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Peer-reviewedCC BY-NC-ND 4.0Microbiome

Comprehensive sequence analysis reveals the vast β-lactam resistome

  • Sevan Gholipour1,2
  • John Z. Chen1,2
  • Dong‐Kyu Lee1,2
  • Naoki Konno3,2
  • Nobuhiko Tokuriki1
  1. 1Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
  2. 2Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T Z4, Canada
  3. 3Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyō, Japan
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Abstract

Most antibiotic-resistance genes (ARGs) evolved in environmental microbes long before humanity’s antibiotic breakthrough, and widespread antibiotic use expedited the dissemination of ARGs among clinical pathogens. While widely discussed, the investigation of environmental ARG distributions lacks the scalability and taxonomic information necessary for a comprehensive analysis. Here, we present a global distribution of all five classes of β-lactamases among microbes and environments. We generated a β-lactamase taxonomy-environment map by identifying >113,000 β-lactamases across diverse bacterial phyla and environmental ecosystems. Remarkably abundant, their occurrence is only ∼2.6-fold lower than the essential recA gene in various environmental ecosystems, with particularly strong enrichment in wastewater and plant samples. The enrichment in plant samples implies an environment where the arms race of β-lactam producers and resistant bacteria occurred over millions of years. We uncover the origins of clinically relevant β-lactamases (mainly in ɣ-Proteobacteria) and expand beyond the previously suggested wastewater samples in plant, terrestrial, and other aquatic settings.

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Cite

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BibTeX
@article{gholipour2026comprehensive,
  title = {{Comprehensive sequence analysis reveals the vast β-lactam resistome}},
  author = {Sevan Gholipour and John Z. Chen and Dong‐Kyu Lee and Naoki Konno and Nobuhiko Tokuriki},
  journal = {Microbiome},
  year = {2026},
  month = oct,
  doi = {10.1186/s40168-026-02566-8},
  url = {https://link.springer.com/article/10.1186/s40168-026-02566-8},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - Comprehensive sequence analysis reveals the vast β-lactam resistome
AU  - Sevan Gholipour
AU  - John Z. Chen
AU  - Dong‐Kyu Lee
AU  - Naoki Konno
AU  - Nobuhiko Tokuriki
PY  - 2026
DA  - 2026/10/26
JO  - Microbiome
DO  - 10.1186/s40168-026-02566-8
UR  - https://link.springer.com/article/10.1186/s40168-026-02566-8
AB  - Most antibiotic-resistance genes (ARGs) evolved in environmental microbes long before humanity’s antibiotic breakthrough, and widespread antibiotic use expedited the dissemination of ARGs among clinical pathogens. While widely discussed, the investigation of environmental ARG distributions lacks the scalability and taxonomic information necessary for a comprehensive analysis. Here, we present a global distribution of all five classes of β-lactamases among microbes and environments. We generated a β-lactamase taxonomy-environment map by identifying >113,000 β-lactamases across diverse bacterial phyla and environmental ecosystems. Remarkably abundant, their occurrence is only ∼2.6-fold lower than the essential recA gene in various environmental ecosystems, with particularly strong enrichment in wastewater and plant samples. The enrichment in plant samples implies an environment where the arms race of β-lactam producers and resistant bacteria occurred over millions of years. We uncover the origins of clinically relevant β-lactamases (mainly in ɣ-Proteobacteria) and expand beyond the previously suggested wastewater samples in plant, terrestrial, and other aquatic settings.
SN  - 2049-2618
ER  -