Reducing Antimicrobial Resistance in Poultry Carcasses Extends Beyond Farm-Level Interventions

Area of Science:

• Food Science
• Microbiology
• Animal Science

Background:

• Antimicrobial use in poultry farming is a significant driver of antimicrobial resistance (AMR).
• Reducing antimicrobial use in livestock is a key strategy to mitigate AMR spread.
• The impact of antimicrobial-free farming on carcass microbiome and AMR profiles requires further investigation.

Purpose of the Study:

• To evaluate the effect of raising chickens without antimicrobials on poultry carcass microbiome composition and antimicrobial resistance gene abundance.
• To compare the microbiome and AMR profiles of caeca and carcass samples from antimicrobial-free chickens.
• To identify potential sources of AMR contamination during post-harvest processing.

Main Methods:

• Shotgun metagenomic sequencing of 151 caeca and neck skin samples from antimicrobial-free chickens.
• Bioinformatic analysis to characterize microbial communities and identify antimicrobial resistance genes (ARGs).
• Comparative analysis of microbiome composition and ARG abundance between caeca and carcasses.

Main Results:

• Chicken caeca were dominated by Bacillota and Bacteroidota, while carcasses by Pseudomonadota.
• Carcass microbiomes showed enrichment in genes for adaptation to limited nutrients and oxidative stress.
• Antimicrobial resistance gene abundance was significantly higher (approx. 49% more) on carcasses than in caeca, with a predominance of multidrug efflux systems and clinically relevant genes.

Conclusions:

• Reducing antimicrobial use at the farm level may not be sufficient to lower AMR on poultry carcasses.
• Post-harvest processing stages can introduce or concentrate antimicrobial resistance genes, potentially compromising farm-level interventions.
• Further research into post-harvest interventions is crucial for effective antimicrobial resistance reduction in the poultry supply chain.