Next-Generation Sequencing Based Gut Resistome Profiling of Broiler Chickens Infected with Multidrug-Resistant .

The study was designed to investigate the fecal microbiome and resistome of broiler chickens infected with multidrug-resistant (MDR) (). Fecal samples ( = 410) from broiler chickens were collected from thirteen randomly selected sites of Khyber Pakhtunkhwa and screened for the presence of MDR . Upon initial screening, thirteen (13) MDR isolates were then subjected to shotgun metagenome next-generation sequencing (NGS). NGS based resistome analysis identified the multidrug efflux pump system-related genes at the highest prevalence (36%) followed by aminoglycoside (26.1%), tetracycline (15.9%), macrolide-lincosamide-streptogramin (9.6%), beta-lactam (6.6%), rifampin (2%), sulphonamide (1.3%), phenicol (0.91%), vancomycin (0.62%), trimethoprim (0.34%), colistin (0.30%), and quinolone (0.33%). The most abundant virulence-associated genes (VAGs) identified were N, A, , and A. NGS based taxonomic profiling at the phylum level revealed the predominance of Proteobacteria (38.9%) followed by Firmicutes (36.4%), Bacteroidetes (15.8%), and Tenericutes (8.9%). Furthermore, pathobionts such as , , , and belonging to the family Enterobacteriaceae were predominantly found. This study revealed the widespread presence of MDR genes, diverse VAGs, and a dysbiotic gut in the broiler chickens infected with MDR of Khyber Pakhtunkhwa for the first time using NGS.