Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Comment
  • Published:

Microbial genomics for antimicrobial resistance ecology and action

The scale-up of microbial genomics has seen notable advances in understanding the dynamics of antimicrobial resistance (AMR) across species, environments and ecosystems. To gain meaningful insights that can ultimately inform AMR control strategies, stronger analytical frameworks are needed that integrate data across temporal, spatial and molecular scales.

This is a preview of subscription content, access via your institution

Access options

Buy this article

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

References

  1. Sati, H. et al. The WHO Bacterial Priority Pathogens List 2024: a prioritisation study to guide research, development, and public health strategies against antimicrobial resistance. Lancet Infect. Dis. 25, 1033–1043 (2025).

    Article  PubMed  PubMed Central  Google Scholar 

  2. Ramírez-Castillo, F. Y., Guerrero-Barrera, A. L. & Avelar-González, F. J. An overview of carbapenem-resistant organisms from food-producing animals, seafood, aquaculture, companion animals, and wildlife. Front. Vet. Sci. 10, 1158588 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Jørgensen, S. L. et al. Diversity and population overlap between avian and human Escherichia coli belonging to sequence type 95. mSphere 4, e00333–18 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Djordjevic, S. P. et al. Genomic surveillance for antimicrobial resistance — a One Health perspective. Nat. Rev. Genet. 25, 142–157 (2024).

    Article  CAS  PubMed  Google Scholar 

  5. Ikhimiukor, O. O., Odih, E. E., Donado-Godoy, P. & Okeke, I. N. A bottom-up view of antimicrobial resistance transmission in developing countries. Nat. Microbiol. 7, 757–765 (2022).

    Article  CAS  PubMed  Google Scholar 

  6. Thorpe, H. A. et al. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nat. Microbiol. 7, 2054–2067 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ludden, C. et al. One Health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock. mBio 10, e02693–18 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hetland, M. A. K. et al. A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs. Genome Med. 17, 42 (2025).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Baker, S., Thomson, N., Weill, F.-X. & Holt, K. E. Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science 360, 733–738 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Liu, C. M. et al. Escherichia coli ST131-H22 as a foodborne uropathogen. mBio 9, 00470–18 (2018).

    Article  Google Scholar 

  11. Lowder, B. V. et al. Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus. Proc. Natl Acad. Sci. USA 106, 19545–19550 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kathryn E. Holt.

Ethics declarations

Competing interests

The author declares no competing interests.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Holt, K.E. Microbial genomics for antimicrobial resistance ecology and action. Nat Rev Genet 27, 7–8 (2026). https://doi.org/10.1038/s41576-025-00909-z

Download citation

  • Published:

  • Version of record:

  • Issue date:

  • DOI: https://doi.org/10.1038/s41576-025-00909-z

This article is cited by

Search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology