Broiler house environment and litter management practices impose selective pressures on antimicrobial resistance genes and virulence factors ofCampylobacter

Abstract

AbstractCampylobacterinfections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir forCampylobacter. Here, we characterized the genetic diversity ofCampylobacterspecies detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance and virulence factor profiles. Antimicrobial susceptibility testing and whole genome sequencing were performed onCampylobacter jejuni(n = 39) andCampylobacter coli(n = 5) isolates. AllC. jejuniisolates were susceptible to all antibiotics tested whileC. coli(n =4) were resistant to only tetracycline and harbored the tetracycline-resistant ribosomal protection protein (TetO). Virulence factors differed within and across grow houses but were explained by the isolates’ flock cohort, species and multilocus sequence type. Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were absent from flock cohort 3C. jejuniisolates as compared to flock 1 and 2 isolates. Our results show that virulence factors and antimicrobial resistance genes differed by the isolates’ multilocus sequence type and by the flock cohort they were present in. These data suggest that the house environment and litter management practices performed imposed selective pressures on antimicrobial resistance genes and virulence factors. In particular, the absence of key virulence factors within the final flock cohort 3 isolates suggests litter reuse selected forCampylobacterstrains that are less likely to colonize the chicken host.ImportanceCampylobacteris a leading cause of foodborne illness in the United States due to the consumption of contaminated food products or from mishandling of food products, often associated with chicken meat.Campylobacteris common in the microbiota of avian and mammalian gut; however, the acquisition of antimicrobial resistance genes and virulence factors may result in strains that pose a significant threat to public health. Although there are studies that have investigated the genetic diversity ofCampylobacterstrains isolated from post-harvest chicken samples, there is limited data on the genome characteristics of isolates recovered from pre-harvest broiler production. In this study, we show thatCampylobacter jejuniandCampylobacter colithat differ in their carriage of antimicrobial resistance and virulence factors may differ in their ability to evade host defense mechanisms and colonize the gut of chickens and humans. Furthermore, we found that differences in virulence factor profiles were explained by the species ofCampylobacterand its multilocus sequence type.