Automated Notifiable Condition Reports: Enhancing Public Health Surveillance

1. Delivery of Automated Notifiable Condition Reports: A Success Story of the Regenstrief Institute's Notifiable Condition Detector Shaun Grannis, MD MS FAAFP Medical Informatics Research Scientist,Regenstrief Institute Assistant Professor of Family Medicine,Indiana University School of Medicine

2. Overview: What We’ll Cover • The Problem: • Underreporting • Incomplete knowledge of disease burden • The Strategy: • Leverage existing flows • Automation • Sustainability • The System: • HIE • NCD • The Results • The Future

3. The Problem (Premises) • To successfully manage the public health disease burden in a community, the true public health disease burden of a community must be ascertained • Disease burden is determined in large part using information generated in clinical care processes • Clinical care processes under-report to public health (Thacker) • Reporters overburdened/under-resourced • Reporters lack knowledge, reporting requirements change • Clinical data is scattered across disparate settings in different (non-standard) formats

4. The Strategy • Leverage (re-use) existing clinical data flows to augment public health reporting • Minimize the need for human intervention in the reporting process by … • Standardizing data in a sustainable fashion so computers can automatically process

5. A Note on Strategy to Consider • Who identifies whether a condition is reportable?

6. The System: Health Information Exchange

7. Regenstrief/INPC/IHIE Timeline • Regenstrief tasked in 1972 to “stitch” silos of medical information together -> the Regenstrief Medical Record System (RMRS/Wishard Memorial Hospital) • In 1994, began stitching together information across institutions (INPC/Indianapolis) • IN 2002 IHIE formed (services organization) • In 2003, working towards stitching the state together (INPC/Indiana)

8. INPC The Indiana Networkfor Patient Care An operational community wide electronic medical record

9. Indianapolis MSA, Indiana • 1.5 million population base • 12th largest city in U.S.A. • Indiana Health Information Exchange • Home to Indiana’s only medical school • Referral center for entire state (7 million) • Regenstrief Institute • State Department of Health

10. INPC Project Goal Demonstrate the feasibility and benefit of a community wide electronic medical record system in patient care.

11. INPC Stakeholders • Indianapolis Med/Surg hospitals • Physician offices • Community health centers • Homeless care network • Public school clinics • County and state public health departments • National laboratories • Pharmacies • PBMs

12. INPC Data sources • 17 hospitals including the 5 major hospital systems (99% of non-office care) and community hospitals • National and regional laboratories • Local imaging centers • All four homeless care systems • Public health departments (county and state) • Approximately 1/3 of ambulatory physicians

13. Classes of Data shared by all Institutions • All ED and outpatient visits • All hospital discharges (dx, procedures) • All inpatient laboratory results • All outpatient laboratory results • Immunizations • All discharge summaries/admissions summaries • All operative notes • All radiology reports • All surgical pathology reports • Inpatient medications • Tumor registry data

14. INPC Data Volumes • 7 million registration “events” • 60 million orders • 900 million coded results • 20 million dictated reports • 8.8 million radiology reports • Hundreds of millions prescriptions • 750,000 EKG tracings • 45 million radiology images

15. Standardizing Clinical Data Jane Doe’s hospital lab: 3/1/04 GC 3/1/04 BloodCx 3/1/04 UrineCx 3/1/04 HepB Patient ID: 123LMNOP Name: Jane Doe DOB: 01/01/04 SSN: N/A Address: 555 Johnson Road City: Indianapolis State: Indiana ZIP: 46202 Gonorrhea: 30936-9 Blood Culture: 30938-5 Urine Culture: 33555-4 Hepatitis B: 30943-5 30936-930938-533555-430943-5 Global Patient Index Hospital Lab Global ID: 45678 Name: Jane Ellen Doe Lots of Demographics.. MRF1 ID: OU81247 MRF2 ID: 4564356 PH MRF ID: 123LMNOP MRF3 ID: 6789XYZ Patient ID: 6789XYZ Name: Jane Ellen Doe DOB: 01/01/04 SSN:123-45-6789 Address: 555 Johnson Road City: Indianapolis State: Indiana ZIP: 46202 Jane Ellen Doe’s clinic labs: 5/1/04 Gonn 5/1/04 BCx 5/1/04 UCx 7/9/04 Hepatits 30936-930938-533555-430943-5 Concept Dictionary Outpatient Clinic Lab

