Acute pyelonephritis and urosepsis · ICU Topics

ICU scene showing a CT abdomen with a swollen streaky kidney and a perinephric collection, a urinary catheter, blood cultures, and broad-spectrum antibiotics with noradrenaline running, clinical-blue lighting — FigurePyelonephritis with urosepsis — source control is decisive: image for obstruction or abscess and drain or stent an obstructed kidney promptly. Empiric anti-pseudomonal cover until sensitivities return; nephrology and urology involvement early.

Background and definitions

The urinary tract is a continuum, and infection is classified by anatomical level and by complexity: [1]

Lower UTI — urethritis, cystitis (bladder). Confined below the bladder neck.
Upper UTI — pyelonephritis (renal parenchyma + collecting system), and prostatitis/epididymitis in men.
Uncomplicated — infection in a structurally and neurologically normal urinary tract in a non-pregnant, immunocompetent adult woman.
Complicated — anything that worsens prognosis: male sex, pregnancy, diabetes, immunocompromise, urinary obstruction, indwelling catheter, recent instrumentation, renal failure, stones, or anatomic abnormality. All upper UTI in men, pregnancy, and the immunocompromised is treated as complicated. [1]

Urosepsis is sepsis (Sepsis-3 definition — life-threatening organ dysfunction caused by a dysregulated host response) arising from a urinary source.[6] It is among the commonest causes of sepsis in ICU patients and accounts for 20-30% of all severe sepsis/septic shock episodes. Urosepsis is notable for a relatively favourable prognosis compared with pulmonary or abdominal sepsis provided source control is achieved early — untreated obstruction, pyonephrosis or emphysematous pyelonephritis carry mortality of 20-40%.[2][3]

Microbiology

Escherichia coli

#1 cause (~80%)

Gram-negative rod; normal bowel flora; uropathogenic clones express virulence factors — P-fimbriae (bind renal epithelium), haemolysin, aerobactin, capsule
Cause >80% of community-acquired uncomplicated pyelonephritis; ~50% of catheter/healthcare-associated
Ascending infection: periurethral colonisation → bladder → ureteric reflux/ascent → renal pelvis → parenchyma
Increasing fluoroquinolone and trimethoprim resistance worldwide — check local antibiogram

Proteus mirabilis

Stone-former

Urease-producing — splits urea to ammonia → alkaline urine → struvite (magnesium ammonium phosphate) and apatite stones
Associated with staghorn calculi and recurrent infection — the "stone is the nidus"
More common in men (BPH), catheterised patients, and those with urinary diversion
Hard to eradicate while the stone remains — source control = stone removal

Klebsiella spp.

Enterobacterales

Gram-negative rod; common in healthcare-associated infection, diabetes, and obstruction
K. pneumoniae increasingly ESBL- and carbapenemase-producing (KPC, NDM) — a major ICU threat
Can be intrinsically resistant to ampicillin; carbapenem or ceftazidime-avibactam may be needed

Enterococcus

Gram-positive

E. faecalis > E. faecium; cause ~5-10% of pyelonephritis, higher after instrumentation/catheterisation
Intrinsically resistant to cephalosporins (low-affinity PBP) — must use ampicillin, vancomycin, or nitrofurantoin
VRE (vancomycin-resistant enterococcus) — linezolid, daptomycin, tigecycline
Often polymicrobial with Gram-negatives in complicated/catheter UTI

Pseudomonas aeruginosa

Catheter / HCA

Classic healthcare-associated pathogen — catheter, instrumentation, stones, obstruction
Intrinsically resistant to many agents; needs anti-pseudomonal beta-lactam (piperacillin-tazobactam, ceftazidime, cefepime, meropenem) ± aminoglycoside
Biofilm formation on catheters — must REMOVE/CHANGE the catheter as source control
Also consider in structurally abnormal tracts and after broad-spectrum antibiotics

Other / special

Less common

Staphylococcus saprophyticus — second commonest cause of UTI in young sexually-active women (usually cystitis)
Staphylococcus aureus in urine — suspect haematogenous seeding / endocarditis unless clearly a contaminant; look for a distant source
Candida spp. — common in catheterised, diabetic, ICU, antibiotic-exposed, TPN patients; treat only if symptomatic, neutropenic, or pre-procedure
Mycobacterium tuberculosis — sterile pyuria with pyuria; consider in endemic areas / immunocompromised

[1] [3]

Pathophysiology

The kidney is normally sterile. Infection reaches it by two routes: [1]

1. Ascending infection (dominant route)

Organisms colonise the periurethral area and distal urethra → ascend the urethra to the bladder (cystitis) → travel up the ureters to the renal pelvis (pyelitis) → invade the renal parenchyma (pyelonephritis) via the collecting ducts. Facilitating factors: [1]

Short urethra in women (hence female predominance).
Sexual activity — mechanical introduction of periurethral bacteria.
Vesicoureteric reflux (VUR) — incompetent ureterovesical junction allows bladder urine (and organisms) to reflux up the ureters during micturition.
Urinary stasis / incomplete emptying — from obstruction (BPH, stones, tumour, neurogenic bladder, pregnancy), reducing the mechanical washout that normally clears organisms.
Bacterial virulence factors — uropathogenic E. coli expresses P-fimbriae (Gal-Gal binding) that adhere to urothelium and resist washout; flagella aid ascent; haemolysin and siderophores (aerobactin) damage tissue and evade innate immunity. [1]

2. Haematogenous spread

Bacteraemia seeds the kidney via the cortical arteries — uncommon in the normal host, but a recognised route in the immunocompromised (endocarditis, IV drug use, disseminated infection) and with Staphylococcus aureus, Candida, Salmonella, and Mycobacterium tuberculosis. S. aureus in the urine with no lower-tract symptoms should prompt a search for an extra-urinary source (endocarditis, osteomyelitis, IV line infection). [1]

Inflammatory cascade

Once in the parenchyma, organisms elicit a neutrophil-predominant interstitial nephritis with tubular oedema, microabscess formation and (in severe disease) papillary necrosis, perinephric abscess extension, or gas production (emphysematous pyelonephritis — fermenting organisms in poorly-controlled diabetics). The inflammatory cytokine response (IL-1, IL-6, TNF-α) drives the systemic features — fever, rigors, and, when dysregulated, septic shock.[6][2]

Risk factors

Female sex

Anatomy

Short urethra + proximity to anus/periurethral flora → ascending colonisation
Lifetime risk of UTI ~50% in women; recurrent in 20-30%
Sexual activity and spermicide use (alters vaginal flora) increase risk

Obstruction

Stasis

Stones (calcium, struvite, uric acid) — act as a nidus and impair washout
BPH in men; urethral stricture; pelvic tumour; retroperitoneal fibrosis
Functional obstruction: neurogenic bladder (spinal cord injury, diabetes, MS), anticholinergics
Pregnancy — progesterone relaxes ureteric smooth muscle + mechanical compression by gravid uterus
Vesicoureteric reflux (VUR) — congenital, may persist into adulthood; causes recurrent pyelonephritis and renal scarring

Diabetes mellitus

Immune + tissue

Impaired neutrophil function (chemotaxis, phagocytosis) and glycosuria (bacterial growth substrate)
Predisposes to severe complications: emphysematous pyelonephritis, papillary necrosis, perinephric abscess, fungal UTI
Higher rates of bacteraemia and antimicrobial-resistant organisms

Pregnancy

Physiological

Physiological ureteric dilation (progesterone) + mechanical compression → stasis; asymptomatic bacteriuria in 2-10%
Untreated ASB progresses to pyelonephritis in 20-30% (vs <1% if treated) — universal screening + treatment
Pyelonephritis in pregnancy: high risk of premature labour, ARDS, septic shock — admit, IV antibiotics

Catheter / instrumentation

Healthcare-associated

Indwelling urinary catheter — biofilm formation; risk ~5% per catheter-day
Catheter-associated UTI (CAUTI) is the commonest healthcare-associated infection
Recent urological procedure (TURP, cystoscopy, stent change, biopsy)
Predisposes to Pseudomonas, Proteus, Enterococcus, Candida, polymicrobial infection

Immunocompromise

Host defence

Transplant (renal, on calcineurin inhibitors + mycophenolate + steroids)
Chemotherapy / neutropenia, haematological malignancy, advanced HIV
High-dose corticosteroids, anti-TNF biologics
Higher risk of atypical organisms (Candida, CMV, BK virus, mycobacteria) and haematogenous spread

[1] [3]

Clinical features

The clinical hallmark is the triad of fever ± rigors, flank pain, and urinary symptoms, with costovertebral angle (CVA) tenderness on examination. [1]

Upper UTI (pyelonephritis)

Kidney

Fever (often >38.5°C) ± rigors — indicates bacteraemia/systemic involvement
Flank / loin pain — unilateral or bilateral; CVA tenderness (Murphy's punch sign)
Nausea, vomiting, anorexia — frequently present; may mimic intra-abdominal pathology
Lower-tract symptoms usually coexist (dysuria, frequency, urgency, suprapubic pain) but may be ABSENT in the elderly, immunocompromised, or catheterised
Ileus, abdominal distension; occasionally a palpable ballotable mass (severe hydronephrosis, abscess)
Septic shock: hypotension, tachycardia, mottled skin, altered mental state, oliguria (urosepsis)

Lower UTI (cystitis)

Bladder

Dysuria, frequency, urgency, suprapubic pain/discomfort
Cloudy or bloody urine, offensive odour
Usually AFEBRILE or low-grade fever (<38°C); no flank pain; no rigors
Presence of fever, rigors, or flank pain suggests UPPER UTI — different management pathway
Haematuria (gross) — think haemorrhagic cystitis, stones, or malignancy if recurrent

Atypical / special

Beware

Elderly: atypical presentation — confusion, falls, incontinence, anorexia without fever (delirium as the only sign)
Pregnancy: may present as preterm labour; respiratory symptoms (ARDS) in severe cases
Diabetic: may be emphysematous — look for gas, crepitus, severe metabolic derangement
Spinal cord injury / neurogenic bladder: absence of pain/dysuria — fever and autonomic dysreflexia may be the only clues
Immunocompromised: blunted inflammatory response — cultures positive with minimal symptoms

[1] [2]

Upper vs lower UTI — exam discriminator

The clinical distinction matters: upper UTI requires longer parenteral therapy, imaging, and source control; lower UTI is usually oral therapy. Discriminators: [1]

Fever >38°C, rigors, flank pain, CVA tenderness, nausea/vomiting → upper UTI.
Afebrile, isolated dysuria/frequency/suprapubic pain → lower UTI (cystitis).
A useful exam point: the presence of systemic features (rigors, high fever, haemodynamic instability) mandates blood cultures, imaging, and admission. [1]

Diagnosis

Diagnostic approach to suspected pyelonephritis / urosepsis

Urinalysis (dipstick + microscopy)

BEDSIDE first test. Positive nitrites (Enterobacterales convert nitrate → nitrite; FALSE NEGATIVE if bladder dwell <4 h, or non-nitrate-formers like Enterococcus, Pseudomonas, Staphylococcus). Leucocyte esterase (neutrophil enzyme — detects pyuria). Microscopy: >10 WBC/high-power field. Haematuria (microscopic) common. Sterile pyuria (pyuria with negative routine culture) → think Mycobacterium tuberculosis, Chlamydia, Ureaplasma, fungal, partially-treated infection, or interstitial nephritis.

