Urinary tract infections span the trivial to the life-threatening. The clinical skill is classifying the infection correctly (uncomplicated vs.
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Urinary tract
infections span the trivial to the life-threatening. The clinical
skill is classifying the infection correctly (uncomplicated vs.
complicated; cystitis vs. pyelonephritis; recurrent vs. persistent),
treating with the narrowest effective agent, recognizing infections
that need drainage, and — most importantly at New Jersey Urology —
knowing when NOT to give an antibiotic at all.
6.1 Classification and microbiology
Type
Definition
Notes
Uncomplicated cystitis
Bladder infection in a healthy, non-pregnant, premenopausal woman
with a normal tract
Short-course oral antibiotics; culture not always required if the
story is classic
Complicated UTI
Any UTI with a structural/functional abnormality, catheter,
stone, obstruction, immunocompromise, pregnancy, recent
instrumentation — or male sex (all male UTIs are complicated)
Culture-directed; longer courses; image if obstruction is
suspected
Culture; consider imaging; admit if septic, obstructed, pregnant,
or unable to tolerate oral intake
Asymptomatic bacteriuria
Positive culture WITHOUT symptoms
Do NOT treat — except in pregnancy or before a urologic
procedure that will traumatize the mucosa
Recurrent UTI (rUTI)
≥ 2 culture-proven infections in 6 months, or ≥ 3 in 12
months
See our practice Beyond-Antibiotics protocol (6.4)
Microbiology
— E. coli causes 75–90% of uncomplicated UTIs. Others:
Klebsiella, Proteus (urease-producing → struvite stones and
alkaline urine), Enterococcus, Staphylococcus saprophyticus (young
women; nitrite-negative), and Pseudomonas (catheters,
instrumentation, prior antibiotics). Candida in the urine of a
catheterized patient is almost always colonization — remove or
change the catheter, do not reflexively treat.
6.2 Empiric treatment of uncomplicated cystitis
Agent
Regimen
Notes
Nitrofurantoin
100 mg BID x 5 days
Excellent bladder concentration; minimal collateral damage. Avoid
if eGFR < 30 or if pyelonephritis is suspected (no tissue
penetration)
TMP-SMX
1 DS tablet BID x 3 days
Use if local resistance < ~20% and no sulfa allergy; check
interactions (warfarin, potassium)
Fosfomycin
3 g single dose
Convenient single dose; somewhat lower efficacy; useful for
resistant organisms
Fluoroquinolones
Reserve
Save for pyelonephritis/complicated cases — resistance plus
tendon, aortic, neuropsychiatric, and dysglycemia warnings
Beta-lactams (cefpodoxime, amox-clav)
5–7 days
Second-line; inferior efficacy to the above
Antibiotic stewardship
Always de-escalate to
culture and sensitivities when they return. Re-check the culture
you sent — do not fire and forget.
Do NOT treat asymptomatic
bacteriuria (except pregnancy or pre-procedure) — it drives
resistance and C. difficile without benefit, and it does not
prevent symptomatic infection.
A positive catheter urine
culture in an asymptomatic patient is colonization, not
infection. Every long-term catheter is colonized. Cloudy, smelly
urine is NOT an indication to treat.
Pyuria alone is not an indication to treat.
6.3 Pyelonephritis
Diagnose:
fever, chills, flank pain, CVA tenderness, often
nausea/vomiting; pyuria and bacteriuria. Always obtain a urine
culture; obtain blood cultures if the patient is ill.
Image
when: the patient is septic, has a known stone or prior
obstruction, has a solitary kidney, is diabetic or
immunocompromised, or fails to improve after 48–72 hours of
appropriate antibiotics. Non-contrast CT to exclude an obstructing
stone; contrast CT to look for abscess or emphysematous
pyelonephritis.
Treat:
outpatient oral therapy (fluoroquinolone 5–7 days, or
culture-directed) for the stable patient who can eat and drink;
admit and give IV therapy for sepsis, pregnancy, intractable
vomiting, or obstruction.
