Longitudinal analysis of surface-associated bacterial ecology and resistome dynamics in a pig slaughterhouse

• 35 S almonella (ST19/ST34) with multidrug resistance profiles were isolated. • Stable, site-specific pig slaughterhouse microbiomes dominated by Moraxellaceae. • Shotgun metagenomics shows co-occurring antibiotic and biocide resistance genes. • Acinetobacter dominates later stages, carrying high levels of resistance genes. Slaughterhouses constitute key stages for the transmission of bacterial pathogens and antimicrobial resistance throughout the meat production chain, with significant implications for food safety. This study investigated the bacterial communities and resistome profiles of surface-associated microbes in a pig slaughterhouse sampled at two-year intervals in 2017 and 2019. Thirty-five strain of Salmonella enterica serovar Typhimurium and its monophasic variant, major pathogenic serovars of the sector, were collected through the slaughtering line in this time frame, and they displayed multidrug resistance profiles characteristic of the pig sector. Whole-genome analysis revealed no clear phylogenetic clustering by site or sampling date. Both 16S rRNA metabarcoding and shotgun metagenomics underlined site-specific bacterial communities dominated by Moraxellaceae family and with a relative stable composition across the sampling period. The upstream of the slaughtering line (dehairing stage) was characterized by aminoglycoside and tetracycline resistance genes, predominantly associated with Acinetobacter , Escherichia , and Clostridium , alongside oxidative stress genes carried by Streptococcus . At the downstream section of the slaughtering process, the red offal platform exhibited increased diversity and abundance of antibiotic and biocide resistance determinants. These included β-lactam and carbapenem resistance genes as well as efflux pump-associated elements ( adeJ ), mainly linked to Acinetobacter which was consistently enriched suggesting its potential role as a reservoir for resistance genes. Overall, these findings provide insights into the composition, stability, and functional potential of bacterial communities in slaughterhouse environments and their possible role in shaping pathogen and resistance gene dynamics along the food production chain.