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<p>We conducted a longitudinal profiling of environmental resistomes and microbiomes from ten Swedish pig farms in a low–antimicrobial usage context. Samples were collected from pig pen environments and analysed using shotgun metagenomic sequencing. Resistome and microbiome profiles showed stronger temporal than farm-specific variation, with several age-associated trends. Age-related trajectories diverged between microbiome and resistome, indicating that resistance dynamics are shaped by factors beyond microbial succession. The highest relative abundance of resistance determinants was observed for tetracyclines, followed by aminoglycosides, macrolide–lincosamide–streptogramin antibiotics, beta-lactams, and folic acid synthesis inhibitors—drug classes commonly used in Swedish pig production. Resistome patterns were partially associated with phenotypic resistance profiles from previous studies, while analysis of antimicrobial usage alone could not fully explain the observed resistome. Overall, these findings suggest that additional factors beyond antimicrobial usage contribute to the persistence and dissemination of antibiotic resistance genes in pig farm environments.</p>

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Longitudinal investigation of the resistomes in Swedish pig farms

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月23日

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  • Valeriia Ladyhina,
  • Susanna Sternberg-Lewerin,
  • Axel Sannö,
  • Erik Bongcam-Rudloff,
  • Johan Dicksved,
  • Elisabeth Rajala

摘要

We conducted a longitudinal profiling of environmental resistomes and microbiomes from ten Swedish pig farms in a low–antimicrobial usage context. Samples were collected from pig pen environments and analysed using shotgun metagenomic sequencing. Resistome and microbiome profiles showed stronger temporal than farm-specific variation, with several age-associated trends. Age-related trajectories diverged between microbiome and resistome, indicating that resistance dynamics are shaped by factors beyond microbial succession. The highest relative abundance of resistance determinants was observed for tetracyclines, followed by aminoglycosides, macrolide–lincosamide–streptogramin antibiotics, beta-lactams, and folic acid synthesis inhibitors—drug classes commonly used in Swedish pig production. Resistome patterns were partially associated with phenotypic resistance profiles from previous studies, while analysis of antimicrobial usage alone could not fully explain the observed resistome. Overall, these findings suggest that additional factors beyond antimicrobial usage contribute to the persistence and dissemination of antibiotic resistance genes in pig farm environments.