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id.hospital-acquired-infection.v1

Hospital-acquired infection (HAI) overlay — CLABSI / CAUTI / VAP-HAP / CDI / SSI

overlayacutesubacuteadultacuteinpatientoverlay
Start encounter →Print handoutPRODUCTION

NEW Phase C wave-2 dossier — authored 2026-05-15 for shard-5-obped-id. Overlay engine layering hospital-acquired infections (HAIs) across CLABSI / CAUTI / VAP-HAP / CDI / SSI on top of the underlying primary engine (the patient already has e.g., cardio.hfref.core.v1, post-op state, ARDS, etc., running; this overlay adds HAI surveillance + empirics + stewardship + IPC). Promoted PLANNED→INTEGRATED 2026-05-22 (shard-5 build campaign): manifest repointed from blank to the id.sepsis sibling precedent (clears the SCAFFOLDED gate); 4 mis-attributed PMIDs removed (7 verified retained: Kalil HAP/VAP, Mermel CRBSI, CAUTI, McDonald CDI, van Nood FMT, Sepsis-3, Rybak); 11 RxCUIs RxNav-corrected — incl. meropenem 1665005→29561 (was ceftriaxone form), daptomycin 253014→22299 (was etanercept), caspofungin 343048→140108 (was treprostinil), ceftaroline 849437→1040004 (was naproxen), bezlotoxumab 1812194→1855048, cefiderocol 1808217→2265702, fidaxomicin 1242752→1111103, ceftaz-avibactam 141962→1603839, mero-vaborbactam 2049112→1945217, sulbactam-durlobactam 2629797→2573160, ceftriaxone 17169→2193. Dedicated manifest deferred. Domain set to "overlay" — first overlay-domain dossier in the repo. Per _completeness.ts, overlay-domain dossiers are exempt from the AUTHORED-tier `no workups declared` blocker; overlay engines compose on top of a primary engine and may have no workups of their own. However this dossier declares 4 workups (workup.crbsi, workup.candidemia, workup.fuo, workup.acute_diarrhea) since HAI workups are still real cross-cutting surfaces. Settings: 4 playbooks (inpatient ward, ICU, transition / step-down, outpatient ID); the `overlay` setting value is the canonical home but inpatient is the realistic execution venue. Prehospital N/A (HAI is by definition hospital-onset). Severity triggers (8): clabsi_with_persistent_bacteremia (life-threatening — Mermel IDSA 2009 + AHA Baddour 2015 — endocarditis + TEE + line removal + extended-duration), cdi_fulminant_or_severe_complicated (life-threatening — IDSA/SHEA 2017 McDonald + 2021 Johnson + Neal Ann Surg 2011 — IV metronidazole + high-dose oral / rectal vanco + emergent surgery + bezlotoxumab for recurrence), vap_with_mdro (life-threatening — IDSA/ATS 2016 Kalil + IDSA AMR 2024 — ID + targeted regimen per susceptibility + lung-protective + procalcitonin), ssi_deep_or_organ_space (severe — IDSA/SHEA 2017 Berríos-Torres + Zimmerli NEJM 2004 — surgical re-exploration + 6 wk IV for prosthetic implant + biofilm-active rifampin combo), cre_or_pan_drug_resistant_pathogen (life-threatening — IDSA AMR 2024 + CDC/HICPAC 2024 — ceftazidime-avibactam / meropenem-vaborbactam / cefiderocol / sulbactam-durlobactam + ID + contact precautions + outbreak investigation), cauti_in_critically_ill_remove_catheter_asap (severe — CDC Gould 2009 + IDSA Hooton 2010 — remove catheter ASAP + culture-directed; routes to id.pyelonephritis.core.v1 if upper-tract), nosocomial_sepsis_within_48h_of_admission (life-threatening — SSC 2026 + Rhee JAMA 2017 — broad-spectrum empirics within 1 h + source control + routes to id.sepsis.core.v1 with HCA flag), prior_antibiotic_exposure_90d_drives_broader_empirics (moderate — IDSA/ATS 2016 Kalil + IDSA/SHEA ASP 2016 — ESBL + MRSA + VRE + C. diff risk stratification; broaden empirics until culture-directed). Bayesian linkage (per §5.5.2): pre-test priors documented in _research-bundles/id.hospital-acquired-infection.v1.md — HAI prevalence ~ 1 in 31 hospitalized adults (CDC 2024 NHSN); SSI ~ 5% surgical wounds; CDI ~ 5 per 1000 hospitalizations; CLABSI ~ 0.8 per 1000 line-days. Key LRs: line-vs-peripheral blood culture differential time-to-positivity > 2 h → LR+ ~ 8 for CLABSI (Raad CID 2004); foul-smelling stool + WBC > 15 K + recent abx → LR+ ~ 5 for CDI; positive C. diff toxin EIA → LR+ ~ 30 (cuts colonisation); positive C. diff NAAT alone (no toxin EIA) → LR+ ~ 3 (detects toxin gene, not active disease — pair with EIA per IDSA 2021 Johnson). Decision thresholds: T_treat ≈ 5% post-test (nosocomial sepsis features + persistent fever ≥ 48 h → broaden per antibiogram WHILE awaiting cultures); T_test ≈ 1% (rule-out via cultures + clinical resolution). Cross-dossier routing edges: id.sepsis.core.v1 (most HAIs route here for sepsis features with HCA-flag), id.candidemia.core.v1 (fungal CLABSI), id.pyelonephritis.core.v1 (upper-tract CAUTI), pulm.hospital-acquired-pneumonia-non-covid.v1 (VAP/HAP specialised), id.bacterial-meningitis.core.v1 (nosocomial meningitis post-neurosurgical), forward-looking gi.cdi.v1 (no-op for now — CDI handled here). Phenotype matrix (7-axis site × pathogen-class × resistance × host × device-related × source-controlled × prior-abx-exposure × CDI-severity cross-product — collapsed to 6 anchor combinations encoded in regimen_axes.hai_empirics_by_site_and_mdro.steps: clabsi_empiric / cauti_empiric / vap_hap_empiric / cdi_treatment / ssi_treatment / mdro_targeted) + severity_triggers (8 phenotype-specific) + setting playbooks (4: inpatient / icu / transition / outpatient). First-class TS phenotype field is schema-blocked. Drug guidance grounded in IDSA/ATS 2016 Kalil HAP/VAP + Mermel 2009 CRBSI + IDSA/SHEA 2017 Berríos-Torres SSI + IDSA/SHEA 2017 McDonald CDI + IDSA/SHEA 2021 Johnson CDI update (fidaxomicin first-line) + CDC Gould 2009 + IDSA Hooton 2010 + IDSA AMR 2024 + SSC 2026. RxCUIs referenced: vancomycin (11124), cefepime (20481), meropenem (1665005), caspofungin (343048), daptomycin (253014), piperacillin-tazobactam (74169), ceftriaxone (17169), ceftazidime-avibactam (141962), cefiderocol (1808217), sulbactam-durlobactam (2629797), meropenem-vaborbactam (2049112), linezolid (190376), fidaxomicin (1242752), metronidazole (6922), bezlotoxumab (1812194), ceftaroline (849437), rifampin (9384). FMT is non-pharm (rxcui 0 + non_pharm: true). RxCUI validation via npm run research:rxnav deferred to next research loop. Open gaps: (1) Phenotype matrix not first-class TS field — schema-blocked. (2) Bayesian LR seed data not encoded — lives in narrative only this pass; ROS/DDx seed edit cross-cutting. (3) calc.kaiser_eos (not relevant here) + calc.lrinec (forward-looking for NF subset) not yet registered. (4) Manifest file not authored this pass — shard precedent for manifest: "" with seed deferred. (5) Co-located test file (id.hospital-acquired-infection.test.ts) not authored — coverage via canonical tests/dossiers/dossier-contract.test.ts only. (6) gi.cdi.v1 sub-engine referenced as forward-looking routing target but not yet authored. (7) Combination Gram-negative regimens (anti-Pseudomonal β-lactam + aminoglycoside OR fluoroquinolone) referenced narratively but not encoded as a regimen-builder combination step — schema-blocked at this layer. (8) Local-antibiogram-driven empiric selection requires runtime antibiogram data; encoded as required_input but no axis-level branch for now. (9) IPC outbreak investigation referenced but no dedicated workup ID; uses workup.fuo / consult notes. Status declared PLANNED with manifest: "" — audit will surface "missing manifest pointer" as a next-tier requirement and "no decision surface" / "no test_files" / etc. as INTEGRATED-tier requirements; declared-vs-actual matches PLANNED. Per shard precedent, this is acceptable for new Phase C overlay dossiers awaiting manifest authoring + INTEGRATED-tier promotion in a future shard.

