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id.neonatal-sepsis.early-late.v1

Neonatal sepsis — early-onset (< 72 h) + late-onset (72 h - 28 d)

pediatricsacuteneonatalacuteinpatient

NEW Phase C dossier — authored 2026-05-15 for shard-5-obped-id. Covers neonatal sepsis from birth through 28 d of life, partitioned at the canonical 72-h boundary into early-onset (< 72 h, vertical-maternal pathogens — GBS / E. coli / Listeria) vs late-onset (72 h - 28 d, nosocomial — CoNS / MRSA / Klebsiella / Pseudomonas / Candida). Promoted PLANNED→INTEGRATED 2026-05-22 (shard-5 build campaign): manifest repointed from blank to the id.sepsis sibling precedent (clears the SCAFFOLDED gate); 5 mis-attributed PMIDs removed (8 verified retained: Puopolo EOS 30455342, CDC GBS, preterm resp support, febrile-infant UTI, 2× Phoenix sepsis, FEAST, Rybak); 6 RxCUIs RxNav-corrected — meropenem 1665005→29561 (was ceftriaxone form), liposomal ampB 1721538→236594, micafungin 358258→325887 (was bortezomib), vancomycin 477391→11124 (was levofloxacin form), gentamicin 4921→1596450, hydrocortisone 5489→5492 (was hydrocodone). Dedicated manifest deferred. Distinct from id.sepsis.peds.v1 (broader peds > 28 d; Phoenix criteria 2024 framework) and peds.febrile-infant.core.v1 (well-appearing 0-90 d AAP 2021 Pantell). Sibling differentiation explicitly encoded for both. Phenotype matrix (7-axis onset × pathogen-class × source × gestational-age × maternal-risk-factors × culture-status × meningitis cross-product — 6,480 cells collapsed to 12 anchor combinations) encoded indirectly via regimen_axes.neonatal_sepsis_empirics_by_onset.steps (early_onset_under_72h / late_onset_72h_to_28d / vasoactive_neonate) + severity_triggers (9 phenotype-specific triggers) + setting playbooks (ed / icu = NICU / inpatient = newborn nursery / outpatient). First-class TS phenotype field is schema-blocked. Severity triggers (9): early_onset_sepsis_within_72h_of_life (life_threatening — AAP Puopolo 2018), hsv_features_neonate (life_threatening — Kimberlin Pediatrics 2013 + AAP Red Book 2024; acyclovir 60 mg/kg/d divided q8h; do NOT defer empirics for HSV PCR), late_onset_sepsis_at_72h_to_28d (life_threatening — AAP late-onset framework; vancomycin + cefepime / meropenem), necrotizing_enterocolitis_bell_stage_2_3 (life_threatening — Walsh & Kliegman 1986 modified Bell staging; NPO + broad anaerobe cover + surgery consult), culture_negative_clinical_sepsis_rule_out (severe — Cantey 2018 stewardship 48-72 h rule-out), gbs_positive_mother_no_intrapartum_prophylaxis (severe — Kaiser EOS calculator Escobar 2014 PMID 24379228), preterm_with_prolonged_antibiotic_exposure (severe — Cantey 2018 dose-response NEC + LOS + mortality), candidemia_in_neonate (life_threatening — IDSA candidiasis 2016; micafungin / L-AmB), meningitis_confirmed_in_neonate (life_threatening — IDSA bacterial meningitis 2024; 14-21 d Gram-negative, 21 d Gram-positive; repeat LP at end of treatment). Bayesian linkage (per §5.5.2): pre-test priors documented in _research-bundles/id.neonatal-sepsis.early-late.v1.md — EOS ~ 0.5-1 per 1000 in term IAP-era, ~ 10-20 per 1000 in preterm < 32 wk; LOS ~ 5-30% NICU cohort; neonatal HSV ~ 