Biostatistics & Population Health
Surveillance systems and public health data sources
— Passive surveillance: providers/labs report to health departments (e.g., notifiable diseases) — cheap, broad, but underreports
— Active surveillance: health department contacts providers/labs (e.g., during outbreaks, measles, polio) — more complete, resource intensive
— Sentinel surveillance: selected reporting sites monitor specific conditions (e.g., ILINet for influenza-like illness)
— Syndromic surveillance: real-time symptom/ED chief-complaint data (BioSense) — early outbreak detection before lab confirmation
— Stem mentions "state health department," "CDC notification," "reportable disease," cluster of cases, or asks "best data source to estimate prevalence/incidence"
— Outbreak investigation steps (Snow-style)
— Vaccine safety signal → think VAERS
— Cancer incidence trends → SEER
— National prevalence of chronic disease/risk factors → BRFSS or NHANES

— Clinician diagnoses or suspects a nationally notifiable condition (NNDSS list maintained by CDC/CSTE)
— Examples: measles, mumps, rubella, pertussis, Neisseria meningitidis, hepatitis A/B/C, HIV (in all states), TB, syphilis, gonorrhea, chlamydia, Lyme, Zika, rabies exposure, foodborne (Salmonella, Shigella, E. coli O157, Listeria), botulism, anthrax, plague, smallpox, viral hemorrhagic fevers
— Mechanism: phone/fax/electronic to local or state health department → state → CDC
— Most reportable infections also trigger lab reporting (positive culture, PCR, serology) — redundancy improves capture
— BRFSS (telephone, adult risk factors), YRBSS (high schoolers), NHANES (exam + labs), NHIS (household interview), NSDUH (substance use), PRAMS (postpartum)
— SEER (cancer, ~48% US coverage), USRDS (ESRD), National Trauma Data Bank

— Proportion of true cases detected by the system
— Low sensitivity = underreporting (typical of passive systems)
— Proportion of reported cases that are true cases
— Drives resource use; low PPV wastes investigations
— Categories: suspected, probable, confirmed (e.g., measles confirmed = lab-positive IgM or PCR or epi-link to confirmed case)
— Tightening definition ↑ specificity/PPV, ↓ sensitivity
— Loosening definition ↑ sensitivity, ↓ PPV

— Weekly MMWR tables; state-level granularity
— FoodNet (active surveillance, 10 sites, ~15% US population) — best for trends in lab-confirmed enteric infections
— PulseNet — molecular subtyping (WGS) to link cases across states → outbreak detection
— NORS — outbreak-level reporting
— SEER (incidence, survival; high-quality, ~48% population)
— NPCR (national coverage, all states) — combined as US Cancer Statistics

— VAERS (Vaccine Adverse Event Reporting System) — co-run by CDC/FDA; passive, anyone can report, used for signal detection only; cannot establish causality
— VSD (Vaccine Safety Datalink) — large integrated health system database (~12M lives); active, used to test hypotheses generated by VAERS
— CISA — clinical consultation for complex vaccine adverse events
— FAERS — FDA Adverse Event Reporting System for drugs/biologics (non-vaccine); MedWatch is the reporting portal
— Sentinel Initiative — FDA's active drug surveillance using claims/EHR (>100M lives); equivalent of VSD for drugs
— PRAMS — postpartum survey on behaviors/experiences
— Pregnancy Mortality Surveillance System (PMSS) — maternal deaths
— MMRCs — state Maternal Mortality Review Committees (case review, preventability)
— NVDRS — National Violent Death Reporting System (homicide, suicide details)
— WISQARS — query tool for injury data
— BRFSS — adults, state-level, telephone, self-report
— YRBSS — high school students
— NSDUH — substance use, mental health
— MTF (Monitoring the Future) — adolescent drug use trends
— NHANES — interview + physical + labs; only source for objectively measured HTN, lipids, HbA1c, lead, BMI
— NHIS — interview only, household-based

— 1. Prepare for fieldwork (supplies, team, contacts)
— 2. Establish existence of outbreak — compare observed to expected (endemic baseline)
— 3. Verify the diagnosis — review labs, exam findings
— 4. Construct a working case definition (person, place, time, clinical/lab criteria)
— 5. Find cases systematically and record information (line list)
— 6. Perform descriptive epidemiology — epidemic curve, person/place/time
— 7. Develop hypotheses
— 8. Evaluate hypotheses — typically retrospective cohort (defined population, e.g., wedding) or case-control (no defined population)
— 9. Refine hypotheses and conduct additional studies (environmental, lab)
— 10. Implement control and prevention measures — can be initiated at any step once sufficient evidence exists
— 11. Communicate findings
— Point source — sharp peak, all cases within one incubation period (potluck salmonella)
— Continuous common source — plateau (contaminated water supply)
— Propagated — successive peaks ~1 incubation apart (measles, person-to-person)
— Defined cohort (wedding guests, cruise ship) → retrospective cohort, calculate attack rates and RR
— Undefined source population (community-wide) → case-control, calculate OR

