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Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria

Author

Listed:
  • Rohan Maddamsetti

    (Duke University
    Duke University)

  • Yi Yao

    (Duke University
    Duke University)

  • Teng Wang

    (Duke University
    Duke University)

  • Junheng Gao

    (Duke University School of Medicine)

  • Vincent T. Huang

    (Duke University
    Duke University)

  • Grayson S. Hamrick

    (Duke University
    Duke University
    Duke University)

  • Hye-In Son

    (Duke University
    Duke University)

  • Lingchong You

    (Duke University
    Duke University
    Duke University
    Duke University School of Medicine)

Abstract

Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.

Suggested Citation

  • Rohan Maddamsetti & Yi Yao & Teng Wang & Junheng Gao & Vincent T. Huang & Grayson S. Hamrick & Hye-In Son & Lingchong You, 2024. "Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45638-9
    DOI: 10.1038/s41467-024-45638-9
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