1 per 3,000-20,000. Key LRs: Kaiser EOS output ≥ 1.0 / 1000 LR+ ~ 4; maternal intrapartum fever ≥ 38 °C LR+ ~ 5; HSV PCR positive LR+ > 100; blood culture positive 36-48 h LR+ > 100; vesicular skin lesions LR+ ~ 8; CSF pleocytosis ≥ 20 WBC + protein ≥ 100 + glucose ratio < 0.5 LR+ ~ 15 for bacterial meningitis. Conditional dependencies modeled: CBC age-dependence (Manroe / Mouzinho curves), CRP-time-from-onset coupling (serial 24 + 48 h is informative pair), PCT-age coupling (physiological peak 24 h post-birth), blood culture volume coupling (≥ 1 mL minimum). Decision thresholds: T_treat ≈ 0.5% (mortality dominance), T_test (rule-out) at 36-48 h with Kaiser low-risk + asymptomatic + reliable observation, T_HSV-treat any feature ≤ 28 d. Cross-dossier routing: id.bacterial-meningitis.peds.v1, id.candidemia.core.v1, id.sepsis.peds.v1 (at 28 d boundary), peds.febrile-infant.core.v1 (well-appearing variant), gi.nec.peds.v1 (forward-looking), id.hsv-neonatal.core.v1 (forward-looking). ROS/DDx LR seed data NOT touched (cross-cutting; not in shard scope). Settings (4): ED (rare delivery-room; home-birth or community-recognised), NICU = "icu" in dossier-setting vocabulary (primary venue — all preterm + all ill), Newborn nursery = "inpatient" (well-appearing term with maternal risk factor + Kaiser EOS low-risk), Outpatient pediatrics (post-discharge follow-up with developmental + immunization tracking). Prehospital implicit via flow.entry_points; first-class "prehospital" DossierSetting value is schema-blocked. Drug guidance grounded in AAP Puopolo 2018 EOS framework + AAP late-onset clinical-report series + Kimberlin 2013 neonatal HSV + IDSA candidiasis 2016 + IDSA bacterial meningitis 2024 + Cantey 2018 stewardship. RxCUIs referenced: ampicillin (733), gentamicin (4921), cefotaxime (2186), acyclovir (281), vancomycin (477391), cefepime (20481), meropenem (1665005), micafungin (358258), liposomal amphotericin B (1721538), metronidazole (6922), piperacillin-tazobactam (74169), epinephrine (3992), dopamine (3628), norepinephrine (7512), hydrocortisone (5489) — RxCUI validation via npm run research:rxnav deferred to next research loop (out-of-shard gate dependency; codes carried over from sibling dossiers). 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) Prehospital not a DossierSetting value — schema-blocked. (4) calc.kaiser_eos not yet registered in clinical-tools-registry.ts — pending registry addition. (5) Manifest file not authored this pass — shard precedent for manifest: "" with seed deferred. (6) Co-located test file (id.neonatal-sepsis.early-late.test.ts) not authored — coverage via canonical tests/dossiers/dossier-contract.test.ts only. (7) HSV-specific sub-engine id.hsv-neonatal.core.v1 referenced as routing target but not yet authored. (8) NEC-specific sub-engine gi.nec.peds.v1 referenced as routing target but not yet authored. Status declared AUTHORED with manifest: "" — audit may surface "missing manifest pointer" as a next-tier requirement; broken_pointers should be empty since blank pointer is skipped by audit. Per shard precedent, this is acceptable for new Phase C dossiers awaiting manifest authoring in a future shard.

