Clinical Commander

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gi.crohns.core.v1

Crohn's Disease

gastroenterologychronicacuteadultoutpatientinpatienttransition
Start encounter →Print handoutPRODUCTION

Manifest is full and current (ACG 2018+2024 + AGA 2021 + ECCO 2023/2024 + BSG 2024 + SONIC + ADVANCE/MOTIVATE + SELECT-CD + SEQUENCE + GALAXI + VARSITY) with 10 phenotypes (Montreal L1/L2/L3/L4 + B2/B3 + perianal + pregnancy + EIM + paediatric) and full medication/dosing tables for biologics + small molecules. Problem-package at src/lib/tier3/problem-package/packages/crohn-s-disease/ has all atoms + phenotypes + regimen + interlinks; no `_design-brief.md`. Gaps for INTEGRATED: no design brief md file; evidence.pmids array empty (manifest cites guideline labels but no numeric PMIDs); no engine-specific test_files; CDAI / Harvey-Bradshaw / SES-CD / Rutgeerts / PDAI calculators are referenced in manifest.classifications but not in clinical-tools-registry. No regimen_axes — induction (budesonide, prednisone, infliximab, ustekinumab, risankizumab, upadacitinib, guselkumab) and maintenance (azathioprine, 6-MP, methotrexate, vedolizumab, certolizumab, adalimumab) wired in manifest.medications without RxCUI verification through regimen-builder.

Entry points (6)

  • symptom
    Chronic diarrhea ± rectal bleeding
    chronic_diarrhea
  • symptom
    RLQ abdominal pain + weight loss
    rlq_abdominal_pain_weight_loss
  • symptom
    Perianal pain / fistula / abscess
    perianal_disease
  • lab_abnormality
    Elevated fecal calprotectin / CRP / iron deficiency
    elevated_calprotectin_crp
  • imaging
    MRE / colonoscopy showing transmural inflammation, skip lesions, granulomas
    mre_inflammation
  • problem_list
    Existing CD on problem list (flare or maintenance visit)
    crohns_disease

Required inputs (20)

  • agerequired
    demographic • used at CONTEXT
    Paediatric onset triggers EEN + transition pathway; elderly drives biologic safety profile
  • temperaturerequired
    vital • used at CONTEXT
    Fever in flare / abscess / sepsis
  • hrrequired
    vital • used at CONTEXT
    Tachycardia in severe flare / sepsis
  • sbprequired
    vital • used at CONTEXT
    Hypotension in obstruction / sepsis / GI bleed
  • crprequired
    lab • used at INITIAL_WORKUP
    Inflammatory marker; tracks disease activity
  • fecal_calprotectinrequired
    lab • used at INITIAL_WORKUP
    Mucosal inflammation surrogate (best for colonic CD)
  • cbcrequired
    lab • used at INITIAL_WORKUP
    Anemia (chronic disease + iron deficiency); leukocytosis in flare
  • albuminrequired
    lab • used at INITIAL_WORKUP
    Nutritional status + protein-losing enteropathy
  • creatininerequired
    lab • used at INITIAL_WORKUP
    Drug dosing; pre-biologic baseline
  • ferritin_iron_studiesrequired
    lab • used at INITIAL_WORKUP
    Iron deficiency anemia common
  • tpmt_nudt15
    lab • used at TREATMENT
    Thiopurine dosing safety
  • tb_quantiferon
    lab • used at TREATMENT
    Pre-biologic latent TB screen
  • hepatitis_b_screen
    lab • used at TREATMENT
    Pre-biologic HBV screen (reactivation risk)
  • ileocolonoscopyrequired
    imaging • used at INITIAL_WORKUP
    Diagnostic + endoscopic activity (SES-CD)
  • mr_enterographyrequired
    imaging • used at INITIAL_WORKUP
    Small-bowel + transmural assessment; stricturing vs penetrating
  • pelvic_mri_perianal
    imaging • used at BRANCHING_WORKUP
    Gold standard for perianal fistula mapping
  • smokingrequired
    history • used at CONTEXT
    Smoking worsens CD course; cessation is high-yield intervention
  • prior_cd_medsrequired
    history • used at CONTEXT
    Steroid exposure, biologic history, response/failure pattern
  • pregnancy_status
    history • used at CONTEXT
    Methotrexate/JAKi/S1P contraindicated; biologic continuation pathway
  • extraintestinal_manifestations
    history • used at CONTEXT
    Joint/skin/eye/PSC EIMs guide therapy choice