The two
things that turn this into an emergency: obstruction (drain it —
Chapter 2) and emphysematous pyelonephritis (gas within the renal
parenchyma, usually in poorly controlled diabetics — a
necrotizing, life-threatening infection requiring drainage,
aggressive resuscitation, and sometimes nephrectomy).
Renal/perinephric
abscess: suspect when fever persists past 72 hours of
appropriate antibiotics. Drain percutaneously if > 3–5 cm.
6.4 Recurrent UTI — the New Jersey Urology
“Beyond Antibiotics” protocol
Recurrent UTI (≥
2 culture-proven infections in 6 months or ≥ 3 in 12 months) is one
of the areas where New Jersey Urology practices deliberately
differently from the reflexive-antibiotic norm. Our position: for
recurrent UTIs, antibiotics are NOT the solution. Repeated courses
breed resistance, disrupt the gut and vaginal microbiome (C.
difficile, yeast), and never reach the bacteria that hide in biofilms
and inside bladder-wall cells — which is exactly why symptoms come
back days after finishing a prescription. We break the cycle by
attacking bacteria locally and restoring the bladder's natural
defenses.
Confirm it is actually an infection first
Bacteriuria is not
infection. Do NOT treat asymptomatic bacteriuria (except in
pregnancy or before a mucosa-traumatizing procedure).
Cloudy or strong-smelling
urine without true symptoms (dysuria, urgency/frequency,
suprapubic/flank pain, fever) is not a UTI — counsel patients
on this before reaching for a prescription.
Confirm each true episode
with a culture so we treat the right thing, the few times
antibiotics are genuinely warranted (symptomatic UTI, fever ≥
100.4°F/chills, pyelonephritis, pregnancy, pre-op).
Distinguish RE-infection (a different organism, or the
same one after a symptom-free interval — the usual pattern)
from PERSISTENCE (the same organism, never cleared — which
implies a nidus: stone, foreign body, fistula, diverticulum —
and demands imaging and cystoscopy).
The core our practice regimen — four things, not
supplements
Our recurrent-UTI
protocol is deliberately focused: Hiprex, vaginal estrogen (Estrace)
for post-menopausal women, reduced sugar, and clean intermittent
catheterization with daily bladder irrigation. We do NOT rely on
D-mannose, cranberry, probiotics, or other over-the-counter
supplements — the evidence does not justify them, and they distract
from what works.
Pillar
What we do
Why it works
Hiprex (methenamine hippurate)
1 g twice daily, taken with food; add vitamin C 500 mg daily to
acidify the urine (this activates Hiprex — it is not a
stand-alone supplement). Caution/avoid in significant renal
impairment — check kidney function first.
In acidic urine (pH < 6) methenamine converts to formaldehyde,
which kills bacteria in the bladder with NO systemic antibiotic
exposure and NO resistance.
Vaginal estrogen (Estrace) — women
For post-menopausal women, low-dose vaginal estradiol cream,
typically 2–3×/week after a loading period (full benefit in
4–12 weeks).
Restores vaginal pH and protective lactobacilli, thickens
urethral/vaginal tissue, and reduces E. coli colonization.
Minimal systemic absorption (FDA removed the boxed warning). See
Chapter 22.
Reduce sugar
Cut dietary sugar and sugary drinks (including cranberry juice
cocktails); manage weight.
Lowers the substrate that feeds bacterial growth and supports
healthier metabolic and bladder function.
CIC with daily bladder irrigation
Clean intermittent self-catheterization with a daily irrigation
of ~300 cc of sterile or distilled water.
Mechanically flushes bacteria, mucus, and debris and disrupts
biofilm on the bladder wall — a physical reset antibiotics
cannot achieve. Especially valuable when emptying is incomplete.
Alongside the
four pillars, always check a post-void residual and fix incomplete
emptying (bladder-outlet obstruction / prostate enlargement) —
retained urine breeds bacteria. Address constipation, and counsel on
post-coital voiding and avoiding spermicide/diaphragm use, which are
genuine modifiable risk factors.
Resistant cases and when to look inside
Intravesical antibiotic
irrigation (gentamicin): for the most resistant infections,
instilling antibiotic directly into the bladder achieves high
local concentration that penetrates biofilm — without systemic
exposure or systemic toxicity.
