Molecular characterization of carbapenemase-producing Enterobacterales from Peshawar City, Khyber Pakhtunkhwa, Pakistan
Stefano Mancini, Irfan Ullah, Helena M B Seth-Smith, Natalia Kolesnik-Goldmann, Vladimira Hinic, Tim Roloff, Adrian Egli, Muhammad Ali Syed, Oliver NolteAbstract
Background/Objectives
The dissemination of multidrug-resistant Enterobacterales poses a critical public health challenge, particularly in resource-limited regions with high antimicrobial use and limited surveillance. We analysed the phenotypic and genotypic resistance profiles of carbapenemase-producing Enterobacterales collected in 2023 from three tertiary care hospitals in Peshawar, Pakistan.
Methods
We performed antimicrobial susceptibility testing on 32 Enterobacterales isolates suspected of carbapenemase production using disk diffusion, gradient diffusion, and broth microdilution according to EUCAST guidelines. We conducted whole-genome sequencing to identify resistance genes, sequence types, and mutations associated with reduced susceptibility to novel β-lactams.
Results
The collection comprised 16 Escherichia coli, 13 Klebsiella pneumoniae, and 3 Proteus mirabilis isolates. The predominant carbapenemase gene was blaNDM-5 (90.6%), frequently combined with blaOXA-48-like variants (46.9%). ESBL genes, mainly blaCTX-M-15, were common (78.1%), while CMY-type AmpC β-lactamases were detected in 28.1% of isolates. Insertions in the PBP3-encoding gene ftsI and CMY co-production were associated with elevated aztreonam–avibactam MICs in E.coli. Reduced cefiderocol susceptibility was observed mainly among NDM-producing E. coli ST2 isolates carrying cirA disruption and ftsI insertions. All isolates remained susceptible to colistin, most of them to gentamicin (84.4%), and exhibited wild-type MIC-distributions for tigecycline, and eravacycline. Genomic analysis identified clustering of high-risk clones, suggesting ongoing local transmission. Notably, 11/13 K. pneumoniae ST147 isolates carried multiple virulence-associated genes consistent with hypervirulence.
Conclusions
High-risk NDM-producing Enterobacterales with increasingly complex resistance and virulence mechanisms are circulating in Pakistan, including determinants compromising last-line β-lactams. Strengthened genomic surveillance is essential to guide therapy and limit further spread.