Coexistence of blaNDM-1, mcr-1 and blaCTX-M-199 in an ST499 multidrug resistant Klebsiella pneumoniae iIsolate

Abstract

The coexistence of multiple resistance genes within a single bacterial strain presents a significant public health challenge, as it complicates treatment options and accelerates the spread of multidrug resistance. While the co-occurrence of bla_NDM-1 and mcr-1 genes in Klebsiella pneumoniae (KP) is uncommon, this study reports the biological characterization of a K. pneumoniae isolate, L5151, derived from a patient with diarrhea. This strain carries bla_NDM-1, mcr-1, and bla_CTX-M-199 resistance genes simultaneously. Multilocus sequence typing (MLST) analysis identified the L5151 strain as an ST499 type. Antimicrobial susceptibility testing (AST) was conducted via agar dilution and the broth microdilution procedure. The AST results revealed that L5151 is resistant to a variety of antibiotics. Whole-genome sequencing (WGS) and bioinformatics analysis were performed to determine the genetic composition of the strain, including the presence and characteristics of resistance genes. The results of S1 nuclease-pulsed field gel electrophoresis (S1-PFGE) and Southern blotting confirmed that the L5151 strain harbors three plasmids and that the plasmid carrying mcr-1 (pL5151_MCR_CTX) is of the IncI2(Delta) type, whereas the plasmid carrying bla_NDM-1 (pL5151_NDM) is of the IncN type. The combination of these plasmids in recipient strains conferred enhanced resistance to carbapenems and colistin, highlighting the potential for increased treatment challenges. This study emphasizes the importance of ongoing surveillance of multidrug-resistant strains to prevent their spread and outbreaks. These findings provide critical insights for clinical treatment strategies and infection prevention and control measures. Enhanced surveillance and targeted interventions are essential to manage the public health risks posed by multidrug-resistant strains.

Keywords: Klebsiella pneumoniae; bla CTX-M-199; bla NDM-1; MCR-1; Multidrug resistance; Whole genome sequencing.

Fig. 1

Comparison of plasmids carrying mcr-1/bla_NDM-1 detected in this study. (A) Circumplex genome comparison of pL5151-NDM with four plasmids carrying bla_NDM-1 (pNDM-1, pNDM-Cf7308, pNDM2963, pNDM-BTR). (B) Genomic mapping of mcr-1 and bla_CTX-M-199 co-carrying IncI2 pL5151_MCR_CTX plasmid with four closely related plasmids (pEC16-50-MCR, pM-199-232, pM-199-C35, pSLDY13). Circular maps were generated by BLAST Ring Image Generator (BRIG) software.

Fig. 2

Plasmid analysis of the ST499 colistin-resistant CRKP strain L5151 via S1-PFGE and Southern blotting using mcr-1 and bla_NDM-1 probes. (A) Analysis of pL5151-NDM-1. (B) Analysis of pL5151-MCR-1. Marker: XbaI digested the total DNA of Salmonella bacterica serotype Braenderup H9812 as a size marker.