16. The Indiana Network for Patient Care Consolidating the Silos Clarian MRF St. Vincent MRF Global Patient Index Hospital Lab Global Patient Index Concept Dictionary Hospital Lab Wishard MRF Concept Dictionary Outpatient Clinic Lab Community MRF Outpatient Clinic

17. Results delivery • Secure document transfer • Shared EMR • Credentialing • Eligibility checking Hospitals Hospital Payers • Results delivery • Secure document transfer • Shared EMR • CPOE • Credentialing • Eligibility checking Health Information Exchange Physicians Labs • Results delivery Labs Data Repository Network Applications • Surveillance • Reportable conditions • Results delivery Public Health Outpatient RX Payer • Secure document transfer Physician Office Public Health Researchers • De-identified, longitudinalclinical data Ambulatory Centers Data Reuse Data Management Data Access & Use Negotiated Access

18. A Note on Sources of Data for NCD • Four percent of physicians have an extensive,fully functional electronic-records system † • 13% reporthaving a basic system† • Identify “low-hanging fruit” for data sources †“Electronic Health Records in Ambulatory Care: A National Survey of Physicians”, NEJM 359:50-60. July 3, 2008

19. Clinical Results ideally should Optimally Standardized, Coded observations Blood culture result in HL7 format: MSH||CHARTLINC|SF_SOFTMED|||$YearMonthDay|| PID|||$patient id$||$patient name$|| PV1|||||||$attending doctor$||$consulting doctor$|| OBR||008^001|M46123|BLC^BLOOD CULTURE^L|| OBX|1|ST|CULT^CULTURE^L^6463-4^Bacteria identified^LN|BLC1|METH. RESISTANT S. AUREUS (MRSA)^115329001^MRSA^SN|||A| LOINC SNOMED

