KPC-2-producing Klebsiella pneumoniae ST147 in a neonatal unit: Clonal isolates with differences in colistin susceptibility attributed to AcrAB-TolC pump

• Published in: International journal of antimicrobial agents 2020-03, Vol.55 (3), p.105903-105903, Article 105903
• Main Authors: Naha, Sharmi, Sands, Kirsty, Mukherjee, Subhankar, Roy, Chayan, Rameez, Moidu Jameela, Saha, Bijan, Dutta, Shanta, Walsh, Timothy R., Basu, Sulagna
• Format: Article
• Language: English
• Subjects: AcrAB-TolC pump; Anti-Bacterial Agents - pharmacology; Bacterial Proteins - biosynthesis; beta-Lactamases - biosynthesis; Carrier Proteins - biosynthesis; Colistin - pharmacology; Colistin Resistance; Drug Resistance, Bacterial - drug effects; Drug Resistance, Bacterial - genetics; Humans; Infant, Newborn; Intensive Care Units, Neonatal; Klebsiella Infections - drug therapy; Klebsiella Infections - microbiology; Klebsiella pneumoniae - drug effects; Klebsiella pneumoniae - genetics; Klebsiella pneumoniae - metabolism; KPC-2; phoP/Q; pmrA/B; ST147
• ISSN: 0924-8579; 1872-7913
• DOI: 10.1016/j.ijantimicag.2020.105903

•First report of clonal KPC-2-producing Klebsiella pneumoniae with varying colistin susceptibility.•blaKPC-2 bracketed between ISKpn7 and ISKpn6 of Tn4401b on non-conjugative IncFII.•Colistin-resistant isolates lack mcr and no mutation in two-component system (TCS) and lipopolysaccharide (LPS) modifying genes.•Isolates were nearly identical (WGS) but colistin-resistant isolate showed decreased MIC of colistin with CCCP.•Colistin resistance was due to overexpression of AcrAB-TolC pump and its regulators. This study characterizes four KPC-2-producing Klebsiella pneumoniae isolates from neonates belonging to a single sequence type 147 (ST147) in relation to carbapenem resistance and explores probable mechanisms of differential colistin resistance among the clonal cluster. Whole genome sequencing (WGS) revealed that the isolates were nearly 100% identical and harbored resistance genes (blaKPC-2,OXA-9,CTX-M-15,SHV-11,OXA-1,TEM-1B, oqxA, oqxB, qnrB1, fosA, arr-2, sul1, aacA4, aac(6′)Ib-cr, aac(6′)Ib), and several virulence genes. blaKPC-2 was the only carbapenem-resistant gene found, bracketed between ISKpn7 and ISKpn6 of Tn4401b on a non-conjugative IncFII plasmid. Remarkably, one of the clonal isolates was resistant to colistin, the mechanistic basis of which was not apparent from comparative genomics. The transmissible colistin resistance gene, mcr, was absent. Efflux pump inhibitor, carbonyl cyanide 3-chlorophenylhydrazone (CCCP) rendered a 32-fold decrease in the minimum inhibitory concentration (MIC) of colistin in the resistant isolate only. acrB, tolC, ramA, and soxS genes of the AcrAB-TolC pump system overexpressed exclusively in the colistin-resistant isolate, although the corresponding homologs of the AcrAB-TolC pump, regulators and promoters were mutually identical. No change was observed in the expression of other efflux genes (kpnE/F and kpnG/H) or two-component system (TCS) genes (phoP/phoQ, pmrA/pmrB). Colistin resistance in one of the clonal KPC-2-producing isolates is postulated to be due to overexpression of the AcrAB-TolC pump. This study is probably the first to report clinical clonal K. pneumoniae isolates with differences in colistin susceptibility. The presence of carbapenem-resistant isolates with differential behavior in the expression of a genomically identical pump system indicates the nuances of the resistance mechanisms and the difficulty of treatment thereof.