Changes in Uropathogen Distribution in Relation to the COVID-19 Pandemic Timeline

Recent research has shown that the COVID-19 virus changes the gastrointestinal microbiome as it is a bacteriophage [1], leading to immune dysregulation and bowel dysbiosis [2]. This creates an environment where opportunistic pathogens thrive while beneficial bowel flora diminish [3]. There is an association among the bowel, vaginal and bladder microbiomes where the bacteria from the bowel are found in the bladder [4]. Urinary tract infections (UTIs) are among the most common bacterial infections, typically caused by Escherichia coli (E. coli), Enterococcus faecalis (E. faecalis), Klebsiella spp, and Proteus mirabilis (P. mirabilis) in women [5]. Changes in the bowel microbiome lead to changes in the bladder microbiome [6]. We aimed to evaluate whether the composition of observed uropathogens differed across the different phases of the COVID-19 pandemic.

This retrospective study analysed positive urine cultures from women before, during and after the COVID-19 pandemic. The leading three causative uropathogens with a count over 10³ cfu/mL were reported.

There were 5543 positive cultures with pre-COVID-19 from 1 January 2019 to 30 January 2020, n = 204, during from 1 February 2020 to 4 May 2023, n = 2518, and after from 5 May 2023 to 1 February 2025, n = 2821. In total, 10,456 bacteria were identified. After May 2023, E. coli prevalence dropped from 27 to 21%, and Pseudomonas spp decreased from 6 to 2% (p value < 0.001). In contrast, Klebsiella spp incidence rose from 8 to 12%. Corynebacterium spp (p < 0.05) and Acinetobacter spp (p < 0.001) were increasingly isolated in symptomatic UTIs after May 2023.

The bacterial organisms found in urinary tract infections detected before and subsequent to the onset of COVID-19 have changed. This may reflect an interaction between changes in the bowel microbiome and pathological urinary tract infections.