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<p>The livestock gut microbiota serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied. Here,&#xa0;we present a large-scale metagenomic analysis of 779 gut samples from Caprinae animals, primarily originating from China (95.38%), including <i>Capra hircus</i> (79.85%) and <i>Ovis aries</i> (17.33%). We reconstruct 17,023 metagenome-assembled genomes (MAGs), and&#xa0;identify 2,440 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). <i>Escherichia coli</i> represents a major host for both. Correlation&#xa0;analyses between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection&#xa0;mechanisms. Although&#xa0;MGEs were detected in only 1.45% of MAGs, likely reflecting limitations in identifying&#xa0;MGEs within incomplete assemblies,&#xa0;19 ARGs are physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs are embedded within viral genomes, implicating bacteriophages in AMR dissemination. Comparative analyses reveal 184 distinct ARGs shared between Caprinae and humans, including 17 clinically&#xa0;critical genes such as <i>tetX</i> and <i>van</i> variants. These findings expand understanding of the Caprinae gut&#xa0;resistome and highlight its potential role in cross-host AMR transmission, and&#xa0;underscore the need for targeted AMR surveillance&#xa0;in this reservoir.</p>

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Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月19日

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  • Jin-Wen Su,
  • Hany M. Elsheikha,
  • Li Guo,
  • Rui Liu,
  • Kai-Meng Shang,
  • Hai-Long Yu,
  • He Ma,
  • Hong-Bo Ni,
  • Bei-Ni Chen,
  • Xiao-Xuan Zhang,
  • Xing Yang

摘要

The livestock gut microbiota serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied. Here, we present a large-scale metagenomic analysis of 779 gut samples from Caprinae animals, primarily originating from China (95.38%), including Capra hircus (79.85%) and Ovis aries (17.33%). We reconstruct 17,023 metagenome-assembled genomes (MAGs), and identify 2,440 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli represents a major host for both. Correlation analyses between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection mechanisms. Although MGEs were detected in only 1.45% of MAGs, likely reflecting limitations in identifying MGEs within incomplete assemblies, 19 ARGs are physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs are embedded within viral genomes, implicating bacteriophages in AMR dissemination. Comparative analyses reveal 184 distinct ARGs shared between Caprinae and humans, including 17 clinically critical genes such as tetX and van variants. These findings expand understanding of the Caprinae gut resistome and highlight its potential role in cross-host AMR transmission, and underscore the need for targeted AMR surveillance in this reservoir.