— Infectious: measles, mumps, rubella, pertussis, diphtheria, polio, smallpox, anthrax, plague, tularemia, botulism, rabies (animal bites), viral hemorrhagic fevers, novel influenza, SARS-CoV-2, TB, N. meningitidis, H. influenzae invasive, hepatitis A/B/C, HIV, syphilis, gonorrhea, chlamydia, Lyme, RMSF, Zika, dengue, malaria, typhoid, cholera, Salmonella, Shigella, STEC, Listeria, C. botulinum
— Non-infectious: elevated blood lead, certain cancers (to state cancer registry), birth defects (state-dependent), occupational lung disease (some states)
— Child abuse/neglect → CPS (mandated, all states, no privilege exceptions)
— Elder abuse / vulnerable adult abuse → APS (most states)
— Intimate partner violence → varies; injury from weapon/burns generally reportable
— Gunshot/stab wounds → law enforcement (most states)
— Suspected impaired driver / specific conditions (e.g., seizures) → state DMV in some states
— Vaccine adverse events meeting VAERS table → VAERS (mandated by NCVIA 1986)
— Serious drug adverse events → FDA MedWatch (mandatory for manufacturers, voluntary but encouraged for providers)
— Class A (urgent: measles, meningococcal, foodborne with public risk) → immediate phone report, often within 24 h
— Most others → within 1–7 days, electronic acceptable

— Single case of high-consequence pathogen (measles, meningococcal, novel influenza, anthrax, VHF, polio) → immediate isolation + health department notification + contact tracing and post-exposure prophylaxis
— Foodborne cluster (PulseNet match) → traceback to common food/facility, recall via FDA/USDA, public advisory
— Healthcare-associated infection signal (NHSN) → infection control bundle review, root cause analysis, public reporting via CMS Hospital Compare
— VAERS signal → VSD or Sentinel hypothesis testing → ACIP review → potential label change/pause (historical: rotavirus tetravalent intussusception 1999; J&J COVID vaccine TTS 2021)
— Cancer incidence rise (SEER) → etiologic investigation, screening guideline review (USPSTF)
— Antibiotic resistance trend (NARMS, NHSN) → antibiotic stewardship, formulary changes
— TB → identify close contacts, IGRA or TST + symptom screen + CXR; treat LTBI
— Pertussis → azithromycin prophylaxis for household and high-risk contacts regardless of vaccination
— Meningococcal → rifampin, ciprofloxacin, or ceftriaxone within 24 h ideally
— HIV → partner notification services; PEP within 72 h
— STIs → expedited partner therapy (EPT) legal in most states for chlamydia/gonorrhea

— Worst for diseases with mild/asymptomatic presentations (chlamydia, hepatitis C)
— True incidence may be 5–50× reported; CDC publishes adjusted estimates (e.g., STIs)
— BRFSS: landline/cell telephone — misses unhoused, institutionalized, non-English speakers (partially addressed by weighting)
— NHANES: oversamples Black, Hispanic, older adults, low-income to improve subgroup estimates — must use sampling weights in analysis
— Increased screening → apparent ↑ incidence without true change (e.g., thyroid cancer with neck ultrasound)
— Improved test sensitivity (PCR vs. culture) → ↑ apparent incidence
— Numerator (cases) ≠ population (denominator) source → biased rates
— Use census or ACS for denominators
— Cancer registry data typically reported with 2–4-year lag
— NVSS mortality has provisional and final files; cause-of-death miscoding common

— PRAMS — postpartum behaviors, contraception, breastfeeding, depression (states + NYC)
— MMRCs — review every pregnancy-associated death for preventability; data → CDC ERASE MM
— NVSS Linked Birth/Infant Death — neonatal/infant mortality with maternal risk factors
— National Immunization Survey (NIS) — vaccination coverage in children 19–35 mo and adolescents
— YRBSS — high schoolers; risk behaviors, mental health, sexual activity, substance use
— Newborn screening programs — state-mandated; data feed back to public health for case management of PKU, CAH, SCD, CF, etc.
— Indian Health Service surveillance; CDC's Tribal Epidemiology Centers
— Historical undercount in NNDSS for AI/AN — now improved race/ethnicity completeness
— NIOSH systems — fatal injuries (CFOI), pneumoconiosis (NIOSH Coal Workers' Health Surveillance), needlestick (EPINet)
— SENSOR — state-based occupational disease (asthma, pesticide poisoning)