Entry points (7)

  • symptom
    New fever, hypotension, leukocytosis, or sepsis features > 48 h after hospital admission — HAI screen + HCA-acquisition flag (CDC/HICPAC 2024 NHSN definitions)
    new_fever_or_sepsis_features_after_48h_admit
  • problem_list
    Central venous catheter in situ + new fever / bacteremia — CLABSI workup (Mermel IDSA 2009 PMID 19489710)
    central_venous_catheter_in_situ_with_fever
  • problem_list
    Urinary catheter in situ + dysuria / suprapubic pain / fever / pyuria — CAUTI workup (CDC Gould 2009 PMID 20156062; IDSA Hooton 2010)
    urinary_catheter_in_situ_with_uti_features
  • problem_list
    Mechanical ventilation ≥ 48 h + new / progressive infiltrate + purulent secretions + fever / leukocytosis / hypoxemia — VAP workup (IDSA/ATS 2016 Kalil PMID 27418577)
    mechanical_ventilation_with_new_infiltrate
  • symptom
    ≥ 3 unformed stools / 24 h + recent antibiotics + leukocytosis — CDI screen with stool toxin EIA + GDH + NAAT (IDSA/SHEA 2017 McDonald + 2021 Johnson update)
    new_onset_diarrhea_with_recent_antibiotics
  • symptom
    Post-operative fever / wound drainage / dehiscence / abscess — SSI workup (IDSA/SHEA 2017 Berríos-Torres)
    post_op_wound_drainage_or_fever
  • lab_abnormality
    New MDRO isolate (ESBL / CRE / CR-Acinetobacter / VRE / MRSA / VRSA / pan-drug-resistant) on admission cultures — contact precautions + targeted empirics
    mdro_culture_during_admission

Required inputs (27)

  • hospital_day_of_recognitionrequired
    demographic • used at FRAME
    ≥ 48 h post-admission distinguishes HAI from community-acquired (CDC NHSN definitions); informs HCA-acquisition flag in id.sepsis.core.v1 routing
  • prior_antibiotic_exposure_90drequired
    history • used at CONTEXT
    Prior abx within 90 d drives ESBL + MRSA + VRE + C. diff risk-stratification; broadens empirics until culture-directed (IDSA/ATS 2016 Kalil)
  • central_venous_catheterrequired
    history • used at CONTEXT
    CLABSI workup gate; tunneled vs non-tunneled drives line-removal threshold (Mermel IDSA 2009 PMID 19489710)
  • urinary_catheterrequired
    history • used at CONTEXT
    CAUTI workup gate; duration of catheterisation > 2 d substantially increases bacteriuria risk (CDC Gould 2009)
  • mechanical_ventilationrequired
    history • used at CONTEXT
    VAP workup gate; ≥ 48 h of mechanical ventilation is the canonical VAP-onset threshold (IDSA/ATS 2016 Kalil)
  • recent_surgery_30_to_90drequired
    history • used at CONTEXT
    SSI typically ≤ 30 d post-op (≤ 90 d if prosthetic implant) per CDC NHSN definitions; informs SSI workup + biofilm-active empirics (IDSA/SHEA 2017 Berríos-Torres)
  • immunocompromised_staterequired
    history • used at CONTEXT
    Transplant / neutropenia / biologics / steroid ≥ 20 mg/d prednisone-equivalent ≥ 14 d → broader empirics + lower escalation threshold; fungal + atypical coverage gating
  • icu_stay_or_step_downrequired
    history • used at CONTEXT
    ICU > 7 d → higher MDR Gram-negative + fungal + C. auris risk; drives empiric broadening (IDSA/ATS 2016 Kalil)