20. Real World Culture Report No LOINC or SNOMED codes MSH|^~\&|PMLW|HNA|NCD||20081016114316||ORU^R01|8|P|2.3|25754 ZVX|K|PF|126134534| PID|1|384854^^^HNA^MRN|519074^^^HNA^MRN||Eccleston^Christopher||20080220|M||W|4784 Main Street^^Neverland^IN^75027||367-433-4206|306-565-8064|EN|S|CAT|710863^^^HNA^FIN NBR|274-387-3363|DL-4750617|902998^^^HNA^FIN NBR|||||||||N OBR|1|989923284^HNALAB|17-494-2482_459053|692571^Resp CX + Stn^CERLB|||20081119100049|||||||20080328201310|&CF&^^^&Sputum&|904379^Cortez^Ana-Lucia^^^^^^HNA^Personnel^^^HNA DOCTOR||||||20080711035105||MB|P|CD:215871426&Cystic Fibrosis Birthday Visit Order Set-RH|1^^^20080123094900^^R~^^^^^R||154768586^HNA_ORDERID|||||||20080305023625 OBX|1|FT|666971^GS^CERLB||Less than 10 epithelial cells per lpf \.br\2+ (moderate) Gram Positive Cocci \.br\1+ (few) Gram Negative Rods \.br\Rare White Blood Cells||||||F|||20080225164740|^CPL Micro^|536146^Tishler^Adair^^^^^^HNA^Personnel^^^HNA DOCTOR|^^220^CPL Micro OBX|2|CE|ORGANISM^^CERLB|1|310784^Staphylococcus aureus^CERLB|||||||||20081116062408|^CPL Micro^||^^220^CPL Micro OBX|3|CE|ORGANISM^^CERLB|3|310307^Haemophilus influenzae^CERLB|||||||||20080106025756|^CPL Micro^||^^220^CPL Micro OBX|4|FT|666972^Final^CERLB||4+ (many) Staphylococcus aureus (MRSA) \.br\2+ (moderate) Escherichia coli Extended spectrum Beta-lactamase producer confirmed \.br\1+ (few) Gram Negative Rods #2 Not identified \.br\4+ (many) Normal flora isolated||||||F|||20080302045155|^CPL Micro^|578549 OBR|2|806483421^HNALAB|16-962-2246_589620|312370^MIC^CERLB|||20080926121606||||||||&CF&|805953^Byrd^Eugene^^^^^^HNA^Personnel^^^HNA DOCTOR||||||20080615131702||MB||692571&Resp CX + Stn^1^310784&Staaur|1^^^^^R~^^^^^R|||||| OBX|1|CE|ORG^^CERLB|1|310784^Staphylococcus aureus^CERLB|||||||||20080615213954|^CPL Micro^||^^^CPL Micro OBX|2|NM|309643^Penicillin^CERLB|1|>=0.5|||R|||F|||20080612075548|^CPL Micro^|209285^Watros^Libby^^^^^^HNA^Personnel^^^HNA DOCTOR|^^^CPL Micro OBX|3|NM|309669^Clindamycin^CERLB|1|<=0.25|||S|||F|||20080222214017|^CPL Micro^|935308^Roundtree^Richard^^^^^^HNA^Personnel^^^HNA DOCTOR|^^^CPL Micro OBX|4|NM|309665^Erythromycin^CERLB|1|>=8|||R|||F|||20080603024932|^CPL Micro^|946525^Fernandez^Nikki^^^^^^HNA^Personnel^^^HNA DOCTOR|^^^CPL Micro OBX|5|NM|309663^Gentamicin^CERLB|1|<=0.5|||S|||F|||20080218160702|^CPL Micro^|354065^French^Colby^^^^^^HNA^Personnel^^^HNA DOCTOR|^^^CPL Micro OBX|6|NM|309644^Oxacillin^CERLB|1|>=4|||R|||F|||20080815093826|^CPL Micro^|716621^Rousseau^Danielle^^^^^^HNA^Personnel^^^HNA DOCTOR|^^^CPL Micro OBX|7|NM|309640^Rifampin^CERLB|1|<=0.5|||S|||F|||20081011194018|^CPL Micro^|296776^Clark^Josh^^^^^^HNA^Personnel^^^HNA DOCTOR|^^^CPL Micro OBX|4|FT|666972^Final^CERLB||4+ (many) Staphylococcus aureus (MRSA) \.br\2+ (moderate) Escherichia coli Extended spectrum Beta-lactamase producer confirmed \.br\1+ (few) Gram Negative Rods #2 Not identified \.br\4+ (many) Normal flora isolated||||||F|||20080302045155|^CPL Micro^|578549 Staphylococcus aureus (MRSA)

21. High-Level Overview of Automated Notifiable Condition Detection

22. Notifiable Condition Detector E-mail Summary Abnormal flag, Organism name in Dwyer II, Value above threshold Realtime Compare to Dwyer I Daily Batch To Public Health Reportable Conditions Databases Inbound Message Potentially Reportable Reportable Condition To Infection Control Record Count as denominator Print Reports

23. Step-By-Step Process • Clinical result received • Test code (OBX-3) mapped to LOINC • LOINC code examined for potential reportability – PHIN NCMT – “Dwyer I” (e.g., Blood culture is potentially reportable; Serum Prolactin Level is not) • If LOINC code is potentially reportable, then look up clinical conditions associated with that code – PHIN-NCMT – “Dwyer II”. • Look for those clinical conditions in the clinical concept field (OBX-5). “Fuzzy” string comparators used • If answer present, look for negation context • If no negation, flag as reportable

24. “Fuzzy” String Comparator • Longest Common Subsequence (LCS) • If LCS (Condition, Result Text) > 0.8, consider it a match • LCS (‘Hepatitis’, ‘Hepaitis’) :Hepatitis contains 9 characters Share subsequences ‘Hepa’ (4) and ‘itis’ (4) ( 4 + 4 ) / ( 9 ) = 88% → Considered a match