Urine culture & susceptibility

Clean-catch midstream urine (MSU) — gold standard. SIGNIFICANT GROWTH: >10^5 CFU/mL in a symptomatic woman (classic Kass criterion); >10^3 in a symptomatic man or on suprapubic aspirate; ANY growth from suprapubic aspirate (normally sterile). Catheter specimen: >10^3 with symptoms. Always collect BEFORE antibiotics if possible. Send Gram stain — rapid clue to Gram-negative rod (E. coli) vs Gram-positive (Enterococcus).

Blood cultures × 2

Send in ALL patients with fever/rigors, sepsis, or immunocompromise BEFORE antibiotics. Positive in ~20-30% of pyelonephritis (higher with obstruction, diabetes, stones). Blood-culture-positive urosepsis: same organism in urine and blood confirms the urinary source. Antibiotics within 1 h of recognition in septic shock (Surviving Sepsis).

Bloods — FBC, CRP, U&E, LFTs, lactate, venous/arterial gas

Leucocytosis with neutrophilia; raised CRP (mirrors severity). U&E: AKI common in sepsis or with bilateral obstruction (post-renal). Lactate: marker of tissue hypoperfusion / severity (Sepsis-3). Venous gas: metabolic acidosis, AKI. Glucose/HbA1c: undiagnosed/poorly-controlled diabetes. Procalcitonin: rising — may help distinguish bacterial infection and guide antibiotic duration.

Imaging — CT abdomen/pelvis with contrast (THE key modality)

INDICATED in: failure to improve within 48-72 h of antibiotics; diabetes; immunocompromise; suspected obstruction/stones; recurrent infection; male; severe sepsis/septic shock; palpable mass. CT with IV contrast is gold standard — identifies obstruction, stones (non-contrast better for tiny calculi), abscess, pyonephrosis, emphysematous change, perinephric extension. Bedside ultrasound (POCUS) is a rapid ICU bedside screen for hydronephrosis (obstruction) but is INSUFFICIENT to exclude parenchymal disease — a normal US does not exclude pyelonephritis.

Exclude obstruction EARLY

Pyonephrosis (pus under pressure in an obstructed kidney) is a urological emergency — every uroseptic patient needs the question "is there obstruction?" answered within hours. Bedside POCUS for hydronephrosis is a rapid triage; CT confirms. Relieve obstruction (JJ stent or percutaneous nephrostomy) — drainage of infected urine often produces dramatic haemodynamic improvement.

Special tests as indicated

Prostatic involvement (tender prostate on PR — avoid vigorous massage to avoid bacteraemia) suggests prostatitis → 4-week course. Renal abscess >3-5 cm → drainage. Atypical organisms (TB: sterile pyuria + AFB/NAAT on morning urines ×3; fungal: Candida with pseudohyphae). Post-treatment culture not routine unless recurrent/complicated.

[1] [2] [6]

Imaging — what to look for

CT with IV contrast

Gold standard

Wedge-shaped areas of decreased enhancement / striated nephrogram — acute pyelonephritis
Round non-enhancing lesion with rim enhancement = abscess
Gas within renal parenchyma/collecting system = emphysematous pyelonephritis (classify class I-IV)
Dilated collecting system with fluid/debris level = pyonephrosis
Perinephric stranding/fluid collection = extension beyond capsule
Non-contrast series identifies radiopaque stones (calcium, struvite)

Ultrasound (incl. POCUS)

Bedside / safe

First-line in pregnancy (no radiation) and the unstable ICU patient at bedside
Detects hydronephrosis (obstruction), large abscesses, gross emphysematous change, stones
NORMAL US does NOT exclude pyelonephritis — parenchymal inflammation often sonographically occult
Use to guide percutaneous nephrostomy and abscess drainage

Plain CT (stone protocol)

Calculus

Highest sensitivity for radiopaque and radiolucent (uric acid) stones
Use when the clinical question is "is there an obstructing stone?"
Low radiation; can be combined with contrast series

MRI / nuclear medicine

Rarely needed

MRI — gadolinium — alternative when iodinated contrast contraindicated; pregnancy (after US)
DMSA / DTPA renal scans — assess renal scarring and differential function (mainly paediatric / recurrent VUR work-up)

[1]

Management

Initial resuscitation (urosepsis / septic shock)

First hour bundle (Surviving Sepsis adapted to urosepsis)

Measure lactate; obtain blood cultures ×2 BEFORE antibiotics

Lactate >2 mmol/L = tissue hypoperfusion; >4 = severe sepsis. Two sets of blood cultures (aerobic + anaerobic) from separate sites, plus urine culture, all before the first antibiotic dose. Do NOT delay antibiotics beyond 45 min to obtain cultures in shock.

Broad-spectrum antibiotics within 1 hour

Empiric IV therapy covering common Gram-negatives + Enterococcus, with anti-pseudomonal cover if healthcare-associated/cathetered/immunocompromised. Options: ceftriaxone 2 g IV daily ± gentamicin (community); piperacillin-tazobactam 4.5 g IV TDS or ceftazidime (HCA/anti-pseudomonal); add ampicillin if Enterococcus risk; meropenem for known ESBL/carbapenemase. De-escalate to culture sensitivities at 48-72 h.

Crystalloid 30 mL/kg for hypotension or lactate ≥4

Balanced crystalloid (Hartmann's / Plasma-Lyte) preferred over 0.9% saline (hyperchloraemic acidosis, AKI). Reassess fluid responsiveness (passive leg raise, IVC POCUS, dynamic indices) before further boluses — uroseptic patients are often elderly with limited cardiac reserve.

Vasopressors for MAP <65 mmHg

Norepinephrine first-line (alpha + modest beta-1 agonist). Target MAP 65 mmHg. Add vasopressin 0.03 U/min if escalating norepinephrine. Do not withhold vasopressors to "fill more" — early vasopressors reduce fluid overload.

Source control — EARLY and definitive

Relieve obstruction (JJ stent or percutaneous nephrostomy — the latter in septic/unstable); drain abscess >3 cm (percutaneous radiologically-guided); remove/replace urinary catheter; nephrectomy for refractory emphysematous pyelonephritis. Aim for source control within 6-12 h of recognition. Drainage of an obstructed infected system often produces dramatic improvement.

Supportive ICU care

Lung-protective ventilation if ARDS; renal replacement therapy for refractory AKI/electrolyte/acid-base; VTE prophylaxis; stress-ulcer prophylaxis if intubated/coagulopathic; glycaemic control 140-180 mg/dL; early enteral nutrition; monitor lactate trend.

[2] [6]

Antimicrobial therapy

Uncomplicated pyelonephritis

Adult non-pregnant woman, mild-moderate

Oral therapy acceptable if able to tolerate PO and no sepsis
Ciprofloxacin 500 mg PO BD × 7 days (check local resistance <10%)
Levofloxacin 750 mg PO daily × 5 days
Co-amoxiclav (amoxicillin-clavulanate) 875/125 mg PO BD × 7-10 days (if organism susceptible)
Trimethoprim-sulfamethoxazole 160/800 mg PO BD × 14 days (if known susceptible & local resistance <20%)
Nitrofurantoin and fosfomycin are NOT reliable for tissue/upper-tract levels — reserve for cystitis

Severe / complicated / urosepsis

IV therapy

Ceftriaxone 2 g IV daily ± gentamicin 5-7 mg/kg IV once daily (synergy + broad Gram-negative cover)
Piperacillin-tazobactam 4.5 g IV TDS (anti-pseudomonal; good for catheter/HCA)
Ceftazidime 2 g IV TDS or cefepime 2 g IV TDS (anti-pseudomonal cephalosporin)
Meropenem 1 g IV TDS — known ESBL, carbapenemase, or critically ill with resistant organism risk
Add ampicillin 2 g IV QID if Enterococcus suspected (cephalosporins do not cover it)
Duration: 7-14 days (7 days for rapid responders with source control; 14 days for slow response, abscess, bacteraemia)

Pregnancy

Special

Ceftriaxone 1-2 g IV daily (or cefuroxime) — cephalosporin first-line
AVOID fluoroquinolones (cartilage/arthropathy), tetracyclines (teeth/bone), trimethoprim 1st trimester (folate antagonist) & 3rd trimester (kernicterus — displaces bilirubin)
AVOID aminoglycosides if possible (fetal ototoxicity) — use only if severe & short course
Always admit; IV therapy; 10-14 day course; test-of-cure culture 1-2 weeks after

Prostatitis / epididymitis

Longer course

Ciprofloxacin or levofloxacin × 4-6 weeks (penetrate prostatic tissue — fluoroquinolones concentrate in prostate)
Acute bacterial prostatitis can cause urosepsis — IV therapy then oral step-down
Consider STI screen (Chlamydia, gonorrhoea) in young sexually-active men

Catheter-associated UTI

CAUTI

REMOVE or replace the catheter FIRST — biofilm-laden catheter is the source
Do NOT treat asymptomatic catheter bacteriuria (does not reduce infection, selects resistance)
Treat only symptomatic infection: fever, rigors, flank pain, new confusion, haemodynamic instability
Catheter specimen culture guides therapy; organisms often polymicrobial (Pseudomonas, Proteus, Enterococcus, Candida)

[1] [5] [3]

Source control — the cornerstone

Source control in urosepsis

Relieve obstruction

Pyonephrosis = pus under pressure in an obstructed kidney = urological emergency. Decompression: percutaneous nephrostomy (radiology-guided — preferred in the unstable/septic patient at bedside or IR suite) OR retrograde JJ ureteric stent (cystoscopy under anaesthetic — requires theatre, may seed infection retrograde). Drainage of thick pus under pressure often produces immediate haemodynamic improvement. Send drained fluid for culture.

