Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Keep us safe: An overview of US public health informatics systems and architectures


Published on

Modern society is highly dependent on the provisioning of clean water, healthy and plentiful food, breathable air, and prompt intervention to curtail disease outbreaks. The public health system is critical in supporting these activities. Today’s information technology provides public health practitioners key capabilities in maintaining the health of the population. This lecture will provide a basic foundation of knowledge about public health practice for clinical informaticians, and highlight specialized information systems and data standards used in public health today. We will explore the existing public health informatics infrastructure including surveillance systems, the process of electronic laboratory reporting (ELR) of notifiable diseases, vital statistics systems, and the critical importance of GIS systems in the public health

Published in: Health & Medicine
  • Be the first to comment

  • Be the first to like this

Keep us safe: An overview of US public health informatics systems and architectures

  1. 1. Keeping us safe: An overview of US public health informatics systems and architectures UCSD DBMI Seminar
  2. 2. Overview • What is public health • How is public health organized? • What is public health informatics • Public health information systems • Public health data sets and open data • Public health specific informatics standards
  3. 3. What is public health? • “...the science and art of preventing disease, prolonging life, and promoting health and efficiency through organized community effort...” • “Public health is not easy to define or to comprehend” – Mary-Jane Schneider Winslow, C. The untilled field of public health. Mod Med. 1920;2:183-191. Mary-Jane Schneider, Introduction to Public Health. Jones and Bartlett Publishers, 2011
  4. 4. Public Health Functions Steering Committee (1994) • What does Public Health provide? – Prevents epidemics and the spread of disease – Protects against environmental hazards – Prevents injuries – Promotes and encourages healthy behaviors – Responds to disasters and assists communities in recovery – Assures the quality and accessibility of health services – Research (communicable disease, population health, etc)
  5. 5. Where did public health come from? • Sir Edwin Chadwick published a widely read and important report on sanitation and disease • He ascribed disease to “miasma”, or bad air, which Dr. Snow later proved to be wrong • However, Dr. Chadwick’s association of disease to sanitation was instrumental in creating boards of health charged with improving sanitation “positive evidence of the propagation of acute disease from putrid emanations”
  6. 6. The UK Public Health Act of 1848 • UK politicians strongly lobbied by Sir. Edwin Chadwick • Chadwick felt that disease was the main cause of poverty, hence preventing disease would reduce poverty. • The Public Health Act of 1848 created a General Health Board to oversee sanitation • Abolished 10 years later, upon the retirement of Chadwick – but established several an important precedent for government to oversee sanitation as a way of reducing the burden of disease
  7. 7. The birth of epidemiology: Cholera 1854 John Snow (1813-1858) Snow’s map of cases
  8. 8. The Value of Public Health
  9. 9. Typical Public Health Practice Responsibilities • WIC – Women, Infants, and Children (98%) • Vital statistics (94%) • Tobacco prevention(94%) • Public Health Laboratories (90%) ================================================== • Food safety (82%) • Drinking water regulation (53%) • Health Facility Regulation (78%) • Environmental Health (76%) ================================================== • Drug/Alcohol Abuse Prevention (37%) • Health Professional Licensing (35%) • Medical Examiner (29%) • Environmental Regulation (25%) • Mental Health (20%) • Medicaid (16%) Bernard Turnock, Essentials of Public Health. Jones and Bartlett Publishers. 2007
  10. 10. Public Health Reporting – California county health profiles
  11. 11. Public health informatics is the systematic application of information, computer science, and technology to public health practice, research, and learning Public Health Informatics — Defined Yasnoff WA, O’Carroll PW, Koo D, Linkins RW, Kilbourne EM. Public health informatics: improving and transforming public health in the information age. J Public Health Manag Pract 2000;6:67–75. Riegelman R, ed. Public health 101: healthy people—healthy populations. Sudbury, MA: Jones & Bartlett Learning; 2010: 40.
  12. 12. The Role of Informatics in Public Health –Information dissemination –Data collection / surveillance systems –Data management systems –Computer security for digital data
  13. 13. Examples of Public Health Information Systems • Electronic death registration System • Electronic birth registration System • Disease Surveillance Systems • Immunization Information System • Electronic Laboratory Reporting System • Disease Registries (cancer, etc..) • Health Information Exchange • Geospatial Information Systems (GIS) • Administrative systems
  14. 14. Vital Records Systems • Vital “Statistics” – “statistics” = ‘data about the state’ – originated from: •need to track populations and their status (health) •need to officially record lineage and thus ownership and entitlements • “Vital Records” systems are managed in public health and typically consist of: – birth certificates – death certificates – marriage certificates
  15. 15. Vital Statistics Today • National Center for Health Statistics (NCHS) – – Part of the CDC – Charged with publishing vital statistics at the federal level – Obtains copies of data from state vital records offices • Responsibilities are defined in state laws •Birth registration – hospital of birth or the birth attendant, or parents in the absence of either •Death registration – varies by state, but usually funeral director on behalf of the family
  16. 16. Death Registration in California Today • In 2005, California implemented an electronic death registration system • Today, 100% of all deaths are registered fully electronically • The system contains death certificate data for over 3.2 million deaths since 2005.
  17. 17. Natality Data and Public Health • Natality Files – Teen childbearing – Non-marital childbearing – Pre-term birth – Low birthweight – Cesarean delivery 1940 1950 1960 1970 1980 1990 2000 0 20 40 60 80 100 Birthrateper1,000women aged15-19 0 100 200 300 400 500 600 700 Numberofbirths(inthousands) Number of births Birth rate Number of births and birth rates for teenagers aged 15-19 years: United States, 1960-2000 te_revisions.htm
  18. 18. Death Files and Public Health • Death Statistics Files – Cause-of-death trends – Leading causes of death – Life expectancy – socio-economic factors – Demographic variation te_revisions.htm
  19. 19. Immunization Information Systems • What are they? – Confidential, population-based, computerized information systems that attempt to collect vaccination data about all residents within a geographic area • Advantages of IIS: – Significantly reduces paperwork and staff time for schools, doctors, public health – Assists in reminding parents of needed immunizations – Allows public health to monitor immunizations
  20. 20. Electronic Immunization Registry in California
  22. 22. What is surveillance? “the ongoing systematic collection, analysis, and interpretation of outcome-specific data for use in planning, implementation, and evaluation of public health practice” Thacker SB, Berkelman RL. Public health surveillance system in the United States. Epidemiol Rev. 1988; 10:164-190
  23. 23. Types of Surveillance Systems • Rapid (Early) Recognition Disease Surveillance – Demands early detection and fast countermeasures to avoid high mortality“ – Premium placed on early detection – tapping data streams for a pattern that we believe means disease *outbreak* (the signal) – Typically need immediate input from multiple disparate data sources that are associated with behavior or actions typically occurring because of the outbreak – Informatics impact: Access to absenteeism data, over-the-counter medications for “the cold”, clinical encounter types, patient ‘complaints’ (symptoms – syndromic surveillance). • Exposure/Disease Monitoring Surveillance System – Surveillance of prolonged exposure to causal factors – Premium placed on understanding the association of a causal factor with the disease – Typically need long term longitudinal data for causal factors – Example: Cancer, diabetes, COPD (emphysema) – Informatics impact: Access to longitudinal data (clinical encounters, cumulative CT radiation dose, etc..)
