Environmental Surveillance of Antimicrobial Resistance in Commercial Poultry Production: Microbiome, Resistome, Antimicrobial Residues, and Avian Pathogenic Escherichia coli Dynamics

Abstract

Antimicrobial Resistance (AMR) is a major global threat to humans, animals, and the environment, often driven by overuse of antimicrobials and environmental contamination, particularly in food animal production. We focused on using the vertically integrated poultry production system as a model to understand the AMR dynamics. Environmental samples representing the inside poultry house (litter) and outside environment (soil and wild or domestic animal fecal samples surrounding the poultry houses) were collected from different stages of production including pullet, breeder and broiler farms. Additionally, flocks from broiler farms were followed to their respective processing plants to collect carcass rinses from post-pick and post-chill stages.

The introductory review chapter underscores the importance of environmental reservoirs in shaping the AMR persistence and development, suggesting the need for comprehensive environmental monitoring for tackling AMR. Further, investigation using shotgun metagenomics revealed distinct microbiome and resistome profiles across different stages of production and environmental samples. Moreover, isolated instances of microbiome and resistome overlap between inside environment and outside poultry house environments were observed, suggesting potential biosecurity breaches.

Complementing metagenomics finding, qPCR analysis demonstrated a higher AMR burden in the litter compared to soil samples particularly in broiler farms. Metagenomics resistome and qPCR results corraborated with each other, both offered insights on AMR diversity and quantification. Furthermore, antimicrobial residue analysis provided opposite trends: antimicrobial residues such as sulfamethoxazole, tetracycline and, oxytetracycline were detected in higher quantity in the early stages of production (pullet and breeder) than in broiler farms. While antimicrobial residues were not associated with antimicrobial resistance genes (ARGs) levels, residues were positively associated with quantification of mobile genetic elements (MGEs), thereby indicating antimicrobial residues may facilitate AMR dissemination via horizontal gene transfer.

Our final approach was to use the culture dependent technique to investigate the prevalence and genomic characterization of avian pathogenic E. coli (APEC), a potential marker organism for AMR surveillance in poultry production settings. APEC was widespread and carried clinically relevant ARGs among different stages of production and sample types. We identified high-risk APEC strains in the farms’ environment as well as in the processing plant. Single nucleotide polymorphism (SNP)-based phylogenetic analysis provided compelling evidence of potential APEC transmission between the inside farm environment and adjacent outside area, as well as between broiler farm litter and processing plant.

Overall, these comprehensive studies highlight the multifaceted and complex nature of AMR. The farms’ environment can act not only as a reservoir of AMR but also as a potential source of AMR spillover. This dissertation highlights the value of a multi-technique approach that integrated metagenomics, qPCR, antimicrobial residue detection, and culture-based technique to comprehensively understand the dynamics of AMR.