Drain abscess

Renal/perinephric abscess >3 cm rarely resolves with antibiotics alone — needs percutaneous catheter drainage (radiology). <3 cm may respond to antibiotics. Surgical drainage reserved for multiloculated/failed percutaneous drainage. Send pus for culture.

Remove/replace urinary catheter

The catheter is often the source in CAUTI/urosepsis. Remove if no longer needed; replace if still required (fresh catheter). Change suprapubic catheters and urological stents that are due. Sample urine from a NEW catheter, not a long-standing one (biofilm).

Treat stones (definitive)

Struvite (infection) stones must be completely removed — residual fragments harbour urease-producing organisms and the stone recurs. Options: ESWL, PCNL, ureteroscopy. Eradicate the nidus to cure the infection. Do NOT leave staghorn calculi in situ.

Nephrectomy for refractory emphysematous pyelonephritis

When medical + percutaneous management fails, or there is extensive destruction (Huang-Tsai class III/IV — extensive gas or gas through kidney + perinephric), emergency nephrectomy is life-saving. Mortality 20-40% overall; highest for extensive disease and delayed intervention.

[2] [4]

Emphysematous pyelonephritis — the surgical emergency

Emphysematous pyelonephritis (EPN) is a necrotising, gas-forming infection of the kidney, almost always in diabetics (90%+), caused by gas-forming organisms (E. coli most common, also Klebsiella, Proteus, Pseudomonas). The gas (CO₂, H₂) results from mixed-acid fermentation of glucose by the organism in tissues with high glucose and impaired perfusion.[8]

Huang-Tsai classification (CT-based)

Class I

Gas in collecting system only

Bubbly/linear gas in the renal parenchyma or collecting system without extension
Best prognosis — often responds to antibiotics + relief of obstruction
Mortality ~20%

Class II

Gas in renal parenchyma

Gas in renal parenchyma without extrarenal extension
Requires antibiotics + percutaneous drainage ± nephrectomy if not improving
Mortality ~35%

Class IIIa

Extension of gas into perinephric space

Gas extends to perinephric space
High risk of abscess, septic shock; aggressive source control required

Class IIIb

Extension of gas into pararenal space

Gas extends beyond Gerota's fascia to pararenal space
Extensive disease — high mortality; early nephrectomy often required

Class IVa/b

Bilateral or solitary kidney

Bilateral EPN or EPN in a solitary kidney
Nephrectomy not possible (would render anuric) — bilateral percutaneous drainage, antibiotics, dialysis if needed
Worst prognosis — mortality approaches 50%+

[7] [8]

Management of EPN

Emphysematous pyelonephritis management

Resuscitate + broad-spectrum antibiotics

ABC; IV fluids (balanced crystalloid); vasopressors for shock; broad-spectrum Gram-negative cover (piperacillin-tazobactam or meropenem) + source control. Aggressive glucose control. These patients are often profoundly septic and acidotic.

CT with contrast — classify

Confirm gas in kidney; classify by Huang-Tsai (extent); look for obstruction, abscess, bilateral involvement. This drives the decision between medical/percutaneous and surgical management.

Percutaneous drainage + medical therapy first-line

Class I-II and many class III: drainage of gas/pus/obstruction via percutaneous nephrostomy or catheter drains (often multiple, repeated) + antibiotics + glycaemic control. Systematic review evidence favours percutaneous drainage over upfront nephrectomy with lower mortality.

Nephrectomy if failure or extensive disease

Indications: clinical deterioration despite 48-72 h of drainage + antibiotics; extensive class IIIb/IV destruction; lack of access to repeated drainage. Emergency nephrectomy is life-saving in refractory disease. Bilateral/solitary kidney: bilateral drainage, avoid nephrectomy.

Correct glycaemia and predisposing factors

Insulin infusion for hyperglycaemia; relieve obstruction; treat the underlying diabetes. Address the reason gas formed — without glycaemic control, recurrence on the contralateral side is a risk.

[4] [7]

2008

Percutaneous drainage vs nephrectomy for emphysematous pyelonephritis (Somani, systematic review, J Urol 2008)

Systematic review of retrospective case series (no RCT possible — rare disease)

Population: Adults with radiologically confirmed emphysematous pyelonephritis across reported series

Key finding

Medical therapy alone had the highest mortality (~50%); addition of percutaneous drainage reduced mortality to ~13.5%, better than emergency nephrectomy (~25%). Combined percutaneous drainage + medical therapy became the new standard first-line; nephrectomy reserved for failure.

Practice change

In emphysematous pyelonephritis, treat with broad-spectrum antibiotics PLUS percutaneous drainage first; reserve nephrectomy for extensive or refractory disease.

[4]

2016

Sepsis-3 definitions (Singer, JAMA 2016)

International consensus task force redefining sepsis and septic shock

Population: Adult patients with suspected infection — derivation and validation cohorts

Key finding

SOFA-based sepsis definition and the septic shock criteria identified a population with mortality ~40% (vs ~10% for sepsis without shock). qSOFA (RR ≥22, altered mentation, SBP ≤100) — a bedside screen — predicted poor outcome outside ICU.

Practice change

Apply Sepsis-3 definitions to urosepsis: organ dysfunction (SOFA ≥2) defines sepsis; vasopressor-dependent hypotension + lactate >2 despite fluids defines septic shock and mandates aggressive resuscitation + early source control.

[6]

Complications

Pyonephrosis

Obstructed infected kidney

Pus under pressure in an obstructed collecting system — urological emergency
Risk: septic shock, irreversible renal destruction, kidney loss
Management: urgent decompression (nephrostomy or JJ stent) + antibiotics
Drainage often produces dramatic haemodynamic improvement

Renal/perinephric abscess

Walled-off infection

Collection of pus within the kidney (renal/cortical) or between kidney and Gerota's fascia (perinephric)
Risk factors: diabetes, obstruction, stones, staphylococcal bacteraemia (haematogenous)
<3 cm may resolve with antibiotics; >3 cm → percutaneous catheter drainage
Surgical drainage for multiloculated/failed percutaneous drainage

Emphysematous pyelonephritis

Gas-forming

Necrotising gas-forming infection — diabetics; mortality 20-40%
Percutaneous drainage + antibiotics first-line; nephrectomy for refractory/extensive
See dedicated section above

Papillary necrosis

Sloughed papillae

Ischaemic necrosis of renal papillae — diabetes, obstruction, analgesic abuse, sickle cell
Sloughed papilla may obstruct ureter (acute obstruction); ring-shadow on imaging
May be asymptomatic or cause haematuria, flank pain, AKI

Septic shock & AKI

Systemic

Vasodilatory shock, multi-organ failure; AKI from sepsis ± post-renal obstruction
Mortality 10-20% in urosepsis with shock (better than pulmonary/abdominal sepsis with source control)
May require vasopressors, RRT, lung-protective ventilation

Renal scarring / CKD / recurrence

Long-term

Recurrent childhood pyelonephritis + VUR → renal scarring, hypertension, CKD (reflux nephropathy)
Adults: residual scarring after severe infection; address predisposing factors to prevent recurrence
Emphysematous/obstructive disease may leave a non-functioning kidney

[1] [4]

Special situations

Pregnancy

High-risk

Universal screening for asymptomatic bacteriuria (treat — prevents pyelonephritis in 20-30%)
Pyelonephritis in pregnancy: ADMIT, IV cephalosporin; risk of premature labour, ARDS, septic shock
Avoid fluoroquinolones, tetracyclines, trimethoprim (1st & 3rd trimester), aminoglycosides
Ultrasound first-line imaging (avoid CT radiation); MRI if needed
Right-sided predilection (right ureter more compressed by gravid uterus, dextro-rotation)

Diabetes mellitus

Severe complications

Higher risk of bacteraemia, emphysematous pyelonephritis, papillary necrosis, perinephric abscess, fungal UTI
Aggressive imaging (CT) — do not miss gas
Tight(ish) glucose control; check feet for source; may have neuropathic bladder (stasis)
Higher incidence of resistant organisms

Catheterised / catheter-associated

HCA

Asymptomatic bacteriuria is universal in long-term catheters — DO NOT treat
Treat only symptomatic infection; remove/replace catheter as source control
Polymicrobial, resistant organisms (Pseudomonas, Proteus, Enterococcus, Candida)
Consider alternative to long-term catheter (suprapubic, condom, intermittent self-catheterisation)

Renal transplant

Immunocompromised

Immunosuppression blunts presentation — cultures positive with few symptoms
Atypical organisms: CMV, BK virus, Candida, mycobacteria; opportunistic infection
Anastomotic stricture / obstruction common; surgical complications (urinoma, leak)
Coordinate with transplant team; avoid drug interactions (calcineurin inhibitors + macrolides/azoles)

Elderly / delirious

Atypical

May present without fever or dysuria — confusion, falls, incontinence, anorexia
High threshold to image; consider obstruction (BPH, cervical/prostate tumour)
Beware over-diagnosis of UTI from asymptomatic bacteriuria — not every positive culture in a confused elderly patient is infection

[1] [3]

Prognosis

Uncomplicated pyelonephritis

Good

Mortality <1% with appropriate therapy
Most respond within 48-72 h; oral step-down after clinical improvement
Test-of-cure culture if recurrent, complicated, or pregnant

Complicated / urosepsis

Moderate

Mortality 10-20% in septic shock — better than pulmonary/abdominal sepsis IF source control achieved
Favourable prognosis reflects the accessibility of the source for control (catheter drainage, stent)
Delayed source control worsens outcome dramatically

Emphysematous pyelonephritis

Poor

Mortality 20-40% overall; higher with extensive (class IIIb/IV) disease, thrombocytopenia, acute renal failure, altered sensorium, shock
Scoring systems (Huang-Tsai class; EPIC score — emphysematous pyelonephritis) guide prognosis and surgical decision-making
Nephrectomy mortality ~25%; medical-only mortality ~50%

Prognostic factors

What matters

Speed of source control; adequacy of initial antibiotics; host factors (age, diabetes, immunocompromise)
Severity of sepsis (lactate, SOFA, vasopressor requirement); presence of bacteraemia
Presence of obstruction, abscess, or gas — all worsen prognosis

[2] [7]

SAQ — Urosepsis with septic shock and obstructive uropathy

SAQ — Urosepsis with septic shock in a post-TURP diabetic patient

10 minutes · 10 marks

A 68-year-old man with type 2 diabetes and benign prostatic hyperplasia is readmitted to ICU on day 4 after a transurethral resection of prostate (TURP) with an indwelling Foley catheter. He is confused, febrile (39.2 °C) and shivering. BP 78/45, HR 128, RR 28, SpO2 94% on room air, capillary refill 5 s. Lactate 4.8 mmol/L, WBC 24.6 x10^9/L, creatinine 220 umol/L (baseline 90), pH 7.28, bicarbonate 16. Urine is cloudy; Gram stain shows Gram-negative rods. Bedside POCUS demonstrates right-sided hydronephrosis with a 1.5 cm obstructing ureteric stone.

