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.

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 bla OXA-48-like and bla NDM-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 (G A TC, G A TGNNNNNNTTG, CA A NNNNNNCATC motifs) and m4C (C C WGG) 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 bla OXA-48 and bla NDM-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.

Background: 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 were characterised. Methods: CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex-PCR, genotyping by Repetitive Element Palindromic-Polymerase Chain Reaction (REP-PCR), plasmid size, number, incompatibility, and mobility analyses, and PacBios SMRT sequencing (n=6). Results & conclusion: 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). These plasmids were of close evolutionary relationship to several plasmids globally whilst the strains also clustered with several global clades, 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. The six strains contained at least 41 virulence genes 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. There is plasmid-mediated, clonal, and multiclonal dissemination of blaOXA-48-like and blaNDM-1 in South Africa, mirroring international epidemiology of similar clones and plasmids. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity, and resistance, threatening infection treatment. RMS influence on antimicrobial and bacteriophage therapy needs urgent investigation.

Background: Mobile genetic elements such as plasmids play a major role in the acquisition and dissemination of antimicrobial resistance determinants in carbapenem-resistant Klebsiella pneumoniae (CRKP). This study aims to determine the frequency of plasmids replicon groups and characterize plasmids mediating carbapenem resistance in K. pneumoniae isolates in South Africa.Methods and materials: A total of 56 K. pneumoniae isolates already identified by the national referral laboratory in Pretoria using the VITEK 2 ® (Biomerieux, France) automated system. Antimicrobial susceptibility testing was performed using the MicroScan Gram-negative MIC 44 panel (Beckman Coulter, United States). All K. pneumoniae resistant to one or more carbapenem(s) were screened for carbapenemase-encoding genes (bla OXA-48 , bla NDM-1 , bla KPC , bla VIM , and bla IMP ) using multiplex-PCR. These isolates were genotyped by REP-PCR. Plasmid extraction was performed on all isolates and electrophoresis was used to determine their number and size. PCR-based replicon typing (PBRT) scheme was used to determine the incompatibility/replicon groups of all the extracted plasmids.Results: The isolates showed reduced susceptibility to tested carbapenems. Multiplex-PCR analysis showed that 55 isolates haboured at least one of the carbapenemase genes, with 41 (73.2%) habouring bla OXA-48 and 18 (32%) habouring bla NDM-1 . The isolates were resolved into four major strains/genotypes by the REP-PCR. Electrophoresis revealed that the isolates carried between one and five plasmids, with the majority carrying 2 or 3 plasmids; the plasmid sizes ranged between 1.6-kb to >48.5-kb. IncF (FII, FIB, FIC), IncL, IncM, and IncA/C plasmid replicons were the most detected. Almost 90% of the isolates showed multi-replicon carriage (Table 1).

Objective: In this study, we sought to determine the source of an outbreak of Achromobacter denitrificans infections in patients at a tertiary-care academic hospital. Design: Outbreak report study with intervention. The study period extended from February 2018 to December 2018. Setting: The study was conducted at a tertiary-care academic hospital in Pretoria, South Africa. Patients and participants: All patients who cultured A. denitrificans from any site were included in this study. During the study period, 43 patients met this criterion. Interventions: Once an outbreak was confirmed, the microbiology laboratory compiled a list of affected patients. A common agent, chlorhexidine-and-water solution, was used as a disinfectant–antiseptic for all affected patients. The laboratory proceeded to culture this solution. Environmental and surface swabs were also cultured from the hospital pharmacy area where this solution was prepared. Repetitive-element, sequence-based, polymerase chain reaction (rep-PCR) was performed on the initial clinical isolates to confirm the relatedness of the isolates. Results: In total, 43 isolates of A. denitrificans were cultured from patient specimens during the outbreak. The laboratory cultured A. denitrificans from all bottles of chlorhexidine-and-water solutions sampled from the wards and the pharmacy. The culture of the dispenser device used to prepare this solution also grew A. denitrificans. The rep-PCR confirmed the clonality of the clinical isolates with 2 genotypes dominating. Conclusions: Contaminated chlorhexidine-and-water solutions prepared at the hospital pharmacy was determined to be the source of the outbreak. Once this item was removed from the hospital, the laboratory did not culture any further A. denitrificans isolates from patient specimens.