Clinical setting comparative analysis of uropathogens and antibiotic resistance: a retrospective study spanning the COVID-19 pandemic

Abstract

Abstract Background Antimicrobial resistance (AMR) in uropathogens has been increasing in Australia. Many nations observed heightened AMR during the COVID-19 pandemic but is not known how this may vary across clinical settings and in nations with lower infection rates. Methods We investigated the uropathogen composition and corresponding antibiotic resistance of 775, 559 Australian isolates from community, hospitals and aged care facilities, before (2016-2019) and during the COVID-19 pandemic (2020-2022). A mathematical model was developed to predict the likelihood of resistance to currently recommended antibiotics for treating urinary tract infections (UTIs). Results Among uropathogens originating from community, hospitals, and aged care facilities, Escherichia coli accounted for 71.4%, 57.6% and 65.2%, respectively. During the COVID-19 pandemic period there was an increase in UTIs caused by E. coli across all settings. Uropathogens from aged care and hospitals frequently showed higher resistance to antibiotics compared to those isolated from the community. Interestingly, AMR among uropathogens showed a declining trend during the COVID-19 pandemic. Based on the resistance patterns of the past three years, our modelling predicted that 30%, 42.6% and 38.8% of UTIs in the community, hospitals and aged care facilities, respectively, would exhibit resistance to trimethoprim treatment as empirical therapy. In contrast, resistance to nitrofurantoin was predicted to be 14.6%, 26% and 24.1% from these three respective settings. Conclusions Empiric therapy of UTIs in Australia with trimethoprim requires evaluation due to high rates of resistance observed across clinical settings.