  24. 24. National Notifiable Disease Surveillance System: A History • 1878: Congress authorizes the US Marine Hospital Service to collect morbidity reports on cholera, smallpox, plague, and yellow fever from US consuls overseas. • 1893: Expanded to include data from states for this list of “notifiable diseases” • 1912: state and public health service begin reporting – 5 diseases by telegraph – 10 diseases by letter
  25. 25. CDC Notifiable Diseases
  26. 26. Computerizing NNDSS • NETSS (1990) – - CDC implemented the National Electronic Telecommunications System for Surveillance for electronic capture of notifiable disease data – Facilitated data collection and submission of case-specific data to the CDC’s National Notifiable Disease Surveillance System – Required *manual* data entry into the computerized system • NEDDS (2001) – launched by the CDC as part of the Public Health Information Network (PHIN), Replaced NETSS – An interoperable surveillance information systems for use at the local, state, and federal levels – Major feature is the ability to capture data already in electronic form (ie, lab results) – 16 States use the CDC NEDDS provided “Base System” – 31 States use their own NEDDS-compatible system
  27. 27. National Electronic Disease Surveillance System (NEDSS) 2018
  28. 28. FoodNet and FoodNet FAST • Foodborne illness in the US – 48 million become ill – 128,000 hospitalized – 3,000 die from foodborne illness • FoodNet – Established 1995 – CDC, 10 state health departments, USDA, FDA – Submit reports of infections diagnosed in the 10 states – Surveillance accounts for 15% of the US population Cryptospridium infections
  29. 29. “Syndromic” Surveillance • Began in response to bio-terrorism (Anthrax attacks 7 days after Sept 11) • “the ongoing, systematic collection, analysis, interpretation, and application of real-time (or near real time) indicators for diseases and outbreaks that allow for their detection before public health authorities would otherwise note them.” • Emphasizes – Timeliness of inbound data (real-time) – Automated analysis – Visualization tools Lee, LM editor. Principles and Practice of Public Health Surveillance, 3rd Ed. Oxford Press. 2010
  30. 30. What is “Syndromic” Surveillance? • Intended to detect a public health emergency as early as possible • Survey by symptoms or signs (syndromes) • GI syndromes, respiratory/influenza like syndrome, etc… • Typically requires: – clinical encounter data – Pharmacy/OTC sales data – Absenteeism data (school) – Laboratory data
  31. 31. Data Sources and “Syndromic Surveillance” systems Yan, Chen, Zeng. Syndromic surveillance systems: Public health and biodefense. Ann Rev Inf Science and Technology. Vol 32. 2008
  32. 32. Evolution of Syndromic Surveillance Systems in the US Gould, Walker, Yoon. Public Health Reports 2018. vol 132(supplement 1) 7S-11S
  33. 33. Electronic Surveillance System for the Early Notification of Community-based Epidemics (ESSENCE) • DoD Global Emerging Infections Surveillance and Response System (DoD-GEIS) funded ESSENCE to assist in influenza outbreak detection and response • ESSENCE I – Uses military beneficiary population outpatient visits data across DoD military treatment facilities (MTFs) – Began in 1999, expanded after Sept 11 2001 – Demonstrated validation against ILI visits to sentinel physicians in South-Atlantic region and military facilities in national capital area – Sept 11, 2002 – ESSENCE began receiving outpatient data from all US MTFs and making syndromic surveillance available through DoD – Design: Graphical user interface, database,
  34. 34. ESSENCE I graphical output
  35. 35. ESSENCE I and ESSENCE II
  36. 36. Public Health Information Network (PHIN)
  37. 37. BioSense 1.0 • A component of PHIN • A national system developed for early detection • Sharing of automated detection and visualization algorithms
  38. 38. BioSense 1.0 (2003-2010)
  39. 39. BioSense 2.0 (2011 – 2015) • Launched Nov 2011 • Provided four main capabilities • HIPAA compliant • “Cather’s Mitt” where health dept can receive and store automated health related data • Analytics tools • Method of accepting data in many forms including HL7 • On-premises web based application (not cloud based)
  40. 40. National Syndromic Surveillance Program (NSSP)
  41. 41. NSSP BioSense Platform (2015-present) • Cloud based • Hosted by CDC • Includes three systems • Data from >4,000 hospitals sent to BioSense platform today • Represents about 55% of all ED visits in the US
