Community-associated quinolone-resistant and extended-spectrum beta-lactamase-producing Escherichia coli isolates are similar to clinical infection isolates by sequence type and resistome.

Escherichia coli is a public health threat capable of causing multiple types of infection, carrying a variety of antimicrobial resistance genes (ARGs), and disseminating ARGs to other microbes. Since ARG-carrying E. coli can exist as a commensal gut microbe, intestinal E. coli in community-associated (CA) members presents an under-appreciated reservoir of ARGs. We cultured 75 CA E. coli isolates from stool of 64 patients lacking inpatient healthcare exposures >24 hours in the previous 12 weeks. Remnant stool submitted to the Barnes-Jewish Hospital (BJH) microbiology laboratory for Clostridioides difficile testing was plated to MacConkey agar with ciprofloxacin and extended-spectrum beta-lactamase (ESBL) Chrome Agar to isolate resistant E. coli colonies, which were whole-genome sequenced. Isolates were compared to ESBL E. coli genomes published by Mahmud et al. (B. Mahmud, M. A. Wallace, K. A. Reske, K. Alvarado, et al., mSystems 7:e00519-22, 2022, https://doi.org/10.1128/msystems.00519-22), which were collected from bloodstream and urinary tract infections. We identified ESBL genes and quinolone resistance elements in E. coli isolates from all patients, 32 (50%) of whom had no recent antibiotic exposure. Sequence type (ST) 131 isolates carried more quinolone resistance elements but fewer ESBL genes than other STs. Eleven patients carried two distinct E. coli lineages simultaneously. CA ESBL E. coli displayed a lower diversity of beta-lactamase genes but similar rates of antibiotic resistance genes compared to ESBL E. coli reported by Mahmud et al. (https://doi.org/10.1128/msystems.00519-22). Carriage of resistance elements without recent antimicrobial exposure suggests the presence of circulating, resistant E. coli. Our results show the continually evolving resistance profile of CA E. coli, demonstrating the importance of characterizing antimicrobial resistance in the community.IMPORTANCEAntimicrobial-resistant Escherichia coli presents a substantial threat to public health, limiting treatment options and potentially horizontally transferring its resistance to other members of the gut microbiome. Resistance to quinolones and beta-lactams, specifically, hinders treatment of urinary tract and gastrointestinal infections, both commonly caused by E. coli. Tracking successful lineages, such as ST131, within the healthcare setting can inform clinicians about resistance patterns among their patients, but this work shows that other STs present an even higher antimicrobial resistance burden than ST131. In addition to monitoring multiple lineages of antimicrobial-resistant E. coli, it is necessary to identify and understand community-associated carriage of this organism, as evidenced by the increasing prevalence of community-associated ESBL E. coli carriage and our specific results showing similar resistance burdens within the clinic and community. This work presents insight into antimicrobial-resistant E. coli among those without significant healthcare exposures, providing important community-focused surveillance that is currently lacking.