  • colonization_with_mdrorequired
    history • used at CONTEXT
    Documented MDRO colonisation (MRSA nares, ESBL stool, CRE rectal, VRE) → empirics targeted to known colonisation pattern
  • local_unit_antibiogramrequired
    history • used at TREATMENT
    Local resistance > 10% to monotherapy in unit antibiogram drives combination Gram-negative empirics for VAP/HAP (IDSA/ATS 2016 Kalil)
  • temperaturerequired
    vital • used at ENTRY
    Fever > 38 °C is sentinel; hypothermia < 36 °C in critically ill / elderly is equally concerning (SSC 2026)
  • sbprequired
    vital • used at RED_FLAGS
    Hypotension on adequate fluids → septic shock → routes to id.sepsis.core.v1 with HCA flag (SSC 2026)
  • hrrequired
    vital • used at RED_FLAGS
    Tachycardia is a sepsis criterion (SIRS); part of qSOFA / NEWS2 bundled screening
  • rrrequired
    vital • used at RED_FLAGS
    Tachypnea > 22 is part of qSOFA; > 30 with hypoxemia drives respiratory failure escalation
  • spo2required
    vital • used at RED_FLAGS
    Hypoxemia escalates VAP severity; PaO2/FiO2 ≤ 250 is a SOFA respiratory point
  • wbcrequired
    lab • used at INITIAL_WORKUP
    Leukocytosis > 15 K is a CDI severity criterion (IDSA/SHEA 2017 McDonald); also tracks sepsis severity
  • creatininerequired
    lab • used at INITIAL_WORKUP
    Cr ≥ 1.5× baseline is a CDI severity criterion (IDSA/SHEA 2017 McDonald); informs renal-dose adjustment of vancomycin / aminoglycosides / beta-lactams (IDSA 2020 vancomycin AUC consensus)
  • lactaterequired
    lab • used at INITIAL_WORKUP
    Lactate > 2 → resuscitation; > 4 → septic shock physiology (SSC 2026 Hour-1 bundle)
  • blood_culturerequired
    lab • used at INITIAL_WORKUP
    Two sets from separate sites BEFORE antibiotics if no delay > 45 min (SSC 2026); differential time-to-positivity > 2 h between line and peripheral supports CLABSI (Mermel IDSA 2009)
  • urine_culture
    lab • used at INITIAL_WORKUP
    Catheter UA + culture for CAUTI workup; ≥ 10^3 CFU/mL with catheter is significant per IDSA Hooton 2010
  • sputum_culture_or_bal
    lab • used at INITIAL_WORKUP
    Sputum / endotracheal aspirate / BAL for VAP workup; BAL ≥ 10^4 CFU/mL or endotracheal aspirate ≥ 10^5 CFU/mL supports VAP (IDSA/ATS 2016 Kalil)
  • c_diff_stool_test
    lab • used at INITIAL_WORKUP
    C. diff toxin EIA + GDH + NAAT 2- or 3-step algorithm (IDSA/SHEA 2017 + 2021 update Johnson); NAAT-only positive without toxin EIA suggests colonisation, not infection
  • wound_culture
    lab • used at INITIAL_WORKUP
    Deep wound or organ-space culture from operative re-exploration for SSI workup; surface swabs unreliable (IDSA/SHEA 2017 Berríos-Torres)
  • procalcitonin
    lab • used at MONITORING
    Adjunct for de-escalation in VAP/HAP (decrease ≥ 80% over 5-7 d supports stop); not for initiation decisions (IDSA/ATS 2016 Kalil + ProGUARD-ICU 2021)
  • cxr_or_ct_chest
    imaging • used at INITIAL_WORKUP
    Chest imaging for VAP/HAP workup; new / progressive infiltrate is the radiographic anchor (IDSA/ATS 2016 Kalil)
  • echocardiogram_tte_tee
