Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains

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 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.

Risk factors for, and molecular epidemiology and clinical outcomes of, carbapenem‐ and polymyxin‐resistant Gram‐negative bacterial infections in pregnant women, infants, and toddlers: a systematic review and meta‐analyses

“…Thus, although E. coli was more common than K. pneumoniae , it is mostly restricted to South Asia, while K. pneumoniae is generally distributed in many countries globally, making K. pneumoniae more likely to mediate the transmission of carbapenem resistance among pregnant women, infants, and neonates. The predominant role of K. pneumoniae , followed by E. coli, Enterobacter spp., and A. baumannii , in spreading carbapenem and polymyxin resistance is well noted in the literature 1,2,9,48 …”

“…Similarly, PR‐GNB infections were also common in the same species, viz., A. baumannii, E. coli, K. pneumoniae, Enterobacter spp., and Pseudomonas spp., although reports on outbreaks were either associated with carbapenem resistance 34,35 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 an NICU in 2016, eight of which were CR K. pneumoniae 34 .…”

“…observed that overexpression of acrB, tolC, ramA, and soxS conferred colistin resistance in a CR K. pneumoniae ST147, which could have been the resistance mechanism in the C. freundii isolate from Malaysia 35,67 . Although mcr genes, and not chromosomal mutations, are the most common mechanisms mediating polymyxin resistance globally, 1,2,4,9 an mcr‐1 was only identified in one study (in E. aerogenes , now K. aerogenes ) and interestingly, from the vaginal secretions of a pregnant woman 38 …”

“…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 is increasing the rate of resistance to these last‐resort antibiotics 2,4,9,11 . The emergence of carbapenem‐resistant (CR) and/or polymyxin‐resistant (PR) MDR infections is thus limiting therapeutic options and increasing hospital stay, healthcare costs, morbidity, and mortality 12–14 .…”

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).…”