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Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria

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Abstract

Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of “last resort” there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.

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Acknowledgements

This work was supported in part by awards to GD through the National Institute of Allergy and Infectious Diseases (NIAID: https://www.niaid.nih.gov/), the Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD: https://www.nichd.nih.gov/), and the National Center for Complementary and Integrative Health (NCCIH: https://nccih.nih.gov/) of the National Institutes of Health (NIH) under award numbers R01AI123394, R01HD092414, and R01AT009741, respectively; the National Institute for Occupational Safety and Health (NIOSH: https://www.cdc.gov/niosh/index.htm) of the US Centers for Disease Control and Prevention (CDC) under award number R01OH011578; and the Congressionally Directed Medical Research Program (CDMRP: https://cdmrp.army.mil/prmrp/default) of the US Department of Defense (DOD) under award number W81XWH1810225. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies.

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  1. Kevin S. Blake and JooHee Choi contributed equally.

Authors and Affiliations

  1. The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA

    Kevin S. Blake, JooHee Choi & Gautam Dantas

  2. Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA

    Gautam Dantas

  3. Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA

    Gautam Dantas

  4. Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA

    Gautam Dantas

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  1. Kevin S. Blake
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Blake, K.S., Choi, J. & Dantas, G. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cell. Mol. Life Sci. 78, 2585–2606 (2021). https://doi.org/10.1007/s00018-020-03717-2

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