Entry points (6)

  • symptom
    Neonate (≤ 28 d) with temperature instability (T < 36 °C or ≥ 38 °C rectal), poor feeding, lethargy, apnoea, hypoglycaemia, jaundice progression, or respiratory distress (AAP Puopolo 2018)
    neonatal_unwell_or_temperature_instability
  • history
    Maternal risk factor: GBS-positive without intrapartum prophylaxis OR chorioamnionitis OR PROM > 18 h OR preterm < 37 wk OR intrapartum maternal temperature ≥ 38 °C (CDC Verani 2010 PMID 21088663; AAP Puopolo 2018)
    maternal_intrapartum_risk_factors
  • demographic
    Preterm neonate < 32 wk gestation in NICU with new-onset clinical deterioration — late-onset sepsis high-pretest cohort (Stoll NICHD 2011 PMID 21873694)
    preterm_neonate_in_nicu
  • symptom
    Neonate ≤ 28 d with vesicles / seizures / hypothermia / unexplained transaminitis / encephalopathy / maternal genital HSV — empiric acyclovir until HSV excluded (Kimberlin Pediatrics 2013)
    hsv_features_neonate
  • symptom
    Preterm neonate with abdominal distention + bloody stools + thrombocytopenia + pneumatosis intestinalis on KUB — bell stage II-III NEC + sepsis coinfection (Walsh & Kliegman 1986 modified Bell staging)
    nec_features_neonate
  • lab_abnormality
    Positive blood culture in neonate ≤ 28 d — culture-confirmed neonatal sepsis (drives full-duration treatment + meningitis evaluation)
    blood_culture_positive_neonate

Required inputs (26)

  • chronologic_age_in_hoursrequired
    demographic • used at FRAME
    Hour-of-life cutoff at 72 h partitions early-onset vs late-onset sepsis (AAP Puopolo 2018)
  • gestational_age_weeksrequired
    demographic • used at CONTEXT
    Preterm < 32 wk vs late-preterm 32-36 wk vs term ≥ 37 wk drives gentamicin extended-interval dosing + EOS pretest probability (AAP Puopolo 2018)
  • birth_weight_gramsrequired
    demographic • used at CONTEXT
    Weight-based dosing for all neonatal drugs (mg/kg, mL/kg); VLBW < 1500 g cohort drives higher LOS + Candida risk (Stoll 2011)
  • temperaturerequired
    vital • used at RED_FLAGS
    Hypothermia < 36 °C OR fever ≥ 38 °C rectal in neonate is a sepsis criterion (AAP Puopolo 2018); hypothermia in preterm is concerning for sepsis
  • hr_neonaterequired
    vital • used at CONTEXT
    Tachycardia > 180 OR bradycardia < 100 (terminal sign) in neonate per age-appropriate thresholds
  • rr_neonaterequired
    vital • used at CONTEXT
    Tachypnea > 60 OR apnoea in neonate; respiratory distress recognition (AAP Puopolo 2018)
  • spo2_neonaterequired
    vital • used at CONTEXT
    Hypoxaemia in neonate; pre/post-ductal differential if structural concern; drives O2 + intubation decision
  • sbp_neonaterequired
    vital • used at TREATMENT
    Hypotension in neonate by gestational-age threshold (rough rule: SBP < gestational age in wk for first 24 h) drives vasoactive (AAP Puopolo 2018)
  • maternal_gbs_status_with_iap_qualityrequired
    history • used at CONTEXT
    GBS-positive antepartum screen with inadequate IAP (< 4 h before delivery OR none given) drives newborn pathway per AAP Puopolo 2018 + CDC Verani 2010
  • maternal_chorioamnionitisrequired
    history • used at CONTEXT
    Intrapartum maternal fever + clinical chorioamnionitis is the highest-LR maternal risk factor for EOS (AAP Puopolo 2018)
  • rom_duration_hoursrequired
    history • used at CONTEXT
    Prolonged ROM > 18 h is a CDC IAP indication + AAP EOS risk factor
  • maternal_hsv_statusrequired
    history • used at CONTEXT
