Genomic surveillance of Klebsiella pneumoniae in poultry
The dissemination of antimicrobial-resistance in World Health Organization (WHO) critical priority pathogens is an emerging public health threat that is a One-Health threat in clinical, veterinarian and environmental settings. is no longer restricted to hospital settings. The rapid spread of antimicrobial-resistance in Escherichia coli from poultry isolates in Pakistan warrants further investigation into other clinically relevant pathogens, such as Klebsiella pneumoniae (K. pneumoniae). We explored commercial healthy broilers in the commercial farms from Faisalabad, Pakistan to identify and characterize strains of the K. pneumoniae, determining clonality, virulence and antimicrobial resistance genes using next generation sequencing. Phylogenomic analysis of global and publicly available genomes were also compared with the dominant sequence type (ST) present in our dataset. K. pneumoniae strains were isolated from 6/100 birds (6%). The antimicrobial susceptibility revealed that all the strains were multi-drug resistant (MDR). Genomic analysis revealed that 3/6 strains belonged to ST152 harbouring acquired resistance aminoglycosides [aadA2, aph(4')-Ia], ß-lactams (blaSHV-187, blaLAP2), fosfomycin (fosA6), tetracycline (tetA), trimethoprim (dfrA12), quinolone (qnrS1), sulphonamides (sul2) and phenicol (floR). All the strains harboured the efflux pump genes oqxA, oqxB, emrR, kpnG, kpnH, kpnF, baeR, mtdB and mtdC. All six strains encoded identical virulence profiles possessing six genes i.e., ureA, iutA, entB, allS, fimH and mrkD. Phylogenomic analysis showed that ST152 clustered to strains isolated mainly from the human and could pose a potential threat to food safety and public health. Antimicrobial-resistant profiles suggested the presence of selective antimicrobial pressure in K. pneumoniae sourced from broiler chickens. Routine surveillance of WHO critical priority pathogens in non-clinical settings is essential to the development of effective control strategies to reduce AMR.