12-phase flow (12)

  1. 1FRAME
    Confirm CD scope (chronic IBD with potential acute flare); distinguish from UC, infectious colitis, IBS, TB
    inputs: age
    advance: IBD pattern recognized
  2. 2ENTRY
    Recognize chronic diarrhea, RLQ pain, weight loss, perianal disease, or known-CD flare visit
    advance: one entry trigger present
  3. 3CONTEXT
    Vitals, smoking status, prior CD therapies + responses, EIMs, vaccinations, pregnancy, NSAID/abx exposure, family hx
    inputs: temperature, hr, sbp, smoking, prior_cd_meds, pregnancy_status, extraintestinal_manifestations
    advance: context captured
  4. 4RED_FLAGS
    Acute obstruction, peritonitis/perforation, intra-abdominal abscess, massive GI hemorrhage, toxic megacolon, severe malnutrition (BMI <16), sepsis, VTE on immunosuppression, adrenal crisis
    inputs: sbp, temperature
    advance: no red flag or escalated to acute pathway
  5. 5INITIAL_WORKUP
    CBC, CRP/ESR, fecal calprotectin, CMP/albumin, iron studies, ferritin, B12/folate/vit D, stool cultures + C. diff + ova/parasites, ileocolonoscopy with biopsies, MRE
    inputs: crp, fecal_calprotectin, cbc, albumin, creatinine, ferritin_iron_studies, ileocolonoscopy, mr_enterography
    actions: panel.lft, panel.renal, panel.cbc
    advance: baseline labs + endoscopy + cross-sectional imaging returned
  6. 6BRANCHING_WORKUP
    Pelvic MRI + EUA for perianal disease; capsule endoscopy if MRE neg; upper GI endoscopy if L4 suspected; CT if acute obstruction/abscess; pre-biologic TPMT/NUDT15, TB, HBV
    inputs: pelvic_mri_perianal, tpmt_nudt15, tb_quantiferon, hepatitis_b_screen
    actions: toxic_megacolon
    advance: phenotype identified (L1/L2/L3/L4, B1/B2/B3, ±perianal)
  7. 7DIFFERENTIAL
    Distinguish CD from UC, IBS, infectious colitis, intestinal TB, celiac, NSAID enteropathy, GI lymphoma, colorectal cancer, Behçet, ischemic / microscopic colitis
    advance: diagnosis confirmed (Montreal location + behaviour)
  8. 8RISK_STRATIFICATION
    Montreal classification; CDAI / Harvey-Bradshaw Index; SES-CD; PDAI for perianal; high-risk features (deep ulcers, perianal, young, extensive)
    inputs: crp
    advance: severity + behaviour documented
  9. 9TREATMENT
    Induction (steroids/budesonide/EEN, anti-TNF, IL-23i, JAKi); maintenance (biologic ± thiopurine per SONIC); surgery for limited stricturing or penetrating; perianal seton + IFX; abscess drainage before biologic
    inputs: creatinine, tpmt_nudt15, tb_quantiferon, hepatitis_b_screen
    advance: induction + maintenance plan agreed
  10. 10DISPOSITION
    ICU / surgical for obstruction, perforation, abscess, fulminant; floor for severe flare; outpatient for mild-moderate
    inputs: sbp
    advance: destination set
  11. 11MONITORING
    Calprotectin + CRP q3-6mo, CBC/LFT/BMP on immunomodulator, biologic trough levels + ADA, endoscopic reassessment 6-12mo, CRC surveillance, DEXA if steroid exposed
    inputs: crp, fecal_calprotectin, cbc
    advance: monitoring cadence set
  12. 12FOLLOWUP
    q2-4w during induction, q3mo first year maintenance, q6mo stable remission; postop colonoscopy 6-12mo (Rutgeerts); annual comprehensive review; preconception counselling
    advance: follow-up scheduled