Spectrum of pathogens and their antimicrobial resistance in cystitis, pyelonephritis, and prostatitis

Kulchavenya E.V., Rafalskiy V.V.

1) Novosibirsk State Medical University, Ministry of Health of Russia, Novosibirsk, Russia; 2) Avicenna Clinical Hospital, Novosibirsk, Russia; 3) Institute of Medicine and Life Sciences (MedBio), Immanuel Kant Baltic Federal University, Kaliningrad, Russia

Introduction. Infectious and inflammatory diseases of the genitourinary tract account for approximately 42% of all outpatient urology cases, and disorders such as cystitis, pyelonephritis, and prostatitis are often characterized by a chronic, recurrent course. One of the key contributors to recurrent urinary tract infections is inappropriate therapy that does not take into account the local microbial spectrum and pathogen resistance profiles.
Aim. To determine the spectrum of uropathogens and their antimicrobial resistance patterns in patients with cystitis, pyelonephritis, and prostatitis.
Materials and methods. We analyzed the results of microbiological urine cultures from outpatient urology patients processed by the Invitro Laboratory between 2022 and 2024. In total, 4031 bacterial isolates were included: 2903 (72.0%) from patients with cystitis, 1017 (25.2%) from patients with pyelonephritis, and 111 (2.8%) from patients with chronic prostatitis.
Results. The structure of the microbial landscape differed by diagnosis. E. coli was the predominant pathogen in all groups, with a detection rate of 73.8–75.3% in cystitis and pyelonephritis, while in chronic prostatitis the rate was markedly lower at 53.1%. Klebsiella pneumoniae and Enterococcus faecalis were more frequently isolated in prostatitis (19.0% and 15.3%, respectively) compared with urinary infections, where their combined frequency ranged from 6.9% to 11.9%. Other pathogens (Proteus mirabilis, Streptococcus agalactiae, Enterobacter cloacae, Pseudomonas aeruginosa) accounted for 6.4% of isolates in cystitis, 7.6% in pyelonephritis, and 12.6% in prostatitis.
Antimicrobial resistance was assessed for E.coli isolates. Resistance to amoxicillin/clavulanate was 24.9% in cystitis, 31.0% in pyelonephritis, and 38.9% in prostatitis. Levofloxacin resistance was observed in approximately one third of isolates from cystitis and in about half of isolates from pyelonephritis, whereas all E.coli isolates from prostatitis cases were susceptible. Resistance to trimethoprim-sulfamethoxazole in prostatitis was approximately twice as high as in cystitis and pyelonephritis.
Conclusion. Urinary tract infections are predominantly caused by E.coli, while chronic prostatitis is associated with a more diverse spectrum of pathogens, with E.coli detected in only 53.1% of cases. Antimicrobial resistance profiles differ substantially between urinary infections and prostatitis, underscoring the importance of tailoring empirical therapy to local pathogen distribution and resistance patterns.

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About the Authors

Corresponding author: Elena V. Kulchavenya – Ph.D., MD, Professor, Department of Phthisiopulmonology, Novosibirsk State Medical University, Ministry of Health of Russia; Scientific Supervisor, Department of Urology, Avicenna Clinical Hospital, Mother and Child Group, Novosibirsk, Russia; e-mail: urotub@yandex.ru

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