MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater
Antibiotic resistance (AMR) in animal agriculture represents a critical One Health challenge, with pig farms serving as major reservoirs for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). While MGEs are known drivers of ARG dissemination, their impact on actual expression of...
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Elsevier
2025-08-01
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| Series: | Environment International |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0160412025004040 |
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| author | Xiulin Wan Qingyang Li Zhi Li Lei Shi Yu Pan Meng Li Zongbao Liu |
| author_facet | Xiulin Wan Qingyang Li Zhi Li Lei Shi Yu Pan Meng Li Zongbao Liu |
| author_sort | Xiulin Wan |
| collection | DOAJ |
| description | Antibiotic resistance (AMR) in animal agriculture represents a critical One Health challenge, with pig farms serving as major reservoirs for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). While MGEs are known drivers of ARG dissemination, their impact on actual expression of resistance in these complex microbial communities is poorly understood. This study aimed to quantify the contribution of MGE-associated ARGs to overall resistance expression and compare their transcriptional efficiency to chromosomally located ARGs in pig farm wastewater. Utilizing deep metagenomic and metatranscriptomic sequencing on wastewater from five typical Chinese pig farms, we comprehensively elucidated ARG presence, genetic context, host association, and transcriptional activity. We identified a vast dataset comprising 811 ARG types conferring resistance to 27 antibiotic classes, with 71.02 % actively transcribed, indicating significant resistance potential. MGEs were associated with 34.87 % of ARG-like ORFs. Crucially, MGE-associated ARGs were responsible for the majority (62.07 %) of total ARG transcript abundance, exhibiting an expression efficiency nearly 2.5 times higher than ARGs on chromosomal non-MGE loci. Taxonomic analysis revealed that these highly expressed MGE-associated ARGs were primarily hosted by genera known to include opportunistic pathogens, such as Enterococcus, Escherichia, and Klebsiella. Differential coverage binning further uncovered diverse draft genomes simultaneously harboring multiple highly expressed ARGs and MGEs, potentially contributing to the persistence and spread of highly resistant bacterial strains. Our findings underscore that MGEs not only propagate ARGs but critically enhance their expression, providing vital data for effective AMR surveillance and mitigation strategies within the One Health framework. |
| format | Article |
| id | doaj-art-ec20bada42cb49bfb93269094b4ea307 |
| institution | DOAJ |
| issn | 0160-4120 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Environment International |
| spelling | doaj-art-ec20bada42cb49bfb93269094b4ea3072025-08-20T02:42:31ZengElsevierEnvironment International0160-41202025-08-0120210965310.1016/j.envint.2025.109653MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewaterXiulin Wan0Qingyang Li1Zhi Li2Lei Shi3Yu Pan4Meng Li5Zongbao Liu6Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education, China) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, ChinaMinistry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, ChinaMinistry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, ChinaShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, ChinaKey Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education, China) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, ChinaArchaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Corresponding author at: Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China.Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education, China) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi Normal University, Guilin, Guangxi, China; Corresponding author at: College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China.Antibiotic resistance (AMR) in animal agriculture represents a critical One Health challenge, with pig farms serving as major reservoirs for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). While MGEs are known drivers of ARG dissemination, their impact on actual expression of resistance in these complex microbial communities is poorly understood. This study aimed to quantify the contribution of MGE-associated ARGs to overall resistance expression and compare their transcriptional efficiency to chromosomally located ARGs in pig farm wastewater. Utilizing deep metagenomic and metatranscriptomic sequencing on wastewater from five typical Chinese pig farms, we comprehensively elucidated ARG presence, genetic context, host association, and transcriptional activity. We identified a vast dataset comprising 811 ARG types conferring resistance to 27 antibiotic classes, with 71.02 % actively transcribed, indicating significant resistance potential. MGEs were associated with 34.87 % of ARG-like ORFs. Crucially, MGE-associated ARGs were responsible for the majority (62.07 %) of total ARG transcript abundance, exhibiting an expression efficiency nearly 2.5 times higher than ARGs on chromosomal non-MGE loci. Taxonomic analysis revealed that these highly expressed MGE-associated ARGs were primarily hosted by genera known to include opportunistic pathogens, such as Enterococcus, Escherichia, and Klebsiella. Differential coverage binning further uncovered diverse draft genomes simultaneously harboring multiple highly expressed ARGs and MGEs, potentially contributing to the persistence and spread of highly resistant bacterial strains. Our findings underscore that MGEs not only propagate ARGs but critically enhance their expression, providing vital data for effective AMR surveillance and mitigation strategies within the One Health framework.http://www.sciencedirect.com/science/article/pii/S0160412025004040Pig farmAntibiotic resistance genesMobile genetic elementsDeep sequencingMetatranscriptomics |
| spellingShingle | Xiulin Wan Qingyang Li Zhi Li Lei Shi Yu Pan Meng Li Zongbao Liu MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater Environment International Pig farm Antibiotic resistance genes Mobile genetic elements Deep sequencing Metatranscriptomics |
| title | MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater |
| title_full | MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater |
| title_fullStr | MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater |
| title_full_unstemmed | MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater |
| title_short | MGE-associated ARGs exhibit higher expression efficiency than chromosomal non-MGE loci and predominantly contribute to resistance expression in pig farm wastewater |
| title_sort | mge associated args exhibit higher expression efficiency than chromosomal non mge loci and predominantly contribute to resistance expression in pig farm wastewater |
| topic | Pig farm Antibiotic resistance genes Mobile genetic elements Deep sequencing Metatranscriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S0160412025004040 |
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