  42. 42. Tracking Influenza Across the US
  43. 43. Influenza Tracking – three data sources • Laboratory Surveillance – “track the micro-organism” – specimens – Cultures, typing • Track mortality – 121 cities mortality reporting system -- influenza/pneumonia mortality report – Death certificates • Influenza-like Illness surveillance – “track the illness” – Example: Outpatient Influenza-like illness (ILI) surveillance – Clinic visits, over the counter meds – FluView
  44. 44. ILINet • 2,800 enrolled outpatient providers in all 50 states • 39 million patient visits • Weekly reporting to CDC on total number of patients seen for any reason plus patients seen for “Influenza-like illness”(ILI) by age group. • ILI definition – Fever – Cough and/or sore throat without known cause other than influenza
  45. 45. Key Aspects of “Early Recognition” • Defining “Signals” –Are we talking about the same thing? –Are we defining it the same way? • Signal Detection –“how do I set thresholds?” • Signal Characterization –“there is an increase in rate, should we sound the alarm?” Mirhaji. Public health meets translational informatics: A desiderata. JALA 2009;14:157-70
  46. 46. Why is Early Recognition surveillance so important? • We live in a time of rapid travel between large urban areas – perfect conditions for a killer communicable disease • 2009 H1N1 Influenza A pandemic had a mortality rate of only 0.01% (1 in 10,000) yet it killed 14,000 worldwide 61 million infected
  47. 47. The deadly viral pandemic • 1918 Influenza pandemic – 20% fatality rate – 50 million died (3% of the world population of 1.86 billion) • Avian flu (H5N1) – H5N1 has a 60% fatality rate (three times that of 1918 virus) – So, 9% of 7 billion 630 million deaths worldwide.... – Wild type Avian Flu, so far, has not demonstrated the ability to have airborne spread, but...... • Dec 2011 - Dr. Fouchier of Erasmus Medical Center modified H5N1 (avian flu) such that it gained the ability to latch onto cells in the respiratory passage ways (making it airborne). File:Colorized_transmission_e lectron_micrograph_of_Avian _influenza_A_H5N1_viruses.j pg H5N1 - electron micrograph 1918 pandemic victim
  49. 49. Cancer Surveillance: National Program of Cancer Registries (NPCR) • Cancer Registries Amendment Act (1992) • Established a national program of cancer registries through cooperative agreements with states, territories, DC • Requires assurances that the state will provide for authorization by law of a statewide cancer registry • All funded programs must meet standards for electronic data exchange, data content/format, completeness/timeliness, quality assurance, and data submission State Cancer Registry Programs by Funding Status
  50. 50. Surveillance Epidemiology and End Results (SEER) • A program of the National Cancer Institute • Goal is to provide information on cancer statistics in an effort to improve cancer prevention • Collects data on cancer cases throughout the US (through 20 jurisdictional registries) • Started in 1973, ongoing today • SEER Funds cancer registries in 15 jurisdictions that include states, counties, and regions – Some receive combined funding from SEER and NPCR
  51. 51. NAACCR and Cancer Reporting Standards • 1987 - North American Association of Central Cancer Registries (US and Canada) • Mission: develops and promotes uniform data standards for cancer registration • Publishes data and coding standards for cancer registry data collection • Provides a certification levels (Gold, Silver) for cancer registries that meet specific data quality targets (completeness, accuracy, timeliness)
  52. 52. CDQS – Cancer Data Query System
  53. 53. Following health of a cohort - CHIS
  54. 54. Injury related deaths
  55. 55. EPICenter Example – Injury Death Trends
  56. 56. Office of Health Planning and Development (OSHPD)
  57. 57. OSHPD Quality Indicators - SacramentoHospitals  Quality  Preventable Hospitalizations  Sacramento
  59. 59. What is GIS? “Geographic Information Systems (GIS) are computer based systems for the integration and analysis of geographic data” Cromley and McLafferty. GIS and Public Health. 2002. Guilford Press
  60. 60. GIS = Geospatial Objects and Data
  61. 61. Combining geospatial and disease data Geospatial data Other data related to the object T. Sutton, O. Dassau, M. Sutton. A Gentle Introduction to GIS. Dept of Land Affairs. Eastern Cape, South Africa.
