Clinical Commander

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id.pyelonephritis.core.v1

Acute pyelonephritis (uncomplicated → complicated)

infectious_diseaseacuteadultacuteinpatientoutpatient
Start encounter →Print handoutPRODUCTION

Cross-engine: id.sepsis.core.v1 for urosepsis escalation; neph.aki.core.v1 for obstructive AKI; neph.nephrolithiasis.core.v1 for stone-driven phenotype. Pediatric pyelo split as urinary-tract-infections-in-children pkg — separate dossier when authored. PRODUCTION blockers: RxCUI verification (npm run research:rxnav:validate); dedicated pyelonephritis duration test pending. Deepened 2026-05-14 (shard-5-obped-id depth-pass-1): added co-located _briefs/id.pyelonephritis.core.v1.md + _research-bundles/id.pyelonephritis.core.v1.md. Refined outpatient setting playbook with 24-72 h structured follow-up, culture-driven de-escalation at day 2-3, pregnancy-specific surveillance, recurrent-UTI prevention counselling (post-coital voiding, topical estrogen, low-dose prophylaxis options), renal imaging at 4-6 wk if recurrent/complicated, urology referral threshold, and ACIP 2024 vaccination check (PCV20, influenza, COVID-19). Added severity triggers: mdro_esbl_or_cre_pathogen (severe — carbapenem for ESBL; ceftazidime-avibactam / meropenem-vaborbactam / cefiderocol for CRE; mandatory ID consult) and kidney_transplant_pyelonephritis (severe — admit regardless of severity, mandatory ID + transplant-nephrology coordination, IS minimisation per protocol). Appended PMIDs 20175247 (Hooton IDSA cUTI 2010 NEEDS_SOURCE_REVIEW), 25920922 (FOCUS 1 ceftolozane-tazobactam NEEDS_SOURCE_REVIEW), 26903338 (Sepsis-3 definitional anchor for urosepsis), 16625125 (Kumar 2006 antibiotic-timing mortality), 32191793 (Rybak IDSA vancomycin consensus 2020), bringing evidence.pmids from 5 to 10. last_reconciled bumped to 2026-05-14. 2026-05-22 citation+drug-code remediation: PubMed-live-verified all PMIDs — corrected FOCUS-1 25920922 (= dermatology case report) -> Wagenlehner ASPECT-cUTI 25931244; corrected placeholder Sandberg 18664623 (= APL ATRA trial) -> Sandberg Lancet 2012 22726802; Hooton cUTI confirmed 20175247; removed mis-attributed 25776532 (ProMISe sepsis EGDT) and 29766750 (POINT stroke). RxNav-corrected wrong RxCUIs: TMP-SMX 10180 (=sulfamethoxazole alone) -> 10831, meropenem 1665005 (=ceftriaxone 500mg) -> 29561, vancomycin 477391 (=levofloxacin oral soln) -> 11124. Phenotype matrix (uncomplicated/complicated × outpatient/inpatient/ICU × pathogen × resistance × pregnant/non-pregnant × diabetic × immunocompromised × kidney-transplant × prostatitis-overlap) encoded indirectly via severity_triggers (mdro_esbl_or_cre_pathogen, kidney_transplant_pyelonephritis, pregnancy_pyelonephritis, emphysematous_pyelonephritis, urosepsis_with_shock, obstructive_uropathy_with_infection, no_improvement_at_72h) and via workups (workup.aki, workup.nephrolithiasis) and via per-setting playbook drug logic. First-class TS field for phenotype matrix is schema-blocked — see docs/framework-audit/shard-5-obped-id-state.md Schema-blocked queue. Bayesian linkage (UA pyuria + nitrites + leukocyte esterase pooled LRs; lactate LR for urosepsis carryover; CT/US LR for obstruction; T_treat = empiric within 1 h for septic shock OR within 3 h for non-shock admitted pyelo; T_test = mild + tolerant of PO + reliable follow-up = outpatient observation; cross-dossier routing to id.sepsis.core.v1 if shock features, ob.* for pregnant complications, neph.aki.core.v1 if AKI, neph.nephrolithiasis.core.v1 if stone-driven) documented in the co-located _research-bundles/id.pyelonephritis.core.v1.md. ROS/DDx LR seed data audited by npm run audit:ros-ddx-coverage (cross-cutting; not touched by this shard). Prehospital recognition encoded via outpatient playbook escalation_triggers (sepsis features / vomiting / pregnancy → ED); first-class "prehospital" DossierSetting value is schema-blocked (cross-shard).

