Comprehensive genomic and metagenomic profiling of antibiotic resistance genes in Klebsiella pneumoniae isolates from whole-genome sequencing
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The rapid global spread of antimicrobial resistance (AMR) threatens the effectiveness of current therapies. Sensitive marker-based metagenomic approaches, such as ShortBRED in combination with curated databases like the Comprehensive Antibiotic Resistance Database (CARD), enable high-resolution profiling of resistomes. In this study, whole-genome sequencing and metagenomic analysis were applied to Klebsiella pneumoniae isolates to characterise resistance gene content. Normalised abundance values (RPKM) were generated across 347 antibiotic resistance gene (ARG) markers. The resistome comprised 347 ARG markers with a total abundance of 16,124.9 RPKM across 22,920 raw hits. β-lactamases (including OXA, CTX-M and SHV), multidrug efflux pumps (AcrA, OqxA, MdfA), and ArnT (associated with polymyxin resistance) were predominant. Resistance was most abundant against cephalosporins, penams, carbapenems and polymyxins. These findings demonstrate the dominance of β-lactam hydrolysing enzymes and efflux systems in K. pneumoniae and underscore the importance of genomic surveillance and One-Health-informed monitoring to track resistance dissemination and support stewardship strategies.
