JMIR Publications

ABSTRACT

Background:

Overuse of antibiotics contributes to antimicrobial resistance (AMR) and is a growing threat to human health worldwide. Prior work suggests a link between antimicrobial use in poultry and human AMR extraintestinal pathogenic Escherichia coli (E. coli) urinary tract infections (UTI). However, few U.S.-based studies exist, and none have comprehensively assessed both foodborne and environmental pathways using advanced molecular and spatial epidemiologic methods in a quasi-experimental design. Recently, California enacted Senate Bill 27 (SB27), which changed prior policy to require a veterinarian’s prescription for use of antibiotic drugs, and which banned antibiotic uses for disease prevention in livestock. This provided an opportunity to evaluate whether SB27 will result in a reduction in human AMR infection.

Objective:

We describe in detail the methods implemented to achieve the overarching objective of this study: to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTI.

Methods:

A summary of the overall approach and the partnerships between Columbia University, George Washington University (GWU), Johns Hopkins Bloomberg School of Public Health (JHU), Kaiser Permanente Southern California (KPSC) Research & Evaluation, the Natural Resources Defense Council, Sanger Institute at Stanford University, Sutter Health Center for Health Systems Research, University of Cambridge, and University of Oxford is presented. The collection, quality control testing, and shipment of retail meat and clinical samples are described. Retail meat (chicken, beef, turkey, and pork) was purchased from stores throughout Southern California from 2017 to 2021. After processing at KPSC it was shipped to GWU for testing. From 2016 to 2021, after clinical specimens were processed for routine clinical purposes and immediately prior to discard, those with isolation colonies of E. coli, Campylobacter, and Salmonella from KPSC members were collected and processed to be shipped for testing at GWU. Detailed methods of the isolation and testing as well as the whole genome sequencing of the meat and clinical samples at GWU are described. KPSC electronic health record (EHR) data was used to track UTI cases and AMR patterns among the cultured specimens. Similarly, Sutter Health EHR data was used to track UTI cases in its Northern California patient population.

Results:

Overall, from 2017-2021, 12,616 retail meat samples were purchased from 472 unique stores across Southern California. In addition, 31,643 positive clinical cultures were collected from KPSC members during the same study period.

Conclusions:

Here, we presented data collection methods for the study which was conducted to evaluate the impact of SB27 on downstream antibiotic resistance rates in human UTI. To date, it is one of the largest studies of its kind to be conducted. The data collected during the course of this study will be used to as the foundation for future analyses specific to the various objectives of this large body of work. Clinical Trial: N/A