Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments.

Affiliation

Mazhar SH(1), Li X(2), Rashid A(3), Su J(4), Xu J(4), Brejnrod AD(5), Su JQ(6), Wu Y(7), Zhu YG(8), Zhou SG(9), Feng R(10), Rensing C(11).
Author information:
(1)Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
(2)Section of Microbiology, University of Copenhagen, Denmark.
(3)Nuclear Institute for Food and Agriculture
(PAEC), Tarnab, Peshawar 25000, Pakistan.
(4)Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
(5)Skaggs School of Pharmacy, University of California San Diego, La Jolla, United States.
(6)Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China.
(7)College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
(8)Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
(9)Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China.
(10)Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China. Electronic address: [Email]
(11)Institute of Environmental Microbiology, College of Agricultural Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China; Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, 361021 Xiamen, China; Fujian Provincial Key Laboratory of Soil and Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China. Electronic address: [Email]

Abstract

Environmental selection of antibiotic resistance genes (ARGs) is considered to be caused by antibiotic or metal residues, frequently used in livestock. In this study we examined three commercial poultry farms to correlate the co-occurrence patterns of antibiotic and metal residues to the presence of ARGs. We quantified 283 ARGs, 12 mobile genetic elements (MGEs), 49 targeted antibiotics, 7 heavy metals and sequenced 16S rRNA genes. The abundance and type of ARG were significantly enriched in manure while soil harbored the most diverse bacterial community. Procrustes analysis displayed significant correlations between ARGs/MGEs and the microbiome. Cadmium (Cd), arsenic (As), zinc (Zn), copper (Cu) and lead (Pb) were responsible for a majority of positive correlations to ARGs when compared to antibiotics. Integrons and transposons co-occurred with ARGs corresponding to 9 classes of antibiotics, especially Class1 integrase intI-1LC. Redundancy analysis (RDA) and Variance partitioning analysis (VPA) showed that antibiotics, metals, MGEs and bacteria explain solely 0.7%, 5.7%, 12.4%, and 21.9% of variances of ARGs in the microbial community, respectively. These results suggested that bacterial composition and horizontal gene transfer were the major factors shaping the composition of ARGs; Metals had a bigger effect on ARG profile than detected antibiotics in this study.