— A new case definition, lab test, or active case-finding push will transiently spike incidence — not a true epidemic
— Example: PCR replacing culture for pertussis ↑ apparent incidence
— HIV name-based reporting initially controversial; balanced by improved care linkage
— Small-cell suppression protects identity in rare disease/small-area data
— VAERS reports used to claim vaccine-autism link — invalid because VAERS lacks denominator, controls, causality assessment
— Missing race/ethnicity in 20–40% of some COVID early reports → inability to detect disparities

— Any case of a Category A bioterrorism agent: anthrax, botulism, plague, smallpox, tularemia, viral hemorrhagic fevers
— Single case of measles, polio, diphtheria, rabies (human), novel influenza A, SARS, MERS, Ebola
— Cluster of unexplained severe illness or death
— Multistate enteric cluster matched by PulseNet WGS
— Healthcare-associated outbreak (NICU, hemodialysis, surgical)
— Clinician → local health department (first call) → state health department → CDC → WHO under International Health Regulations (IHR 2005) for events of international concern
— Health Alert (highest), Health Advisory, Health Update, Info Service
— Clinicians should subscribe; HAN messages frequently appear as question stem framing
— Suspected high-consequence pathogen → single-patient airborne isolation room, PPE per pathogen, notify hospital epidemiology and infection prevention immediately, do not transport through general areas
— Specimen handling per BSL level; alert lab before sending
— Governors and HHS Secretary can declare emergencies enabling EUAs, quarantine orders, crisis standards of care
— Quarantine (asymptomatic exposed) vs. isolation (symptomatic/infectious) — terminology tested

— NNDSS: passive, national, all notifiable conditions, less complete
— FoodNet: active, 10 sites, enteric pathogens only, gold-standard trends
— VAERS: passive, hypothesis-generating, no denominator
— VSD: active cohort, hypothesis-testing, has denominator
— CISA: clinical consultation for individual complex cases
— FAERS: passive drug AE reports (MedWatch portal)
— Sentinel: active distributed database, drug safety hypothesis testing
— SEER: depth (survival, treatment), ~48% population
— NPCR: breadth (all 50 states), incidence only historically
— USCS: combined SEER+NPCR for national incidence/mortality
— BRFSS: state-level, telephone, adult risk behaviors
— NHIS: national, in-person interview, health conditions/access
— NHANES: national, interview + physical exam + labs, only source for measured biomarkers
— NVSS: aggregate vital statistics
— NDI (National Death Index): record-level matching for research follow-up
— NHSN is the HAI system (CLABSI, CAUTI, SSI, C. diff, MRSA bacteremia) tied to CMS payment
— NNDSS captures community-acquired notifiable pathogens

— Surveillance: population-level ongoing data collection
— Screening: individual-level testing of asymptomatic persons (USPSTF domain)
— Registry: organized collection of data on persons with a specific condition (often clinical-quality focus, e.g., STS cardiac surgery, NCDR cardiology)
— Some registries (SEER) function as surveillance systems
— Surveillance is exempt from IRB review when used for routine public health practice
— When surveillance data are analyzed for generalizable knowledge beyond program evaluation, it becomes research requiring IRB
— Active case finding: seek undetected cases in a population (TB in shelters)
— Contact tracing: identify exposed individuals from a known case
— Cluster: aggregation of cases that may or may not exceed expected — investigate to determine
— Outbreak: occurrence above expected baseline
— Epidemic = outbreak, often larger geographic scope
— Pandemic = epidemic across multiple countries/continents
— Endemic: usual baseline level
— Hyperendemic: persistently high
— Holoendemic: nearly universal in early life (some malaria settings)

— VAERS/VSD signals on rotavirus (RotaShield, 1999) → withdrawal
— VSD/CISA on RZV, mpox, COVID vaccines → schedule changes
— NIS coverage data → identify undervaccinated areas, drive outreach
— BRFSS/NHIS smoking trends → MPOWER, taxation, cessation coverage mandates
— Youth e-cigarette surge (NYTS) → flavor restrictions, Tobacco 21
— SEER incidence/mortality trends → USPSTF updates (e.g., 2021 lung cancer screening expansion to 50–80 y, 20 pack-year; 2021 colon cancer to start at 45 y)
— NHANES BP/lipid trends → JNC/ACC-AHA targets; statin eligibility
— NHANES HbA1c data, USRDS ESRD trends → diabetes prevention program coverage, SGLT2 use in CKD
— NVSS overdose mortality, prescription drug monitoring programs (PDMPs), DAWN ED data → CDC 2016/2022 prescribing guidelines, naloxone distribution
— MMRCs → AIM bundles (hemorrhage, hypertension, sepsis); Medicaid extension to 12 mo postpartum
— NHSN/NARMS data → Joint Commission stewardship requirement (2017)