25. Additional Detail • “Report All” sources • Abnormal Flag • ICD-9 diagnostic codes • Key words • Challenges

26. standardize patient (MPI) Push data to recipients via clinical messaging standardize vocabulary Load data into repository standardize provider Evaluate for Public Health Notifiable status Monitor data flows P1 P2 P3 P4 P5 P6 P7 Processor/ Consumer Layer Access Layer Access Layer Access Layer Access Layer DataReceiver Raw MessageQueue NormalizedMessage Queue Inbounddata Data Layer Receive data by a variety of potential means: TCP port, directory harvester, sFTP, HTTP, email, etc Raw, non-normalized data Normalized data available for multiple uses /stakeholders/applications • WORKFLOW (from left to right in image): • Dr. Orders Chlamydia Culture • Lab performs test, generates electronic result • Electronic result sent via secure real-time connection to data receiver • Rates of flow from lab are monitored, alerts sent if rate falls outside expected range (P1) • Data receiver performs minimal validation of inbound message, stores message in raw queue • Raw-queue processors augment/normalize data where necessary, eg: • Augment result with additional provider data present in the HIE (P2) • convert local Chlamydia code to common vocabulary eg, LOINC, SNOMED, etc. (P3) • Augment patient data with additional information in the HIE - MPI (P4) • Message is place in normalized queue where 1 to N consumers can access each message for a specified use case: • results are pushed back to Dr. through clinical messaging (P5) • results are stored in patient-centric community repository for access at point of care (P6) • results are analyzed and if Chlamydia test is positive, is automatically sent to public health (P7) and reporting form can be sent to provider (P5)

28. Results

29. Public Health Reportable Conditions

30. ELR Completeness† 4,785 total reportable cases INPC– 4,625 (97%) Health Dept – 905 (19%) Hospitals – 1,142 (24%) †Overhage, Grannis, McDonald. A Comparison of the Completeness and Timeliness of Automated ELR and Spontaneous Reporting of Notifiable Conditions. Am J Pub Health 2008 98:344-350.

31. Next Steps • Evolving NCD / Open Source • Critic Architecture • Delivering reporting forms to providers • Administrative/operational improvements • Monitoring • Denominator Counts • Cross jurisdictional reporting

32. Open Source

33. Public Health ?

34. New “REX Critic” Architecture • Ability to identify more complex result structures • More robust “conditional” negation (using an ontology of negation) • Addresses at least 3 types of results categories: • Numeric • “Varicella Zoster IgG titre: 1.51”, “Lead level: 22”, “Absolute CD 4 Helper: 284” • Discrete / Categorical • “Hep B surface Ag: Present”, “N gonorrhoeae, DNA Probe: Positive” • Freeform Text • e.g., Blood culture reports

35. MRSA Evaluation† 64,554 total reports Sensitivity, Specificity, PPV > 99% †Friedlin J, Grannis S, Overhage JM. Using Natural Language Processing to Improve Accuracy of Automated Notifiable Disease Reporting. AMIA Proc Sym 2008. In Press.

