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

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.

Prevalence of insertion sequence elements in plasmids relating to mgrB gene disruption causing colistin resistance in Klebsiella pneumoniae

“…Nucleotide position 75 represents a hotspot for IS5 element insertion among clonally unrelated K. pneumoniae isolates (Cannatelli et al, 2013; Poirel et al, 2014). Mobilization of IS5 elements from plasmids into the mgrB gene of colistin resistant K. pneumoniae has been speculated owing to the similarity between the IS5 element inserted into mgrB and the IS5 element present on K. pneumoniae carbapenemase (KPC)‐encoding and other Gram‐negative bacterial plasmids (Azam et al, 2021; Cannatelli et al, 2013; Hala et al, 2019), and endogenous presence of IS5‐like elements in the genome of colistin resistant K. pneumoniae (Choi & Ko, 2020).…”

Prevalence of colistin resistance of Klebsiella pneumoniae isolates in Iran: a systematic review and meta-analysis

“…A study by Bshabshe et al from Saudi Arabia showed 34.5% resistance to colistin [ 21 ]. Poudyal et al In Australia examined 21 MDR K. pneumoniae , of which 6 isolates were resistant to colistin (28.5%) [ 22 ].Other studies from India, Poland, Pakistan, and Spain reported 16, 0, 4.8 and 13% colistin resistance in K. pneumoniae isolates [ 23 – 26 ]. Although a similar meta-analysis is needed to compare the resistance of colistin to other countries, the study of resistance to this antibiotic in Iran showed a moderate resistance level compared to other countries.…”

Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates from Two Romanian Hospitals Co-Presenting Resistance and Heteroresistance to Colistin

“…Meanwhile, other researchers have mentioned the deleterious L26Q substitution in the phoP gene [ 55 ]. Furthermore, some mutations closely related to those above were detected in the phoQ gene (such as L30Q, L26P, L96R, and L257P substitutions) [ 31 , 56 , 57 , 58 ] and the phoP gene (V3F) [ 58 ] and have previously been described as mediating colistin resistance.…”