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Does Antibiotic Resistance Evolve in Hospitals?

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Abstract

Nosocomial outbreaks of bacteria are well documented. Based on these incidents, and the heavy usage of antibiotics in hospitals, it has been assumed that antibiotic resistance evolves in hospital environments. To test this assumption, we studied resistance phenotypes of bacteria collected from patient isolates at a community hospital over a 2.5-year period. A graphical model analysis shows no association between resistance and patient information other than time of arrival. This allows us to focus on time-course data. We introduce a hospital transmission model, based on negative binomial delay. Our main contribution is a statistical hypothesis test called the Nosocomial Evolution of Resistance Detector (NERD). It calculates the significance of resistance trends occurring in a hospital. It can inform hospital staff about the effects of various practices and interventions, can help detect clonal outbreaks, and is available as an R package. We applied the NERD method to each of the 16 antibiotics in the study via 16 hypothesis tests. For 13 of the antibiotics, we found that the hospital environment had no significant effect on the evolution of resistance; the hospital is merely a piece of the larger picture. The p-values obtained for the other three antibiotics (cefepime, ceftazidime, and gentamicin) indicate that particular care should be taken in hospital practices with these antibiotics. One of the three, ceftazidime, was significant after accounting for multiple hypotheses, indicating a trend of decreased resistance for this drug.

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Acknowledgements

We thank Dignity Health Mercy Medical Center and especially Robert Salcido, Glenn Bruss, and Robert Streeter for providing clinical data and strains. We thank Joe Kileel for help organizing the data and defining the final data set. We are grateful to Lior Pachter for very helpful comments on an earlier version of this paper. This study was funded by CITRIS Seed Grant #: 2015-324. Anna Seigal and Bernd Sturmfels were supported by the National Science Foundation (DMS-1419018).

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Authors and Affiliations

  1. Department of Mathematics, University of California, Berkeley, Berkeley, CA, USA

    Anna Seigal & Bernd Sturmfels

  2. School of Natural Sciences, University of California, Merced, Merced, CA, USA

    Portia Mira & Miriam Barlow

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  1. Anna Seigal
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  2. Portia Mira
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  3. Bernd Sturmfels
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Correspondence to Anna Seigal.

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Seigal, A., Mira, P., Sturmfels, B. et al. Does Antibiotic Resistance Evolve in Hospitals?. Bull Math Biol 79, 191–208 (2017). https://doi.org/10.1007/s11538-016-0232-7

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