Characterization of the pig lower respiratory tract antibiotic resistome

Yunyan Zhou, Jingquan Li, Fei Huang, Huashui Ai, Jun Gao, Congying Chen () and Lusheng Huang ()
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Yunyan Zhou: Jiangxi Agricultural University
Jingquan Li: Jiangxi Agricultural University
Fei Huang: Jiangxi Agricultural University
Huashui Ai: Jiangxi Agricultural University
Jun Gao: Jiangxi Agricultural University
Congying Chen: Jiangxi Agricultural University
Lusheng Huang: Jiangxi Agricultural University

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.

Date: 2023
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DOI: 10.1038/s41467-023-40587-1

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