[1]

SAQ — Obstructive uropathy with pyonephrosis and post-obstructive diuresis

10 minutes · 10 marks

A 72-year-old man with bladder-outlet obstruction from advanced prostate cancer presents with a 3-day history of right flank pain, anuria, fever 38.9 °C and new confusion. BP 96/58, HR 112, RR 24. Creatinine 340 umol/L (baseline 110), K+ 5.9 mmol/L, pH 7.22, lactate 3.2. WBC 22 x10^9/L. Urine Gram stain shows Gram-negative rods. Bedside ultrasound shows bilateral hydronephrosis with a markedly distended bladder; in-and-out catheterisation drains 1.4 L of cloudy urine. A subsequent CT urogram confirms bilateral hydroureteronephrosis with a large obstructing mass at the bladder neck and a right perinephric fluid collection suggestive of pyonephrosis.

[1]

Clinical pearls

High-yield pyelonephritis/urosepsis points for the CICM/FFICM exam

E. coli is the #1 organism (~80% of community pyelonephritis).[1]
Source control is the cornerstone — relieve obstruction (stent/nephrostomy), drain abscess, remove catheter. Antibiotics alone fail against an obstructed infected kidney.[2]
Emphysematous pyelonephritis (diabetic + gas on CT) is a surgical emergency — percutaneous drainage + antibiotics first-line; nephrectomy for refractory/extensive disease (Huang-Tsai III/IV).[4]
Pyonephrosis = obstructed infected kidney = urological emergency. Urgent decompression (percutaneous nephrostomy or JJ stent).[1]
Severe/urosepsis antibiotics: ceftriaxone 2 g IV ± gentamicin; piperacillin-tazobactam or meropenem if anti-pseudomonal/carbapenemase risk. De-escalate at 48-72 h.[3]
CT abdomen/pelvis with contrast is essential in urosepsis — exclude obstruction, abscess, gas, stones. Bedside POCUS for hydronephrosis is a rapid triage but a normal US does NOT exclude pyelonephritis.[1]
Catheter-associated UTI: remove/replace the catheter (source control). Do NOT treat asymptomatic catheter bacteriuria.[3]
Diabetes increases risk of severe complications — emphysematous pyelonephritis, papillary necrosis, perinephric abscess, fungal UTI. Image aggressively.[1]
Pregnancy: pyelonephritis is high-risk — admit, IV cephalosporin (avoid fluoroquinolones, tetracyclines, trimethoprim, aminoglycosides). Risk of premature labour & ARDS.[1]
Proteus = urease producer → alkaline urine → struvite (staghorn) stones. You cannot cure the infection while the stone remains — the stone IS the nidus.[1]
Enterococcus is intrinsically resistant to cephalosporins — use ampicillin or vancomycin. Add ampicillin empirically if Enterococcus suspected in severe infection.[3]
Blood cultures positive in 20-30% of pyelonephritis — always send before antibiotics. Same organism in urine + blood confirms the urinary source.[2]
Sterile pyuria (pyuria + negative routine culture) → think TB, Chlamydia/Ureaplasma, fungal, partially-treated infection, or interstitial nephritis. Send AFB/NAAT on 3 early-morning urines if TB suspected.[1]
Mortality: uncomplicated <1%; urosepsis with shock 10-20%; emphysematous 20-40%.[7]
Nitrite dipstick is false-negative for Enterococcus, Pseudomonas, Staphylococcus (non-nitrate-reducers) and with short bladder dwell time (<4 h). A negative dipstick does NOT exclude UTI.[1]
Significant bacteriuria thresholds: >10^5 CFU/mL symptomatic woman; >10^3 symptomatic man; ANY growth from suprapubic aspirate. Lower counts matter in the symptomatic male.[5]
Duration: 7 days for rapid responders with source control; 14 days for slow response, abscess, bacteraemia; prostatitis 4-6 weeks.[1]
S. aureus in the urine without lower-tract symptoms → suspect haematogenous seeding; look for endocarditis, osteomyelitis, IV line infection. Do not dismiss as contamination.[1]
Acute prostatitis causes urosepsis and needs a longer course (4 weeks+); fluoroquinolones penetrate the prostate well. Avoid vigorous prostate massage (bacteraemia).[3]
Candida UTI: treat only if symptomatic, neutropenic, or pre-procedure. Fluconazole first-line (renal excretion); amphotericin B bladder irrigation for resistant cystitis; remove urinary catheter.[3]
Recurrent UTI: address predisposing factors (post-menopausal vaginal atrophy — topical oestrogen; voiding dysfunction; stones; diabetes). Prophylaxis: trimethoprim or nitrofurantoin post-coital or nightly; consider cranberry (limited evidence).[1]
Nitrofurantoin and fosfomycin are NOT reliable for pyelonephritis — poor renal tissue levels. Reserve for cystitis. (Nitrofurantoin also contraindicated if eGFR <30-45.)[5]
Right ureter more often obstructed in pregnancy (dextro-rotation of gravid uterus compresses the right ovarian venous plexus) — but bilateral ureteric dilation is physiological.[1]
POCUS (point-of-care ultrasound) for hydronephrosis in the unstable uroseptic patient is a rapid bedside test that can trigger emergency nephrostomy before formal CT — but CT remains gold standard for parenchymal disease.[2]
Vesicoureteric reflux (VUR) in adults causes recurrent pyelonephritis and reflux nephropathy (renal scarring, hypertension, CKD) — consider in recurrent childhood-onset infections.[1]
qSOFA (RR ≥22, altered mentation, SBP ≤100) at the bedside flags high-risk sepsis outside ICU and should prompt urgent escalation in suspected urosepsis.[6]
Reassess at 48-72 h — if no improvement, RE-IMAGE (CT), reconsider organism/resistance, check source control adequacy, and look for abscess/emphysematous change/obstruction that was missed.[1]

Red flags

Critical pyelonephritis/urosepsis points

Obstructed infected kidney (pyonephrosis) = urological emergency — urgent decompression (nephrostomy/stent) within hours.[1]
Emphysematous pyelonephritis (diabetic + gas on CT) = surgical emergency — percutaneous drainage + antibiotics; nephrectomy if refractory.[4]
Source control is critical — relieve obstruction, drain abscess, remove/replace catheter. Antibiotics alone fail against an obstructed infected system.[2]
CT with contrast in ALL uroseptic/severe patients — exclude obstruction, abscess, gas. A normal bedside US does NOT exclude pyelonephritis.[1]
Remove the urinary catheter — it is often the source. Do not treat asymptomatic catheter bacteriuria.[3]
Blood cultures positive in 20-30% — send before antibiotics; same organism in blood + urine confirms source.[2]
Enterococcus is cephalosporin-resistant — add ampicillin empirically if suspected; cephalosporin monotherapy will fail.[3]
Proteus + struvite stone — you cannot cure the infection without removing the stone (the nidus).[1]
S. aureus in urine without lower-tract symptoms → hunt for endocarditis/osteomyelitis/line infection (haematogenous).[1]
Pregnancy pyelonephritis — admit, IV cephalosporin; avoid fluoroquinolones, tetracyclines, trimethoprim, aminoglycosides. Risk of premature labour & ARDS.[1]
Sterile pyuria → consider TB, atypicals, fungal, interstitial nephritis; do not repeatedly re-treat as "UTI".[1]
Emphysematous pyelonephritis mortality 20-40% — classify (Huang-Tsai), drain percutaneously first-line, reserve nephrectomy for extensive/refractory disease.[7]
Antibiotics within 1 hour of recognising septic shock (Surviving Sepsis) — after cultures, but do not delay beyond 45 min.[6]
Reassess at 48-72 h — no improvement mandates re-imaging and re-evaluation of source control.[1]

Exam practice — viva-style questions

One-minute viva prompts

A 55-year-old diabetic woman presents with fever, rigors, right flank pain and hypotension. Outline your immediate management. (Sepsis-6 in the first hour: cultures before antibiotics, broad-spectrum IV antibiotics [piperacillin-tazobactam ± gentamicin], fluids, vasopressors, lactate; early source control — CT with contrast looking for obstruction/gas/abscess; emergency nephrostomy if pyonephrosis; aggressive glucose control.)
A diabetic patient with pyelonephritis has "gas in the kidney" on CT. What is this and how do you manage it? (Emphysematous pyelonephritis — necrotising gas-forming infection in diabetics. Classify by Huang-Tsai. Treat with broad-spectrum antibiotics + percutaneous drainage first-line; nephrectomy for extensive [class IIIb/IV] or refractory disease. Mortality 20-40%.)
Why is source control central in urosepsis? (Antibiotics cannot penetrate an obstructed, pus-filled, pressure-laden collecting system, and a biofilm-laden catheter or an infected stone is a persistent nidus. Relief of obstruction, drainage of abscess and removal of catheter dramatically improve outcomes — drainage of pyonephrosis often produces immediate haemodynamic improvement.)
A pregnant woman at 28 weeks has fever and right flank pain. What is your approach? (Admit; IV cephalosporin [ceftriaxone]; avoid fluoroquinolones, tetracyclines, trimethoprim, aminoglycosides. Ultrasound first-line imaging; consider risk of premature labour/ARDS — obstetric involvement. Right-sided predilection. Treat asymptomatic bacteriuria in pregnancy to prevent this.)
A 70-year-old man with an indwelling catheter and a positive urine culture is confused. Is this a UTI? (Not necessarily — asymptomatic catheter bacteriuria is universal and should not be treated. Diagnose CAUTI only with symptoms: fever, rigors, flank pain, new confusion, haemodynamic instability. Remove/replace the catheter; treat with anti-pseudomonal/Enterococcus cover; sample from a fresh catheter.)
Justify your empirical antibiotic choice for uroseptic shock from a likely urinary source. (Broad-spectrum Gram-negative + Enterococcus cover with anti-pseudomonal activity if catheter/HCA/immunocompromised: piperacillin-tazobactam or ceftazidime + ampicillin ± gentamicin; meropenem if known ESBL/carbapenemase. De-escalate at 48-72 h on culture results. Always culture before antibiotics.)
What is the significance of Staphylococcus aureus in a urine culture? (Unless clearly a contaminant from poor collection, suspect haematogenous seeding — search for endocarditis, osteomyelitis, IV line infection. Do not dismiss as a contaminant or treat as simple UTI.)
A patient with recurrent pyelonephritis and sterile pyuria. What are you thinking? (Genitourinary tuberculosis — sterile pyuria with pyuria; send 3 early-morning urines for AFB + NAAT. Also Chlamydia/Ureaplasma, fungal, partially-treated infection, interstitial nephritis. Isolate until TB excluded.)

