Comparative Profiling of Antibiotic Resistance Genes and Microbial Communities in Pig and Cow Dung from Rural China: Insights into Environmental Dissemination and Public Health Risks

TL;DR

Pig dung from rural China contains more antibiotic resistance genes and harmful microbes than cow dung, posing a higher risk to the environment and public health.

Contribution

The study provides localized evidence on the higher risk of ARG and pathogen spread from pig dung compared to cow dung in rural livestock systems.

Findings

Pig dung had 56 enriched ARGs, including β-lactamase and macrolide resistance genes, while cow dung had only eight.

Pig dung contained higher levels of mobile genetic elements like intI1 and IS613, promoting ARG transfer.

Pig dung was enriched in potential pathogens like Escherichia coli and Leptospira, indicating higher health risks.

Abstract

Livestock dung is an important source of nutrients for agriculture but can also act as a reservoir for antibiotic resistance genes (ARGs) and harmful microorganisms that threaten environmental and public health. In this study, we compared pig and cow dung collected from small farms in rural China using high-throughput PCR arrays and 16S rDNA sequencing. We found that pig dung contained far more ARGs and potential pathogens than cow dung. Genes related to β-lactam and macrolide resistance were particularly abundant in pig dung, which also showed higher levels of mobile genetic elements that can promote ARG transfer. Cow dung, by contrast, was dominated by microorganisms associated with digestion in ruminants. These findings highlight that pig dung represents a higher risk of spreading antibiotic resistance and pathogens to the environment. Our results provide useful information for developing safer dung management practices, such as composting and biogas treatment, to reduce antibiotic resistance risks in rural livestock systems.

Antibiotic resistance genes (ARGs) and microbial communities in pig and cow dung from rural China were systematically profiled using high-throughput quantitative PCR arrays and 16S rDNA amplicon sequencing to assess their environmental dissemination and public health risks. The abundance and diversity of ARGs were markedly higher in pig dung than in cow dung. A total of 56 ARGs were enriched in pig dung, including β-lactamase genes (blaCMY, blaCTX-M) and macrolide resistance genes (ermB, ermF), along with several genes related to aminoglycoside and macrolide–lincosamide–streptogramin B resistance. In contrast, only eight ARGs were enriched in cow dung. Microbial community analysis revealed that cow dung was dominated by UCG-005, UCG-010, Methanocorpusculum, and Fibrobacter, taxa typically associated with ruminant digestion. In pig dung, Ignatzschineria, Lactobacillus, Pseudomonas, Streptococcus, Treponema, and conditional pathogens such as Escherichia coli and Leptospira were significantly enriched, indicating higher pathogen-related risks. Functional prediction identified 26 KEGG level-2 and 136 level-3 pathways, showing stronger xenobiotic degradation and amino acid metabolism in pig dung, whereas cow dung was enriched in energy metabolism and chemotaxis pathways. Moreover, the higher abundance of mobile genetic elements (e.g., intI1 and IS613) in pig dung suggests a greater potential for horizontal ARG transfer. Integrating ARG, microbial, and pathogen data reveals that pig dung acts as a composite source of “ARG–pathogen” contamination with enhanced transmission potential. These findings provide localized, data-driven evidence for developing safer livestock waste management practices, such as composting and biogas utilization, and contribute to antibiotic resistance mitigation strategies in rural China.

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