Clinical Commander

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uro.pyelonephritis.v1

Acute pyelonephritis (upper UTI; outpatient + inpatient + complicated + urosepsis)

urologyacuteadultpregnancyacuteoutpatientinpatient

shard-3-neuro-sym Phase C wave-7 2026-05-15 — initial author at INTEGRATED with full §5.5 contract depth. 9 acuity / context phenotypes encoded as severity_triggers: uncomplicated_outpatient_pyelo, uncomplicated_inpatient_pyelo, complicated_pyelo, urosepsis_with_obstruction (the central operational emergency), emphysematous_pyelo, renal_perinephric_abscess, pregnancy_pyelo, xanthogranulomatous_pyelo, acute_lobar_nephronia, esbl_or_mdr_pyelo. Pivot from sibling rows because per-phenotype dossiers do not exist (same engine, different management branch). 5 setting playbooks span the full journey: home (recognition + ED routing) → outpatient (IDSA 2010 FQ-eligible 5–7 d) → ed (STAT UA + culture + blood culture + lactate + renal US + triage) → inpatient (IV ceftriaxone × 24–72 h then PO step-down; total 7–14 d) → icu (urosepsis with shock + obstruction — SCC 2026 bundle + STAT decompression). IDSA 2010 outpatient first-line: ciprofloxacin 500 mg PO BID × 7 d OR levofloxacin 750 mg PO daily × 5 d if local FQ resistance <10%; initial IV ceftriaxone 1 g × 1 then oral step-down if FQ R >10%; TMP-SMX DS BID × 14 d if susceptible alternative. IDSA 2010 inpatient: IV ceftriaxone 1 g q24h × 24–72 h until afebrile + PO tolerance, then PO step-down per culture; total 7–14 d course. ESBL → ertapenem 1 g IV q24h (Tamma IDSA 2019); carbapenem-sparing principle — reserve meropenem for severe / non-ertapenem susceptible. Pseudomonas concern (healthcare-associated, prior MDR, immunocompromised) → cefepime 2 g IV q8h OR pip-tazo 4.5 g IV q6h. Pregnancy → admit + IV ceftriaxone 1 g q24h; PO step-down cephalexin × 10–14 d total; AVOID FQ throughout (cartilage), AVOID nitrofurantoin (no renal penetration regardless of trimester), AVOID sulfa near term. Emphysematous pyelo (gas in parenchyma on CT in diabetic) → STAT urology + IR for drainage / nephrectomy; broad-spectrum (pip-tazo or cefepime + metronidazole); high mortality without source control. Renal / perinephric abscess (CT or US) → percutaneous drainage + 4–6 wk culture-directed abx. AVOID-NITROFURANTOIN-IN-PYELO doctrine — load-bearing distinction from cystitis; nitrofurantoin concentrates in urine but NOT renal tissue (IDSA 2010). AVOID-FQ-IN-PREGNANCY doctrine — cartilage toxicity throughout pregnancy (FDA). Source control mandatory for obstruction (PCN / stent), abscess (drainage), emphysematous pyelo (drainage or nephrectomy), XGP (nephrectomy) (EAU 2020). Schema-blocked downstream: calc.qsofa_pyelo, protocol.pyelo_iv_to_po_bridge, uro.cauti.v1, uro.emphysematous-pyelo.v1, uro.renal-abscess.v1, uro.xgp.v1 — none yet in clinical-tools-registry.ts. Tickets surfaced in depth brief §9. 2026-05-22 citation remediation — all PMIDs live-verified on PubMed; mis-attributed placeholders replaced with verified anchors; RxCUIs reverse-verified on RxNav. Sibling pivots: uro.uti.uncomplicated.v1 (cystitis — nitrofurantoin pivot), symptom.fuo.v1 (FUO differential when no urinary sx), id.sepsis.core.v1 (urosepsis is most common gram-negative sepsis source) — all resolve to real engines in ALL_DOSSIERS. Dossier NOT registered in _registry.ts per shard scope (DO NOT TOUCH _registry.ts). Registration deferred to subsequent commit by shard-0 / cross-shard registry maintainer.