[1]

Summary answer (for the oral exam)

"Acute pyelonephritis is infection of the renal parenchyma and collecting system, most commonly by ascending E. coli, and urosepsis is sepsis arising from a urinary source — one of the commonest causes of sepsis in ICU. I would diagnose it at the bedside with a history of fever, rigors, flank pain and urinary symptoms plus costovertebral angle tenderness, confirm it with urinalysis showing nitrites, leucocyte esterase and pyuria, a urine culture with significant growth, blood cultures that are positive in 20-30%, and a contrast CT of the abdomen and pelvis to exclude obstruction, abscess, gas and stones — remembering that a normal bedside ultrasound does not exclude parenchymal disease. My management follows the first-hour sepsis bundle: cultures before antibiotics, broad-spectrum intravenous therapy covering common Gram-negatives and Enterococcus — ceftriaxone with or without gentamicin for community disease, piperacillin-tazobactam or meropenem for healthcare-associated or anti-pseudomonal cover, with ampicillin added if Enterococcus is suspected — balanced crystalloid for hypotension or lactate above four, norepinephrine for a MAP below 65, and above all EARLY SOURCE CONTROL: relief of obstruction by percutaneous nephrostomy or stent for pyonephrosis, drainage of any abscess greater than three centimetres, removal or replacement of an indwelling catheter, and definitive treatment of any struvite stone. I would treat for seven to fourteen days, de-escalating to oral therapy as the patient improves and cultures return. In a diabetic with gas in the kidney I would diagnose emphysematous pyelonephritis — a surgical emergency — classify it by the Huang-Tsai system, treat with antibiotics and percutaneous drainage first-line, and reserve emergency nephrectomy for extensive or refractory disease, knowing the mortality is twenty to forty per cent. In pregnancy I would admit, give an intravenous cephalosporin and avoid fluoroquinolones, tetracyclines, trimethoprim and aminoglycosides. Throughout, I would reassess at 48 to 72 hours and re-image if the patient is not improving, because the prognosis of urosepsis — mortality under one per cent when uncomplicated, ten to twenty per cent in septic shock, and twenty to forty per cent in emphysematous disease — hinges on rapid antibiotics and definitive source control." [1]

Sepsis and septic shock — apply Sepsis-3 definitions and the Surviving Sepsis one-hour bundle to urosepsis.[6]
Acute kidney injury — post-renal AKI from obstruction; septic AKI from hypoperfusion; may require RRT.
Asymptomatic bacteriuria — screen and treat in pregnancy and before urological instrumentation; otherwise do NOT treat (catheter, elderly).
Vesicoureteric reflux / reflux nephropathy — congenital; recurrent childhood pyelonephritis → renal scarring, hypertension, CKD.
Renal/perinephric abscess — complication needing percutaneous or surgical drainage.
Prostatitis — acute bacterial (urosepsis source) and chronic; longer antibiotic course (4-6 weeks).

References

[1]Johnson JR, Russo TA Acute Pyelonephritis in Adults N Engl J Med, 2018.PMID 29298155
[2]Wagenlehner FM, Lichtenstern C, Rolfes C, et al. Urosepsis--from the view of the urologist Int J Antimicrob Agents, 2011.PMID 21993485
[3]Wagenlehner FM, Tandogdu Z, Bjerklund Johansen TE An update on classification and management of urosepsis Curr Opin Urol, 2017.PMID 27846034
[4]Somani BK, Nabi G, Thorpe P, et al. Is percutaneous drainage the new gold standard in the management of emphysematous pyelonephritis? Evidence from a systematic review J Urol, 2008.PMID 18353396
[5]Gupta K, Hooton TM, Naber KG, et al. International clinical practice guidelines for the treatment of acute uncomplicated cystitis and pyelonephritis in women: A 2010 update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases Clin Infect Dis, 2011.PMID 21292654
[6]Singer M, Deutschman CS, Seymour CW, et al. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) JAMA, 2016.PMID 26903338
[7]Chen CC, Lin SH, Huang HC, et al. Performance of Scoring Systems in Predicting Clinical Outcomes of Patients with Emphysematous Pyelonephritis: A 14-Year Hospital-Based Study J Clin Med, 2022.PMID 36555916
[8]Tsu JH, Ma WK, Chan WC, et al. Emphysematous pyelonephritis: an 8-year retrospective review across four acute hospitals Asian J Surg, 2013.PMID 23810162

[1]

Background and definitions

The urinary tract is a continuum, and infection is classified by anatomical level and by complexity: [1]

Lower UTI — urethritis, cystitis (bladder). Confined below the bladder neck.
Upper UTI — pyelonephritis (renal parenchyma + collecting system), and prostatitis/epididymitis in men.
Uncomplicated — infection in a structurally and neurologically normal urinary tract in a non-pregnant, immunocompetent adult woman.
Complicated — anything that worsens prognosis: male sex, pregnancy, diabetes, immunocompromise, urinary obstruction, indwelling catheter, recent instrumentation, renal failure, stones, or anatomic abnormality. All upper UTI in men, pregnancy, and the immunocompromised is treated as complicated. [1]

Microbiology

Escherichia coli

#1 cause (~80%)

Gram-negative rod; normal bowel flora; uropathogenic clones express virulence factors — P-fimbriae (bind renal epithelium), haemolysin, aerobactin, capsule
Cause >80% of community-acquired uncomplicated pyelonephritis; ~50% of catheter/healthcare-associated
Ascending infection: periurethral colonisation → bladder → ureteric reflux/ascent → renal pelvis → parenchyma
Increasing fluoroquinolone and trimethoprim resistance worldwide — check local antibiogram

Proteus mirabilis

Stone-former

Urease-producing — splits urea to ammonia → alkaline urine → struvite (magnesium ammonium phosphate) and apatite stones
Associated with staghorn calculi and recurrent infection — the "stone is the nidus"
More common in men (BPH), catheterised patients, and those with urinary diversion
Hard to eradicate while the stone remains — source control = stone removal

Klebsiella spp.

Enterobacterales

Gram-negative rod; common in healthcare-associated infection, diabetes, and obstruction
K. pneumoniae increasingly ESBL- and carbapenemase-producing (KPC, NDM) — a major ICU threat
Can be intrinsically resistant to ampicillin; carbapenem or ceftazidime-avibactam may be needed

Enterococcus

Gram-positive

E. faecalis > E. faecium; cause ~5-10% of pyelonephritis, higher after instrumentation/catheterisation
Intrinsically resistant to cephalosporins (low-affinity PBP) — must use ampicillin, vancomycin, or nitrofurantoin
VRE (vancomycin-resistant enterococcus) — linezolid, daptomycin, tigecycline
Often polymicrobial with Gram-negatives in complicated/catheter UTI

Pseudomonas aeruginosa

Catheter / HCA

Classic healthcare-associated pathogen — catheter, instrumentation, stones, obstruction
Intrinsically resistant to many agents; needs anti-pseudomonal beta-lactam (piperacillin-tazobactam, ceftazidime, cefepime, meropenem) ± aminoglycoside
Biofilm formation on catheters — must REMOVE/CHANGE the catheter as source control
Also consider in structurally abnormal tracts and after broad-spectrum antibiotics

Other / special

Less common

Staphylococcus saprophyticus — second commonest cause of UTI in young sexually-active women (usually cystitis)
Staphylococcus aureus in urine — suspect haematogenous seeding / endocarditis unless clearly a contaminant; look for a distant source
Candida spp. — common in catheterised, diabetic, ICU, antibiotic-exposed, TPN patients; treat only if symptomatic, neutropenic, or pre-procedure
Mycobacterium tuberculosis — sterile pyuria with pyuria; consider in endemic areas / immunocompromised

[1] [3]

Pathophysiology

The kidney is normally sterile. Infection reaches it by two routes: [1]

1. Ascending infection (dominant route)

Short urethra in women (hence female predominance).
Sexual activity — mechanical introduction of periurethral bacteria.
Vesicoureteric reflux (VUR) — incompetent ureterovesical junction allows bladder urine (and organisms) to reflux up the ureters during micturition.
Urinary stasis / incomplete emptying — from obstruction (BPH, stones, tumour, neurogenic bladder, pregnancy), reducing the mechanical washout that normally clears organisms.
Bacterial virulence factors — uropathogenic E. coli expresses P-fimbriae (Gal-Gal binding) that adhere to urothelium and resist washout; flagella aid ascent; haemolysin and siderophores (aerobactin) damage tissue and evade innate immunity. [1]

2. Haematogenous spread

Inflammatory cascade

Risk factors

Female sex

Anatomy

Short urethra + proximity to anus/periurethral flora → ascending colonisation
Lifetime risk of UTI ~50% in women; recurrent in 20-30%
Sexual activity and spermicide use (alters vaginal flora) increase risk

Obstruction

Stasis

Stones (calcium, struvite, uric acid) — act as a nidus and impair washout
BPH in men; urethral stricture; pelvic tumour; retroperitoneal fibrosis
Functional obstruction: neurogenic bladder (spinal cord injury, diabetes, MS), anticholinergics
Pregnancy — progesterone relaxes ureteric smooth muscle + mechanical compression by gravid uterus
Vesicoureteric reflux (VUR) — congenital, may persist into adulthood; causes recurrent pyelonephritis and renal scarring

