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Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece. Microorganisms 2023; 11:microorganisms11020516. [PMID: 36838481 PMCID: PMC9959086 DOI: 10.3390/microorganisms11020516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of blaNDM1-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of blaNDM-1, the isolates carried a combination of various to β-lactams encoding resistance genes: blaTEM-1B, blaCTX-15, blaOXA-1, blaVIM-1, blaSHV-5, blaOXA-16, blaOXA-10 and blaVEB-1. Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of blaNDM-1 genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). Τhis latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer.
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Merhi G, Amayri S, Bitar I, Araj GF, Tokajian S. Whole Genome-Based Characterization of Multidrug Resistant Enterobacter and Klebsiella aerogenes Isolates from Lebanon. Microbiol Spectr 2023; 11:e0291722. [PMID: 36651778 PMCID: PMC9927356 DOI: 10.1128/spectrum.02917-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Enterobacter spp. and Klebsiella aerogenes are rod-shaped Gram-negative opportunistic pathogens. This study aimed at the molecular and genomic characterization of multidrug resistant Enterobacter spp. and K. aerogenes isolates recovered from hospitalized patients in a tertiary care hospital in Lebanon. A total of 59 Enterobacter spp. clinical isolates consisting of 41 carbapenem-resistant and 18 susceptible by Etest were included in this study. Genotypic identification through whole-genome sequencing (WGS) was performed and confirmed in silico. Resistance and plasmid profiles were studied using ResFinder4.0 and Plasmid-Finder2.1. Multilocus sequence typing (MLST) was used to determine the isolates' clonality. Using the average nucleotide identity (ANI) we identified and confirmed that 47 (80%) isolates were E. hormaechei, 11 (18%) were Klebsiella aerogenes and 1 (2%) was an E. cloacae. Carbapenem-resistance was detected among 41 isolates all showing an MIC90 of ≥ 32 μg/mL for ertapenem, imipenem, and meropenem. blaNDM-1 (58.5%), blaACT-16 (54%), and blaOXA-1 (54%) were the most common detected β-lactamases, while blaCTX-M-15 (68%) was the main detected extended-spectrum β-lactamase (ESBL) encoding gene. Chromosomal ampC, carbapenemase encoding genes, and porin modifications were among the detected carbapenem resistance determinants. The carbapenemase encoding genes were linked to three well-defined plasmid Inc groups, IncFII/IncFIB, IncX3, and IncL. MLST typing revealed the diversity within the studied isolates, with ST114 being the most common among the studied E. hormaechei.: The spread of carbapenem-resistant isolates in clinical settings in Lebanon is a serious challenge. Screening and continuous monitoring through WGS analysis could effectively limit the dissemination of drug-resistant isolates in hospitalized patients. IMPORTANCE Drug resistance is an increasing global public health threat that involves most disease-causing organisms and antimicrobial drugs. Drug-resistant organisms spread in health care settings, and resistance to multiple drugs is common. Our study demonstrated the mechanisms leading to resistance against the last resort antimicrobial agents among members of the Enterobacteriaceae family. The spread of carbapenem-resistant bacteria in clinical settings is a serious challenge. Screening and continuous monitoring could effectively limit the dissemination of drug-resistant isolates in hospitalized patients.
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Affiliation(s)
- Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
| | - Sara Amayri
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - George F. Araj
- Department of Pathology & Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Byblos, Lebanon
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Chen L, Ai W, Zhou Y, Wu C, Guo Y, Wu X, Wang B, Rao L, Xu Y, Zhang J, Chen L, Yu F. Outbreak of IncX8 Plasmid-Mediated KPC-3-Producing Enterobacterales Infection, China. Emerg Infect Dis 2022; 28:1421-1430. [PMID: 35731165 PMCID: PMC9239885 DOI: 10.3201/eid2807.212181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) infection is highly endemic in China; Klebsiella pneumoniae carbapenemase (KPC) 2-producing CRE is the most common, whereas KPC-3-producing CRE is rare. We report an outbreak of KPC-3-producing Enterobacterales infection in China. During August 2020-June 2021, 25 blaKPC-3-positive Enterobacteriale isolates were detected from 24 patients in China. Whole-genome sequencing analysis revealed that the blaKPC-3 genes were harbored by IncX8 plasmids. The outbreak involved clonal expansion of KPC-3-producing Serratia marcescens and transmission of blaKPC-3 plasmids across different species. The blaKPC-3 plasmids demonstrated high conjugation frequencies (10-3 to 10-4). A Galleria mellonella infection model showed that 2 sequence type 65 K2 K. pneumoniae strains containing blaKPC-3 plasmids were highly virulent. A ceftazidime/avibactam in vitro selection assay indicated that the KPC-3-producing strains can readily develop resistance. The spread of blaKPC-3-harboring IncX8 plasmids and these KPC-3 strains should be closely monitored in China and globally.
