Trends in Uropathogenic Escherichia coli Genotype and Antimicrobial Resistance from 2019-2022 in a San Francisco Public Hospital Network

Background Uropathogenic Escherichia coli (UPEC) is the predominant pathogen causing urinary tract infections (UTI) and frequently exhibits antimicrobial resistance (AMR). Amongst UTIs caused by UPEC, four genotypes – so-called pandemic sequence types (ST) – cause over 50% of infections, with ST131 particularly prone to exhibiting antimicrobial resistance. To investigate the role of pandemic sequence type 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 obtained from patients with bacteriuria who received care in a public healthcare network (N=997). Multiplex PCR was used to identify presence of UPEC pandemic sequence types 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 chi-squared testing. Multivariable logistic regression modelling 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 = <0.001) even after controlling for confounding variables (adjusted OR: 6.01, 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.