing isolates was evaluated on the LBA plates with various level of colistin. Genetic deletion was used to test the requirement of the initial "ATG" codon for the MCR-1 function. RESULTS Here, we report full genomes of over 10 mcr-1-harboring plasmids with diversified replication incompatibilities. A novel hybrid IncI2/IncFIB plasmid pGD17-2 was discovered and characterized from a swine isolate with colistin resistance. Intriguingly, co-occurrence of two unique mcr-1-bearing plasmids (pGD65-3, IncI2, and pGD65-5, IncX4) was detected in a single isolate GD65, which might accelerate dissemination of the mcr-1 under environmental selection pressure. Genetic analyses of these plasmids mapped mobile elements in the context of antibiotic resistance and determined two insertion sequences (ISEcp1 and ISApl1) that are responsible for the mobilization of mcr-1. Gene deletion also proved that the first ATG codon is redundant in the mcr-1 gene. CONCLUSIONS Collectively, our results extend landscapes of the diversified mcr-1-bearing plasmid reservoirs.
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Affiliation(s)
- Qingjing Wang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jun Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
| | - Youfa Ding
- Lishui People's Hospital, Lishui, 323000, Zhejiang, China
| | - Xing-Ping Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jingxia Lin
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | | | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
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