Diabetes mellitus

Immune + tissue

Impaired neutrophil function (chemotaxis, phagocytosis) and glycosuria (bacterial growth substrate)
Predisposes to severe complications: emphysematous pyelonephritis, papillary necrosis, perinephric abscess, fungal UTI
Higher rates of bacteraemia and antimicrobial-resistant organisms

Pregnancy

Physiological

Physiological ureteric dilation (progesterone) + mechanical compression → stasis; asymptomatic bacteriuria in 2-10%
Untreated ASB progresses to pyelonephritis in 20-30% (vs <1% if treated) — universal screening + treatment
Pyelonephritis in pregnancy: high risk of premature labour, ARDS, septic shock — admit, IV antibiotics

Catheter / instrumentation

Healthcare-associated

Indwelling urinary catheter — biofilm formation; risk ~5% per catheter-day
Catheter-associated UTI (CAUTI) is the commonest healthcare-associated infection
Recent urological procedure (TURP, cystoscopy, stent change, biopsy)
Predisposes to Pseudomonas, Proteus, Enterococcus, Candida, polymicrobial infection

Immunocompromise

Host defence

Transplant (renal, on calcineurin inhibitors + mycophenolate + steroids)
Chemotherapy / neutropenia, haematological malignancy, advanced HIV
High-dose corticosteroids, anti-TNF biologics
Higher risk of atypical organisms (Candida, CMV, BK virus, mycobacteria) and haematogenous spread

[1] [3]

Clinical features

The clinical hallmark is the triad of fever ± rigors, flank pain, and urinary symptoms, with costovertebral angle (CVA) tenderness on examination. [1]

Upper UTI (pyelonephritis)

Kidney

Fever (often >38.5°C) ± rigors — indicates bacteraemia/systemic involvement
Flank / loin pain — unilateral or bilateral; CVA tenderness (Murphy's punch sign)
Nausea, vomiting, anorexia — frequently present; may mimic intra-abdominal pathology
Lower-tract symptoms usually coexist (dysuria, frequency, urgency, suprapubic pain) but may be ABSENT in the elderly, immunocompromised, or catheterised
Ileus, abdominal distension; occasionally a palpable ballotable mass (severe hydronephrosis, abscess)
Septic shock: hypotension, tachycardia, mottled skin, altered mental state, oliguria (urosepsis)

Lower UTI (cystitis)

Bladder

Dysuria, frequency, urgency, suprapubic pain/discomfort
Cloudy or bloody urine, offensive odour
Usually AFEBRILE or low-grade fever (<38°C); no flank pain; no rigors
Presence of fever, rigors, or flank pain suggests UPPER UTI — different management pathway
Haematuria (gross) — think haemorrhagic cystitis, stones, or malignancy if recurrent

Atypical / special

Beware

Elderly: atypical presentation — confusion, falls, incontinence, anorexia without fever (delirium as the only sign)
Pregnancy: may present as preterm labour; respiratory symptoms (ARDS) in severe cases
Diabetic: may be emphysematous — look for gas, crepitus, severe metabolic derangement
Spinal cord injury / neurogenic bladder: absence of pain/dysuria — fever and autonomic dysreflexia may be the only clues
Immunocompromised: blunted inflammatory response — cultures positive with minimal symptoms

[1] [2]

Upper vs lower UTI — exam discriminator

The clinical distinction matters: upper UTI requires longer parenteral therapy, imaging, and source control; lower UTI is usually oral therapy. Discriminators: [1]

Fever >38°C, rigors, flank pain, CVA tenderness, nausea/vomiting → upper UTI.
Afebrile, isolated dysuria/frequency/suprapubic pain → lower UTI (cystitis).
A useful exam point: the presence of systemic features (rigors, high fever, haemodynamic instability) mandates blood cultures, imaging, and admission. [1]

Diagnosis

Diagnostic approach to suspected pyelonephritis / urosepsis

Urinalysis (dipstick + microscopy)

Urine culture & susceptibility

Blood cultures × 2

Bloods — FBC, CRP, U&E, LFTs, lactate, venous/arterial gas

Imaging — CT abdomen/pelvis with contrast (THE key modality)

Exclude obstruction EARLY

Special tests as indicated

[1] [2] [6]

Imaging — what to look for

CT with IV contrast

Gold standard

Wedge-shaped areas of decreased enhancement / striated nephrogram — acute pyelonephritis
Round non-enhancing lesion with rim enhancement = abscess
Gas within renal parenchyma/collecting system = emphysematous pyelonephritis (classify class I-IV)
Dilated collecting system with fluid/debris level = pyonephrosis
Perinephric stranding/fluid collection = extension beyond capsule
Non-contrast series identifies radiopaque stones (calcium, struvite)

Ultrasound (incl. POCUS)

Bedside / safe

First-line in pregnancy (no radiation) and the unstable ICU patient at bedside
Detects hydronephrosis (obstruction), large abscesses, gross emphysematous change, stones
NORMAL US does NOT exclude pyelonephritis — parenchymal inflammation often sonographically occult
Use to guide percutaneous nephrostomy and abscess drainage

Plain CT (stone protocol)

Calculus

Highest sensitivity for radiopaque and radiolucent (uric acid) stones
Use when the clinical question is "is there an obstructing stone?"
Low radiation; can be combined with contrast series

MRI / nuclear medicine

Rarely needed

MRI — gadolinium — alternative when iodinated contrast contraindicated; pregnancy (after US)
DMSA / DTPA renal scans — assess renal scarring and differential function (mainly paediatric / recurrent VUR work-up)

[1]

Management

Initial resuscitation (urosepsis / septic shock)

First hour bundle (Surviving Sepsis adapted to urosepsis)

Measure lactate; obtain blood cultures ×2 BEFORE antibiotics

Broad-spectrum antibiotics within 1 hour

Crystalloid 30 mL/kg for hypotension or lactate ≥4

Vasopressors for MAP <65 mmHg

Source control — EARLY and definitive

Supportive ICU care

[2] [6]

Antimicrobial therapy

Uncomplicated pyelonephritis

Adult non-pregnant woman, mild-moderate

Oral therapy acceptable if able to tolerate PO and no sepsis
Ciprofloxacin 500 mg PO BD × 7 days (check local resistance <10%)
Levofloxacin 750 mg PO daily × 5 days
Co-amoxiclav (amoxicillin-clavulanate) 875/125 mg PO BD × 7-10 days (if organism susceptible)
Trimethoprim-sulfamethoxazole 160/800 mg PO BD × 14 days (if known susceptible & local resistance <20%)
Nitrofurantoin and fosfomycin are NOT reliable for tissue/upper-tract levels — reserve for cystitis

Severe / complicated / urosepsis

IV therapy

Ceftriaxone 2 g IV daily ± gentamicin 5-7 mg/kg IV once daily (synergy + broad Gram-negative cover)
Piperacillin-tazobactam 4.5 g IV TDS (anti-pseudomonal; good for catheter/HCA)
Ceftazidime 2 g IV TDS or cefepime 2 g IV TDS (anti-pseudomonal cephalosporin)
Meropenem 1 g IV TDS — known ESBL, carbapenemase, or critically ill with resistant organism risk
Add ampicillin 2 g IV QID if Enterococcus suspected (cephalosporins do not cover it)
Duration: 7-14 days (7 days for rapid responders with source control; 14 days for slow response, abscess, bacteraemia)

Pregnancy

Special

Ceftriaxone 1-2 g IV daily (or cefuroxime) — cephalosporin first-line
AVOID fluoroquinolones (cartilage/arthropathy), tetracyclines (teeth/bone), trimethoprim 1st trimester (folate antagonist) & 3rd trimester (kernicterus — displaces bilirubin)
AVOID aminoglycosides if possible (fetal ototoxicity) — use only if severe & short course
Always admit; IV therapy; 10-14 day course; test-of-cure culture 1-2 weeks after

Prostatitis / epididymitis

Longer course

Ciprofloxacin or levofloxacin × 4-6 weeks (penetrate prostatic tissue — fluoroquinolones concentrate in prostate)
Acute bacterial prostatitis can cause urosepsis — IV therapy then oral step-down
Consider STI screen (Chlamydia, gonorrhoea) in young sexually-active men

Catheter-associated UTI

CAUTI

REMOVE or replace the catheter FIRST — biofilm-laden catheter is the source
Do NOT treat asymptomatic catheter bacteriuria (does not reduce infection, selects resistance)
Treat only symptomatic infection: fever, rigors, flank pain, new confusion, haemodynamic instability
Catheter specimen culture guides therapy; organisms often polymicrobial (Pseudomonas, Proteus, Enterococcus, Candida)

[1] [5] [3]

Source control — the cornerstone

Source control in urosepsis

Relieve obstruction

Drain abscess

Remove/replace urinary catheter

Treat stones (definitive)

Nephrectomy for refractory emphysematous pyelonephritis

[2] [4]

Emphysematous pyelonephritis — the surgical emergency

Huang-Tsai classification (CT-based)

Class I

Gas in collecting system only

Bubbly/linear gas in the renal parenchyma or collecting system without extension
Best prognosis — often responds to antibiotics + relief of obstruction
Mortality ~20%

Class II

Gas in renal parenchyma

Gas in renal parenchyma without extrarenal extension
Requires antibiotics + percutaneous drainage ± nephrectomy if not improving
Mortality ~35%

Class IIIa

Extension of gas into perinephric space

Gas extends to perinephric space
High risk of abscess, septic shock; aggressive source control required

Class IIIb

Extension of gas into pararenal space

Gas extends beyond Gerota's fascia to pararenal space
Extensive disease — high mortality; early nephrectomy often required

Class IVa/b

Bilateral or solitary kidney

Bilateral EPN or EPN in a solitary kidney
Nephrectomy not possible (would render anuric) — bilateral percutaneous drainage, antibiotics, dialysis if needed
Worst prognosis — mortality approaches 50%+

[7] [8]

Management of EPN

Emphysematous pyelonephritis management

Resuscitate + broad-spectrum antibiotics

CT with contrast — classify

Confirm gas in kidney; classify by Huang-Tsai (extent); look for obstruction, abscess, bilateral involvement. This drives the decision between medical/percutaneous and surgical management.

