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Genomic surveillance for antimicrobial resistance — a One Health perspective

Nature Reviews Genetics volume 25, pages 142–157 (2024)Cite this article

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Abstract

Antimicrobial resistance (AMR) — the ability of microorganisms to adapt and survive under diverse chemical selection pressures — is influenced by complex interactions between humans, companion and food-producing animals, wildlife, insects and the environment. To understand and manage the threat posed to health (human, animal, plant and environmental) and security (food and water security and biosecurity), a multifaceted ‘One Health’ approach to AMR surveillance is required. Genomic technologies have enabled monitoring of the mobilization, persistence and abundance of AMR genes and mutations within and between microbial populations. Their adoption has also allowed source-tracing of AMR pathogens and modelling of AMR evolution and transmission. Here, we highlight recent advances in genomic AMR surveillance and the relative strengths of different technologies for AMR surveillance and research. We showcase recent insights derived from One Health genomic surveillance and consider the challenges to broader adoption both in developed and in lower- and middle-income countries.

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Fig. 1: Development of antimicrobial resistance.
Fig. 2: One Health antimicrobial resistance.
Fig. 3: One Health genomics toolbox.
Fig. 4: Plasmids as mobile genetic elements that drive antimicrobial resistance.

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Acknowledgements

The authors thank F. MacIver from the University of Technology Sydney for assistance with preparing and editing the manuscript and S. Zufan from the University of Melbourne for assistance with preparation of Fig. 3. This work was supported by the Medical Research Future Fund (MRFF)-supported AusPathoGen Program (FSPGN000049) and by the Australian Centre for Genomic Epidemiological Microbiology (Ausgem), a collaborative research initiative between the New South Wales Department of Primary Industries and the University of Technology Sydney. B.P.H. is supported by a National Health and Medical Research Council (NHMRC) Fellowship (GNT1196103).

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Authors and Affiliations

  1. Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia

    Steven P. Djordjevic, Veronica M. Jarocki, Max L. Cummins, Ethan R. Wyrsch & Cameron J. Reid

  2. Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Sydney, New South Wales, Australia

    Steven P. Djordjevic, Veronica M. Jarocki, Max L. Cummins, Ethan R. Wyrsch & Cameron J. Reid

  3. Centre for Pathogen Genomics, University of Melbourne, Melbourne, Victoria, Australia

    Torsten Seemann & Benjamin P. Howden

  4. Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia

    Torsten Seemann, Anne E. Watt & Benjamin P. Howden

  5. UniSA STEM, University of South Australia, Adelaide, South Australia, Australia

    Barbara Drigo

  6. Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia

    Barbara Drigo & Erica Donner

  7. Cooperative Research Centre for Solving Antimicrobial Resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia

    Erica Donner

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Contributions

S.P.D., V.M.J., T.S., M.L.C., A.E.W., B.D., E.D. and B.P.H. researched the literature. S.P.D., V.M.J., T.S., M.L.C., A.E.W., E.R.W., C.J.R., E.D. and B.P.H. contributed substantially to discussions of the content. S.P.D., V.M.J., T.S., M.L.C., E.D. and B.P.H. wrote the article. S.P.D., V.M.J., T.S., A.E.W., B.D., C.J.R., E.D. and B.P.H. reviewed and/or edited the manuscript before submission.

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Djordjevic, S.P., Jarocki, V.M., Seemann, T. et al. Genomic surveillance for antimicrobial resistance — a One Health perspective. Nat Rev Genet 25, 142–157 (2024). https://doi.org/10.1038/s41576-023-00649-y

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