Entry points (7)

  • symptom
    Fever + flank pain ± N/V ± dysuria — classic acute pyelonephritis (IDSA 2010 Gupta PMID 21292654)
    fever_with_flank_pain
  • symptom
    Costovertebral angle tenderness on exam (IDSA 2010)
    cva_tenderness
  • symptom
    Dysuria + fever — pyelo concern over cystitis (IDSA 2010)
    dysuria_with_fever
  • symptom
    Hypotension + fever + flank pain / dysuria — urosepsis (SCC 2026)
    urosepsis_presentation
  • lab_abnormality
    Positive urine culture + systemic features (fever, leukocytosis, AKI) (IDSA 2010)
    urine_culture_positive_with_systemic_sx
  • imaging
    CT shows gas in renal parenchyma (emphysematous pyelo) or abscess (EAU 2020)
    ct_renal_emphysema_or_abscess
  • history
    Pregnancy + UTI symptoms + fever — admit per USPSTF / IDSA
    pregnancy_with_uti_symptoms

Required inputs (24)

  • pregnancy_statusrequired
    demographic • used at FRAME
    Pregnancy + pyelo → admit; IV ceftriaxone; AVOID FQ (cartilage); fetal monitoring (IDSA 2010; USPSTF 2019)
  • sexrequired
    demographic • used at FRAME
    Men with pyelo → always complicated workup (anatomic / prostate concern) (IDSA 2010)
  • agerequired
    demographic • used at CONTEXT
    Geriatric / pediatric workflows differ; aminoglycoside dose adjustment in elderly (IDSA 2010)
  • diabetesrequired
    history • used at CONTEXT
    Diabetic + pyelo → emphysematous pyelo risk; CT if non-resolving fever; broad-spectrum + IR consult (EAU 2020)
  • immunosuppressionrequired
    history • used at CONTEXT
    Immunocompromised → complicated pathway; broaden empirics; ID consult low threshold (IDSA 2010)
  • recent_antibioticsrequired
    history • used at CONTEXT
    Recent FQ → avoid empiric FQ; recent broad-spectrum → ESBL / Pseudomonas concern (Tamma 2019)
  • anatomic_anomaly_or_stonesrequired
    history • used at CONTEXT
    Obstruction → STAT decompression (PCN / stent); recurrent pyelo with stones → urology referral (AUA 2016)
  • prior_esbl_or_mdr_culturerequired
    history • used at CONTEXT
    Prior ESBL → empiric ertapenem; prior CRE → ID consult + tailored agent (Tamma 2019)
  • catheter_or_instrumentationrequired
    history • used at CONTEXT
    Indwelling catheter or recent instrumentation → complicated pathway + healthcare-associated empiric coverage (IDSA 2019 CAUTI)
  • transplant_status
    history • used at CONTEXT
    Renal transplant or other SOT → ID + transplant team co-management; broaden empirics (IDSA)
  • temprequired
    vital • used at RED_FLAGS
    Fever curve drives IV-to-PO step-down (typically afebrile × 24 h); persistent fever >72 h → imaging for abscess / obstruction (IDSA 2010)
  • sbprequired
    vital • used at RED_FLAGS
    Hypotension → urosepsis ICU; SCC 2026 bundle (SCC 2026)
  • hrrequired
    vital • used at RED_FLAGS
    Tachycardia component of qSOFA / SIRS / sepsis screen (SCC 2026)
  • rr
    vital • used at RED_FLAGS
    Tachypnea component of qSOFA (SCC 2026)
  • urinalysisrequired
    lab • used at INITIAL_WORKUP
    Leuk-esterase + nitrite + WBC casts (pyelo) vs cystitis pattern; sterile pyuria → STI / TB / contamination pivot (IDSA 2010)
  • urine_culturerequired
    lab • used at INITIAL_WORKUP
    Always obtain in pyelo before abx; drives narrowing + duration (IDSA 2010)
  • blood_culturesrequired
    lab • used at INITIAL_WORKUP
    Bacteremia in ~25% of pyelo; mandatory if febrile / septic appearance (SCC 2026; IDSA 2010)
  • cbcrequired
    lab • used at INITIAL_WORKUP
    Leukocytosis confirms inflammation; thrombocytopenia → sepsis severity (SCC 2026)
  • bmprequired
    lab • used at INITIAL_WORKUP
    AKI staging + dose adjustment for renal-excreted abx (KDIGO AKI 2026)
  • lactaterequired
    lab • used at INITIAL_WORKUP
    qSOFA / sepsis bundle; ≥2 mmol/L → repeat q4–6h until cleared (SCC 2026)
  • pregnancy_hcgrequired
    lab • used at INITIAL_WORKUP
    Reproductive-age women — must check; drives regimen (USPSTF 2019)
  • renal_us
    imaging • used at INITIAL_WORKUP
    First-line for obstruction; safe in pregnancy; no contrast (EAU 2020)
  • ct_abdomen_pelvis
    imaging • used at BRANCHING_WORKUP
    For non-resolving fever at 72 h, abscess concern, or emphysema concern (gas in parenchyma) (EAU 2020)
  • current_medsrequired
    medication • used at TREATMENT
    Warfarin + TMP-SMX INR rise; methotrexate + sulfa toxicity; FQ + steroid → tendinopathy (FDA 2016)