Cystoscopy (often under
anesthesia) + upper-tract imaging/urodynamics: for rUTI despite
prevention, UTI-type symptoms with repeatedly negative cultures,
hematuria, or new-onset recurrent infections over age 50 (rule
out stone, foreign body, diverticulum, stricture, fistula, IC, or
malignancy). A normal exam is reassuring and supports continued
conservative management.
Think anatomically when the SAME organism keeps returning:
that is persistence, and it means a nidus — an infected stone,
a retained stent, a bladder diverticulum, a urachal remnant, or a
fistula (pneumaturia or fecaluria = colovesical fistula until
proven otherwise).
The one-line version for patients
We prevent recurrent UTIs with Hiprex, vaginal estrogen, less
sugar, and daily catheter irrigation with sterile/distilled water
— not antibiotics and not a cabinet of supplements — and we
save antibiotics for the rare true, symptomatic infection.
6.5 Prostatitis / male pelvic pain
Category (NIH)
Features
Management
Acute bacterial prostatitis
Acutely ill: fever, chills, dysuria, pelvic/perineal pain, an
exquisitely tender, boggy prostate, possible retention
Prompt antibiotics with good prostate penetration
(fluoroquinolone or TMP-SMX; IV if septic) for 2–4 weeks; avoid
vigorous prostate massage (can precipitate bacteremia); watch for
abscess and sepsis. If retention, prefer a suprapubic tube over
repeated urethral instrumentation
Chronic bacterial prostatitis
Recurrent UTIs with the SAME organism; the prostate is a
reservoir
By far the most common (> 90%). Chronic pelvic pain WITHOUT
infection; IIIa inflammatory, IIIb non-inflammatory
Multimodal — antibiotics generally do NOT help. Use the UPOINT
approach: alpha-blockers, pelvic-floor physical therapy,
neuromodulators (amitriptyline, gabapentin), stress/cognitive
therapy, and lifestyle. See Chapter 27
IV — Asymptomatic inflammatory
Incidental (e.g., found on biopsy or in a semen analysis)
No treatment
Acute bacterial prostatitis cautions
Avoid aggressive prostatic
massage in suspected acute bacterial prostatitis — it can
precipitate bacteremia.
Consider a prostatic abscess
if there is no improvement after 48–72 hours on appropriate
antibiotics — image (transrectal ultrasound or CT) and drain.
PSA is often markedly
elevated during acute prostatitis. Do NOT check it, and do not
act on one drawn during the illness — wait at least 4–6 weeks
after resolution.
Do not label a man with chronic pelvic pain as “chronic
prostatitis” and cycle him through antibiotics. That is
category III and antibiotics are not the answer (Chapter 27).
Clinical Pathway
Click any node to expand
Urinary infections run from trivial to life-threatening. The skill is classifying the infection correctly, treating with the narrowest effective agent, recognizing what needs drainage, and — most importantly at New Jersey Urology — knowing when NOT to give an antibiotic at all.
Classify first, then pick the narrowest agent — and decide whether this patient needs an antibiotic at all.
Select a box to open its teaching details.
The five categories
Uncomplicated cystitis — bladder infection in a healthy, non-pregnant, premenopausal woman with a normal tract
Complicated UTI — any UTI with a structural/functional abnormality, catheter, stone, obstruction, immunocompromise, pregnancy, recent instrumentation — or male sex (all male UTIs are complicated)
Candida in the urine of a catheterized patient is almost always colonization — remove or change the catheter, do not reflexively treat.