— Annual evaluation against CDC's 9 attributes
— Completeness audits (compare to lab data, hospital discharge data)
— Capture-recapture methods estimate true case counts from overlapping sources
— Subscribe to CDC HAN, state health department alerts, MMWR
— Use EHR-integrated electronic case reporting (eCR) — increasingly mandatory; reduces clinician burden, improves timeliness
— Explain that diagnosis triggers public health notification and possible contact outreach
— Reassure about confidentiality protections — only public health personnel receive identifiers
— STIs: discuss partner notification options (provider-referral, patient-referral, EPT)
— TB: explain DOT and household contact testing
— Date of report, person notified, control measures initiated
— In CCS, write "report to public health department" as an explicit order
— Health department typically contacts clinician within 24–72 h for class A diseases
— Provide additional clinical data (exposures, travel, vaccination history) as requested
— Lead poisoning (BLL ≥3.5 µg/dL CDC reference value, 2021): recheck per CDC schedule, environmental investigation if ≥5
— Newborn screening positive: confirmatory testing within days; subspecialty referral
— Active TB: monthly clinical visits during therapy, sputum monthly until conversion, DOT

— HIPAA Privacy Rule §164.512 permits disclosure to public health authorities without patient authorization
— Patients cannot opt out of communicable disease reporting
— Clinicians have a duty to report; failure can incur fines and licensure action
— Provider-referral, patient-referral, or contract referral
— EPT legal in most states for chlamydia and gonorrhea; never for syphilis or HIV
— HIV partner notification is voluntary in most states; partners contacted without revealing index identity
— Newborn screening: typically opt-out (varies by state); ethical tension between parental autonomy and state interest in child welfare
— Public health emergency: EUAs require disclosure of investigational status, alternatives, right to refuse
— Rare disease in small geography → cell suppression in published data
— Genomic data in PulseNet: case-level identifiers protected
— Patient with newly diagnosed TB discharged home: ensure DOT handoff to health department, written follow-up date, medication in hand, household contacts list given to public health
— Failure to complete public health handoff = high-risk transition error
— Surveillance can stigmatize (HIV reporting, immigration concerns) — counter with assurances and culturally appropriate outreach
— Missing demographic data (race, ethnicity, sex/gender) hides disparities; ASTHO and CDC push for complete data


— Stem: researcher wants measured prevalence of obesity, HbA1c, lead → NHANES
— State-level adult smoking → BRFSS
— National cancer survival → SEER
— Vaccine adverse event after EUA approval → VAERS → VSD
— Multistate Salmonella outbreak detection → PulseNet
— Suspected measles in clinic → call local health department immediately, isolate (airborne), order IgM and PCR
— Single case meningococcemia → droplet isolation, ceftriaxone, notify public health, contact chemoprophylaxis
— TB suspect on chest x-ray → airborne isolation, AFB ×3, notify public health, IGRA on contacts
— Gunshot wound presenting to ED → stabilize and notify law enforcement
— Suspected child abuse → CPS report, hospital admission for safety if needed
— Step ordering: establish outbreak → verify diagnosis → case definition → line list → epi curve → hypothesis → analytic study → control → communicate
— Defined cohort (wedding) → retrospective cohort with attack rates and RR
— Undefined population → case-control with OR
— Rising thyroid cancer incidence with stable mortality → overdiagnosis / surveillance artifact
— VAERS used to claim causation → no denominator, no causality — invalid
— State-level correlation extended to individuals → ecological fallacy
— Refusal of consent for STI reporting → report anyway; HIPAA permits
— Newborn screening parental refusal → varies by state but generally mandatory with limited exemptions
— EPT for chlamydia → legal in most states, not for syphilis or HIV

Public health surveillance is the ongoing, systematic collection and analysis of population health data — chosen by question type, evaluated by CDC's 9 attributes, mandated by reporting laws that override HIPAA, and acted upon through outbreak investigation and policy — and the Step 3 task is to match the right source to the right question and trigger the right next step.
— Measured biomarker prevalence → NHANES; state behavioral → BRFSS; notifiable disease incidence → NNDSS; vaccine AE → VAERS → VSD; drug AE → FAERS/Sentinel; cancer → SEER/NPCR/USCS; foodborne → FoodNet/PulseNet; HAIs → NHSN
— Passive = cheap, undersensitive; active = complete, costly; sentinel = focused providers; syndromic = real-time symptoms
— HIPAA explicitly permits public health disclosures; clinicians must report Class A diseases immediately, others within days; failure carries legal consequences
— Establish → verify → define → line list → epi curve → hypothesize → test (cohort if defined population, case-control if not) → control → communicate
— Case definition changes, new tests, screening programs all inflate apparent incidence — always rule out before declaring a true trend
— For every reportable diagnosis, write three orders: treat the patient, isolate appropriately, notify public health — and document the handoff so transition-of-care is safe

