Uropathogens and prognosis among patients with hospital-diagnosed acute pyelonephritis: insights from a 19-year population-based cohort study

Purpose The microbial aetiologies of acute pyelonephritis (APN) may change over time. We aimed to describe long-term trends in microbiological diagnostics and pathogen distribution in patients with hospital-diagnosed APN, and to characterise clinical outcomes by pathogens. Methods We conducted a population-based, serial cross-sectional and cohort study of patients with hospital-diagnosed APN in North Denmark across three periods covering 2000-2018. National health registries were linked with microbiological data to describe temporal trends in microbiological diagnostics and pathogen distribution, and to provide a descriptive comparison of median length of stay (LOS) with interquartile range (IQR) and 30-day cumulative mortality with 95% confidence interval (CI) between Escherichia coli and non- E. coli APN. Results We identified 5338 APN episodes among 4773 patients. The proportion with urine culture increased from 75.1% in 2000-2006 to 92.9% in 2013-2018, with a concomitant increase in the proportion with a positive urine culture from 44.4% to 56.7%. The median LOS declined by 2 days across calendar periods. E. coli remained the predominant pathogen with a prevalence in the range 77.3%-81.9%. Non- E. coli APN was more common in male, older, and comorbid patients, and was characterised by longer LOS (median 5 days [IQR: 3-8] vs. 4 days [IQR: 2-6]) and higher 30-day mortality (3.7% [95% CI 2.3%-5.2%] vs. 1.0% [95% CI 0.6%-1.5%]) compared with E. coli . Conclusion Microbiological testing increased during the study period, and the pathogen distribution remained largely stable with E. coli as the predominant uropathogen. Non- E. coli infections were associated with slightly less favourable short-term outcomes.