Metagenomic insights into the influence of goose farming on the gut microbiome and antibiotic resistome of workers

Antimicrobial resistance (AMR) seriously threatens the health of humans and animals. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were enriched in the goose farms. However, the influence of goose farming exposure on the gut microbiota and ARGs of workers was unclear. In this study, metagenomic analysis was used to characterize gut microbiome structures, annotate bacterial taxa, and quantify the abundances of ARGs and MGEs in geese and human samples. Results showed that goose feces harbored more abundant ARGs and ARB than human feces. Significantly higher abundances of special ARGs (such as vanY, lsaE, AAC3-IId and ampC) were identified in workers compared to villagers. Compositions of gut bacteria were significantly different between workers and villagers, and some certain gut pathogens were abundant in the feces of workers, including Bacillus anthracis, Clostridium perfringens, and Escherichia coli O45:K1:H7. A total of 51 ARGs were pinpointed in the metagenome-assembled genomes (MAGs). Based on ARG-MGE associations and co-occurrence signals in MAGs, the potential for horizontal gene transfer (HGT) was inferred. With this transfer capacity and ubiquitous gut colonization, E. coli carrying 38 ARGs is proposed as a putative AMR indicator for the goose farm. This study demonstrates that goose farming had non-ignorable influences on the gut microbiome and antibiotic resistome of workers. More efforts should be made to control the ARGs and ARB in the goose farm.