Emergence of drug-resistant <i>Klebsiella pneumoniae</i> phylogroups ( <i>K. quasipneumoniae</i> and <i>K. variicola</i> ) causing human infections

This prospective, cross-sectional study was undertaken to identify the emerging <i>K. pneumoniae</i> phylogeny groups (KpI, KpII, KpIII) and characterize their drug resistance. Phylogeny groups of 150 clinical isolates of biochemically identified <i>K. pneumoniae</i> were detected by targeting their chromosomal class A, β-lactamase genes <i>bla</i>_SHV, <i>bla</i>_LEN, and <i>bla</i>_OKP, respectively, and their flanking gene (<i>deoR</i>). Antimicrobial susceptibility testing was done by disk diffusion and broth microdilution methods and statistically analyzed. Carbapenemases (Classes A, B, and D) were detected by multiplex PCR. Colistin resistance mechanisms to detect alteration in <i>PhoP</i>/<i>PhoQ</i>, <i>pmrAB</i> two-component signaling pathways, and <i>mgrB</i> were done by PCR and sequencing. Of the total, KpI, <i>K. pneumoniae</i> were 93 (62%), KpII, <i>K. quasipneumoniae</i> were 36 (24%), and KpIII, <i>K. variicola</i> were 21 (14%). Carbapenem resistance was in 77 (51.3%); 52 (55.9%), 17 (47.2%), and 8 (38%) in KpI, KpII, and KpIII, respectively. Colistin resistance was in 16 (10.6%), 11 (68.75%) in KpI and 5 (31.25%) in KpIII. <i>K. variicola</i> was resistant to polymyxin B as compared with KpI (<i>P</i> = 0.0008). <i>bla</i>_NDM (63, 81.8%) was the commonest. Co-harboring of multiple carbapenemase genes was significant in all the phylogroups (<i>P</i> < 0.001). The majority of the cases of <i>K. variicola</i> were males (<i>P</i> = 0.0139) and in the intensive care unit (<i>P</i> = 0.0091). Several non-synonymous mutations were observed in the colistin-resistant isolates in <i>PhoP</i> and <i>PhoQ</i> genes, with the phylogenetic tree revealing different evolutionary relationships among the isolates. There is considerable emergence of <i>K. quasipneumoniae</i> and <i>K. variicola</i> as prominent human pathogens along with drug resistance, which requires attention.IMPORTANCEThese epidemiological data add to the extremely scarce literature on the occurrence of the two phylogeny groups of <i>K. pneumoniae</i>, namely <i>K. quasipneumoniae</i> and <i>K. variicola</i>, in infections and highlight their widespread dissemination as prominent human pathogens, beyond agriculture and environment as their common habitat. There was significant drug resistance in the phylogeny groups, including colistin resistance in <i>K. variicola</i>, which was studied for the first time.