Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):E11988-E11995. doi: 10.1073/pnas.1810840115.


Bystander selection-the selective pressure for resistance exerted by antibiotics on microbes that are not the target pathogen of treatment-is critical to understanding the total impact of broad-spectrum antibiotic use on pathogenic bacterial species that are often carried asymptomatically. However, to our knowledge, this effect has never been quantified. We quantify bystander selection for resistance for a range of clinically relevant antibiotic-species pairs as the proportion of all antibiotic exposures received by a species for conditions in which that species was not the causative pathogen ("proportion of bystander exposures"). Data sources include the 2010-2011 National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey, the Human Microbiome Project, and additional carriage and etiological data from existing literature. For outpatient prescribing in the United States, we find that this proportion over all included antibiotic classes is over 80% for eight of nine organisms of interest. Low proportions of bystander exposure are often associated with infrequent bacterial carriage or concentrated prescribing of a particular antibiotic for conditions caused by the species of interest. Applying our results, we roughly estimate that pneumococcal conjugate vaccination programs result in nearly the same proportional reduction in total antibiotic exposures of Streptococcus pneumoniae, Staphylococcus aureus, and Escherichia coli, despite the latter two organisms not being targeted by the vaccine. These results underscore the importance of considering antibiotic exposures of bystanders, in addition to the target pathogen, in measuring the impact of antibiotic resistance interventions.

Keywords: antibiotic resistance; microbiome; vaccines.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adolescent
  • Adult
  • Anti-Bacterial Agents / immunology
  • Anti-Bacterial Agents / pharmacology*
  • Bacteria / classification
  • Bacteria / drug effects*
  • Bacteria / immunology
  • Child
  • Child, Preschool
  • Drug Resistance, Bacterial / drug effects*
  • Drug Resistance, Bacterial / immunology
  • Escherichia coli / drug effects
  • Humans
  • Infant
  • Infant, Newborn
  • Microbial Sensitivity Tests / methods
  • Microbiota / drug effects*
  • Microbiota / immunology
  • Pneumococcal Infections
  • Pneumococcal Vaccines / immunology
  • Species Specificity
  • Staphylococcus aureus / drug effects
  • Streptococcus pneumoniae / drug effects
  • United States
  • Vaccination
  • Vaccines, Conjugate / immunology
  • Young Adult


  • Anti-Bacterial Agents
  • Pneumococcal Vaccines
  • Vaccines, Conjugate