36. Example 1: All results found in OBX-5 OBX|1|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Source: ABSCESS Collected: 09/09/08 00:55 OBX|2|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Site: ABDOMINAL abcess Received : 09/09/08 00:55||||||F|||200809090055 OBX|3|TX|CLDWD^CULTURE WOUND, Deep^SERH||CULT Anaerobe ** FINAL * 09/14/08 06:53||||||F|||200809090055 OBX|4|TX|CLDWD^CULTURE WOUND, Deep^SERH||09/14/08 No anaerobes isolated in 5 days.||||||F|||200809090055 OBX|5|TX|CLDWD^CULTURE WOUND, Deep^SERH||CULTURE WOUND, Deep ** FINAL * 09/12/08 06:29||||||F|||200809090055 OBX|6|TX|CLDWD^CULTURE WOUND, Deep^SERH|| # 01 Staphylococcus aureus-mrsa||||||F|||200809090055 OBX|7|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Moderate.||||||F|||200809090055 OBX|8|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Negative for inducible||||||F|||200809090055 OBX|9|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Clindamycin resistance.||||||F|||200809090055 OBX|1|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Source: ABSCESS Collected: 09/09/08 00:55 OBX|2|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Site: ABDOMINAL abcess Received : 09/09/08 00:55||||||F|||200809090055 OBX|3|TX|CLDWD^CULTURE WOUND, Deep^SERH||CULT Anaerobe ** FINAL * 09/14/08 06:53||||||F|||200809090055 OBX|4|TX|CLDWD^CULTURE WOUND, Deep^SERH||09/14/08 No anaerobes isolated in 5 days.||||||F|||200809090055 OBX|5|TX|CLDWD^CULTURE WOUND, Deep^SERH||CULTURE WOUND, Deep ** FINAL * 09/12/08 06:29||||||F|||200809090055 OBX|6|TX|CLDWD^CULTURE WOUND, Deep^SERH|| # 01 Staphylococcus aureus-mrsa||||||F|||200809090055 OBX|7|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Moderate.||||||F|||200809090055 OBX|8|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Negative for inducible||||||F|||200809090055 OBX|9|TX|CLDWD^CULTURE WOUND, Deep^SERH|| Clindamycin resistance.||||||F|||200809090055

37. Example 2: Results found in both OBX and NTE segments OBX|1|CE|SDES^SPECIMEN DESCRIPTION^MIDAM|1|BLUDC^BLOOD(C) CENTRL LINE DRAW^SQS||||||F|||200809090810|^| OBX|2|CE|SREQ^SPECIAL REQUESTS^MIDAM|1|OONLY^Aerobic bottle only received - unable todetermine presence or absence of^SQD||||||F|||200809090810|^| NTE|1|| strict anaerobic organisms. OBX|3|CE|CULT^CULTURE^MIDAM|1|ENT^ ENTEROCOCCUS SPECIES ^SQMO||||||F|||200809090810|^| NTE|1||METHICILLIN RESISTANT STAPH AUREUS NTE|2||PRESUMPTIVE NTE|3||VANCOMYCIN RESISTANT ENTEROCOCCUS NTE|4|| NTE|5||GPC CALLED 9/10/08 1009AM AT 555-3244 TO MARY SMITH RN, NTE|6|| NTE|7||MRSA CALLED TO 555-3244 TO MARY SMITH, RN. 09/14/08 1044 OBX|1|CE|SDES^SPECIMEN DESCRIPTION^MIDAM|1|BLUDC^BLOOD(C) CENTRL LINE DRAW^SQS||||||F|||200809090810|^| OBX|2|CE|SREQ^SPECIAL REQUESTS^MIDAM|1|OONLY^Aerobic bottle only received - unable to determine presence or absence of^SQD||||||F|||200809090810|^| NTE|1|| strict anaerobic organisms. OBX|3|CE|CULT^CULTURE^MIDAM|1|ENT^ ENTEROCOCCUS SPECIES ^SQMO||||||F|||200809090810|^| NTE|1||METHICILLIN RESISTANT STAPH AUREUS NTE|2||PRESUMPTIVE NTE|3||VANCOMYCIN RESISTANT ENTEROCOCCUS NTE|4|| NTE|5||GPC CALLED 9/10/08 1009AM AT 555-3244 TO MARY SMITH RN, NTE|6|| NTE|7||MRSA CALLED TO 555-3244 TO MARY SMITH, RN. 09/14/08 1044

