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Published on: March 3, 2023
Genomic Epidemiology of Multidrug-Resistant Clinical Klebsiella pneumoniae From Pakistan
Hakeem Zada1, Muhammad Qasim1, Mubashir Hussain1
1Department of Microbiology, Kohat University of Science and Technology, Kohat, 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.
Insights
Genomic surveillance of antimicrobial-resistant Klebsiella pneumoniae in Pakistan reveals diverse lineages carrying resistance genes like blaCTX-M-15 and blaNDM-1. Findings highlight multiple multidrug-resistant backgrounds, not a single clonal expansion, informing future genomic surveillance efforts.
Area of Science:
- Genomics
- Microbiology
- Infectious Diseases
- Public Health
Background:
- Antimicrobial-resistant Klebsiella pneumoniae poses a significant clinical threat in Pakistan and South Asia.
- Genomic surveillance for this pathogen remains limited in the region.
- Analysis of 122 whole-genome sequencing datasets from Pakistan was conducted.
Purpose of the Study:
- To define the lineage structure of Klebsiella pneumoniae in Pakistan.
- To identify antimicrobial-resistance determinants, virulence factors, and plasmid replicons.
- To assess genomic relatedness and provide a baseline for surveillance.
Main Methods:
- Whole-genome sequencing data from 122 human clinical isolates were analyzed.
- Assemblies were quality-filtered and characterized using Kleborate and ABRicate.
- Single nucleotide polymorphism (SNP) analysis was performed to calculate genomic distances.
Main Results:
- Twenty-three sequence types (STs) were identified, dominated by ST15 (33.61%).
- Near-universal carriage of blaCTX-M-15 (99.18%) was observed; blaNDM-1 was present in 13.11% of isolates.
- Frequent siderophore loci (yersiniabactin, aerobactin) and diverse plasmid replicon profiles were detected.
Conclusions:
- The study revealed broad genomic diversity and multiple co-circulating multidrug-resistant Klebsiella pneumoniae backgrounds.
- Lineage-structured blaNDM-1 backgrounds were identified.
- These findings establish a crucial reference for future genomic surveillance in Pakistan.
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