  62. 62. GIS Layers • GIS systems typically store information about the world in layers • Each layer has additional geospatial objects • One can add/remove layers in a GIS system • As layers are added, a picture of the real world emerges
  63. 63. Choropleth Maps
  64. 64. GIS Data and Image Basics • Ways GIS systems represent geospatial objects – Vector Data • geometric approximations of objects on the earth • Objects are described by their type, and their geometric shape • The GIS system uses this information to ‘draw’ the objects with correct proportions and geographic orientation – Raster Data • Data is stored in as individual pixels, which individually carry color and position information • Provides more of a ‘real world’ view – looks like a satellite photograph
  65. 65. Vector Data Types T. Sutton, O. Dassau, M. Sutton. A Gentle Introduction to GIS. Dept of Land Affairs. Eastern Cape, South Africa.
  66. 66. Vector Layers Vector map with road Road layer only T. Sutton, O. Dassau, M. Sutton. A Gentle Introduction to GIS. Dept of Land Affairs. Eastern Cape, South Africa.
  67. 67. Raster Data • Raster data is used when information is contiguous across an area and is not easily divided into vector features • Raster data set is composed of rows and columns of pixels, with the value in the pixel representing some characteristic (snow level, temperature, depth, etc..) T. Sutton, O. Dassau, M. Sutton. A Gentle Introduction to GIS. Dept of Land Affairs. Eastern Cape, South Africa. Sacramento Area Raster image: created with Google Earth
  68. 68. Raster Data • Provides for analysis that cannot be done easily with vector data – Water flow over land to calculate watersheds – Identification of areas where plants are growing poorly – Areas of deforestation – Areas under risk of flooding
  69. 69. GIS System Types • GIS Tools to create geospatial data files – Authoring GIS files – ArcGIS – QGIS (open source) • GIS Tools to consume geospatial data files and create thematic maps – Map Creation – Google Earth – Arc GIS (viewing capability) • Interactive GIS Tools to provide geospatial information to accomplish a task – Google maps, Mapquest, etc..
  70. 70. Common GIS File Formats • Shapefile • KML (Keyhole Markup Language)
  71. 71. ESRI Shapefile • A popular geospatial vector data format for GIS systems • Developed and managed by ESRI (Environmental Systems Research Institute) • Does not store topological information • Was introduced with ArcVIEW GIS v2.0 in the early 1990’s • Today, a variety of free and commercial programs will read and write shapefiles
  72. 72. The .shp File • Contains geographic reference data • Consists of a single fixed length header then one or more variable length records • Each record includes a header and content • The variable record content depends on the shape type – Point, polyline, polygon, multipoint • Detailed information on the shapefile format: – file.pdf
  73. 73. What is KML? • Keyhole Markup Language (KML) – created by Keyhole, Inc – Keyhole acquired by Google in 2004 – Keyhole is a reference to a type of satellite • XML-based schema (layout) designed to express geographic annotation and visualization information • KMZ is a ‘zipped’ KML file – .kmz = zipped kml file – Google Earth can ‘open’ either a KML or KMZ file
  74. 74. KML Tags – the XML tags of KML files
  75. 75. KML <description> and ‘markup’
  76. 76. Google Earth <Descriptions>
  78. 78. PHIN Standards
  79. 79. PHIN Reportable Condition Messages
  80. 80. PHIN Example: Tb Notification
  81. 81. Immunizations HL7 Messages CDC Implementation Guide Message Types Involved • VXU – unsolicited request immunization record • VXQ – unsolicited immunization record update • QBP – Query by parameter • RSP – Respond to QBP • ADT – Admit, Discharge, Transfer message • ACK – Acknowledgement message
