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InfectionsStandardLast updated 29 May 2026

Infections & Inflammation

Cystitis is infection confined to the bladder mucosa. This tab covers the uncomplicated and complicated forms, cystitis in men, and the special problems of unresolved and recurrent infection, asymptomatic bacteriuria, pyocystis, and infected urachal cysts.

Risk Factors

  • Reduced urine flow — outflow obstruction (BPH, prostate cancer, urethral stricture, foreign body/calculus), neurogenic bladder, inadequate fluid intake (dehydration).
  • Promote colonisation — sexual activity (increased inoculation), spermicide (increased binding), estrogen depletion (increased binding), antibiotic use (depletes indigenous flora).
  • Facilitate ascent — catheterisation, urinary incontinence, faecal incontinence.
  • Residual urine with ischaemia of the bladder wall.

Uncomplicated Acute Bacterial Cystitis

Diagnosis requires both laboratory confirmation of significant bacteriuria and acute-onset lower urinary tract symptoms.

Pathogens

  • E. coli causes 75–90% of acute cystitis in young women.
  • S. saprophyticus (a skin commensal) is second at 10–20%; Klebsiella, Proteus, and Enterococcus are less common.
  • In men, E. coli and other Enterobacteriaceae predominate. Sexual transmission of uropathogens is suggested by finding identical E. coli in the bowel and urinary flora of sexual partners.

Diagnosis and Evaluation

The differential diagnosis is broad: interstitial cystitis/bladder pain syndrome, overactive bladder, urinary calculi, bacterial or fungal vaginitis, STI urethritis, vulvar dermatitis, non-infectious vulvovestibulitis, vulvodynia, hypertonic pelvic-floor dysfunction, genitourinary syndrome of menopause, and (less commonly) bladder CIS.

  • Symptoms — variable, usually dysuria, frequency, and/or urgency; suprapubic pain, incontinence, haematuria, or foul-smelling urine may develop. In older adults symptoms are less clear, and nonspecific chronic complaints (cloudy urine, vaginal dryness/burning, pelvic discomfort) are often misread as UTI. Acute-onset dysuria with new or worsening storage symptoms remains a reliable criterion in older women, both community-dwelling and in long-term care. By definition acute cystitis is a superficial mucosal infection, so fever, chills, and signs of dissemination are absent.
  • Examination — usually no diagnostic findings; some have suprapubic tenderness. The pelvic exam looks for prolapse, urethral tenderness or diverticulum, Skene's-gland or other vulvar/vaginal cysts, vaginitis/dermatitis/herpes/atrophy, and pelvic-floor tone, tenderness, and trigger points.
  • Labs — urinalysis gives the presumptive diagnosis (microscopic pyuria, bacteriuria, occasionally haematuria); urine culture is definitive. The >10⁵ CFU/mL threshold is arbitrary — useful to distinguish bacteriuria from contamination in asymptomatic premenopausal women, but a lower 10² CFU/mL threshold is appropriate in symptomatic patients. Suspect contamination when there are mixed cultures (≥2 organisms), low counts (<10³ CFU/mL) of a pathogen in an asymptomatic patient, or growth of normal vaginal flora (lactobacilli, group B streptococci, corynebacteria, non-saprophyticus coagulase-negative staphylococci) — these are not treated. Epithelial cells or mucus on urinalysis also suggest contamination; obtain a catheterised specimen when suspicion is high. Specimens should not sit at room temperature for >30 minutes.

Management

  • Preferred first-line: fosfomycin 3 g PO single dose; nitrofurantoin 100 mg PO BID ×5 days; or TMP-SMX DS 1 tab PO BID ×3 days.
  • Alternative (when resistant to the above): ciprofloxacin 250 mg BID ×3 days. Fluoroquinolones should not be first-line for uncomplicated cystitis.
  • About 90% of women are asymptomatic within 72 hours. No follow-up visit or culture is needed in young women who are asymptomatic after therapy; a follow-up visit, urinalysis, and culture are recommended in older women, those with risk factors, and men.
  • Urologic evaluation is unnecessary in women and usually unnecessary in young men who respond — but UTIs in most men should be considered complicated until proven otherwise. If there is no response, pursue the microbiologic and urologic work-up for unresolved/complicated UTI.

Complicated Cystitis in Females

A UTI is complicated if any one of five features is present: an anatomic/functional abnormality, urinary instrumentation or a foreign body, systemic disease (renal insufficiency, diabetes, immunodeficiency, transplant), pregnancy, or multidrug-resistant bacteria.

  • Evaluation — urine culture is mandatory to identify the organism and susceptibilities; review prior cultures to guide empiric selection.
  • Management (outpatient candidates): oral ciprofloxacin 500 mg BID ×7 days; a once-daily fluoroquinolone (ciprofloxacin 1000 mg ER ×7 days or levofloxacin 750 mg ×5 days); or oral TMP-SMX DS BID ×14 days (not for Enterococcus or Pseudomonas).

