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

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.