Genomic characterization of plasmids harboring bla NDM-1, bla NDM-5, and bla NDM-7 carbapenemase 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 6 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 sequence types (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 antimicrobial resistance (AMR) genes conferring resistance to aminoglycosides, cephalosporins, and fluoroquinolones. We identified the plasmidome of the K. pneumoniae isolates and characterized the New Delhi metallo-beta-lactamase (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 low-middle income countries, infection control measures, and adherence to the “Access,” “Watch,” and “Reserve” guidelines in antibiotics use. IMPORTANCE Infections caused by NDM-producing Klebsiella pneumoniae are a significant challenge to treat and represent a crucial health burden in low- and middle-income countries (LMICs). Most of the bla NDM are located on plasmids that promote horizontal gene transfer. However, there is a lack of comprehensive information on the genetic context of the NDM-carrying plasmids in Pakistan. This study presents a detailed analysis of seven NDM-plasmids in clinical K. pneumoniae isolates, shedding light on their high-risk sequence types and multiple resistance determinants. We also describe the plasmid-bearing NDM alleles ( bla NDM-1 , bla NDM-5 , and bla NDM-7 ). Notably, we are the first to report bla NDM-7 on the hybrid IncFIB/IncHI1B backbone in Pakistan, a plasmid that has rarely been reported previously globally. Understanding the plasmid genomic landscape is paramount to comprehensively understanding the AMR scenario in this LMIC.