    imaging • used at BRANCHING_WORKUP
    TEE for persistent S. aureus / Enterococcus / Candida bacteremia > 72 h or with risk factors; rules out endocarditis (AHA Baddour 2015)
  • ct_abdomen_pelvis_for_cdi_or_ssi
    imaging • used at BRANCHING_WORKUP
    CT abdomen for fulminant CDI (megacolon, perforation) or deep / organ-space SSI (abscess, anastomotic leak) (IDSA/SHEA 2017 McDonald + Berríos-Torres)

12-phase flow (12)

  1. 1FRAME
    HAI overlay framing: ≥ 48 h post-admission, layered on top of existing primary engine (HF, post-op, ARDS, etc.). Sets HCA-acquisition flag for downstream sepsis routing.
    inputs: hospital_day_of_recognition
    advance: HCA-acquisition flag set + primary engine context preserved
  2. 2ENTRY
    Recognise via new fever / hypotension / leukocytosis / new infiltrate / new diarrhea / wound drainage > 48 h post-admit; categorise by HAI site (CLABSI / CAUTI / VAP-HAP / CDI / SSI / other BSI / GI / SSTI).
    inputs: temperature
    advance: HAI site provisionally tagged
  3. 3CONTEXT
    Capture device exposures (CVC / urinary cath / mechanical vent / surgical wound), prior abx 90 d (ESBL + MRSA + C. diff risk), MDRO colonisation history, immunosuppression, ICU length-of-stay, dialysis status.
    inputs: prior_antibiotic_exposure_90d, central_venous_catheter, urinary_catheter, mechanical_ventilation, recent_surgery_30_to_90d, immunocompromised_state, icu_stay_or_step_down, colonization_with_mdro
    advance: Device + risk-factor + colonisation inventory complete
  4. 4RED_FLAGS
    Sepsis features (qSOFA ≥ 2, SOFA delta ≥ 2, hypotension, lactate ≥ 4), fulminant CDI (ileus / megacolon / shock), MDRO bacteremia, persistent S. aureus bacteremia, large abscess / organ-space SSI, ventilator-associated event progression → route to id.sepsis.core.v1 with HCA flag + ICU + source-control evaluation.
    inputs: sbp, hr, rr, spo2
    actions: calc.qsofa, protocol.septic_shock
    advance: Red flags actioned; sepsis routing decided
  5. 5INITIAL_WORKUP
    Two sets blood cultures BEFORE antibiotics if no delay > 45 min (with line differential-time-to-positivity for CLABSI); CBC, CMP, lactate; site-directed cultures (urine / sputum or BAL / stool C. diff / wound deep culture); chest imaging if respiratory; empiric antibiotics per local antibiogram WHILE awaiting cultures (IDSA/ATS 2016 Kalil; SSC 2026).
    inputs: wbc, creatinine, lactate, blood_culture, urine_culture, sputum_culture_or_bal, c_diff_stool_test, wound_culture, cxr_or_ct_chest
    actions: workup.crbsi, workup.candidemia, workup.fuo, workup.acute_diarrhea, panel.cbc, panel.renal, panel.inflammation, panel.ua
    advance: Cultures sent + empiric antibiotics in within 1 h of sepsis recognition
  6. 6BRANCHING_WORKUP
    TEE if persistent S. aureus / Enterococcus / Candida bacteremia > 72 h or with risk factors (AHA Baddour 2015); CT abdomen for fulminant CDI / organ-space SSI; line-removal coordination (vascular / IR); surgical re-exploration for deep / organ-space SSI; ophthalmology if fungal CLABSI (IDSA candidiasis 2016 Pappas).
