Trends in Uropathogenic Escherichia coli Genotype and Antimicrobial Resistance From 2019 to 2022 in a San Francisco Public Hospital Network.

Background: Uropathogenic Escherichia coli (UPEC) is the predominant pathogen causing urinary tract infections and frequently exhibits antimicrobial resistance (AMR). Among urinary tract infections caused by UPEC, 4 genotypes-so-called pandemic sequence types (STs)-cause >50% of infections, with ST131 particularly prone to exhibiting AMR. To investigate the role of pandemic ST prevalence in driving AMR, we prospectively collected and genotyped UPEC isolated from patient urine samples.

Methods: Over separate periods in 2019 and 2022, we collected and analyzed community-onset UPEC samples from patients with bacteriuria who received care in a public health care network (N = 997). Multiplex polymerase chain reaction was used to identify the presence of UPEC pandemic STs, including ST131, while patient characteristics and antibiotic susceptibilities of the UPEC samples were collected from electronic medical records. Differences in pandemic ST prevalence and AMR between years were assessed through χ² testing. Multivariable logistic regression modeling was performed for odds of AMR.

Results: Pandemic ST prevalence remained stable between collection years, while resistance to any antimicrobial and trimethoprim-sulfamethoxazole generally decreased. However, within pandemic ST131, fluoroquinolone resistance increased significantly (45.6% to 76.8%, P < .001) even after controlling for confounding variables (adjusted odds ratio, 6.01; 95% CI, 2.41-15.01).

Conclusions: Steady ST prevalence and stable or decreased AMR prevalence masked significant increased fluoroquinolone resistance with ST131, which may represent unmeasured patient characteristics, bacterial factors, or new exposure to resistant ST131 in the community. Antimicrobial surveillance of UPEC at the ST level may be important for monitoring otherwise unnoticed AMR trends.