A comparative metagenomic analysis of antibiotic resistance in the fecal microbiome of pigs raised with and without antibiotics

PurposeThe use of antibiotics in swine production has raised concerns about its impact on animal health, microbial ecology, and the emergence of antibiotic resistance. The gut microbiome, a critical component of animal health, is susceptible to disruptions caused by antibiotic use. The fecal microbiome can provide a snapshot of changes in the gut microbiome and provide information on the spread of antibiotic resistance from pig feces to the environment. MethodsWe investigated the differences between the fecal microbiome of pigs raised with (AB+) and without (AB-) antibiotics to assess how antibiotic exposure influenced the microbial community, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). ResultsOur findings revealed that the use of antibiotics combined with study-specific conditions alters the fecal microbiome. Antibiotic usage in pigs explains 20% of the variation in the diversity of bacterial species detected between AB+ and AB- pigs. Similarly, variations in ARGs were observed in the two groups. The RND efflux pump gene family was abundant in both groups. The OXA {beta}-lactamase gene and associated plasmids were more prevalent in the AB- group. We also identified integrons linked to chloramphenicol resistance and transposon-associated integrative elements that can facilitate the spread of antibiotic resistance genes within and between bacterial species. ConclusionThese findings highlight that antibiotics influence both the microbial community and the antibiotic resistance gene repertoire, regardless of study-specific or environmental conditions. This emphasises the potential for fecal matter to contribute to the spread of antibiotic resistance in the environment, underscoring the need for more research to fully understand these dynamics in agricultural settings.