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Fuga B, Cerdeira L, Moura Q, Fontana H, Fuentes-Castillo D, Carvalho AC, Lincopan N. Genomic data reveals the emergence of an IncQ1 small plasmid carrying bla KPC-2 in Escherichia coli of the pandemic sequence type 648. J Glob Antimicrob Resist 2021; 25:8-13. [PMID: 33662640 PMCID: PMC8213540 DOI: 10.1016/j.jgar.2021.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/21/2021] [Accepted: 02/16/2021] [Indexed: 11/17/2022] Open
Abstract
Epidemiological success of KPC has been linked to plasmids carrying blaKPC genes. An IncQ1 small plasmid carrying blaKPC-2 was found in pandemic Escherichia coli ST648. Plasmid analysis revealed blaKPC-2 on an NTEKPC-IId element with the aph(3')-VIa gene. Plasmid phylogeny confirmed >99% identity with IncQ/blaKPC-2 from Klebsiella pneumoniae. The emergence and rapid expansion of IncQ1/blaKPC-2 to novel hosts is discussed.
Objectives The global success of carbapenem-resistant pathogens has been attributed to large plasmids carrying blaKPC genes circulating among high-risk clones. In this study, we sequenced the genome of a carbapenem-resistant Escherichia coli strain (Ec351) isolated from a human infection. Phylogenomic analysis based on single nucleotide polymorphisms (SNPs) as well as the comparative resistome and plasmidome of globally disseminated blaKPC-2-positive E. coli strains with identical sequence type (ST) were further investigated. Methods Total DNA was sequenced using an Illumina NextSeq 500 platform and was assembled using Unicycler. Genomic data were evaluated through bioinformatics tools available from the Center of Genomic Epidemiology and by in silico analysis. Results Genomic analysis revealed the convergence of a wide resistome and virulome in E. coli ST648, showing a high-level phylogenetic relationship with a KPC-2-positive ST648 cluster identified in the USA and association with international clade 2. Additionally, the emergence of an IncQ1 small plasmid (pEc351) carrying blaKPC-2 (on an NTEKPC-IId element), aph(3')-VIa, and plasmid regulatory and replication genes in the pandemic clone ST648 is reported. Conclusion Identification of a blaKPC-2-positive IncQ1 plasmid in a high-risk E. coli clone represents rapid adaptation and expansion of these small plasmids encoding carbapenemases to novel bacterial hosts with global distribution, which deserves continued monitoring.
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Affiliation(s)
- Bruna Fuga
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil.
| | - Louise Cerdeira
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Quézia Moura
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Faculty of Health Sciences, Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Pathology, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Albalúcia C Carvalho
- Clinical Laboratory, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil
| | - Nilton Lincopan
- Departmentof Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil.
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Polemis M, Tryfinopoulou K, Giakkoupi P, Vatopoulos A. Eight-year trends in the relative isolation frequency and antimicrobial susceptibility among bloodstream isolates from Greek hospitals: data from the Greek Electronic System for the Surveillance of Antimicrobial Resistance - WHONET-Greece, 2010 to 2017. Euro Surveill 2020; 25:1900516. [PMID: 32856583 PMCID: PMC7453683 DOI: 10.2807/1560-7917.es.2020.25.34.1900516] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/15/2020] [Indexed: 11/20/2022] Open
Abstract
BackgroundAntimicrobial resistance (AMR) changes over time and continuous monitoring provides insight on trends to inform both empirical treatment and public health action.AimsTo survey trends in relative isolation frequency (RIF) and AMR among key bloodstream pathogens using data from the Greek Electronic System for the Surveillance of AMR (WHONET-Greece).MethodsThis observational study looked into routine susceptibility data of 50,488 blood culture isolates from hospitalised patients in 25 tertiary hospitals, participating in the WHONET-Greece for trends over time between January 2010 and December 2017. Only the first isolate per species from each patient was included. Hospital wards and intensive care units (ICUs) were analysed separately.ResultsDuring the study, the RIF of Acinetobacter baumannii increased in wards, as did the proportion of A. baumannii isolates, which were non-susceptibleto most antibiotics in both wards and ICUs. Coincidently, Klebsiella pneumoniae RIF declined while the respective rates of non-susceptible isolates to carbapenems and gentamicin increased. Pseudomonas aeruginosa RIF remained stable but decreasing proportions of non-susceptible isolates to all studied antibiotics, except imipenem were observed. Escherichia coli RIF increased as did the proportion of isolates non-susceptible to third-generation cephalosporins, carbapenems and fluoroquinolones. Concerning Staphylococcus aureus, a decline in the percentage of meticillin resistant isolates in ICUs was found, while the percentages of Enterococcus faecium isolates with non-susceptibility to vancomycin stayed stable.ConclusionsRecognising these trends over time is important, since the epidemiology of AMR is complex, involving different 'bug and drug' combinations. This should be taken into consideration to control AMR.
