Antimicrobial resistance profiles and genomic insights of phenotypically extended spectrum β-lactamase-positive Klebsiella pneumoniae from cattle farms.

Abstract

Klebsiella pneumoniae, identified by the World Health Organization (WHO) as a critical priority pathogen, presents a growing public health concern due to increasing multidrug-resistant (MDR) and extended spectrum β-lactamase (ESBL)-producing strains. This study assessed the antimicrobial resistance (AMR) profiles of K. pneumoniae isolates from 288 cattle farm samples in Punjab, India. The bacterium was detected in 10.06% (29/288) of the samples, with 65.51% (19/29) of the isolates being MDR and 6.89% (2/29) exhibiting an ESBL-like phenotype. Resistance genes for β-lactams (bla_TEM-62.06%, bla_AmpC-51.72%, bla_SHV-51.72%), quinolones (qnrS-13.79%), and tetracyclines (tetA-10.34%) were identified. Whole-genome sequencing (WGS) was conducted on two representative phenotypically ESBL-positive and MDR K. pneumoniae isolates, selected for detailed genomic analysis within the limitations of available funding. The analysis revealed the presence of multiple antimicrobial resistance genes (ARGs) conferring resistance to quinolones, cephalosporins, carbapenems, tetracyclines, macrolides, and several other antibiotic classes. Virulence factors detected included Type I and Type III fimbriae, capsules, efflux systems, siderophores, and secretion systems. Plasmid replicon types (IncFIB(K), IncFIB, IncFII(K)), integrons harboring ARGs, and insertion sequences (ISKpn24, ISKpn1, ISKpn19, IS26) were also identified. Multilocus Sequence Typing (MLST) assigned isolates to sequence types ST-160 and ST-4232, with core-genome MLST identifying additional types ST-14,733 and ST-13,365. These findings highlight the potential risk of transmission of resistant K. pneumoniae strains between animals and humans and underscore the urgent need for integrated One Health surveillance and intervention strategies to contain the spread of AMR across sectors.