Please be advised that the site will be down for maintenance on Sunday, September 1, 2024, from 08:00 to 18:00, and again on Monday, September 2, 2024, from 08:00 to 09:00. We apologize for any inconvenience this may cause.
dc.contributor.author | Kopotsa, Katlego![]() |
|
dc.contributor.author | Mbelle, Nontombi Marylucy![]() |
|
dc.contributor.author | Osei Sekyere, John![]() |
|
dc.date.accessioned | 2021-06-25T11:57:00Z | |
dc.date.available | 2021-06-25T11:57:00Z | |
dc.date.issued | 2020-11-10 | |
dc.description.abstract | Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio’s SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/ disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both blaOXA-48 and blaNDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation. | en_ZA |
dc.description.department | Medical Microbiology | en_ZA |
dc.description.sponsorship | The NHLS, NRF (National Research Foundation) and the University of Pretoria. | en_ZA |
dc.description.uri | https://www.microbiologyresearch.org/content/journal/mgen | en_ZA |
dc.identifier.citation | Kopotsa, K, Mbelle, NM & Sekyere, JO 2020, 'Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains', Microbial Genomics, vol. 6, pp. 1-19. | en_ZA |
dc.identifier.issn | 2057-5858 | |
dc.identifier.other | 10.1099/mgen.0.000474 | |
dc.identifier.uri | http://hdl.handle.net/2263/80606 | |
dc.language.iso | en | en_ZA |
dc.publisher | Microbiology Society | en_ZA |
dc.rights | © 2020 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. | en_ZA |
dc.subject | Bacteriophage | en_ZA |
dc.subject | Carbapenemase | en_ZA |
dc.subject | DNA methylation | en_ZA |
dc.subject | Evolutionary epidemiology | en_ZA |
dc.subject | Resistance plasmids | en_ZA |
dc.subject | Carbapenem-resistant Klebsiella pneumoniae (CRKP) | en_ZA |
dc.subject | Repetitive element palindromic (REP) | en_ZA |
dc.subject | Polymerase chain reaction (PCR) | en_ZA |
dc.subject | Restriction modification systems (RMS) | en_ZA |
dc.title | Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains | en_ZA |
dc.type | Article | en_ZA |