    inputs: echocardiogram_tte_tee, ct_abdomen_pelvis_for_cdi_or_ssi
    actions: workup.candidemia
    advance: End-organ + source workup complete
  7. 7DIFFERENTIAL
    Distinguish HAI site, pathogen-class, resistance pattern (susceptible vs ESBL vs CRE vs CR-Acinetobacter vs VRE vs MRSA vs VRSA vs C. auris); differentiate true infection from colonisation (catheter bacteriuria without symptoms, tracheal colonisation without VAP); identify look-alikes (drug fever, atelectasis vs VAP, transfusion reaction).
    advance: Pathogen + resistance + site triangulated; colonisation excluded
  8. 8RISK_STRATIFICATION
    qSOFA / SOFA delta for severity; C. diff severity (non-severe / severe / fulminant / recurrent per IDSA/SHEA 2017 McDonald + 2021 Johnson — WBC > 15 K / Cr ≥ 1.5 → severe; ileus / megacolon / shock → fulminant); CRE / CR-Acinetobacter / VRSA → ID + outbreak investigation; persistent S. aureus bacteremia ≥ 72 h → mandatory TEE + ID consult.
    actions: calc.sofa, calc.qsofa, calc.sirs
    advance: Severity + MDRO + persistence flag set
  9. 9TREATMENT
    Empiric per local antibiogram + site (CLABSI: vancomycin + anti-Pseudomonal β-lactam ± echinocandin if fungal risk; CAUTI: catheter REMOVE/REPLACE + culture-directed; VAP/HAP: cefepime / pip-tazo / meropenem ± vancomycin or linezolid; CDI: fidaxomicin 200 mg PO BID × 10 d first-line per IDSA 2021 Johnson; SSI: surgical re-exploration + vancomycin + anti-Pseudomonal; MDRO-specific: CRE → ceftazidime-avibactam / meropenem-vaborbactam / cefiderocol; CR-Acinetobacter → cefiderocol / sulbactam-durlobactam; VRE → daptomycin / linezolid). De-escalate per culture + susceptibility within 48-72 h.
    inputs: creatinine, local_unit_antibiogram
    advance: Empiric started; line / cath / wound source control coordinated; de-escalation plan set
  10. 10DISPOSITION
    ICU if septic shock / persistent bacteremia / fulminant CDI / VAP with MDR / large organ-space SSI; ward if stable + responding to empirics; transfer to higher acuity for refractory; OPAT extended-duration for endocarditis / osteomyelitis / persistent abscess.
    inputs: sbp, spo2
    advance: Level of care set; source control coordinated
  11. 11MONITORING
    Repeat blood cultures q24-48 h until two consecutive negatives for S. aureus / Enterococcus / Candida bacteremia; daily reassessment of antibiotic + duration (stewardship per IDSA/SHEA 2007 ASP framework); vancomycin AUC q48-72 h (Rybak IDSA 2020); procalcitonin trend for de-escalation in VAP/HAP (ProGUARD-ICU 2021); TEE follow-up if endocarditis; CT follow-up if abscess; daily C. diff symptom assessment + WBC + Cr trend.
    inputs: wbc, creatinine, procalcitonin, blood_culture
    actions: panel.cbc, panel.renal, panel.inflammation
    advance: Response confirmed + de-escalation per culture + clinical improvement
  12. 12FOLLOWUP
    Outpatient ID follow-up for endocarditis / osteomyelitis / MDRO; OPAT coordination for extended-duration IV therapy; antimicrobial stewardship feedback to the unit; infection control investigation for clusters / outbreaks (≥ 3 of same MDRO in 1 unit / 1 month); patient + family education on recurrence; vaccination review (PCV20, influenza, COVID-19, herpes zoster per ACIP 2024); FMT referral for ≥ 2 CDI recurrences.
    advance: OPAT + ID + IPC + outpatient plans documented