38. Example 3: Incomplete sentences; Punctuation lacking Source: SWAB FROM SYNOVIAL/JOINT FLD Collected: 02/16/07 Site: Left Knee Received : 02/16/07 BACT. CULT- BODY FLUID 02/17/07 Notified MMS, Kathy 02/17/2007 07:09. 02/18/07 **COPY OF REPORT SENT TO INFECTIONS CONTROL** Called to Carol 02/18/2007 16:42 . Called corrected report to Carol 02/18/2007 16:48 . ORGANISM 01 Staph aureus MANY SUSCEPTIBILITY TESTING TO FOLLOW. ***Please note, previously reported MRSA in error. After further testing, isolate is not MRSA*** Source: SWAB FROM SYNOVIAL/JOINT FLD Collected: 02/16/07 Site: Left Knee Received : 02/16/07 BACT. CULT- BODY FLUID 02/17/07 Notified MMS, Kathy 02/17/2007 07:09. 02/18/07 **COPY OF REPORT SENT TO INFECTIONS CONTROL** Called to Carol 02/18/2007 16:42 . Called corrected report to Carol 02/18/2007 16:48 . ORGANISM 01 Staph aureus MANY SUSCEPTIBILITY TESTING TO FOLLOW. ***Please note, previously reported MRSA in error. After further testing, isolate is not MRSA***

39. Example 4: Ambiguous Phrases MRSA^MRSA by PCR Source: NOSE/NPH Collected: 12/31/07 14:25 Site: NOSE Received : 12/31/07 14:32 CALLED 01/01/2008, 00:27, positive mrsa called to mary at 0028, By CCBL7 MRSA by PCR ** FINAL * 01/02/08 08:18 12/31/07 POSITIVE 01/02/08 No viable methicillin resistant S. aureus (MRSA) for isolation and/or susceptibility studies. MRSA^MRSA by PCR Source: NOSE/NPH Collected: 12/31/07 14:25 Site: NOSE Received : 12/31/07 14:32 CALLED 01/01/2008, 00:27, positive mrsa called to kathy at 0028, By CCAT1 MRSA by PCR ** FINAL * 01/02/08 08:18 12/31/07 POSITIVE 01/02/08 No viable methicillin resistant S. aureus (MRSA) for isolation and/or susceptibility studies. MRSA^MRSA by PCR Source: NOSE/NPH Collected: 12/31/07 14:25 Site: NOSE Received : 12/31/07 14:32 CALLED 01/01/2008, 00:27, positive mrsa called to kathy at 0028, By CCAT1 MRSA by PCR ** FINAL * 01/02/08 08:18 12/31/07 POSITIVE 01/02/08 No viable methicillin resistant S. aureus (MRSA) for isolation and/or susceptibility studies.

40. Example 5: No Punctuation EYE CULTURE No Collection Times Given No anaerobes seen ORG #5 MRSA Staphylococcus coagulase negative Enterococcus sp GNR ID to follow Bacillus species EYE CULTURE No Collection Times Given No anaerobes seen ORG #5 MRSA Staphylococcus coagulase negative Enterococcus sp GNR ID to follow Bacillus species

41. Augmenting MRSA reporting with NLP Average Monthly MRSA reporting rate = 1540 NLP detecting average of 1,157 more reports of MRSA/month MRSA Reports Average Monthly MRSA reporting rate = 383 Months Is MRSA more prevalent than current estimates predict?

42. Results Delivery – An Illustration

45. Administrative / Operational improvements • Monitoring reporting rates • Denominator Counts • Cross jurisdictional reporting • Public Health Feedback

46. Take Home Points • If we seek a better assessment of community health, a more complete picture is needed. Then either: • Address the reasons humans don’t report or • Un-encumber the human and begin to automate the process • If we seek to automate the reporting process, then standardized codes (test, not answer) are needed • If we want to sustainable management of standardized codes, we must find the multiple use cases (value propositions) that will support the ongoing mapping process

47. Take Home Points • Notifiable disease surveillance is one such function that can be highly leveraged: Public health Notifiable Condition Detection shares many similarities with clinical decision support processes • In the near- to mid-term, public health information technology will become largely indistinguishable from clinical information technology

48. Questions / DiscussionThank You! Shaun Grannis, MD MS FAAFP Medical Informatics Research Scientist,Regenstrief Institute Assistant Professor of Family Medicine,Indiana University School of Medicine