Epigenomics, Genomics, Resistome, Mobilome, Virulome and Evolutionary Phylogenomics of Carbapenem-resistant Klebsiella pneumoniae clinical strains

Abstract

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.

Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae : a Systematic Review of Current Reports

“…These enzymes are frequently plasmid-borne genes, allowing for the dissemination of genes within and between Gram-negative bacteria species. This results in resistance toward penicillin, cephalosporins, carbapenems, and/or monobactams ( 29 , 202 , 203 ). Carbapenem resistance in Enterobacteriaceae is mediated mainly by the production of carbapenemases ( 11 ).…”

Molecular Epidemiology, Risk Factors and Clinical Outcomes of Carbapenem- and Polymyxin-Resistant Gram-negative Bacterial Infections in Pregnant Women and Infants: A Systematic Review

“…and Pseudomonas sp ., although reports on outbreaks were either associated with carbapenem resistance 34,36 or absent. Hence, outbreaks involving CR-GNB that were also polymyxin resistant could also be referred to as PR-GNB outbreaks, which makes such infections very difficult to manage 1,2,4,9 . The largest collection of PR-GNB was recorded in Malaysia from preterm infants in a NICU in 2016, eight of which were carbapenem-resistant K. pneumoniae 34 .…”

“…The immediate genetic environment of the NDM-5 on these plasmids were exactly the same or similar, suggesting that same plasmids and/or clones were mediating the spread of NDM-5 within and between species 31,45 . The higher mobility of these carbapenemases may explain their faster dissemination between neonates in wards and hospitals during outbreaks and evinces the need to undertake molecular analyses of isolates to comprehend their epidemiology 1,2,4,9,69 .…”

“…Resistance to antimicrobials remain a major challenge to public health, veterinary medicine, agriculture and aquaculture globally, owing to the limited or no therapeutic option available to treat multidrug-resistant (MDR) infections [1][2][3][4][5] . To avoid depleting our antibiotics arsenals against infectious pathogens, certain agents are reserved as last-line drugs to fight difficult-totreat infections [6][7][8] .…”

“…Currently, carbapenems, polymyxins (colistin) and tigecycline are used as reserved agents for MDR infections 9,10 . However, the continual use of carbapenems and polymyxins to treat bacterial infections resistant to penicillins, cephalosporins, and carbapenems are increasing the rate of resistance to these last-resort antibiotics 2,4,9,11 . The emergence of carbapenem-and/or polymyxin-resistant MDR infections is thus limiting therapeutic options and increasing hospital stay, healthcare costs, morbidity, and mortality [12][13][14] .…”