  82. 82. Standardizing Lists of Vaccines and Manufacturers Standard vaccine codes (CVX) Standard manufacturer codes (MVX)
  83. 83. Example IIS HL-7 Message MSH|^~&||GA0000||VAERS PROCESSOR|20010331605||ORU^RO1|20010422GA03|T|2.3.1|||AL| PID|||1234^^^^SR~1234-12^^^^LR~00725^^^^MR||Doe^John^Fitzgerald^JR^^^L||20001007|M||2106-3^White^HL70005|123 Peachtree St^APT 3B^Atlanta^GA^30210^^M^^GA067||(678) 555-1212^^PRN| NK1|1|Jones^Jane^Lee^^RN|VAB^Vaccine administered by (Name)^HL70063| NK1|2|Jones^Jane^Lee^^RN|FVP^Form completed by (Name)-Vaccine provider^HL70063|101 Main Street^^Atlanta^GA^38765^^O^^GA121||(404) 554-9097^^WPN| ORC|CN|||||||||||1234567^Welby^Marcus^J^Jr^Dr.^MD^L|||||||||Peachtree Clinic|101 Main Street^^Atlanta^GA^38765^^O^^GA121|(404) 554- 9097^^WPN|101 Main Street^^Atlanta^GA^38765^^O^^GA121| OBR|1|||^CDC VAERS-1 (FDA) Report|||20010316| OBX|1|NM|21612-7^Reported Patient Age^LN||05|mo^month^ANSI| OBX|1|TS|30947-6^Date form completed^LN||20010316| OBX|2|FT|30948-4^Vaccination adverse events and treatment, if any^LN|1|fever of 106F, with vomiting, seizures, persistent crying lasting over 3 hours, loss of appetite| OBX|3|CE|30949-2^Vaccination adverse event outcome^LN|1|E^required emergency room/doctor visit^NIP005| OBX|4|CE|30949-2^Vaccination adverse event outcome^LN|1|H^required hospitalization^NIP005| OBX|5|NM|30950-0^Number of days hospitalized due to vaccination adverse event^LN|1|02|d^day^ANSI| OBX|6|CE|30951-8^Patient recovered^LN||Y^Yes^ HL70239| OBX|7|TS|30952-6^Date of vaccination^LN||20010216| OBX|8|TS|30953-4^Adverse event onset date and time^LN||200102180900| OBX|9|FT|30954-2^Relevant diagnostic tests/lab data^LN||Electrolytes, CBC, Blood culture| OBR|2|||30955-9^All vaccines given on date listed in #10^LN| OBX|1|CE30955-9&30956-7^Vaccine type^LN|1|08^HepB-Adolescent/pediatric^CVX| OBX|2|CE|30955-9&30957-5^Manufacturer^LN|1|MSD^Merck^MVX| OBX|3|ST|30955-9&30959-1^Lot number^LN|1|MRK12345| OBX|4|CE|30955-9&30958-3^ Route^LN|1|IM^Intramuscular ^HL70162| OBX|5|CE|30955-9&31034-2^Site^LN|1|LA^Left arm^ HL70163| OBX|6|NM|30955-9&30960-9^Number of previous doses^LN|1|01I OBX|7|CE|CE|30955-9&30956-7^Vaccine type^LN|2|50^DTaP-Hib^CVX| OBX|8|CE|30955-9&30957-5^ Manufacturer^LN|2|WAL^Wyeth_Ayerst^MVX| OBX|9|ST|30955-9&30959-1^Lot number^LN|2|W46932777| OBX|10|CE|30955-9&30958-3^ Route^LN|2|IM^Intramuscular^HL70162|
  84. 84. Causes of Death Coding - ICD • Causes of Death are coded using the International Classification of Disease, 10th edition (ICD-10) • ACME – Automated Classification of Medical Entities – Developed to improve consistency – Developed with experienced nosologists – SuperMICAR: a software system that automates the classification and allows the use of literal text from the death certificate • Used today to expedite the coding of causes of death on certificate information submitted by states to the National Center for Health Statistics (NCHS).
  85. 85. PHIN - VADS • A one-stop shop for obtaining vocabularies related to public health • Main purpose is to distribute value sets developed by the CDC for use in v2.x and CDA messages in public health • 592 value sets supporting 60 HL7 and CDA message implementation guides • Value sets are function specific and derived from a number of vocabularies (LOINC, SNOMED, CPT, ICD, etc..)
  86. 86. VADS Microorganism Value Set
  87. 87. Jurisdictions – FIPS and ANSI Codes • Federal Information Processing Standard (FIPS) • Uniquely identifies counties and county equivalents in the US and territories • NIST has withdrawn FIPS and recommends using ANSI codes (INCITS) ANSI Codes: