Clinical Commander

All dossiers
gi.acute-gastroenteritis.core.v1

Acute Infectious Gastroenteritis / Acute Diarrhoea (viral, bacterial incl. invasive/inflammatory, traveller's, toxin food poisoning, C. difficile pointer) — adult + pediatric

gastroenterologyacuteadultpediatricacuteinpatientoutpatient

Authored 2026-05-16 (autonomous, shard-3). acuity acute (acute-only) — full 12-phase canonical order (FRAME…FOLLOWUP) for depth; mandatory acute phases RED_FLAGS/INITIAL_WORKUP/TREATMENT/DISPOSITION all present per _completeness.ts checkIntegrated. domain gastroenterology; population adult+pediatric. Two load-bearing pivots encoded: (1) clinical dehydration/volume severity (mild/moderate/severe-shock; pediatric % weight loss) drives the rehydration route + disposition; (2) watery-vs-inflammatory/invasive pivot drives stool testing + the antibiotic decision. Most AGE is self-limited viral → supportive only, NO routine stool testing, NO antibiotics (ACG 2016 PMID 27068718; IDSA 2017 PMID 29053792). Anti-patterns hard-coded as contraindication_substitute drugs + contraindication_rules: NO empiric antibiotics in suspected STEC/EHEC O157 (HUS RR 14.3, 95% CI 2.9-70.7; adjusted 17.3 — Wong NEJM 2000 PMID 10874060); NO antimotility in dysentery / C. difficile / pediatric bloody diarrhoea; antibiotics for traveller's only moderate-severe; quinolones avoided in pregnancy/pediatric; rising Campylobacter fluoroquinolone resistance → prefer azithromycin; ondansetron QT caution; probiotics honestly stated uncertain/limited (not standard of care). Effect sizes wired: reduced-osmolarity ORS unscheduled-IV OR 0.61 (Hahn PMID 11869639); ondansetron cessation-of-vomiting OR 0.28 / avoiding-admission OR 2.93 (Niño-Serna Pediatrics 2020 PMID 32132152) + Freedman NEJM 2006 RCT PMID 16625009; STEC-antibiotic HUS RR 14.3 (Wong NEJM 2000 PMID 10874060); multiplex PCR sens ≥94.5%/spec ≥97%, 35.3% vs 6.0% culture, 18 vs 47 h (Buss JCM 2015 PMID 25588652); 12 quantitative anchors total in the research bundle. PMID corrections vs build spec: IDSA 2017 lead author is Shane (not "Shane/Riddle"; Riddle leads the separate ACG adult guideline) — PMID 29053792 correct; traveller's diarrhoea corrected to ISTM/IDSA 2017 PMID 28521004 (spec hint 28218008 wrong); reduced-osmolarity ORS PMID 11869639 (Hahn BMJ/Cochrane; an early draft 11451781 was a different paper, corrected). All RxCUIs curl-verified via RxNav REST forward+reverse 2026-05-16: loperamide 6468, bismuth subsalicylate 19478, azithromycin 18631, ciprofloxacin 2551, ceftriaxone 2193, rifaximin 35619, ondansetron 26225, metronidazole 6922, vancomycin 11124, fidaxomicin 1111103, zinc sulfate 39954. ORS returned NO single RxCUI ({"idGroup":{}}) → non_pharm (also IV rehydration, refeeding, probiotics, stewardship/anti-pattern entries). fluids: applicability applicable — rehydration is the core intervention (LR primary; deficit+maintenance+ongoing losses; pediatric Holliday-Segar; icu setting_override = SSC 2026 Hour-1 bundle; escalation/de-escalation triggers; evidence_anchor ESPGHAN/ESPID 2014 + WHO ORS + IDSA 2017). No dedicated C. difficile engine on disk — CDI pointer routes to registry workup.fulminant_cdiff + symptom.diarrhea.ed.v1; oral vancomycin/fidaxomicin encoded in regimen Step 4 for completeness only (IDSA/SHEA 2021 PMID 34164674). Registry ids confirmed-resolving only: workups workup.acute_diarrhea (required, INITIAL_WORKUP), workup.acute_vomiting, workup.fulminant_cdiff, workup.returning_traveler_fever, workup.chronic_diarrhea; calculators calc.qsofa/calc.sirs/calc.ckd_epi_2021/calc.phq9; panels panel.cbc/cmp/renal/inflammation/lft; cascades cascade.fluid/electrolyte/labs_command; protocol protocol.septic_shock. Manifest is the required stub per spec; no panel file created (per build spec).

Entry points (6)

  • symptom
    Acute diarrhoea (≤14 d, usually <7) ± nausea/vomiting (IDSA 2017 PMID 29053792; ACG 2016 PMID 27068718)
    acute_diarrhea
  • symptom
    Bloody / mucoid (dysenteric) stool ± fever ± tenesmus — invasive/inflammatory bacterial pivot (IDSA 2017 PMID 29053792)
    bloody_dysentery
  • symptom
    Fever + diarrhoea — inflammatory/invasive or systemic enteric infection (IDSA 2017 PMID 29053792)
    fever_with_diarrhea
  • symptom
    Vomiting-predominant short-incubation illness after shared meal — preformed-toxin food poisoning (ACG 2016 PMID 27068718)
    vomiting_predominant
  • history
    Returning traveller with diarrhoea — ETEC/EAEC/Campylobacter/protozoal (ISTM/IDSA 2017 PMID 28521004)
    recent_travel
  • history
    Diarrhoea with recent antibiotics / hospitalisation / healthcare exposure — C. difficile trigger (IDSA/SHEA 2021 PMID 34164674)
    recent_antibiotics_or_healthcare

Required inputs (21)

  • agerequired
    demographic • used at CONTEXT
    Pediatric vs adult vs elderly — weight-based ORS/zinc/antiemetic dosing; age extremes raise complicated-course and mortality risk (ESPGHAN/ESPID 2014 PMID 24739189; IDSA 2017 PMID 29053792)
  • weight
    demographic • used at CONTEXT
    Pediatric ORS deficit/maintenance, zinc and ondansetron dosing; % weight loss is the pediatric dehydration metric (ESPGHAN/ESPID 2014 PMID 24739189)
  • pregnancy_status
    demographic • used at CONTEXT
    Drug safety — avoid fluoroquinolones; ceftriaxone/azithromycin preferred parenteral/oral; Listeria/Salmonella considerations (ACG 2016 PMID 27068718; ISTM/IDSA 2017 PMID 28521004)
  • hrrequired
    vital • used at CONTEXT
    Tachycardia — dehydration/hypovolaemia and sepsis screen (qSOFA/SIRS) for invasive enteric infection (IDSA 2017 PMID 29053792)
  • sbprequired
    vital • used at CONTEXT
    Hypotension/orthostasis → severe dehydration / hypovolaemic or septic shock route (IDSA 2017 PMID 29053792)
  • temperaturerequired
    vital • used at CONTEXT
    Fever component of the inflammatory/invasive pivot and the sepsis screen (IDSA 2017 PMID 29053792)
  • urine_output
    vital • used at RED_FLAGS
    Oliguria flags severe dehydration and volume-depletion AKI / HUS surveillance (KDIGO; IDSA 2017 PMID 29053792)
  • dehydration_signsrequired
    symptom • used at RED_FLAGS
    Clinical dehydration assessment (capillary refill, mucous membranes, skin turgor, sunken eyes, mental status, % weight loss) sets severity tier and rehydration route — load-bearing pivot #2 (ESPGHAN/ESPID 2014 PMID 24739189; WHO ORS PMID 11869639)
  • bloody_stoolrequired
    symptom • used at RED_FLAGS
    Bloody/dysenteric stool raises invasive bacterial probability AND (if low/no fever) the STEC/HUS prior — drives stool testing and the no-empiric-antibiotic STEC anti-pattern (IDSA 2017 PMID 29053792; Wong NEJM 2000 PMID 10874060)
  • vomiting_severity
    symptom • used at CONTEXT
    Intractable vomiting limits ORS and is an antiemetic + admission trigger (Freedman NEJM 2006 PMID 16625009)
  • symptom_durationrequired
    symptom • used at FRAME
    Acute (≤14 d) vs persistent (>14 d) — persistent routes to chronic-diarrhoea/post-infectious workup (ACG 2016 PMID 27068718)
  • immunocompromise
    history • used at CONTEXT
    HIV/transplant/chemo/biologic → broader pathogen spectrum, lower antibiotic threshold, prolonged course, admit (IDSA 2017 PMID 29053792)
  • recent_antibiotic_healthcare_exposure
    history • used at CONTEXT
    Recent antibiotics / hospitalisation → C. difficile pivot — toxin/NAAT testing, no antimotility, route to dedicated CDI pathway (IDSA/SHEA 2021 PMID 34164674)
  • travel_history
    history • used at CONTEXT
    Travel raises ETEC/EAEC/Campylobacter/protozoal priors and enteric-fever consideration (ISTM/IDSA 2017 PMID 28521004)
  • food_exposure_outbreak
    history • used at CONTEXT
    Shared-meal/sick-contact/outbreak history — toxin food poisoning, public-health reportable pathogens, food-handler considerations (ACG 2016 PMID 27068718)
  • comorbidity
    history • used at CONTEXT
    Significant comorbidity (CKD, cirrhosis, IBD, cardiac) raises complicated-course risk and modifies disposition + drug dosing (IDSA 2017 PMID 29053792)
  • creatinine
    lab • used at INITIAL_WORKUP
    Baseline + serial creatinine — volume-depletion AKI / STEC-HUS detection and renal antibiotic dose adjustment (CKD-EPI 2021)
  • electrolytes
    lab • used at INITIAL_WORKUP
    Na/K/HCO3 — hypo/hypernatraemic dehydration, hypokalaemia, metabolic acidosis from losses guide rehydration solution choice (ESPGHAN/ESPID 2014 PMID 24739189)
  • cbc
    lab • used at INITIAL_WORKUP
    Leukocytosis/left-shift supports invasive bacterial disease; falling Hb + thrombocytopenia + rising creatinine = HUS (Wong NEJM 2000 PMID 10874060)
  • lactate
    lab • used at INITIAL_WORKUP
    Elevated lactate flags hypoperfusion/septic shock from invasive enteric infection (Sepsis-3)
  • stool_studies
    lab • used at INITIAL_WORKUP
    Stool culture-independent multiplex PCR (sens ≥94.5%/spec ≥97% — Buss JCM 2015 PMID 25588652) vs culture; Shiga-toxin/STEC; fecal leukocytes/lactoferrin/calprotectin; O&P selectively; C. diff toxin/NAAT — only when inflammatory/severe/immunocompromised/traveller/public-health/persistent (IDSA 2017 PMID 29053792; ACG 2016 PMID 27068718)

12-phase flow (12)

  1. 1FRAME
    Establish scope — acute (≤14 d) infectious diarrhoea, adult vs pediatric; set the watery-vs-inflammatory and dehydration-severity frame; persistent (>14 d) or surgical-abdomen/IBD mimic forks to a different pathway (IDSA 2017 PMID 29053792; ACG 2016 PMID 27068718)
    inputs: age, symptom_duration
    advance: acute infectious-diarrhoea context confirmed and adult/pediatric set; persistent/mimic rerouted
  2. 2ENTRY
    Capture acute diarrhoea ± vomiting, bloody/dysenteric stool, fever + diarrhoea, vomiting-predominant food poisoning, returning traveller, or recent antibiotic/healthcare exposure (C. diff trigger) (IDSA 2017 PMID 29053792)
    advance: one entry trigger present
  3. 3CONTEXT
    Age/weight (pediatric dosing), pregnancy, immunocompromise, recent antibiotics/hospitalisation (C. diff), travel, food/sick-contact/outbreak exposure, comorbidity, vitals + vomiting severity; baseline renal/hepatic function for drug dosing (IDSA 2017 PMID 29053792; ISTM/IDSA 2017 PMID 28521004)
    inputs: age, weight, pregnancy_status, hr, sbp, temperature, vomiting_severity, immunocompromise, recent_antibiotic_healthcare_exposure, travel_history, food_exposure_outbreak, comorbidity
    actions: panel.cmp, cascade.labs_command
    advance: vitals + host-risk + exposure history captured
  4. 4RED_FLAGS
    Screen severe dehydration/hypovolaemic shock, sepsis/septic shock from invasive enteric infection, bloody diarrhoea + high fever + severe pain/tenesmus (dysentery), suspected STEC/HUS (bloody stool + low/no fever + oliguria + pallor → AVOID antibiotics & antimotility), volume-depletion AKI, intractable vomiting, immunocompromised host (IDSA 2017 PMID 29053792; Wong NEJM 2000 PMID 10874060)
    inputs: sbp, hr, temperature, urine_output, dehydration_signs, bloody_stool
    actions: calc.qsofa, calc.sirs, protocol.septic_shock
    advance: no red flag OR escalation route (IV resuscitation / sepsis bundle / STEC-safe pathway / admission) activated
  5. 5INITIAL_WORKUP
    Most cases: clinical only — NO routine stool testing, NO antibiotics (viral self-limited; ACG 2016 PMID 27068718). Test only if inflammatory/bloody/febrile/severe/immunocompromised/traveller/public-health/persistent: stool multiplex PCR (preferred — sens ≥94.5%/spec ≥97%, Buss PMID 25588652) vs culture, Shiga-toxin/STEC, fecal leukocytes/lactoferrin/calprotectin (limited), O&P selectively, C. diff toxin/NAAT if antibiotic/healthcare exposure; CBC/CMP/electrolytes/creatinine/lactate + blood cultures if severe/septic/immunocompromised (IDSA 2017 PMID 29053792)
    inputs: creatinine, electrolytes, cbc, lactate, stool_studies
    actions: workup.acute_diarrhea, panel.cbc, panel.cmp, panel.renal, panel.inflammation
    advance: supportive-only pathway chosen OR targeted stool/lab studies sent
  6. 6BRANCHING_WORKUP
    Branch by pivot — watery/non-febrile → supportive, no testing; inflammatory/dysenteric → culture/PCR + consider empiric azithromycin (NOT if STEC suspected); traveller → ETEC/EAEC/protozoal pathway; vomiting-predominant → toxin food poisoning vs acute-vomiting workup; recent abx/healthcare → fulminant-CDI workup; persistent >14 d → chronic-diarrhoea workup; returning-traveller fever → enteric-fever/malaria rule-out (IDSA 2017 PMID 29053792; ISTM/IDSA 2017 PMID 28521004; IDSA/SHEA 2021 PMID 34164674)
    inputs: bloody_stool, travel_history, recent_antibiotic_healthcare_exposure, symptom_duration
    actions: workup.acute_diarrhea, workup.acute_vomiting, workup.fulminant_cdiff, workup.returning_traveler_fever, workup.chronic_diarrhea
    advance: phenotype identified (viral-watery / inflammatory-bacterial / toxin food poisoning / traveller / C. diff / persistent)
  7. 7DIFFERENTIAL
    Viral AGE (commonest) vs inflammatory bacterial (Salmonella/Shigella/Campylobacter/STEC/Yersinia/Vibrio) vs preformed-toxin food poisoning vs traveller's (ETEC/EAEC/protozoal) vs C. difficile vs non-infectious mimics (early IBD/UC flare, ischaemic colitis, appendicitis with diarrhoea, DKA/thyrotoxicosis, medication/laxative, overflow, HUS/TTP) (IDSA 2017 PMID 29053792; ACG 2016 PMID 27068718)
    inputs: bloody_stool, stool_studies
    advance: infectious AGE phenotype confirmed or alternative diagnosis routed
  8. 8RISK_STRATIFICATION
    Dehydration severity tier (mild/moderate/severe — pediatric % weight loss) + sepsis screen (qSOFA/SIRS) + volume-depletion AKI (CKD-EPI 2021) + host-risk modifiers (age extremes, immunocompromise, comorbidity, pregnancy) → disposition + antibiotic decision (IDSA 2017 PMID 29053792; ESPGHAN/ESPID 2014 PMID 24739189)
    inputs: dehydration_signs, sbp, hr, creatinine, immunocompromise
    actions: calc.qsofa, calc.sirs, calc.ckd_epi_2021
    advance: severity tier + host-risk documented and management/disposition fork chosen
  9. 9TREATMENT
    Rehydration cornerstone: reduced-osmolarity ORS for mild-moderate (unscheduled-IV OR 0.61, Hahn PMID 11869639); IV isotonic crystalloid (LR/NS) for severe/shock — deficit + maintenance + ongoing losses. Early refeeding, continue breastfeeding. Ondansetron for vomiting limiting ORS (peds ED — OR 0.28 cessation, OR 2.93 avoiding admission; Freedman PMID 16625009, Niño-Serna PMID 32132152; QT caution). Selective antimicrobials: empiric azithromycin (febrile dysentery / moderate-severe traveller's), ciprofloxacin where susceptible, ceftriaxone for severe/bacteraemic/enteric fever/pregnancy, rifaximin (non-invasive traveller's); pathogen-directed de-escalation. Zinc (pediatric LMIC). Loperamide/bismuth ONLY for mild non-bloody non-febrile. C. diff → oral vancomycin/fidaxomicin via dedicated pathway. Anti-patterns enforced: NO empiric abx in STEC (HUS RR 14.3 — Wong PMID 10874060); NO antimotility in dysentery/C.diff/peds-bloody (IDSA 2017 PMID 29053792; ACG 2016 PMID 27068718; ISTM/IDSA 2017 PMID 28521004)
    inputs: dehydration_signs, creatinine, pregnancy_status, bloody_stool, vomiting_severity
    actions: protocol.septic_shock, cascade.fluid, cascade.electrolyte
    advance: rehydration route executed, antiemetic/antimicrobial decision made (incl. anti-pattern exclusions), C. diff routed if applicable
  10. 10DISPOSITION
    Outpatient with ORS + return precautions for most (mild-moderate, tolerating PO, no red flag); admit for severe dehydration/shock, sepsis, AKI, intractable vomiting, inability to maintain hydration, significant comorbidity, immunocompromise, social; ICU for septic shock / fulminant disease. Public-health reportable pathogens + outbreak/food-handler considerations (IDSA 2017 PMID 29053792; ACG 2016 PMID 27068718)
    inputs: dehydration_signs, sbp, immunocompromise, vomiting_severity
    advance: destination set (home / ward / ICU) and public-health reporting addressed
  11. 11MONITORING
    Hydration status / urine output / weight (pediatric), electrolytes + renal function (AKI, antibiotic dosing), clinical course/response, antibiotic stewardship + QT with ondansetron, HUS surveillance (CBC/smear/creatinine) if STEC, response to de-escalation (IDSA 2017 PMID 29053792; Wong NEJM 2000 PMID 10874060)
    inputs: dehydration_signs, urine_output, creatinine, electrolytes, cbc
    actions: panel.renal, panel.cbc, cascade.electrolyte
    advance: clinical improvement documented or escalation per failure/HUS criteria
  12. 12FOLLOWUP
    Most: complete recovery, return precautions, hygiene/food-safety counselling, no routine test-of-cure; public-health reporting + food-handler clearance for reportable pathogens; persistent/post-infectious symptoms → reassess (post-infectious IBS — gi.ibs.core.v1; persistent → chronic-diarrhoea workup); rotavirus-vaccine context (pediatric) (IDSA 2017 PMID 29053792; ACG 2016 PMID 27068718)
    inputs: symptom_duration, food_exposure_outbreak, age
    actions: workup.chronic_diarrhea, calc.phq9
    advance: recovery confirmed or persistent/post-infectious pathway routed, public-health/food-handler addressed, follow-up scheduled