Percutaneous drainage + medical therapy first-line

Nephrectomy if failure or extensive disease

Correct glycaemia and predisposing factors

Insulin infusion for hyperglycaemia; relieve obstruction; treat the underlying diabetes. Address the reason gas formed — without glycaemic control, recurrence on the contralateral side is a risk.

[4] [7]

2008

Percutaneous drainage vs nephrectomy for emphysematous pyelonephritis (Somani, systematic review, J Urol 2008)

Systematic review of retrospective case series (no RCT possible — rare disease)

Population: Adults with radiologically confirmed emphysematous pyelonephritis across reported series

Key finding

Practice change

In emphysematous pyelonephritis, treat with broad-spectrum antibiotics PLUS percutaneous drainage first; reserve nephrectomy for extensive or refractory disease.

[4]

2016

Sepsis-3 definitions (Singer, JAMA 2016)

International consensus task force redefining sepsis and septic shock

Population: Adult patients with suspected infection — derivation and validation cohorts

Key finding

Practice change

[6]

Complications

Pyonephrosis

Obstructed infected kidney

Pus under pressure in an obstructed collecting system — urological emergency
Risk: septic shock, irreversible renal destruction, kidney loss
Management: urgent decompression (nephrostomy or JJ stent) + antibiotics
Drainage often produces dramatic haemodynamic improvement

Renal/perinephric abscess

Walled-off infection

Collection of pus within the kidney (renal/cortical) or between kidney and Gerota's fascia (perinephric)
Risk factors: diabetes, obstruction, stones, staphylococcal bacteraemia (haematogenous)
<3 cm may resolve with antibiotics; >3 cm → percutaneous catheter drainage
Surgical drainage for multiloculated/failed percutaneous drainage

Emphysematous pyelonephritis

Gas-forming

Necrotising gas-forming infection — diabetics; mortality 20-40%
Percutaneous drainage + antibiotics first-line; nephrectomy for refractory/extensive
See dedicated section above

Papillary necrosis

Sloughed papillae

Ischaemic necrosis of renal papillae — diabetes, obstruction, analgesic abuse, sickle cell
Sloughed papilla may obstruct ureter (acute obstruction); ring-shadow on imaging
May be asymptomatic or cause haematuria, flank pain, AKI

Septic shock & AKI

Systemic

Vasodilatory shock, multi-organ failure; AKI from sepsis ± post-renal obstruction
Mortality 10-20% in urosepsis with shock (better than pulmonary/abdominal sepsis with source control)
May require vasopressors, RRT, lung-protective ventilation

Renal scarring / CKD / recurrence

Long-term

Recurrent childhood pyelonephritis + VUR → renal scarring, hypertension, CKD (reflux nephropathy)
Adults: residual scarring after severe infection; address predisposing factors to prevent recurrence
Emphysematous/obstructive disease may leave a non-functioning kidney

[1] [4]

Special situations

Pregnancy

High-risk

Universal screening for asymptomatic bacteriuria (treat — prevents pyelonephritis in 20-30%)
Pyelonephritis in pregnancy: ADMIT, IV cephalosporin; risk of premature labour, ARDS, septic shock
Avoid fluoroquinolones, tetracyclines, trimethoprim (1st & 3rd trimester), aminoglycosides
Ultrasound first-line imaging (avoid CT radiation); MRI if needed
Right-sided predilection (right ureter more compressed by gravid uterus, dextro-rotation)

Diabetes mellitus

Severe complications

Higher risk of bacteraemia, emphysematous pyelonephritis, papillary necrosis, perinephric abscess, fungal UTI
Aggressive imaging (CT) — do not miss gas
Tight(ish) glucose control; check feet for source; may have neuropathic bladder (stasis)
Higher incidence of resistant organisms

Catheterised / catheter-associated

HCA

Asymptomatic bacteriuria is universal in long-term catheters — DO NOT treat
Treat only symptomatic infection; remove/replace catheter as source control
Polymicrobial, resistant organisms (Pseudomonas, Proteus, Enterococcus, Candida)
Consider alternative to long-term catheter (suprapubic, condom, intermittent self-catheterisation)

Renal transplant

Immunocompromised

Immunosuppression blunts presentation — cultures positive with few symptoms
Atypical organisms: CMV, BK virus, Candida, mycobacteria; opportunistic infection
Anastomotic stricture / obstruction common; surgical complications (urinoma, leak)
Coordinate with transplant team; avoid drug interactions (calcineurin inhibitors + macrolides/azoles)

Elderly / delirious

Atypical

May present without fever or dysuria — confusion, falls, incontinence, anorexia
High threshold to image; consider obstruction (BPH, cervical/prostate tumour)
Beware over-diagnosis of UTI from asymptomatic bacteriuria — not every positive culture in a confused elderly patient is infection

[1] [3]

Prognosis

Uncomplicated pyelonephritis

Good

Mortality <1% with appropriate therapy
Most respond within 48-72 h; oral step-down after clinical improvement
Test-of-cure culture if recurrent, complicated, or pregnant

Complicated / urosepsis

Moderate

Mortality 10-20% in septic shock — better than pulmonary/abdominal sepsis IF source control achieved
Favourable prognosis reflects the accessibility of the source for control (catheter drainage, stent)
Delayed source control worsens outcome dramatically

Emphysematous pyelonephritis

Poor

Mortality 20-40% overall; higher with extensive (class IIIb/IV) disease, thrombocytopenia, acute renal failure, altered sensorium, shock
Scoring systems (Huang-Tsai class; EPIC score — emphysematous pyelonephritis) guide prognosis and surgical decision-making
Nephrectomy mortality ~25%; medical-only mortality ~50%

Prognostic factors

What matters

Speed of source control; adequacy of initial antibiotics; host factors (age, diabetes, immunocompromise)
Severity of sepsis (lactate, SOFA, vasopressor requirement); presence of bacteraemia
Presence of obstruction, abscess, or gas — all worsen prognosis

[2] [7]

SAQ — Urosepsis with septic shock and obstructive uropathy

SAQ — Urosepsis with septic shock in a post-TURP diabetic patient

10 minutes · 10 marks

[1]

SAQ — Obstructive uropathy with pyonephrosis and post-obstructive diuresis

10 minutes · 10 marks

[1]

Clinical pearls

High-yield pyelonephritis/urosepsis points for the CICM/FFICM exam

E. coli is the #1 organism (~80% of community pyelonephritis).[1]
Source control is the cornerstone — relieve obstruction (stent/nephrostomy), drain abscess, remove catheter. Antibiotics alone fail against an obstructed infected kidney.[2]
Emphysematous pyelonephritis (diabetic + gas on CT) is a surgical emergency — percutaneous drainage + antibiotics first-line; nephrectomy for refractory/extensive disease (Huang-Tsai III/IV).[4]
Pyonephrosis = obstructed infected kidney = urological emergency. Urgent decompression (percutaneous nephrostomy or JJ stent).[1]
Severe/urosepsis antibiotics: ceftriaxone 2 g IV ± gentamicin; piperacillin-tazobactam or meropenem if anti-pseudomonal/carbapenemase risk. De-escalate at 48-72 h.[3]
CT abdomen/pelvis with contrast is essential in urosepsis — exclude obstruction, abscess, gas, stones. Bedside POCUS for hydronephrosis is a rapid triage but a normal US does NOT exclude pyelonephritis.[1]
Catheter-associated UTI: remove/replace the catheter (source control). Do NOT treat asymptomatic catheter bacteriuria.[3]
Diabetes increases risk of severe complications — emphysematous pyelonephritis, papillary necrosis, perinephric abscess, fungal UTI. Image aggressively.[1]
Pregnancy: pyelonephritis is high-risk — admit, IV cephalosporin (avoid fluoroquinolones, tetracyclines, trimethoprim, aminoglycosides). Risk of premature labour & ARDS.[1]
Proteus = urease producer → alkaline urine → struvite (staghorn) stones. You cannot cure the infection while the stone remains — the stone IS the nidus.[1]
Enterococcus is intrinsically resistant to cephalosporins — use ampicillin or vancomycin. Add ampicillin empirically if Enterococcus suspected in severe infection.[3]
Blood cultures positive in 20-30% of pyelonephritis — always send before antibiotics. Same organism in urine + blood confirms the urinary source.[2]
Sterile pyuria (pyuria + negative routine culture) → think TB, Chlamydia/Ureaplasma, fungal, partially-treated infection, or interstitial nephritis. Send AFB/NAAT on 3 early-morning urines if TB suspected.[1]
Mortality: uncomplicated <1%; urosepsis with shock 10-20%; emphysematous 20-40%.[7]
Nitrite dipstick is false-negative for Enterococcus, Pseudomonas, Staphylococcus (non-nitrate-reducers) and with short bladder dwell time (<4 h). A negative dipstick does NOT exclude UTI.[1]
Significant bacteriuria thresholds: >10^5 CFU/mL symptomatic woman; >10^3 symptomatic man; ANY growth from suprapubic aspirate. Lower counts matter in the symptomatic male.[5]
Duration: 7 days for rapid responders with source control; 14 days for slow response, abscess, bacteraemia; prostatitis 4-6 weeks.[1]
S. aureus in the urine without lower-tract symptoms → suspect haematogenous seeding; look for endocarditis, osteomyelitis, IV line infection. Do not dismiss as contamination.[1]
Acute prostatitis causes urosepsis and needs a longer course (4 weeks+); fluoroquinolones penetrate the prostate well. Avoid vigorous prostate massage (bacteraemia).[3]
Candida UTI: treat only if symptomatic, neutropenic, or pre-procedure. Fluconazole first-line (renal excretion); amphotericin B bladder irrigation for resistant cystitis; remove urinary catheter.[3]
Recurrent UTI: address predisposing factors (post-menopausal vaginal atrophy — topical oestrogen; voiding dysfunction; stones; diabetes). Prophylaxis: trimethoprim or nitrofurantoin post-coital or nightly; consider cranberry (limited evidence).[1]
Nitrofurantoin and fosfomycin are NOT reliable for pyelonephritis — poor renal tissue levels. Reserve for cystitis. (Nitrofurantoin also contraindicated if eGFR <30-45.)[5]
Right ureter more often obstructed in pregnancy (dextro-rotation of gravid uterus compresses the right ovarian venous plexus) — but bilateral ureteric dilation is physiological.[1]
POCUS (point-of-care ultrasound) for hydronephrosis in the unstable uroseptic patient is a rapid bedside test that can trigger emergency nephrostomy before formal CT — but CT remains gold standard for parenchymal disease.[2]
Vesicoureteric reflux (VUR) in adults causes recurrent pyelonephritis and reflux nephropathy (renal scarring, hypertension, CKD) — consider in recurrent childhood-onset infections.[1]
qSOFA (RR ≥22, altered mentation, SBP ≤100) at the bedside flags high-risk sepsis outside ICU and should prompt urgent escalation in suspected urosepsis.[6]
Reassess at 48-72 h — if no improvement, RE-IMAGE (CT), reconsider organism/resistance, check source control adequacy, and look for abscess/emphysematous change/obstruction that was missed.[1]

