Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms

• Published in: Environmental science and pollution research international Vol. 30; no. 18; pp. 52087 - 52106
• Main Authors: Ji, Bingzhen, Qin, Junjun, Ma, Yijia, Liu, Xin, Wang, Tian, Liu, Guiming, Li, Bugao, wang, Guoliang, Gao, Pengfei
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.04.2023; Springer Nature B.V
• Subjects: Aminoglycoside antibiotics; Aminoglycosides; Animals; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Aquatic Pollution; Atmospheric Protection/Air Quality Control/Air Pollution; Bacteria; Bacteria - genetics; Bacteroides; Butyrivibrio; China; Drug Resistance, Bacterial - genetics; Earth and Environmental Science; Ecotoxicology; Environment; Environmental Chemistry; Environmental Health; Environmental science; family; Farms; Genes; Genes, Bacterial; Genetic analysis; human health; Humans; Macrolides; Manure; Manures; Metagenomics; Microbial activity; Microorganisms; phenol; Phenols; Pig manure; Pollution control; Prevotella; Research Article; Swine; tetracycline; Waste Water Technology; Water Management; Water Pollution Control; China; Pig manure; Bacterial host; Mobility; Antibiotic resistance genes; Metagenomic
• ISSN: 1614-7499; 0944-1344; 1614-7499
• DOI: 10.1007/s11356-023-25962-1

In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum , Butyrivibrio , and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella , Bacteroides , and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.