TY - JOUR
T1 - Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses
AU - Gaire, Tara N.
AU - Odland, Carissa
AU - Zhang, Bingzhou
AU - Slizovskiy, Ilya
AU - Jorgenson, Blake
AU - Wehri, Thomas
AU - Meneguzzi, Mariana
AU - Wass, Britta
AU - Schuld, Jenna
AU - Hanson, Dan
AU - Doster, Enrique
AU - Singer, Jacob
AU - Cannon, Jerry
AU - Asmus, Aaron
AU - Ray, Tui
AU - Dee, Scott
AU - Nerem, Joel
AU - Davies, Peter
AU - Noyes, Noelle R.
N1 - Publisher Copyright:
© 2024 Elsevier B.V.
PY - 2024/10/10
Y1 - 2024/10/10
N2 - 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.
AB - 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.
KW - Abattoir environment
KW - Antimicrobial resistance (AMR)
KW - Antimicrobial use
KW - Food safety
KW - Metagenomics
KW - Metal resistance genes
KW - Swine
UR - http://www.scopus.com/inward/record.url?scp=85197537370&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85197537370&partnerID=8YFLogxK
U2 - 10.1016/j.scitotenv.2024.174394
DO - 10.1016/j.scitotenv.2024.174394
M3 - Article
C2 - 38955276
AN - SCOPUS:85197537370
SN - 0048-9697
VL - 946
JO - Science of the Total Environment
JF - Science of the Total Environment
M1 - 174394
ER -