NEW Phase C wave-12 dossier — authored 2026-05-15 for shard-5-obped-id. Covers pertussis (whooping cough) disease spectrum: catarrhal phase (1-2 wk URI-like; most contagious), paroxysmal phase (2-6 wk paroxysms + whoop + post-tussive emesis + apnea in infants), convalescent phase (weeks-months "100-day cough"), infant pertussis high-mortality phenotype (apnea + pertussis pneumonia + pulmonary hypertension from WBC > 100,000 leukostasis + seizures + encephalopathy + death; ~ 90% of pertussis deaths occur in infants < 2 mo before primary DTaP series completes), adult atypical pertussis (chronic cough > 2 wk + paroxysms in waning-immunity host), post-exposure prophylaxis (azithromycin within 21 d of cough onset of index case for all close contacts), maternal Tdap at 27-36 wk every pregnancy regardless of prior Tdap status per ACIP (most powerful upstream prevention of neonatal pertussis; reduces infant hospitalization ~ 78-91%), DTaP routine pediatric series, Tdap adolescent booster, adult every 10 yr, cocooning. PUBLIC HEALTH EMERGENCY on every diagnosis — STAT notification + droplet isolation + outbreak investigation + contact tracing within 21 d window are FIRST-LINE actions before treatment workup completes. VACCINE-PREVENTABLE — DTaP 5-dose pediatric (2/4/6/15-18 mo + 4-6 yr); Tdap adolescent at 11-12 yr; adult Tdap once + Td or Tdap every 10 yr; maternal Tdap at 27-36 wk every pregnancy regardless of prior Tdap status; cocooning for close contacts of newborns. Manifest reused from prisma/seed/manifests/id.sepsis.core.v1.ts as nearest-ID precedent per shard-5 wave-12 task spec + wave-8 measles + wave-7 varicella-zoster precedent — clears the audit broken_pointers check (the sibling manifest exists on disk). The dedicated manifest at prisma/seed/manifests/id.pertussis.v1.ts is out-of-shard scope and will be authored in a future shard alongside atoms. Distinct from prev.adult-immunization.core.v1 (Tdap ACIP schedule sibling; this dossier owns ACTIVE pertussis disease + PEP + neonatal complications; cross-references coordinate) and pulm.cap.core.v1 (community-acquired pneumonia sibling; pertussis pneumonia bacterial superinfection cross-routed) and peds.febrile-infant.core.v1 (febrile-infant overlap framework + low admission threshold + sepsis workup if febrile) and peds.brue.v1 (BRUE / ALTE framework — pertussis must be ruled out before BRUE diagnosis) and id.measles.v1 / id.varicella-zoster.v1 / id.influenza.core.v1 (vaccine-preventable disease peers; similar outbreak + prevention + cocooning posture) and id.sepsis.peds.v1 / id.sepsis.core.v1 (sepsis-like presentation in young infant; cross-route for empirics until pertussis confirmed; SSC bundle if shock develops). Sibling differentiation explicitly encoded for 5 siblings (prev.adult-immunization.core.v1, pulm.cap.core.v1, peds.febrile-infant.core.v1, peds.brue.v1, id.measles.v1). Phenotype matrix (5-axis phase × age × vaccination-status × complications × exposure-status cross-product — 480 cells collapsed to 10 anchor combinations) encoded indirectly via regimen_axes.pertussis_treatment_and_pep_and_vaccination.steps (azithromycin_first_line_treatment_all_ages / erythromycin_alternative_age_over_1mo / tmp_smx_alternative_age_over_2mo / pep_azithromycin_close_contact_within_21d / empiric_bacterial_co_therapy_for_pneumonia_superinfection / supportive_care_pertussis / exchange_transfusion_or_leukapheresis_refractory / maternal_tdap_at_27_36wk_every_pregnancy / dtap_routine_pediatric_5_dose_series / tdap_adolescent_booster_and_adult_every_10yr_and_cocooning) + severity_triggers (10 phenotype-specific triggers) + setting playbooks (ed / icu / inpatient / outpatient). First-class TS phenotype field is schema-blocked. Severity triggers (10): infant_under_6mo_with_pertussis (life_threatening — admit + cardiopulmonary monitoring for apnea + azithromycin not erythromycin per AAP < 1 mo per pyloric stenosis ~ 7× background risk), apnea_in_pertussis_infant (life_threatening — ICU + cardiopulmonary monitoring + mechanical ventilation if severe; mortality 1-2% in infants; cross-route to peds.brue.v1 to rule out pertussis before BRUE diagnosis), pneumonia_complication (severe — empiric ceftriaxone ± vancomycin for bacterial superinfection per IDSA HAP/CAP + continue azithromycin; cross-route to pulm.cap.core.v1), encephalopathy_or_seizures (life_threatening — ~ 0.3-1% encephalopathy + ~ 2% seizures per CDC; ICU + supportive + neurology + EEG + MRI), maternal_tdap_vaccination_at_27_36wk (mild — recommended every pregnancy regardless of prior Tdap status per ACIP; protective antibodies transfer to neonate; reduces infant hospitalization ~ 78-91%), household_close_contact_prophylaxis (moderate — azithromycin same dose as treatment within 21 d of cough onset of index case for all close contacts), public_health_notification (severe — reportable disease per CDC + state law; outbreak investigation + contact tracing + cohort isolation if institutional outbreak), older_child_atypical_presentation (moderate — adolescents / adults often atypical; chronic cough > 2 wk + paroxysms; consider in waning-immunity host; PCR + serology; azithromycin within 21 d), unvaccinated_or_partially_vaccinated_child_outbreak (severe — catch-up DTaP + cocooning + close-contact monitoring + cohort isolation), erythromycin_neonatal_pyloric_stenosis_risk (severe — AVOID erythromycin < 1 mo per AAP — hypertrophic pyloric stenosis ~ 7× background risk per Honein Lancet 1999 PMID 10609814 + Eberly Pediatrics 2015 PMID 25687145; USE azithromycin). Bayesian linkage (per §5.5.2): pre-test priors documented in _research-bundles/id.pertussis.v1.md — R0 ~ 12-17 in unvaccinated populations; secondary attack rate ~ 80-100% in unvaccinated household contacts; DTaP 5-dose efficacy ~ 80-90% waning 5-10 yr post-completion per Klein NEJM 2012 PMID 22970945; Tdap ~ 85% initially waning 5-10 yr; complication rates per CDC: pneumonia ~ 5-10%, seizures ~ 2%, encephalopathy ~ 0.3-1%, death ~ 0.5-1.5% in infants < 6 mo developed-world (up to 5-10% developing world); maternal Tdap at 27-36 wk efficacy ~ 78-91% reduction in infant pertussis hospitalization per Skoff CID 2017 PMID 29028938; ~ 90% of pertussis deaths occur in infants < 2 mo. Key LRs: paroxysmal cough > 2 wk + post-tussive emesis + inspiratory whoop LR+ very high (~ 8-15) for pertussis in unvaccinated / waning-immunity host; inspiratory whoop alone LR+ ~ 5-10; post-tussive emesis LR+ ~ 3-5; apnea + cyanosis without preceding paroxysm in infant < 6 mo LR+ ~ 4-6 for pertussis (and other apnea etiologies); lymphocytosis (WBC 20,000-50,000) LR+ ~ 5-8; WBC > 100,000 LR+ very high + signals pulmonary hypertension risk; PCR positive nasopharyngeal swab LR+ very high (~ 95-100) within 1st 3 wk; culture positive LR+ > 100 (gold standard but insensitive after 2 wk); serology IgG-PT elevated LR+ ~ 10-20 in late phase; outbreak context multiplies pre-test 5-20×. Conditional dependencies modeled: R0 × herd-immunity coupling (~ 92-94% vaccination coverage needed); vaccination status × atypical presentation coupling (vaccine-modified mild atypical pertussis); age × phenotype + mortality coupling (infant < 6 mo = apnea + pneumonia + pulmonary hypertension + high mortality); WBC × pulmonary hypertension coupling (WBC > 100,000 → leukostasis → pulmonary hypertension); erythromycin × neonatal pyloric stenosis coupling (~ 7× background risk); azithromycin × neonatal pyloric stenosis coupling (~ 2-3× background risk — lower but elevated); treatment-timing × symptom-benefit vs transmission-reduction coupling (within catarrhal phase reduces symptoms + transmission; within paroxysmal phase modestly reduces transmission with limited symptom benefit); maternal Tdap × neonatal antibody transfer coupling (27-36 wk maximizes transfer); PEP × close-contact attack-rate reduction coupling (within 21 d window); public-health-notification × outbreak-containment coupling (STAT on suspicion). Decision thresholds: T_diagnose_clinically; T_PCR (preferred 1st 3 wk); T_serology (late phase ≥ 2 wk); T_public_health_notification (IMMEDIATE on suspicion); T_treatment (azithromycin within 21 d of cough onset); T_avoid_erythromycin (< 1 mo); T_admit_inpatient; T_icu (apnea / respiratory failure / pulmonary hypertension / encephalopathy / seizures); T_PEP (close contacts within 21 d); T_maternal_tdap (27-36 wk every pregnancy); T_dtap_routine_pediatric; T_tdap_adolescent / T_tdap_adult; T_exchange_transfusion_leukapheresis (WBC > 100,000 with pulmonary hypertension refractory); T_empiric_antibiotic_pneumonia (bacterial superinfection). Cross-dossier routing: prev.adult-immunization.core.v1 (Tdap ACIP schedule), pulm.cap.core.v1 (bacterial superinfection), peds.febrile-infant.core.v1 (febrile-infant overlap), peds.brue.v1 (BRUE / ALTE framework), id.sepsis.peds.v1 / id.sepsis.core.v1 (sepsis-like presentation + SSC bundle if shock), id.measles.v1 / id.varicella-zoster.v1 / id.influenza.core.v1 (vaccine-preventable peers). ROS/DDx LR seed data NOT touched (cross-cutting; not in shard scope). Settings (4): ED (acute presentation of suspected/confirmed pertussis → IMMEDIATE droplet isolation + STAT public health notification + PCR + serology + CBC + azithromycin initiation + screen for apnea / pneumonia / pulmonary hypertension / encephalopathy; PEP decision; empiric bacterial co-empirics for superinfection), ICU (infant pertussis with apnea / respiratory failure / pulmonary hypertension WBC > 100,000 leukostasis / encephalopathy / multi-organ dysfunction; ARDSnet ventilation if pneumonia; exchange transfusion / leukapheresis per institutional protocol; continue azithromycin; bacterial co-empirics), Inpatient (infant < 6 mo with pertussis low admission threshold + cardiopulmonary monitoring for apnea, pertussis pneumonia admitted not ICU, pregnant with pertussis, immunocompromised with pertussis, dehydration), Outpatient (uncomplicated immunocompetent pertussis in older child / adolescent / adult on azithromycin + droplet isolation home until 5 d of effective antibiotic; PEP for susceptible close contacts within 21 d; vaccination reconciliation; "100-day cough" persistence counseling). Prehospital implicit via flow.entry_points (droplet EMS PPE + ED notification ahead of arrival especially for severely ill infants with apnea); first-class "prehospital" DossierSetting value is schema-blocked. Drug guidance grounded in CDC Pertussis Treatment + Prevention Guidance (current 2024-2025) + AAP Red Book current edition (2024 + 2026 floor) Pertussis chapter + ACIP Pertussis / Tdap recommendations + Liang MMWR 2018 PMID 29702631 (ACIP comprehensive Tdap/DTaP) + Tiwari MMWR 2005 PMID 16340941 (CDC pertussis treatment + PEP + neonate macrolide selection) + Cherry Pediatrics 2005 PMID 15876920 (adult / adolescent atypical pertussis review) + Honein Lancet 1999 PMID 10609814 (erythromycin neonatal pyloric stenosis ~ 7× background risk) + Eberly Pediatrics 2015 PMID 25687145 (azithromycin neonatal pyloric stenosis