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Affiliation(s)
- Michalis Polemis
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Kyriaki Tryfinopoulou
- Central Public Health Laboratory, National Public Health Organization, Athens, Greece
| | - Panagiota Giakkoupi
- Department of Public Health Policies, School of Public Health, University of West Attica, Athens, Greece
| | - Alkiviadis Vatopoulos
- Department of Public Health Policies, School of Public Health, University of West Attica, Athens, Greece
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Tang L, Shen W, Zhang Z, Zhang J, Wang G, Xiang L, She J, Hu X, Zou G, Zhu B, Zhou Y. Whole-Genome Analysis of Two Copies of bla NDM-1 Gene Carrying Acinetobacter johnsonii Strain Acsw19 Isolated from Sichuan, China. Infect Drug Resist 2020; 13:855-865. [PMID: 32273730 PMCID: PMC7106997 DOI: 10.2147/idr.s236200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose To characterize the genetic feature of the carbapenems resistant Acinetobacter johnsonii strain Acsw19 isolated from municipal sludge. This strain was found to carry two copies of bla NDM-1, cmlB1-like gene, and bla OXA-211-like gene along with other 8 antimicrobial resistance genes, 3 plasmids, 15 genomic islands and 8 prophages. Methods A carbapenem-resistant Acinetobacter johnsonii strain Acsw19 isolated from municipal sludge was subjected to whole-genome sequencing (WGS) via the PacBio and Illumina MiSeq platforms. Thereafter, the characteristic was analyzed by a series of bioinformatics software. Results The results showed that the genome of Acsw19 was consisted of a 3,433,749 bp circular chromosome and 3 circular plasmids, pAcsw19-1 (11,161 bp), pAcsw19-2 (351,885 bp) and pAcsw19-3 (38,391bp), respectively. Resistome analysis showed that Acsw19 carried 12 antimicrobial resistance genes, including 6 [cmlB1-like, bla NDM-1, bla OXA-58, aph (3')-VIa, msr(E) and mph(E)] in the plasmid pAcsw19-2 and 6 (bla OXA-211-like, bla NDM-1, aph(3")-Ib, aph(6)-Id, sul2, and floR) in the chromosome genome. Specifically, the cmlB1-like gene shared 86.33%, 71.7% and 71.9% similarities with the cmlB1, cmlA4 and cmlA8 gene, and the bla OXA-211-like gene shared 94.4%, 95.39% and 96.36% similarities with bla OXA-211, bla OXA-643 and bla OXA-652, at the nucleotide level, respectively. Phylogenetic analysis showed that the bla OXA-211-like gene and cmlB1-like gene had the closest evolutionary relationship with bla OXA-643 and cmlB1, respectively. These results indicated that the bla OXA-211-like and cmlB1-like genes identified in the current study should be the novel variant resistance genes. Conclusion Carrying of two copies of bla NDM-1, cmlB1-like, bla OXA-211-like and along with other 8 antimicrobial resistance genes, 3 plasmids, 15 genomic islands and 8 prophages Acinetobacter johnsonii strain might increase the possibility of spreading of resistance genes.
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Affiliation(s)
- Lingtong Tang
- Department of Clinical Laboratory, The People's Hospital of Gao County, Sichuan 644000, People's Republic of China.,Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Wei Shen
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China.,Department of Clinical Laboratory, The First People's Hospital of Yibin, Yibin 644000, Sichuan, People's Republic of China
| | - Zhikun Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Jingping Zhang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Guangxi Wang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Li Xiang
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Junping She
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Xiaoyan Hu
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
| | - Guoyuan Zou
- Institute of Plant Nutrition and Resources, Beijing Academy of Agriculture and Forestry Science, Beijing, People's Republic of China
| | - Baoli Zhu
- Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yingshun Zhou
- Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, Luzhou, Sichuan, People's Republic of China
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Kopotsa K, Osei Sekyere J, Mbelle NM. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review. Ann N Y Acad Sci 2019; 1457:61-91. [PMID: 31469443 DOI: 10.1111/nyas.14223] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. blaKPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; blaKPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. blaCTX-M , blaTEM , blaSHV , blaOXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa.,National Health Laboratory Service, Tshwane Division, Department of Medical Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Assessing genetic diversity and similarity of 435 KPC-carrying plasmids. Sci Rep 2019; 9:11223. [PMID: 31375735 PMCID: PMC6677891 DOI: 10.1038/s41598-019-47758-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/22/2019] [Indexed: 01/01/2023] Open
Abstract
The global spread and diversification of multidrug-resistant Gram-negative (MRGN) bacteria poses major challenges to healthcare. In particular, carbapenem-resistant Klebsiella pneumoniae strains have been frequently identified in infections and hospital-wide outbreaks. The most frequently underlying resistance gene (blaKPC) has been spreading over the last decade in the health care setting. blaKPC seems to have rapidly diversified and has been found in various species and on different plasmid types. To review the progress and dynamics of this diversification, all currently available KPC plasmids in the NCBI database were analysed in this work. Plasmids were grouped into 257 different representative KPC plasmids, of which 79.4% could be clearly assigned to incompatibility (Inc) group or groups. In almost half of all representative plasmids, the KPC gene is located on Tn4401 variants, emphasizing the importance of this transposon type for the transmission of KPC genes to other plasmids. The transposons also seem to be responsible for the occurrence of altered or uncommon fused plasmid types probably due to incomplete transposition. Moreover, many KPC plasmids contain genes that encode proteins promoting recombinant processes and mutagenesis; in consequence accelerating the diversification of KPC genes and other colocalized resistance genes.
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