Investigation of swine caecal microbiomes in the northern region of Thailand

IntroductionThe northern region of Thailand serves as a crucial area for swine production, contributing to the global food supply. Previous studies have highlighted the presence of foodborne pathogens originating from swine farms in this region, posing a threat to both human and animal health. Gap statementMultiple swine pathogens have been studied at a species level, but the distribution and co-occurrence of pathogens in agricultural swine has not been well established. AimOur study employed the intestinal scraping technique to directly examine the microorganisms interacting with the swine host. MethodologyWe used shotgun metagenomic sequencing to analyse the caecal microbiomes of swine from five commercial farms in northern Thailand. ResultsSwine caecal microbiomes contained commensal bacteria such as Bifidobacterium, Lactobacillus, and Faecalibacterium, which are associated with healthy physiology and feed utilisation. We also identified multiple pathogenic and opportunistic bacteria present in all samples, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus, and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides which have historically been used extensively in swine farming. ConclusionThe findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.