Genomic Epidemiology of Multidrug-Resistant Clinical Klebsiella pneumoniae From Pakistan.

BACKGROUND

Antimicrobial-resistant Klebsiella pneumoniae is a major clinical threat in Pakistan and the wider South Asian region, where genomic surveillance remains limited. We analyzed 122 publicly available human clinical K. pneumoniae whole-genome sequencing datasets from Pakistan to define lineage structure, antimicrobial-resistance determinants, virulence-associated loci, surface-antigen profiles, plasmid replicons, and genomic relatedness.

METHODS

Reads were extracted, quality-filtered and assembled de novo, and assembly quality was assessed. Assemblies were characterized using Kleborate and ABRicate with the PlasmidFinder database. Trimmed reads were mapped to the K. pneumoniae MGH 78578 reference genome, and high-confidence biallelic SNPs (QUAL ≥ 30; per-isolate depth ≥ 10) were used to calculate pairwise genomic distances.

RESULTS

The cohort contained 23 sequence types and was dominated by ST15 (41/122, 33.61%), followed by ST48 (17/122, 13.93%), ST336 (11/122, 9.02%), ST711 (7/122, 5.74%), and ST3805 (7/122, 5.74%). Acquired resistance profiling detected 48 distinct antimicrobial-resistance genes. blaCTX-M-15 was present in 121 isolates (99.18%), blaVEB-5 in 45 (36.89%), and blaNDM-1 in 16 (13.11%). blaNDM-1-positive isolates occurred in four principal ST/capsule/O-locus backgrounds. Yersiniabactin and aerobactin loci were detected in 48 (39.34%) and 43 (35.25%) isolates, respectively; 43 isolates had a Kleborate virulence score ≥ 3, whereas colibactin and rmpADC were not detected. IncFIB(K)_1_Kpn3 was the most frequent plasmid replicon marker (101/122, 82.79%). Analysis of 169,220 high-confidence biallelic SNP sites yielded 7381 pairwise comparisons, with a median distance of 30,224 SNPs and no pairs differing by ≤ 10 SNPs.

CONCLUSION

The cohort showed broad genomic diversity, near-universal blaCTX-M-15 carriage, lineage-structured blaNDM-1 backgrounds, frequent siderophore-associated virulence loci, and distinct plasmid-replicon profiles. The findings support multiple co-circulating multidrug-resistant genomic backgrounds rather than a single clonal expansion and provide a reference point for genomic surveillance in Pakistan.