Ch 6.1 — microbiology
Culture rules by category
Uncomplicated cystitis — culture not always required if the story is classic
Complicated UTI — culture-directed, longer courses; image if obstruction is suspected
Pyelonephritis — always culture; blood cultures if the patient is ill
Ch 6.1 — classification
Empiric agent for uncomplicated cystitis
Dosing
Nitrofurantoin 100 mg BID x 5 days
Do not use if
eGFR < 30
Pyelonephritis is suspected — no tissue penetration
Ch 6.2
Dosing
TMP-SMX 1 DS tablet BID x 3 days
Check first
Local resistance < ~20%
No sulfa allergy
Interactions — warfarin, potassium
Ch 6.2
Dosing
Fosfomycin 3 g single dose
Second-line beta-lactams
Cefpodoxime or amox-clav for 5–7 days — second-line, inferior efficacy to the agents above
Ch 6.2
Why we reserve them
Resistance
Tendon warnings
Aortic warnings
Neuropsychiatric warnings
Dysglycemia warnings
Ch 6.2
Stewardship rules
Always de-escalate to culture and sensitivities — do not fire and forget
Do NOT treat asymptomatic bacteriuria — it drives resistance and C. difficile without benefit, and it does not prevent symptomatic infection
A positive catheter urine culture in an asymptomatic patient is colonization, not infection. Every long-term catheter is colonized
The only exceptions to "don't treat asymptomatic bacteriuria"
Pregnancy
Before a urologic procedure that will traumatize the mucosa
Ch 6.2 — antibiotic stewardship
Diagnose, decide who needs imaging, decide who needs admission — and never miss the two emergencies.
Select a box to open its teaching details.
Diagnostic features
Fever, chills, flank pain, CVA tenderness
Often nausea/vomiting
Pyuria and bacteriuria
Ch 6.3
Orders
Urine culture — always
Blood cultures if the patient is ill
Ch 6.3
Image when
Septic
Known stone or prior obstruction
Solitary kidney
Diabetic or immunocompromised
Fails to improve after 48–72 hours of appropriate antibiotics
Which study
Non-contrast CT — exclude an obstructing stone
Contrast CT — look for abscess or emphysematous pyelonephritis
Ch 6.3
Outpatient or admit?
Regimen
Fluoroquinolone 5–7 days, or culture-directed therapy
Pitfall
Nitrofurantoin has no tissue penetration — it does not treat pyelonephritis
Ch 6.3
Admission triggers
Sepsis
Pregnancy
Intractable vomiting
Obstruction
Ch 6.3
Time-critical
What to do
Obstruction is one of the two things that turn pyelonephritis into an emergency. Drain it — see Chapter 2.
Ch 6.3 — the two emergencies
Time-critical
Why this is different
A necrotizing, life-threatening infection requiring drainage, aggressive resuscitation, and sometimes nephrectomy.
Ch 6.3 — the two emergencies
Action
Suspect abscess when fever persists past 72 hours of appropriate antibiotics
Drain percutaneously if > 3–5 cm
Ch 6.3 — abscess
The New Jersey Urology "Beyond Antibiotics" protocol. Our position: for recurrent UTIs, antibiotics are NOT the solution.
Select a box to open its teaching details.
Why antibiotics fail here
Repeated courses breed resistance, disrupt the gut and vaginal microbiome (C. difficile, yeast), and never reach the bacteria that hide in biofilms and inside bladder-wall cells — which is exactly why symptoms come back days after finishing a prescription. We break the cycle by attacking bacteria locally and restoring the bladder's natural defenses.
Ch 6.4
Local policy
Our rules
Do NOT treat asymptomatic bacteriuria — except in pregnancy or before a mucosa-traumatizing procedure
Cloudy or strong-smelling urine without true symptoms (dysuria, urgency/frequency, suprapubic/flank pain, fever) is not a UTI — counsel patients on this before reaching for a prescription
Confirm each true episode with a culture
When antibiotics ARE genuinely warranted
Symptomatic UTI
Fever ≥ 100.4°F / chills
Pyelonephritis
Pregnancy
Pre-op
Ch 6.4 — confirm it is actually an infection
Re-infection or persistence?
What it means
Re-infection is the usual pattern and is what the prevention protocol is built for.
Ch 6.4
Think anatomically
Infected stone
Retained stent / foreign body
Bladder diverticulum
Urachal remnant
Fistula — pneumaturia or fecaluria = colovesical fistula until proven otherwise
Ch 6.4 — resistant cases
Local policy
Dosing
Hiprex (methenamine hippurate) 1 g twice daily, taken with food
Add vitamin C 500 mg daily to acidify the urine — this activates Hiprex; it is not a stand-alone supplement
Why it works
In acidic urine (pH < 6) methenamine converts to formaldehyde, which kills bacteria in the bladder with NO systemic antibiotic exposure and NO resistance.
