Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses

Tara N. Gaire, Carissa Odland, Bingzhou Zhang, Ilya Slizovskiy, Blake Jorgenson, Thomas Wehri, Mariana Meneguzzi, Britta Wass, Jenna Schuld, Dan Hanson, Enrique Doster, Jacob Singer, Jerry Cannon, Aaron Asmus, Tui Ray, Scott Dee, Joel Nerem, Peter Davies, Noelle R. Noyes

Research output: Contribution to journalArticlepeer-review

Abstract

Several steps in the abattoir can influence the presence of microbes and associated resistance genes (ARGs) on the animal carcasses used for further meat processing. We investigated how these processes influence the resistome-microbiome of groups of pigs with different on-farm antimicrobial exposure status, from the moment they entered the abattoir until the end of carcass processing. Using a targeted enrichment metagenomic approach, we identified 672 unique ARGs conferring resistance to 43 distinct AMR classes from pooled skin (N = 42) and carcass swabs (N = 63) collected sequentially before, during, and after the slaughter process and food safety interventions. We observed significant variations in the resistome and microbial profiles of pigs before and after slaughter, as well as a significant decline in ARG counts, diversity, and microbial DNA load during slaughter and carcass processing, irrespective of prior antimicrobial treatments on the farm. These results suggest that existing interventions in the abattoir are effective in reducing not only the pathogen load but also the overall bacterial burden, including ARGs on pork carcasses. Concomitant with reductions in microbial and ARG counts, we observed an increase in the relative abundance of non-drug-specific ARGs, such as those conferring resistance to metals and biocides, and in particular mercury. Using a strict colocalization procedure, we found that most mercury ARGs were associated with genomes from the Pseudomonadaceae and Enterobacteriaceae families. Collectively, these findings demonstrate that slaughter and processing practices within the abattoir can shape the microbial and ARG profiles of pork carcasses during the transition from living muscle to meat.

Original languageEnglish (US)
Article number174394
JournalScience of the Total Environment
Volume946
DOIs
StatePublished - Oct 10 2024

Bibliographical note

Publisher Copyright:
© 2024 Elsevier B.V.

Keywords

  • Abattoir environment
  • Antimicrobial resistance (AMR)
  • Antimicrobial use
  • Food safety
  • Metagenomics
  • Metal resistance genes
  • Swine

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