Occurrence, antimicrobial resistance and genomic features offrom broiler chicken in Faisalabad, Pakistan.

Abstract

INTRODUCTION: The dissemination of antimicrobial resistance (AMR) in critical priority pathogens is a significant threat. Non-clinical reservoirs of AMR, such as agriculture and food production facilities, may contribute to the transmission of clinically relevant pathogens such as multidrug-resistant (MDR). There is currently very limited knowledge regarding the population structure and genomic diversity ofin poultry production in Pakistan. METHODS: We explored healthy broilers in a commercial farm from Faisalabad, Pakistan, and identified sixstrains from 100 broiler birds. We characterized the strains, determining clonality, virulence and antimicrobial resistance genes using next generation sequencing. RESULTS: The evaluation of antimicrobial susceptibility revealed that all the strains were MDR. Genomic analysis showed that 3/6 strains belonged to ST152, harbouring acquired resistance aminoglycosides [,], β-lactams (,), fosfomycin (), tetracycline (), trimethoprim (), quinolone (), sulphonamides () and phenicol (). All the strains harboured the efflux pump genes,,,,,,,and. All six strains encoded identical virulence profiles possessing six genes, i.e.,,,,,and. Phylogenomic analysis of the dominant sequence type (ST152) present in our dataset with publicly available genomes showed that the isolates clustered to strains mainly from human sources and could pose a potential threat to food safety and public health. DISCUSSION: The combination of these findings with antimicrobial use data would allow a better understanding of the selective pressures that may be driving the spread of AMR. This is the first report of MDRisolated from broiler hens in Pakistan, and the finding suggests that routine surveillance of WHO critical priority pathogens in such settings would be beneficial to the development of effective control strategies to reduce AMR.