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

Valentina Indio1, Yitagele Terefe Mekonnen1, Chiara Oliveri1

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Summary
This summary is machine-generated.

Raising chickens without antimicrobials did not reduce antimicrobial resistance (AMR) gene abundance on carcasses. Post-harvest processing stages appear to compromise farm-level AMR reduction efforts in poultry production.

Keywords:
antibiotic-free flocksbroiler caecabroiler carcassesresistomeshotgun sequencing

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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.