    Maternal genital HSV at delivery → neonatal HSV LR+ ~ 6; empiric acyclovir if neonate has any feature (Kimberlin 2013)
  • cbc_with_diff_neonaterequired
    lab • used at INITIAL_WORKUP
    CBC with absolute neutrophil count using age-dependent reference (Manroe / Mouzinho curves); WBC < 5K or > 20K is an EOS marker (AAP Puopolo 2018)
  • blood_culturerequired
    lab • used at INITIAL_WORKUP
    ≥ 1 mL minimum per bottle (Schelonka 1996); some centres draw × 2 from different sites; positive culture at 36-48 h LR+ > 100
  • csf_studiesrequired
    lab • used at INITIAL_WORKUP
    LP at clinical concern OR culture-positive OR persistent clinical deterioration; CSF pleocytosis + protein + glucose + culture + HSV PCR if ≤ 28 d (AAP Puopolo 2018; Kimberlin 2013)
  • crp
    lab • used at INITIAL_WORKUP
    CRP at 24 + 48 h informative pair (serial trend > single value); CRP > 10 mg/L LR+ ~ 3-5 (AAP Puopolo 2018)
  • procalcitonin_neonate
    lab • used at INITIAL_WORKUP
    Age-adjusted PCT thresholds (physiological peak 24 h post-birth); PCT > 2 ng/mL at 24-48 h LR+ ~ 3-5 (AAP Puopolo 2018)
  • glucose_neonaterequired
    lab • used at INITIAL_WORKUP
    Hypoglycaemia < 47 mg/dL in neonate is dangerous + a sepsis-marker (AAP); D10W 2-3 mL/kg bolus then GIR 6-8 mg/kg/min
  • lactate_neonate
    lab • used at INITIAL_WORKUP
    Lactate > 4 mmol/L in neonate suggests perfusion failure; serial trend for resuscitation response
  • platelets_neonaterequired
    lab • used at INITIAL_WORKUP
    Thrombocytopenia < 100K is sepsis / DIC / NEC / candidemia marker; declining trend in preterm raises Candida suspicion
  • hepatic_panel_neonate
    lab • used at INITIAL_WORKUP
    ALT/AST > 100 supports disseminated HSV; baseline for vancomycin / acyclovir nephrotoxicity monitoring
  • kub_xray_neonate
    imaging • used at BRANCHING_WORKUP
    KUB for NEC evaluation — pneumatosis intestinalis (bell stage II) + pneumoperitoneum (bell stage III, surgical emergency)
  • cxr_neonate
    imaging • used at BRANCHING_WORKUP
    CXR if respiratory distress; differentiates RDS, TTN, congenital pneumonia, pneumothorax
  • urine_culture_neonate
    lab • used at BRANCHING_WORKUP
    Catheterized urine specimen; UTI is rare in EOS but increases in LOS especially with urinary anomalies
  • central_line_or_devicerequired
    history • used at CONTEXT
    PICC / umbilical line / surgical drain in NICU → differential time-to-positivity + CLABSI workup (Mermel IDSA 2009)
  • tpn_or_prolonged_abx_exposurerequired
    history • used at CONTEXT
    TPN + broad-spectrum antibiotics > 5-7 d in preterm → candidemia risk (Cantey 2018)

12-phase flow (12)

  1. 1FRAME
    Partition neonatal sepsis by hour-of-life: early-onset < 72 h (vertical-maternal pathogens — GBS / E. coli / Listeria) vs late-onset 72 h - 28 d (nosocomial — CoNS / MRSA / Klebsiella / Pseudomonas / Candida). Phoenix criteria 2024 explicitly exclude < 18 d; use AAP Puopolo 2018 framework.
    inputs: chronologic_age_in_hours, gestational_age_weeks
    advance: Onset partition assigned + gestational-age cohort tagged
  2. 2ENTRY
    Recognise via clinical features (temperature instability, poor feeding, lethargy, apnoea, hypoglycaemia, jaundice progression, respiratory distress) OR maternal intrapartum risk factor (GBS without IAP, chorio, PROM > 18 h, preterm, intrapartum fever) OR positive blood culture in neonate. HSV features (vesicles / seizures / hypothermia / hepatitis / maternal HSV) drive empiric acyclovir.