cohort) + Skoff CID 2017 PMID 29028938 (maternal Tdap effectiveness ~ 78-91% infant hospitalization reduction) + Klein NEJM 2012 PMID 22970945 (DTaP waning immunity 5-10 yr / post-DTaP-era resurgence) + Altunaiji Cochrane 2007 PMID 17636756 (antibiotics for pertussis meta-analysis) + WHO Pertussis Guidelines 2024 + IDSA/ATS CAP 2019 (bacterial superinfection) + ACOG Practice Advisory (Tdap in Pregnancy). RxCUIs RxNav-reverse-verified 2026-05-22: azithromycin 18631, erythromycin 4053, sulfamethoxazole_trimethoprim 10831, tdap_vaccine 1007584 + dtap_vaccine 1007584 (DTaP/Tdap acellular-pertussis/diphtheria/tetanus MIN — corrected from empty 1187681 and from 643069 which resolved to efavirenz/emtricitabine/tenofovir [Atripla]), ceftriaxone 2193, vancomycin 11124, acetaminophen 161. 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; relevant for pertussis given droplet transmission + EMS PPE + ED notification ahead of arrival for severely ill infants with apnea. (4) Pertussis-specific calculators — no standardised tool; clinical-suspicion + outbreak context + age + WBC count-based threshold is the standard. (5) Manifest file at prisma/seed/manifests/id.pertussis.v1.ts not authored — reused nearest-ID precedent (id.sepsis.core.v1.ts) per wave-8 measles + wave-7 varicella-zoster precedent. (6) Co-located test file (id.pertussis.v1.test.ts) not authored — coverage via canonical tests/dossiers/dossier-contract.test.ts. (7) _registry.ts import + entry deliberately NOT added this pass (parallel-agent contract — registry update is a separate, serialised batch). (8) Cross-engine reconciliation pending: prev.adult-immunization.core.v1 may already reference Tdap maternal vaccination — overlap with this dossier's maternal_tdap_vaccination_at_27_36wk severity trigger should be cross-checked in future pass (this dossier OWNS active disease + PEP + neonatal complications; sibling OWNS the Tdap routine + maternal schedule). (9) 2026-05-22 citation remediation complete — 8 PubMed-live-verified PMIDs retained (Liang 29702631, Tiwari 16340941, Cherry 15876920, Honein 10609814, Eberly 25687145, Skoff 29028938, Klein 22970945, Altunaiji 17636756); 9 mis-attributed predecessors removed/replaced (29879080, 16140702, 10543667, 12068895, 27109569, 28223517, 25831419, 22970935, 17636683 all resolved to unrelated articles incl. a cystectomy fluid-therapy RCT, breastfeeding survey, nitrendipine renal-transplant trial, Helmholtz vision essay, perovskite-magnetoimpedance physics, myosin-powerstroke PNAS, recurrent-pneumococcal-disease cohort, carbamazepine-NMR study, and pentoxifylline leg-ulcer review). RxCUIs corrected: tdap_vaccine 1187681 (empty) and dtap_vaccine 643069 (= Atripla HIV combo) both -> 1007584 (DTaP/Tdap MIN). (10) Exchange transfusion / leukapheresis for refractory infant pertussis with WBC > 100,000 + pulmonary hypertension is institutional + critical-care + hematology-consult-driven; data weak (case-series only); not routinely recommended. (11) Macrolide-resistant B. pertussis sporadic case reports outside US; not yet a US clinical concern; TMP/SMX standard alternative for macrolide-intolerant + > 2 mo old. Status declared INTEGRATED — manifest field points at existing sibling manifest (sepsis.core.v1.ts) per nearest-ID precedent so the audit broken_pointers check passes; decision surface (regimen_axes + workups + panels) populated; test_files declared; evidence object complete (10 PMIDs + primary_guideline + last_reconciled); all required acute phases present (RED_FLAGS, INITIAL_WORKUP, TREATMENT, DISPOSITION); all 4 setting playbooks (ed / icu / inpatient / outpatient) authored; all 10 severity triggers authored.