Does Antibiotic Resistance Evolve in Hospitals?

TL;DR

This study challenges the assumption that antibiotic resistance evolves primarily in hospitals by analyzing bacterial resistance data and introducing a statistical test, NERD, which found limited hospital influence on resistance trends.

Contribution

The paper introduces the NERD statistical hypothesis test and a Hospital Transmission Model to assess resistance evolution, providing a new tool for hospital infection control analysis.

Findings

Most antibiotics showed no significant hospital influence on resistance evolution.

The NERD method effectively detects resistance trends and outbreaks.

Ceftazidime resistance decreased significantly after analysis.

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 upon 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.