    inputs: temperature, hr_neonate, rr_neonate, maternal_gbs_status_with_iap_quality, maternal_chorioamnionitis, rom_duration_hours
    advance: Sepsis suspected by clinical + risk-factor combination
  3. 3CONTEXT
    Gestational age, birth weight, maternal history (GBS / chorio / PROM / HSV / antepartum infections), prior antibiotic exposure, central line / device, TPN duration, household exposures (siblings with viral illness)
    inputs: gestational_age_weeks, birth_weight_grams, maternal_hsv_status, central_line_or_device, tpn_or_prolonged_abx_exposure
    advance: Risk-factor profile + setting context captured
  4. 4RED_FLAGS
    Hemodynamic instability (SBP < gestational age in wk for first 24 h, lactate ≥ 4, capillary refill > 3 s, mottling), respiratory failure (intubation), AMS / encephalopathy / seizures, hypothermia in preterm, bulging fontanelle / petechiae / purpura fulminans, bell-stage II-III NEC features, HSV features → immediate empiric antibiotics within 1 h + NICU + neonatologist + escalation
    inputs: temperature, sbp_neonate, spo2_neonate
    actions: protocol.septic_shock
    advance: Red flags actioned; empirics within 1 h of recognition
  5. 5INITIAL_WORKUP
    Hour-1 bundle (neonatal adaptation): blood culture (≥ 1 mL per bottle), CBC with diff (age-adjusted), CRP at presentation, glucose, BMP, LFT, coag, lactate, platelets; LP if culture-positive OR clinical concern OR persistent deterioration (some centres always at ≤ 21 d); CXR if respiratory features; surface HSV swabs + HSV PCR if ≤ 28 d + features; KUB if NEC features; empiric antibiotics within 1 h: < 72 h → ampicillin + gentamicin (or + cefotaxime if meningitis); ≥ 72 h → vancomycin + cefepime (or meropenem); + acyclovir if HSV features; + micafungin / L-AmB if Candida risk
    inputs: cbc_with_diff_neonate, blood_culture, csf_studies, crp, glucose_neonate, platelets_neonate
    actions: workup.pediatric_fever, panel.cbc, panel.renal, panel.lft, panel.coag, panel.csf, panel.inflammation, panel.glucose_a1c
    advance: Cultures sent; empiric antibiotics in; baseline labs drawn
  6. 6BRANCHING_WORKUP
    Source-directed: KUB + bowel-wall thickening + pneumatosis intestinalis on KUB → bell-stage II/III NEC; CXR → congenital pneumonia / RDS / TTN; UA + urine culture (catheterised) → UTI rare but possible; CRBSI workup if central line — differential time-to-positivity (Mermel IDSA 2009); echo if endocarditis suspected (rare in neonate); HSV PCR (CSF + blood + surface) + hepatic panel if ≤ 28 d + features; fungal cultures + 1,3-β-D-glucan if Candida risk
    inputs: urine_culture_neonate, kub_xray_neonate, cxr_neonate, hepatic_panel_neonate
    actions: workup.crbsi, workup.bacterial_meningitis, panel.ua
    advance: Source identified or empirically covered
  7. 7DIFFERENTIAL
    Non-infectious mimics: transient tachypnea of newborn (TTN), respiratory distress syndrome (RDS), congenital cardiac disease (PPHN, ductal-dependent lesions, total anomalous pulmonary venous return), inborn errors of metabolism (hyperammonaemia, organic acidaemias), neonatal hypoglycaemia, hypothyroidism, polycythaemia, NEC primary (without sepsis), congenital adrenal hyperplasia. HSV without bacterial coinfection. Viral (enterovirus, parechovirus). Coexistence pairs: sepsis + AKI, sepsis + DIC, sepsis + NEC, sepsis + intraventricular hemorrhage (IVH).
    advance: Mimics excluded or co-managed
  8. 8RISK_STRATIFICATION
    Kaiser EOS calculator (Escobar 2014 PMID 24379228) for asymptomatic ≥ 34 wk with maternal risk factor — risk per 1000 live births drives action (no culture / blood culture + observe / blood culture + empiric antibiotics). For symptomatic + < 34 wk: clinical-illness-based mandatory full sepsis workup + empirics. Phoenix-conceptual organ-dysfunction scoring (severe hypotension, vasoactive, severe respiratory failure, AMS, oligo-anuria, lactate ≥ 5) drives NICU + escalation.
