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Urinary Tract Infection

Recurrent cystitis may not be repeated cystitis. A Korean urobiome study found the two look like different diseases

Conventional culture found an organism in 16.4 percent of recurrent cases. Sequencing found one in 82.4 percent — and the organisms it found were not the same ones.

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In short

In the Korean urobiome platform study comparing urine next-generation sequencing with conventional culture in symptom-free control women, women with sporadic uncomplicated cystitis and women with recurrent uncomplicated cystitis, all sampled by transurethral catheterisation, sequencing detected a urinary microbiome in 83.3 percent of controls with Lactobacillus and Prevotella most abundant, and was far more sensitive than culture in both disease groups (91.2 against 32.4 percent in sporadic cystitis and 82.4 against 16.4 percent in recurrent cystitis) — with distinct organism profiles in each group leading the authors to conclude that sporadic and recurrent uncomplicated cystitis might represent entirely separate pathological processes.

Key takeaways

  • Urine next-generation sequencing was compared with conventional urine culture in control women and in women with sporadic and recurrent uncomplicated cystitis, sampled by transurethral catheterisation.
  • A urinary microbiome was detected by sequencing in 83.3 percent of symptom-free controls, with Lactobacillus and Prevotella the most abundant genera.
  • In sporadic cystitis, sequencing detected an organism in 91.2 percent of cases against 32.4 percent by culture.
  • In recurrent cystitis, sequencing detected an organism in 82.4 percent against 16.4 percent by culture.
  • Sporadic cases additionally showed Enterobacterales, Prevotella and Escherichia or Shigella.
  • Recurrent cases showed Lactobacillus, Prevotella, Enterobacterales, Escherichia or Shigella, and Propionibacterium.
  • The authors conclude that sporadic and recurrent uncomplicated cystitis might be entirely separate pathological processes rather than the same illness repeating.

Two assumptions sit underneath how recurrent cystitis is treated. The first is that healthy urine is sterile. The second is that recurrent cystitis is sporadic cystitis happening again. This study undermines both, and the second one has consequences for treatment.

Urine is not sterile

Sequencing found a urinary microbiome in 83.3 percent of women with no symptoms and normal urinalysis, dominated by Lactobacillus and Prevotella. The sterility assumption was never a finding; it was an artefact of culture, which grows the organisms it is set up to grow and reports nothing about the rest.

82.4% vs 16.4%

detection rate in recurrent cystitis — urine sequencing against conventional cultureYoo JJ et al., Investigative and Clinical Urology, 2024

That gap describes a familiar clinical situation from the laboratory end. A woman with burning, urgency and frequency is told her culture is negative, and is left either untreated or treated blind. On this data the culture was negative in more than four-fifths of recurrent cases in which sequencing found an organism.

The claim that matters

The organism profiles differed between the groups. Sporadic cases showed Enterobacterales, Prevotella and Escherichia or Shigella added to the background. Recurrent cases showed those plus Lactobacillus and Propionibacterium — a different community, not a heavier dose of the same one.

What the design cannot carry

This is a retrospective review of patients who happened to have had both tests, which selects for cases where a clinician was already dissatisfied with the culture result. Sequencing detects genetic material and cannot distinguish a live organism from a dead one, or an invader from a resident. And the study itself notes that patterns differed by menopausal status and by whether antibiotics or probiotics had been taken before sampling, which are large enough influences to account for some of the group differences on their own.

Set beside the national resistance data — where recurrent cystitis carried 59.8 percent fluoroquinolone resistance, the highest of any subgroup — the two findings converge on the same patient. The women in whom antibiotics work least well are also the women whose infection may not be the thing antibiotics were designed to treat.

Sources

  1. 1

    Yoo JJ, Shin HB, Moon JE, Lee SH, Jeong H, Yang HJ, Kim WB, Lee KW, Kim JH, Kim YH

    Korean urobiome platform (KUROM) study for acute uncomplicated sporadic versus recurrent cystitis in women: Clinical significance

    Investigative and Clinical Urology 2024;65(4):378-390

    doi:10.4111/icu.20230369 · PMID:38978218

    https://doi.org/10.4111/icu.20230369
  2. 2

    Yu SH, Jung SI, Lee SJ, Oh MM, Choi JB, Choi CI, Kim YJ, Park DJ, Bae S, Min SK

    Nationwide surveillance of antimicrobial resistance for uncomplicated cystitis in 2023: Conducted by the Korean Association of Urogenital Tract Infection and Inflammation

    Investigative and Clinical Urology 2025;66(2):161-171

    doi:10.4111/icu.20240302 · PMID:40047130

    https://doi.org/10.4111/icu.20240302