Red flags

Critical pyelonephritis/urosepsis points

Obstructed infected kidney (pyonephrosis) = urological emergency — urgent decompression (nephrostomy/stent) within hours.[1]
Emphysematous pyelonephritis (diabetic + gas on CT) = surgical emergency — percutaneous drainage + antibiotics; nephrectomy if refractory.[4]
Source control is critical — relieve obstruction, drain abscess, remove/replace catheter. Antibiotics alone fail against an obstructed infected system.[2]
CT with contrast in ALL uroseptic/severe patients — exclude obstruction, abscess, gas. A normal bedside US does NOT exclude pyelonephritis.[1]
Remove the urinary catheter — it is often the source. Do not treat asymptomatic catheter bacteriuria.[3]
Blood cultures positive in 20-30% — send before antibiotics; same organism in blood + urine confirms source.[2]
Enterococcus is cephalosporin-resistant — add ampicillin empirically if suspected; cephalosporin monotherapy will fail.[3]
Proteus + struvite stone — you cannot cure the infection without removing the stone (the nidus).[1]
S. aureus in urine without lower-tract symptoms → hunt for endocarditis/osteomyelitis/line infection (haematogenous).[1]
Pregnancy pyelonephritis — admit, IV cephalosporin; avoid fluoroquinolones, tetracyclines, trimethoprim, aminoglycosides. Risk of premature labour & ARDS.[1]
Sterile pyuria → consider TB, atypicals, fungal, interstitial nephritis; do not repeatedly re-treat as "UTI".[1]
Emphysematous pyelonephritis mortality 20-40% — classify (Huang-Tsai), drain percutaneously first-line, reserve nephrectomy for extensive/refractory disease.[7]
Antibiotics within 1 hour of recognising septic shock (Surviving Sepsis) — after cultures, but do not delay beyond 45 min.[6]
Reassess at 48-72 h — no improvement mandates re-imaging and re-evaluation of source control.[1]

Exam practice — viva-style questions

One-minute viva prompts

A 55-year-old diabetic woman presents with fever, rigors, right flank pain and hypotension. Outline your immediate management. (Sepsis-6 in the first hour: cultures before antibiotics, broad-spectrum IV antibiotics [piperacillin-tazobactam ± gentamicin], fluids, vasopressors, lactate; early source control — CT with contrast looking for obstruction/gas/abscess; emergency nephrostomy if pyonephrosis; aggressive glucose control.)
A diabetic patient with pyelonephritis has "gas in the kidney" on CT. What is this and how do you manage it? (Emphysematous pyelonephritis — necrotising gas-forming infection in diabetics. Classify by Huang-Tsai. Treat with broad-spectrum antibiotics + percutaneous drainage first-line; nephrectomy for extensive [class IIIb/IV] or refractory disease. Mortality 20-40%.)
Why is source control central in urosepsis? (Antibiotics cannot penetrate an obstructed, pus-filled, pressure-laden collecting system, and a biofilm-laden catheter or an infected stone is a persistent nidus. Relief of obstruction, drainage of abscess and removal of catheter dramatically improve outcomes — drainage of pyonephrosis often produces immediate haemodynamic improvement.)
A pregnant woman at 28 weeks has fever and right flank pain. What is your approach? (Admit; IV cephalosporin [ceftriaxone]; avoid fluoroquinolones, tetracyclines, trimethoprim, aminoglycosides. Ultrasound first-line imaging; consider risk of premature labour/ARDS — obstetric involvement. Right-sided predilection. Treat asymptomatic bacteriuria in pregnancy to prevent this.)
A 70-year-old man with an indwelling catheter and a positive urine culture is confused. Is this a UTI? (Not necessarily — asymptomatic catheter bacteriuria is universal and should not be treated. Diagnose CAUTI only with symptoms: fever, rigors, flank pain, new confusion, haemodynamic instability. Remove/replace the catheter; treat with anti-pseudomonal/Enterococcus cover; sample from a fresh catheter.)
Justify your empirical antibiotic choice for uroseptic shock from a likely urinary source. (Broad-spectrum Gram-negative + Enterococcus cover with anti-pseudomonal activity if catheter/HCA/immunocompromised: piperacillin-tazobactam or ceftazidime + ampicillin ± gentamicin; meropenem if known ESBL/carbapenemase. De-escalate at 48-72 h on culture results. Always culture before antibiotics.)
What is the significance of Staphylococcus aureus in a urine culture? (Unless clearly a contaminant from poor collection, suspect haematogenous seeding — search for endocarditis, osteomyelitis, IV line infection. Do not dismiss as a contaminant or treat as simple UTI.)
A patient with recurrent pyelonephritis and sterile pyuria. What are you thinking? (Genitourinary tuberculosis — sterile pyuria with pyuria; send 3 early-morning urines for AFB + NAAT. Also Chlamydia/Ureaplasma, fungal, partially-treated infection, interstitial nephritis. Isolate until TB excluded.)

[1]

Summary answer (for the oral exam)

Sepsis and septic shock — apply Sepsis-3 definitions and the Surviving Sepsis one-hour bundle to urosepsis.[6]
Acute kidney injury — post-renal AKI from obstruction; septic AKI from hypoperfusion; may require RRT.
Asymptomatic bacteriuria — screen and treat in pregnancy and before urological instrumentation; otherwise do NOT treat (catheter, elderly).
Vesicoureteric reflux / reflux nephropathy — congenital; recurrent childhood pyelonephritis → renal scarring, hypertension, CKD.
Renal/perinephric abscess — complication needing percutaneous or surgical drainage.
Prostatitis — acute bacterial (urosepsis source) and chronic; longer antibiotic course (4-6 weeks).

References

[1]Johnson JR, Russo TA Acute Pyelonephritis in Adults N Engl J Med, 2018.PMID 29298155
[2]Wagenlehner FM, Lichtenstern C, Rolfes C, et al. Urosepsis--from the view of the urologist Int J Antimicrob Agents, 2011.PMID 21993485
[3]Wagenlehner FM, Tandogdu Z, Bjerklund Johansen TE An update on classification and management of urosepsis Curr Opin Urol, 2017.PMID 27846034
[4]Somani BK, Nabi G, Thorpe P, et al. Is percutaneous drainage the new gold standard in the management of emphysematous pyelonephritis? Evidence from a systematic review J Urol, 2008.PMID 18353396
[5]Gupta K, Hooton TM, Naber KG, et al. International clinical practice guidelines for the treatment of acute uncomplicated cystitis and pyelonephritis in women: A 2010 update by the Infectious Diseases Society of America and the European Society for Microbiology and Infectious Diseases Clin Infect Dis, 2011.PMID 21292654
[6]Singer M, Deutschman CS, Seymour CW, et al. The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3) JAMA, 2016.PMID 26903338
[7]Chen CC, Lin SH, Huang HC, et al. Performance of Scoring Systems in Predicting Clinical Outcomes of Patients with Emphysematous Pyelonephritis: A 14-Year Hospital-Based Study J Clin Med, 2022.PMID 36555916
[8]Tsu JH, Ma WK, Chan WC, et al. Emphysematous pyelonephritis: an 8-year retrospective review across four acute hospitals Asian J Surg, 2013.PMID 23810162

Your progress

Background and definitions

Microbiology

Escherichia coli

Proteus mirabilis

Klebsiella spp.

Enterococcus

Pseudomonas aeruginosa

Other / special

Pathophysiology

1. Ascending infection (dominant route)

2. Haematogenous spread

Inflammatory cascade

Risk factors

Female sex

Obstruction

Diabetes mellitus

Pregnancy

Catheter / instrumentation

Immunocompromise

Clinical features

Upper UTI (pyelonephritis)

Lower UTI (cystitis)

Atypical / special

Upper vs lower UTI — exam discriminator

Diagnosis

Urinalysis (dipstick + microscopy)

Urine culture & susceptibility

Blood cultures × 2

Bloods — FBC, CRP, U&E, LFTs, lactate, venous/arterial gas

Imaging — CT abdomen/pelvis with contrast (THE key modality)

Exclude obstruction EARLY

Special tests as indicated

Imaging — what to look for

CT with IV contrast

Ultrasound (incl. POCUS)

Plain CT (stone protocol)

MRI / nuclear medicine

Management

Initial resuscitation (urosepsis / septic shock)

Measure lactate; obtain blood cultures ×2 BEFORE antibiotics

Broad-spectrum antibiotics within 1 hour

Crystalloid 30 mL/kg for hypotension or lactate ≥4

Vasopressors for MAP <65 mmHg

Source control — EARLY and definitive

Supportive ICU care

Antimicrobial therapy

Uncomplicated pyelonephritis

Severe / complicated / urosepsis

Pregnancy

Prostatitis / epididymitis

Catheter-associated UTI

Source control — the cornerstone

Relieve obstruction

Drain abscess

Remove/replace urinary catheter

Treat stones (definitive)

Nephrectomy for refractory emphysematous pyelonephritis

Emphysematous pyelonephritis — the surgical emergency

Huang-Tsai classification (CT-based)

Class I

Class II

Class IIIa

Class IIIb

Class IVa/b

Management of EPN

Resuscitate + broad-spectrum antibiotics

CT with contrast — classify

Percutaneous drainage + medical therapy first-line

Nephrectomy if failure or extensive disease

Correct glycaemia and predisposing factors

Percutaneous drainage vs nephrectomy for emphysematous pyelonephritis (Somani, systematic review, J Urol 2008)

Sepsis-3 definitions (Singer, JAMA 2016)

Complications

Pyonephrosis

Renal/perinephric abscess

Emphysematous pyelonephritis

Papillary necrosis

Septic shock &amp; AKI

Renal scarring / CKD / recurrence

Septic shock & AKI