Genomic characterization of plasmids harboring blaNDM-1,-5,-7carbapenemase alleles in clinical Klebsiella pneumoniae in Pakistan

ABSTRACT Klebsiella pneumoniae is notorious for causing healthcare-associated infections, which become more complicated by the acquisition of bla NDM genes via mobile genetic elements. Although Pakistan is a well-established hot spot of bla NDM -positive K. pneumoniae , detailed molecular descriptions of bla NDM -carrying plasmids are scarce. Seven K. pneumoniae isolates harboring bla NDM were recovered from clinical sample sources during a six-month period and tested for antimicrobial susceptibility. A long-read approach was used for whole genome sequencing to obtain circularized plasmids and chromosomes for typing, annotation, and comparative analysis. The isolates were susceptible to colistin and tigecycline only among the tested antibiotics. We identified five STs: ST11, ST16, ST716, ST464, and ST2856. Notably, three strains possessed the hypervirulent capsule KL2, while five were classified as O locus type O2a. Evidence of genetic diversity was further highlighted by the presence of four IncC plasmids harboring bla NDM-1 , two IncX3 plasmids harboring bla NDM-5 , and a single hybrid IncFIB/IncHI1B plasmid harboring bla NDM-7 . These plasmids also carried additional ARGs conferring resistance to aminoglycosides, cephalosporins, and fluoroquinolones. We identified the plasmidome of the K. pneumoniae isolates and characterized the NDM-carrying plasmids. Genetic analysis confirmed the presence of bla NDM-1 and bla NDM-5 on broad host range plasmids and bla NDM-7 in a previously unreported hybrid plasmid backbone. We emphasized the critical role of plasmids in spreading bla NDM in the clinical setting in Pakistan. Hence, we stressed the urgent need for enhanced surveillance, not least in LMICs, infection control measures, and adherence to the AWaRe guidelines in antibiotics use.