Cystitis in Males

  • Evaluation — urine culture is mandatory. Complicated UTI in an older male warrants urologic evaluation (CT urogram and cystoscopy) because of the high rate of associated abnormalities — obstruction from urethral or ureteral stricture, tumour, or stones; ≈50% of males with UTIs have a significant abnormality. Uncomplicated cystitis in a young, sexually active male may need nothing beyond a follow-up urine culture.
  • Management — preferred: TMP-SMX DS (160/800 mg) 1 tab PO BID; alternatives levofloxacin 500 mg daily, ciprofloxacin 500 mg BID, or ciprofloxacin ER 1000 mg daily. Treat for 7–14 days (optimal duration unknown).

Unresolved UTI

An unresolved UTI means initial therapy failed to clear symptoms and/or bacterial growth. If symptoms do not resolve by the end of treatment or recur shortly after, obtain urinalysis and culture with susceptibilities; if symptoms are significant, start empirical fluoroquinolone pending results.

Causes, in descending order of importance:

  • Pre-existing bacterial resistance to the chosen drug.
  • Development of resistance from initially susceptible bacteria.
  • Bacteriuria from two species with mutually exclusive susceptibilities.
  • Rapid reinfection with a new, resistant species during initial therapy.
  • Renal failure (cannot deliver adequate antibiotic concentration to the tract).
  • Papillary necrosis from analgesic abuse (impaired medullary concentrating ability dilutes the antibiotic).
  • Staghorn calculi (large bacterial mass).
  • Self-inflicted infection or deception about taking the drug (a Munchausen variant).

The first four (resistance-associated) need no further evaluation. If re-culture shows the bacteria are sensitive to the drug the patient is taking, perform renal-function and radiologic evaluation for a renal or urinary-tract abnormality.

Management: assume resistance and choose an antibiotic different from the original; fluoroquinolones cover most cases — give for 7 days, adjust to susceptibilities, and culture during and 7 days after therapy.

Recurrent UTI

Recurrent UTI is caused by either bacterial persistence (re-emergence from a site within the tract) or reinfection (new bacteria from outside). The pattern distinguishes them: persistence is the same organism at close intervals, whereas reinfection is different species at varying or long intervals. This distinction is critical — persistence is usually curable by finding and surgically removing/correcting the focus, whereas reinfection (typically in women) usually has no alterable abnormality and needs long-term medical management. Recurrence probability rises with the number of prior infections and falls in inverse proportion to the interval between the first and second.

Bacterial persistence — after the urine shows no growth for several days off antibiotics, recurrence with the same organism arises from a focus shielded from high urinary drug concentrations. Correctable causes include:

  • Infection stones; chronic bacterial prostatitis; foreign bodies.
  • Urethral diverticula and infected periurethral glands.
  • Unilateral infected atrophic kidney; ureteral duplication and ectopic ureters; unilateral medullary sponge kidney.
  • Non-refluxing, normal-appearing infected ureteral stumps after nephrectomy.
  • Infected urachal cysts; infected communicating calyceal cysts.
  • Papillary necrosis; perivesical abscess with fistula to the bladder.

Reinfection — different species or long intervals; most often in females via ascending colonisation from bowel flora, while reinfection in men is often associated with a urinary-tract abnormality. Consider a vesicoenteric or vesicovaginal fistula with any history of pneumaturia, faecaluria, diverticulitis, obstipation, prior pelvic surgery, or radiation. Evaluation is individualised.

Asymptomatic Bacteriuria

Definition: bacteriuria of any magnitude without symptoms.

  • Do not routinely screen or treat — there is no evidence that treatment improves outcomes.
  • Screen and treat in two settings: pregnant women, and patients undergoing elective urologic surgery.
  • Neonatal candiduria (not strictly bacteriuria) should be treated even if asymptomatic — with parenteral fluconazole.
  • Struvite stones: routine treatment of urease-producing bacteriuria, absent UTI symptoms or documented stones, is not recommended — there is no clear evidence it prevents struvite stones (urease producers: Proteus, Pseudomonas, Klebsiella, Mycoplasma, Staphylococcus). In selected patients with recurrent struvite stones, however, screening and treating urease-producing bacteriuria may be indicated when other measures have failed.

Pyocystis and Urachal Cyst Infection

Pyocystis occurs in ≈20% of patients after supravesical diversion (the defunctionalised bladder fills with purulent material). Patients have a malodorous discharge and may become septic. Management is conservative with routine bladder irrigations; if that fails, a vaginal vesicostomy (creation of a large vesicovaginal fistula) effectively prevents pyocystis in women.

Urachal cyst infection — the cyst contains desquamated epithelial cells that can become infected; Staphylococcus aureus is the most common organism.