Entry points (3)

  • symptom
    Flank pain + fever
    flank_pain_fever
  • symptom
    Costovertebral angle tenderness with systemic symptoms
    cva_tenderness
  • lab_abnormality
    Pyuria/bacteriuria with fever, tachycardia, or rigors
    pyuria_with_systemic_signs

Required inputs (13)

  • temperaturerequired
    vital • used at CONTEXT
    Fever ≥38°C is core; drives sepsis screen
  • sbprequired
    vital • used at RED_FLAGS
    Hypotension → urosepsis pathway + SSC bundle
  • hrrequired
    vital • used at CONTEXT
    Tachycardia component of SIRS / qSOFA
  • pregnancy_statusrequired
    symptom • used at CONTEXT
    Pregnancy → admit, avoid fluoroquinolones, narrower antibiotic options
  • recent_abxrequired
    history • used at CONTEXT
    Resistance risk; informs empiric choice + IDSA 2025 4-step framework
  • urologic_abnormality_or_stentrequired
    history • used at CONTEXT
    Complicated phenotype; stent / nephrolithiasis → urology
  • diabetes_or_immunocompromiserequired
    history • used at CONTEXT
    Emphysematous pyelo / abscess risk
  • urinalysis_with_microrequired
    lab • used at INITIAL_WORKUP
    Pyuria + bacteriuria + nitrites supports diagnosis
  • urine_culturerequired
    lab • used at INITIAL_WORKUP
    Anchors targeted therapy + susceptibility
  • blood_culture
    lab • used at INITIAL_WORKUP
    Bacteremia in 15-30%; required when admitting / sepsis features
  • creatininerequired
    lab • used at TREATMENT
    Baseline renal + obstructive AKI screen + dose adjustment
  • lactate
    lab • used at INITIAL_WORKUP
    Sepsis bundle when SIRS positive
  • renal_ultrasound_or_ct
    imaging • used at BRANCHING_WORKUP
    Imaging if no improvement at 48-72h, recurrent pyelo, suspected obstruction / abscess / emphysematous

12-phase flow (12)

  1. 1FRAME
    Adult acute pyelonephritis. Pediatric pyelo and prostatitis covered by sibling engines
    advance: scope confirmed
  2. 2ENTRY
    Recognize flank pain + fever / CVAT + UA evidence
    advance: entry trigger present
  3. 3CONTEXT
    Pregnancy, immunocompromise, diabetes, urologic devices, prior antibiotic exposure, MDRO risk factors
    inputs: temperature, hr, pregnancy_status, recent_abx, urologic_abnormality_or_stent, diabetes_or_immunocompromise
    advance: risk factors + IDSA 2025 patient-factor row complete
  4. 4RED_FLAGS
    Sepsis (qSOFA ≥2 / SIRS), obstructive uropathy with infection, emphysematous pyelo, pregnancy with sepsis → admit + STAT decompression / pressors / SSC bundle
    inputs: sbp
    actions: calc.qsofa
    advance: red flags addressed; urology engaged for obstruction
  5. 5INITIAL_WORKUP
    UA + culture + blood cultures if admit / sepsis, CBC, BMP, lactate if SIRS, beta-hCG if reproductive age
    inputs: urinalysis_with_micro, urine_culture, creatinine, lactate
    actions: panel.ua, panel.cbc, panel.renal
    advance: workup sent; empirics started ≤1h if septic
  6. 6BRANCHING_WORKUP
    Renal US / CT abdomen/pelvis if no clinical improvement at 48-72h, suspected obstruction, abscess, or emphysematous pyelo; nephrolithiasis branch
    inputs: renal_ultrasound_or_ct
    actions: workup.aki, workup.nephrolithiasis
    advance: imaging done when criteria met
  7. 7DIFFERENTIAL
    Lower UTI, perinephric abscess, renal stone with obstruction, prostatitis, PID, herpes zoster, MSK flank pain
    advance: mimics excluded
  8. 8RISK_STRATIFICATION
    Uncomplicated vs complicated; outpatient vs admit per IDSA 2025 4-step (severity → resistance risk → patient factors → antibiogram)
    inputs: temperature, sbp
    advance: tier + disposition set
  9. 9TREATMENT
    Outpatient uncomplicated: ciprofloxacin 500 mg BID × 5-7 d (or 1 g ER × 7d), levofloxacin 750 mg × 5-7 d. Where local resistance ≥10% — single-dose IV ceftriaxone 1 g or aminoglycoside before oral PO. TMP-SMX × 14 d only if susceptibility confirmed. Inpatient: ceftriaxone 1-2 g IV q24h or piperacillin/tazobactam if MDRO risk; carbapenem if ESBL; vancomycin/daptomycin only if Enterococcus on culture. Pregnancy: avoid FQ; use ceftriaxone IV → step-down per culture. Source control: relieve obstruction urgently. Step-down to PO when afebrile + improving 48-72h; total 5-7 d (short-course non-inferior, CMI 2025)
    inputs: creatinine, pregnancy_status
    advance: antibiotic + dispo set; obstruction relieved if present
  10. 10DISPOSITION
    Discharge well-appearing tolerating PO; admit pregnancy / sepsis / obstruction / failed outpatient / pediatric / immunocompromised
    inputs: sbp
    advance: level of care set
  11. 11MONITORING
    Resolution of fever within 48-72h; if not — re-image and broaden empirics; trend creatinine + WBC; vancomycin AUC if used
    inputs: creatinine
    actions: panel.renal, panel.cbc
    advance: response confirmed at 48-72h
  12. 12FOLLOWUP
    Test of cure not routinely needed unless pregnant or relapse; prevention counseling; recurrent UTI workup if ≥2 episodes/year
    advance: follow-up plan documented