Caution
Caution/avoid in significant renal impairment — check kidney function first
Ch 6.4 — the core our practice regimen
Local policy
How we use it
Low-dose vaginal estradiol cream, typically 2–3×/week after a loading period
Full benefit in 4–12 weeks — set that expectation
Why it works
Restores vaginal pH and protective lactobacilli, thickens urethral/vaginal tissue, and reduces E. coli colonization. Minimal systemic absorption — the FDA removed the boxed warning. See Chapter 22.
Ch 6.4 — the core our practice regimen
Local policy
Why it works
Lowers the substrate that feeds bacterial growth and supports healthier metabolic and bladder function.
Ch 6.4 — the core our practice regimen
Local policy
The regimen
Clean intermittent self-catheterization with a daily irrigation of ~300 cc of sterile or distilled water
Why it works
Mechanically flushes bacteria, mucus, and debris and disrupts biofilm on the bladder wall — a physical reset antibiotics cannot achieve. Especially valuable when emptying is incomplete.
Ch 6.4 — the core our practice regimen
Local policy
Our position
We do NOT rely on D-mannose, cranberry, probiotics, or other over-the-counter supplements — the evidence does not justify them, and they distract from what works.
The one-line version for patients
We prevent recurrent UTIs with Hiprex, vaginal estrogen, less sugar, and daily catheter irrigation with sterile/distilled water — not antibiotics and not a cabinet of supplements — and we save antibiotics for the rare true, symptomatic infection.
Ch 6.4 — the core our practice regimen
Always do
Check a post-void residual and fix incomplete emptying (bladder-outlet obstruction / prostate enlargement)
Address constipation
Counsel on post-coital voiding
Counsel on avoiding spermicide/diaphragm use — genuine modifiable risk factors
Ch 6.4 — the core our practice regimen
Why
Instilling antibiotic directly into the bladder achieves high local concentration that penetrates biofilm — without systemic exposure or systemic toxicity.
Ch 6.4 — resistant cases
Indications
rUTI despite prevention
UTI-type symptoms with repeatedly negative cultures
Hematuria
New-onset recurrent infections over age 50
What you are ruling out
Stone, foreign body, diverticulum, stricture, fistula, IC, or malignancy
A normal exam
A normal exam is reassuring and supports continued conservative management.
Ch 6.4 — when to look inside
Four NIH categories. Getting the category right decides whether antibiotics are the answer — and usually they are not.
Select a box to open its teaching details.
The categories
Acute bacterial prostatitis — acutely ill
Chronic bacterial prostatitis — recurrent UTIs with the same organism
IV — asymptomatic inflammatory — incidental, no treatment
Ch 6.5
Which category is this?
Time-critical
Treatment
Antibiotics with good prostate penetration — fluoroquinolone or TMP-SMX; IV if septic
Duration 2–4 weeks
If retention
Prefer a suprapubic tube over repeated urethral instrumentation
Pitfalls
Avoid vigorous/aggressive prostate massage — it can precipitate bacteremia
Watch for abscess and sepsis
Ch 6.5
Treatment
Prolonged 4–6 weeks culture-directed antibiotics
Consider Hiprex suppression
Ch 6.5
The UPOINT approach
Alpha-blockers
Pelvic-floor physical therapy
Neuromodulators — amitriptyline, gabapentin
Stress/cognitive therapy
Lifestyle
See also
Chapter 27.
Ch 6.5
Action
No treatment.
Ch 6.5
Time-critical
Action
Consider a prostatic abscess if there is no improvement after 48–72 hours on appropriate antibiotics
Image with transrectal ultrasound or CT and drain
Ch 6.5 — acute bacterial prostatitis cautions
The rule
Do NOT check a PSA during acute prostatitis, and do not act on one drawn during the illness
Wait at least 4–6 weeks after resolution
Ch 6.5 — acute bacterial prostatitis cautions
Pitfall
Do not label a man with chronic pelvic pain as "chronic prostatitis" and cycle him through antibiotics. That is category III and antibiotics are not the answer (Chapter 27).