Short- and long-read metagenomics insight into the genetic contexts and hosts of mobile antibiotic resistome in Chinese swine farms
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Short- and long-read metagenomics insight into the genetic contexts and hosts of mobile antibiotic resistome in Chinese swine farms. / Li, Lili; Xiao, Yawen; Olsen, Rikke Heidemann; Wang, Chong; Meng, Hecheng; Shi, Lei.
In: Science of the Total Environment, Vol. 827, 154352, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - Short- and long-read metagenomics insight into the genetic contexts and hosts of mobile antibiotic resistome in Chinese swine farms
AU - Li, Lili
AU - Xiao, Yawen
AU - Olsen, Rikke Heidemann
AU - Wang, Chong
AU - Meng, Hecheng
AU - Shi, Lei
N1 - Publisher Copyright: © 2022
PY - 2022
Y1 - 2022
N2 - Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Intensive swine farms are recognized as hotspots for antibiotic resistance genes (ARGs). However, antibiotic resistome and their genetic contexts, hosts, and transferability in Chinese swine farms remain largely unexplored. Here, we used Illumina and Oxford Nanopore metagenomics sequencing to investigate the antibiotic resistome context of 14 distantly located large-scale (10,000 animals per year) commercial swine farms in China. We identified high abundant and diverse ARGs (609,966.8 with 1433 types, belonging to 38 different antibiotic classes) in all samples, including those encoding resistance to clinically critical important antibiotics (such as mcr, tetX, optrA, poxtA, qnr and blaCTX-M). About 75% of the ARGs detected were carried by mobile genetic elements (mainly plasmids), suggesting their high transmission potential into receiving environments. Host-tracking analysis identified Clostridiales, Faecalibacterium prausnitzii and Escherichia coli as the predominant bacterial hosts of mobile ARGs. Notably, genome binning generated 246 high-completeness draft genomes. Genetic context analysis of the multiple resistant (MDR) genes in binned genomes showed the involvement of insertion sequences (ISs), integron and SGI2 genomic island, implying their importance role in promoting the development of MDR bacteria. Overall, these findings substantially expand our current knowledge of mobile antibiotic resistome in Chinese swine farms, and suggest reasonable management of animal wastes in swine farms to reduce the dissemination of antibiotic resistance to the environment.
AB - Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Intensive swine farms are recognized as hotspots for antibiotic resistance genes (ARGs). However, antibiotic resistome and their genetic contexts, hosts, and transferability in Chinese swine farms remain largely unexplored. Here, we used Illumina and Oxford Nanopore metagenomics sequencing to investigate the antibiotic resistome context of 14 distantly located large-scale (10,000 animals per year) commercial swine farms in China. We identified high abundant and diverse ARGs (609,966.8 with 1433 types, belonging to 38 different antibiotic classes) in all samples, including those encoding resistance to clinically critical important antibiotics (such as mcr, tetX, optrA, poxtA, qnr and blaCTX-M). About 75% of the ARGs detected were carried by mobile genetic elements (mainly plasmids), suggesting their high transmission potential into receiving environments. Host-tracking analysis identified Clostridiales, Faecalibacterium prausnitzii and Escherichia coli as the predominant bacterial hosts of mobile ARGs. Notably, genome binning generated 246 high-completeness draft genomes. Genetic context analysis of the multiple resistant (MDR) genes in binned genomes showed the involvement of insertion sequences (ISs), integron and SGI2 genomic island, implying their importance role in promoting the development of MDR bacteria. Overall, these findings substantially expand our current knowledge of mobile antibiotic resistome in Chinese swine farms, and suggest reasonable management of animal wastes in swine farms to reduce the dissemination of antibiotic resistance to the environment.
KW - Genetic context
KW - Host-tracking
KW - Illumina sequencing
KW - Nanopore sequencing
KW - Resistome
U2 - 10.1016/j.scitotenv.2022.154352
DO - 10.1016/j.scitotenv.2022.154352
M3 - Journal article
C2 - 35259381
AN - SCOPUS:85126052677
VL - 827
JO - Science of the Total Environment
JF - Science of the Total Environment
SN - 0048-9697
M1 - 154352
ER -
ID: 304150890