Colistin Resistance Among Multiple Sequence Types of Klebsiella pneumoniae Is Associated With Diverse Resistance Mechanisms: A Report From India

<b>Background:</b> The resistance to colistin and carbapenems in <i>Klebsiella pneumoniae</i> infections have been associated with increased morbidity and mortality worldwide. A retrospective observational study was conducted to determine the prevalence and molecular events contributing to colistin resistance. <b>Methods:</b> Clinical samples were screened for colistin resistance and underlying mechanisms were studied by PCR-based amplification and sequence analysis of genes of two-component regulatory system (<i>phoPQ</i> and <i>pmrAB</i>), regulatory transmembrane protein-coding <i>mgrB</i>, and mobilized colistin resistance genes (<i>mcr-1-8</i>). Gene expression of <i>pmrC</i> and <i>pmrK</i> was analyzed by qRT-PCR, and the genetic relationship was assessed by MLST. The putative effect of amino-acid substitutions was predicted by a combination of bioinformatics tools. <b>Results:</b> Of 335 <i>Klebsiella</i> spp. screened, 11 (3.2%) were identified as colistin-resistant (MIC range, 8 to >128 μg/ml). <i>K. pneumoniae</i> isolates belonged to clonal complex-11 (CC11) with sequence types (STs): 14, 16, 43, 54, 147 and 395, whereby four isolates conferred three novel STs (3986, 3987 and 3988) profiles. Sequence analysis revealed non-synonymous potentially deleterious mutations in <i>phoP</i> (T151A), <i>phoQ</i> (del87-90, del263-264, L30Q, and A351D), <i>pmrA</i> (G53S), <i>pmrB</i> (D150V, T157P, L237R, G250C, A252G, R315P, and Q331H), and <i>mgrB</i> (C28G) genes. The <i>mgrB</i> gene in three strains was disrupted by insertion sequences encoding IS<i>1</i>-like and IS<i>5</i>/IS<i>1182</i> family-like transposase genes. All 11 isolates showed an elevation in the transcription level of <i>pmrC</i> gene. Mobilized colistin-resistance (<i>mcr</i>) genes were not detected. All but one of the colistin-resistant isolates was also resistant to carbapenems; β-lactamase genes <i>bla_NDM-1-like</i> , <i>bla_OXA-48-like</i> , and <i>bla_CTX-M-like</i> were detected in eight, five, and nine isolates, respectively. <b>Conclusion:</b> All the studied colistin- and carbapenem-resistant <i>K. pneumoniae</i> isolates were genetically distinct, and various mechanisms of colistin resistance were detected, indicating its spontaneous emergence in this bacterial species.