12-phase flow (12)

  1. 1FRAME
    Adult or pregnant patient with fever + flank pain + N/V → acute pyelonephritis differential. Explicit pivots: men / pregnancy / immunocompromise / obstruction / DM with gas → complicated phenotype branch (IDSA 2010)
    inputs: pregnancy_status, sex
    advance: engine scope confirmed
  2. 2ENTRY
    Fever + flank pain + CVA tenderness ± dysuria ± N/V — rule in pyelo (IDSA 2010 Gupta)
    inputs: age
    advance: entry captured
  3. 3CONTEXT
    Pregnancy, DM (emphysematous risk), immunocompromise, recent abx, anatomic anomaly / stones, prior ESBL / MDR, catheter / instrumentation, transplant (IDSA 2010; EAU 2020; Tamma 2019)
    inputs: diabetes, immunosuppression, recent_antibiotics, anatomic_anomaly_or_stones, prior_esbl_or_mdr_culture, catheter_or_instrumentation, transplant_status, current_meds
    advance: context complete
  4. 4RED_FLAGS
    Hypotension + fever → urosepsis ICU; obstruction on imaging → STAT decompression; gas on CT → emphysematous pyelo (surgical / IR); pregnancy → admit (SCC 2026; AUA 2016; EAU 2020)
    inputs: temp, sbp, hr, rr
    advance: no red flags OR escalate
  5. 5INITIAL_WORKUP
    STAT UA + urine culture + blood cultures × 2 + CBC + BMP + lactate + pregnancy test; renal US for obstruction (IDSA 2010; SCC 2026; EAU 2020)
    inputs: urinalysis, urine_culture, blood_cultures, cbc, bmp, lactate, pregnancy_hcg, renal_us
    actions: panel.ua, panel.renal, panel.cbc
    advance: workup complete
  6. 6BRANCHING_WORKUP
    Obstruction → STAT urology + IR decompression; abscess on CT → percutaneous drainage; emphysematous → surgical / IR; non-responder at 72 h → repeat imaging + ID consult; ESBL → ertapenem; Pseudomonas concern → cefepime / pip-tazo (Tamma 2019; EAU 2020)
    inputs: ct_abdomen_pelvis
    advance: pathway selected
  7. 7DIFFERENTIAL
    Pyelo vs renal colic (no fever; severe colic + hematuria) vs perinephric abscess vs basal pneumonia (referred pain) vs intra-abdominal (cholecystitis, appendicitis); pregnancy: chorio vs HELLP vs preterm labor differential (IDSA 2010)
    advance: differential narrowed
  8. 8RISK_STRATIFICATION
    IDSA 2010 uncomplicated vs complicated; qSOFA / SOFA for sepsis; CrCl for dose adjustment; pregnancy + obstruction always complicated (IDSA 2010; SCC 2026)
    advance: tier selected
  9. 9TREATMENT
    Outpatient FQ 5–7 d (if local R <10%) OR ceftriaxone IV bridge; inpatient ceftriaxone 1 g IV q24h × 24–72 h then PO step-down; ESBL → ertapenem; Pseudomonas → cefepime / pip-tazo; pregnancy → ceftriaxone; total 7–14 d; abscess 4–6 wk; XGP nephrectomy (IDSA 2010; Tamma 2019; EAU 2020)
    inputs: current_meds
    advance: regimen prescribed
  10. 10DISPOSITION
    Outpatient if FQ-eligible, low-risk, PO tolerant, reliable; admit if severe, pregnancy, obstruction, immunocompromise, sepsis; ICU for urosepsis with shock (IDSA 2010; SCC 2026)
    advance: disposition documented
  11. 11MONITORING
    Fever curve, lactate, urine output, creatinine, culture results; PO step-down when afebrile + tolerating PO; imaging if non-resolving at 72 h (IDSA 2010; KDIGO AKI 2026)
    advance: monitoring plan documented
  12. 12FOLLOWUP
    Outpatient urology if obstruction / recurrent; pregnancy → repeat culture at 1–2 wk; counsel recurrent pyelo prevention; recurrent breakthrough → urology workup (IDSA 2010; AUA 2022)
    advance: follow-up scheduled