# Spatial clusters of dominant lineages of uropathogenic Escherichia coli in a community dwelling patient population

## TL;DR

The study found spatial clusters of antibiotic-resistant Escherichia coli causing urinary tract infections in a community, suggesting possible common-source outbreaks.

## Contribution

This study introduces a novel geospatial approach to identify clusters of antimicrobial-resistant uropathogenic Escherichia coli lineages in community settings.

## Key findings

- 45% of UPEC isolates were identified as pandemic ST lineages, with ST131 being the most prevalent.
- Significant spatial clusters were found for ST95, ST131, and ST69, indicating localized outbreaks.
- The findings suggest that community transmission of AMR UPEC may be influenced by spatial clustering rather than just antimicrobial use.

## Abstract

Antimicrobial resistance (AMR) is a major public health concern, especially in the clinical management of urinary tract infections (UTIs). While use of antimicrobial agents selects for AMR bacterial strains, it remains unclear if this factor alone drives the prevalence of UTIs caused by AMR uropathogenic Escherichia coli (UPEC) in community settings. Local prevalence of AMR UTIs may be largely influenced by spatial clusters of already-resistant sequence types within a community rather than by the initial selection of resistant strains by antimicrobial agents. The goal of this study is to examine geospatial clustering of UTI by common AMR UPEC ST lineages.

We collected 551 UPEC isolates from patients receiving care in a San Francisco public healthcare system from April to September 2019. Isolates underwent multiplex PCR for rapid identification of pandemic UPEC STs (ST69, ST73, ST95, ST131) and were linked with electronic health records data. We conducted Global Moran’s I and Local Moran’s I to detect spatial clusters of each pandemic ST lineage.

45% of UPEC isolates (N = 247) were identified as pandemic ST lineages. ST131 comprised 72 (29%) of the pandemic ST lineages and contributed the most multidrug resistant isolates (resistant to ≥ 3 classes of antibiotics) (N = 29). Spatial clusters of ST95, ST131 and ST69 (p < 0.001, p < 0.001, p = 0.008, respectively) were identified.

We found spatial clusters of community-onset bacteriuria caused by predominant ST lineages, suggesting common-source outbreaks. This novel approach may inform future surveillance efforts to reduce community transmission of AMR UPEC and provides the basis for future investigations of environmental risk factors for AMR UTI.

The online version contains supplementary material available at 10.1186/s12879-025-11734-4.