Deciphering of microbial diversity and antibiotic resistome of bioaerosols in swine confinement buildings

Abstract Cumulative evidence has revealed that particulate matter from swine confinement buildings (SCBs) is a reservoir of zoonotic pathogens and antibiotic resistance genes (ARGs) from feces, which have been associated with the growth stage of pigs. SCB bioaerosols can spread over long distances to the external environment, posing a significant risk to public health. However, the bacterial microbiome and resistome profiles of SCB bioaerosols and their relationship with the growth stages of pigs are not well understood. In this study, 24 bioaerosol samples from buildings separately housing weaning piglets (WP), growing-finishing pigs (FP), gestation sows (GS), and farrowing sows (FS) were used to determine the bacterial microbiome and resistome of the indoor air of SCBs using next-generation high-throughput sequencing approaches. The results indicated that FP bioaerosols exhibited the highest alpha diversity and ARG abundance. The composition of the bacterial microbiome and resistome of SCB bioaerosols varied according to the growth stage of the pigs. The most abundant phyla and ARG types were Proteobacteria and aminoglycosides, respectively, across the four types of SCBs. Three potential pathogens and 18 possible ARG host genera were found to occur in the SCB bioaerosols. The highest abundances of dominant potential pathogens (Acinetobacter) and ARG subtypes (aph(3”')-III) were observed in the FP bioaerosols. Moreover, there is a strong correlation between the bacterial microbiome and the resistome in bioaerosols from the SCBs. It can be concluded that the growth stage of pigs exerted a significant effect on the bacterial microbiome and resistome profiles of the indoor air of SCBs.