Abstract
Background: The resistance to colistin and carbapenems in Klebsiella pneumoniae 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.Methods: 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 (phoPQ and pmrAB), regulatory transmembrane protein-coding mgrB, and mobilized colistin resistance genes (mcr-1-8). Gene expression of pmrC and pmrK 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.Results: Of 335 Klebsiella spp. screened, 11 (3.2%) were identified as colistin-resistant (MIC range, 8 to >128 μg/ml). K. pneumoniae 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 phoP (T151A), phoQ (del87–90, del263–264, L30Q, and A351D), pmrA (G53S), pmrB (D150V, T157P, L237R, G250C, A252G, R315P, and Q331H), and mgrB (C28G) genes. The mgrB gene in three strains was disrupted by insertion sequences encoding IS1-like and IS5/IS1182 family-like transposase genes. All 11 isolates showed an elevation in the transcription level of pmrC gene. Mobilized colistin-resistance (mcr) genes were not detected. All but one of the colistin-resistant isolates was also resistant to carbapenems; β-lactamase genes blaNDM-1-like, blaOXA-48-like, and blaCTX-M-like were detected in eight, five, and nine isolates, respectively.Conclusion: All the studied colistin- and carbapenem-resistant K. pneumoniae isolates were genetically distinct, and various mechanisms of colistin resistance were detected, indicating its spontaneous emergence in this bacterial species.
Highlights
Klebsiella pneumoniae, a nosocomial pathogen, accounts for one-third of worldwide reported Gram-negative infections (Navon-Venezia et al, 2017)
Molecular identification confirmed the isolates as K. pneumoniae and Multilocus sequence typing (MLST) analysis revealed the sequence types ST14 (n = 1), ST16 (n = 1), ST43 (n = 1), ST54 (n = 1), ST147 (n = 1), and ST395 (n = 2; Table 1)
Comparative and clustering analysis by eBURST v3 of query dataset with a total of 3,550 already reported MLST profiles of K. pneumoniae suggested that all 11 isolates of the query dataset belonged to the most prominent and diverse clonal complex 11 (CC11)
Summary
Klebsiella pneumoniae, a nosocomial pathogen, accounts for one-third of worldwide reported Gram-negative infections (Navon-Venezia et al, 2017). Available data showcase a significant increase in K. pneumoniae in India’s carbapenem-resistant isolates from 29% in 2008 to 57% in 2016, limiting the treatment of life-threatening infections (Gandra et al, 2016; Dixit et al, 2019). The unavailability of new antimicrobial agents to combat carbapenem-resistant K. pneumoniae infections has revived the use of polymyxins (colistin and polymyxin B). Colistin-resistant K. pneumoniae exhibits a high degree of genetic plasticity where a point mutation and/or genetic disruption in two-component regulatory systems (TCRS), i.e., pmrAB and phoPQ, are known to confer polymyxin resistance (Cannatelli et al, 2014a; Jayol et al, 2014). The resistance to colistin and carbapenems in Klebsiella pneumoniae 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
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