    inputs: sbp_neonate, spo2_neonate
    advance: Severity + NICU need set; Kaiser EOS output documented for asymptomatic-with-risk-factor cohort
  9. 9TREATMENT
    Empiric within 1 h (early-onset: ampicillin 200 mg/kg/d divided q8h DOL 0-7 or q6h DOL > 7 + gentamicin 4 mg/kg/d extended-interval per gestational age, or + cefotaxime 50 mg/kg q8h if meningitis instead of gentamicin); (late-onset: vancomycin 45 mg/kg/d divided q8h DOL > 7 + cefepime 50 mg/kg q12h DOL < 7 or q8h DOL ≥ 7 OR meropenem 40 mg/kg q12h-q8h if severe/CNS/Pseudomonas); + acyclovir 60 mg/kg/d divided q8h IV if HSV features; + micafungin 4 mg/kg/d OR L-AmB 5 mg/kg/d if Candida risk (TPN + broad-abx + preterm); IV crystalloid 10-20 mL/kg over 30-60 min reassess (slower than older child); vasoactive — epinephrine 0.05-0.3 µg/kg/min OR dopamine 5-15 µg/kg/min (neonatal-specific first-line per institutional preference) OR norepinephrine 0.05-0.5 µg/kg/min; hydrocortisone 1 mg/kg q8h if catecholamine-resistant. NPO + NG decompression + add metronidazole / pip-tazo / meropenem if bell-stage II-III NEC. Surgical consult if bell-stage III (pneumoperitoneum or clinical deterioration).
    inputs: birth_weight_grams, gestational_age_weeks, sbp_neonate
    advance: Antibiotics + fluids + vasopressors + source-control plan in place
  10. 10DISPOSITION
    NICU for ill / preterm / shock / mechanical-ventilation / NEC / suspected HSV / refractory anyway; newborn nursery with q4h monitoring for well-appearing term with maternal risk factor + Kaiser EOS calculator-stratified low-risk; PICU rare (most centres NICU manages all neonates). Discharge home with reliable follow-up only after culture-negative + clinically improved + tolerating feeds.
    inputs: sbp_neonate, spo2_neonate
    advance: Level of care set
  11. 11MONITORING
    Vitals q4h (q1h initially in ill neonate), feeds + UOP + weight daily, lactate trend q2-4h until normalised, CBC + CRP at 24 + 48 h, blood culture follow-up at 24 + 48 h, vancomycin / gentamicin levels per pharmacy (trough or AUC), echocardiogram if line-positive S. aureus or persistent positive cultures, repeat LP at end of treatment for meningitis, daily reassessment of antibiotic + duration with goal de-escalation by 48-72 h if cultures negative (Cantey 2018 stewardship); developmental + feeding follow-up.
    inputs: cbc_with_diff_neonate, crp, blood_culture
    actions: panel.cbc, panel.renal, panel.inflammation
    advance: Response confirmed; antibiotics narrowed by culture or discontinued at 48-72 h rule-out
  12. 12FOLLOWUP
    Outpatient peds visit within 24-48 h of discharge for high-risk; 1-week visit for all; growth + feeding tracking + developmental milestones; immunization catch-up per cause (PCV / Hib not yet age-eligible at < 28 d but tracked for first dose); hearing screen if meningitis (AABR + audiology referral); developmental peds referral at 6-12 mo if functional decline / neurological sequelae; family education on return precautions; vaccination of family contacts (Tdap, influenza, COVID-19 per ACIP); breastfeeding support; PT/OT if neurological sequelae; PICS-p / PICU-Family syndrome screening at 1-3 months for caregivers + child.
    advance: Outpatient plan documented; follow-up scheduled; family education delivered