LIMS and Public Health

The current H1N1 flu pandemic has put a spotlight on public health agencies as they work to identify and contain the outbreak. The United States public health infrastructure was well prepared to handle the emerging crisis, with a remarkably large percentage of state laboratories using the same informatics infrastructure to effectively share information in real time. Nevertheless, a jittery public seemed to find little reassurance in the due diligence and processes followed by those agencies entrusted with controlling such public health emergencies. The public seemed to assume that news about emerging cases and the severity of the outbreak was being discovered and transmitted by the mainstream media itself, with public agencies lagging behind in processing the constantly shifting stream of information. On the contrary, a sophisticated collaborative information network made information on each new suspected case available across the country, to a large percentage of the country’s public health agencies. This was possible due to the implementation, over the course of the past several years, of a far-reaching public health information network, which facilitates information-sharing and collaboration among agencies operating at the local, regional, state, and national levels.

For example, the San Diego County Public Health Laboratory (SDCPHL) relies on the Health Level Seven (HL7) messaging capability of its STARLIMS public health laboratory information management system (STARLIMS, Hollywood, FL) to communicate reportable disease conditions automatically to Community Epidemiology. “The swine flu outbreak was the lab’s first crisis challenge in processing large numbers of samples and rapidly reporting the results,” stated Jonna Allen, Senior Public Health Microbiologist QA at SDCPHL. “Within just a couple of days of the beginning of the outbreak, we were able to set up a streamlined work flow using PCR results to finalize testing and allow electronic reporting. Our ability to create reports and communicate efficiently during this public health emergency was improved by the quick response of STARLIMS’s technical support team.”

In a similar vein, David Smalley, Public Health Laboratory Director, Tennessee Department of Health, described how during the initial phase of the novel H1N1 outbreak, his department developed a spreadsheet from data entered into the program that was consistent with the linelisting directed by the Centers for Disease Control and Prevention (CDC) in reporting confirmed cases. “STARLIMS programmers developed the spreadsheet and within a day, we were able to automatically upload our new data directly into the CDC reporting system,” he noted.

Historical perspective: The CDC sets the stage

The active Public Health Information Network (PHIN) that is in place today originated when the House of Representatives Government Reform Committee Subcommittee on Technology and Procurement Policy and the Association of Public Health Laboratories (APHL) met to discuss the National Electronic Disease Surveillance System (NEDSS) and the important role it would play in rebuilding the information technology capability of public health laboratories. The testimony included a justification of the role of a LIMS in the NEDSS framework, together with a commitment to work with the APHL to define and document the relationship between LIMS and NEDSS. This helps ensure that state LIMS are developed according to NEDSS standards.

The major conclusion from this testimony (subsequently confirmed by the anthrax scare in fall 2001) was that the state of information technology in the nation’s PHLs was not adequate for large-scale emergencies. The advent of the West Nile Virus and Severe Acute Respiratory Syndrome (SARS) reaffirmed the critical need for efficient electronic laboratory information management systems and the need for enhanced electronic reporting and communications.

The events surrounding the 2001 anthrax bioterrorism (BT) threat emphasized the urgency of achieving these goals as rapidly as possible. Health and Human Services Secretary Tommy Thompson’s announcement on January 31, 2002, of $1.1 billion in funding to states for bioterrorism preparedness, to be provided mainly through the CDC’s bioterrorism cooperative agreements, created an unprecedented opportunity for developing modern IT capacity within the nation’s public health community.

This was driven by recognition by the CDC’s Office of the Director that a substantial amount of these resources would probably be spent on information technology. Accelerating progress toward defining and implementing IT standards for public health could improve the likelihood that these expenditures would result in effective information flow through interoperable systems. Consequently, the CDC decided to incorporate the “Public Health Information Technology Functions and Specifications (for Emergency Preparedness and Bioterrorism)” into the BT guidance as an attachment.

The CDC Information Council (CIC) took an important first step at its April 2002 meeting by deciding that the CDC would work to adopt IT standards and specifications that would apply to all CDC cooperative agreement programs.

Historical perspective: The APHL defines LIMS requirements

In a parallel process, funded by the Robert Wood Johnson Foundation (RWJF), the APHL, the Public Health Informatics Institute (PHII), and a number of partner PHLs began the “PHL Collaborative for Laboratory Information Management Systems” project. Nine state PHLs and one local PHL provided full partner collaboration involving significant time and material support. Six other state PHLs supplied participation support.

One of the main goals of the project was to identify, if possible, common business processes among PHLs that could be used to specify shared LIMS requirements. The Project Team published its seminal work identifying the following 16 common business processes in 2003:

  1. Laboratory test processing (clinical and environmental)
  2. Test scheduling
  3. Proactive specimen/sample collection (prescheduled tests)
  4. Specimen and sample tracking/chain of custody
  5. Media, reagents, stains, controls, etc., manufacturing
  6. Inventory control, including kits and forms management
  7. General laboratory reporting
  8. Statistical analysis and surveillance
  9. Billing for laboratory services
  10. Contract and grant management
  11. Training, education, and resource management
  12. Laboratory certifications/licensing
  13. Customer concerns/suggestions
  14. Quality control (QC) and quality assurance (QA) management
  15. Laboratory safety and accident investigation
  16. Laboratory mutual assistance/disaster recovery.

Historical perspective: The CDC adopts communication standards

The CDC introduced the Public Health Information Network as a means to define a standards-based approach to the exchange of information among public health partners. From a LIMS perspective, the PHIN-adopted standards added two key requirements:

  1. The LIMS must be able to incorporate standardized messaging services. The LIMS was required to receive messages from public health partners and then to process the content of the messages into LIMS-relevant events (e.g., prelogging samples). The LIMS was required to assemble information from LIMS-relevant events (e.g., results reporting) into standardized message format and then to transmit the message(s) to the associated public health partner(s). Rather than create a new standard, PHIN selected the existing HL7 as the messaging standard.
  2. The LIMS must be able to adopt standardized vocabularies in order to minimize inconsistencies and ambiguities. Again, PHIN selected existing tools: the Systematic Nomenclature for Medicine (SNOMED) and the Logical Observation Identifiers Names and Codes (LOINC) in order to establish standard, version- controlled coded concepts.

Therefore, by 2007, the role of LIMS within public health organizations was coming closer to its promise of offering central repositories of public health information with the ability to exchange the information with other public health partners. To date, 20 of the 50 state public health agencies in the U.S. have implemented STARLIMS systems.

Challenges in implementing a nationwide public health LIMS

In practice, harmonization of the public health LIMS environment faces many challenges, including:

  • Organizational challenges: Each country and, indeed, each U.S. state, presents a unique organizational structure. For example, some state PHLs run clinics but most do not; some charge for services and some do not; some are organized within their state’s Health Agency and some are not. Organizational differences require significant flexibility within a LIMS to accommodate the resulting differences in reporting rules.


STARLIMS configuration tools allow each PHL to define its own organizational structure with regard to the names and staffing of multiple facilities and teams (including outsource laboratories). STARLIMS uses these configuration settings to minimize manual laboratory and business activities. Other configuration tools are used to map reporting requirements to specific tests and clients, permitting each PHL using STARLIMS to create a unique, rules-driven reporting and notification environment.

  • Vocabulary challenges: Prior to the PHIN requirement, the use of LOINC and SNOMED codes was rare in public health. Virtually every state PHL has developed its own unique vocabulary to describe test names and results. Further, many PHLs are required to use additional coding standards such as the Current Procedural Terminology (CPT) and the International Statistical Classification of Diseases (ICD9). Complicating matters further, the clients of PHLs often use their own unique vocabularies. Moreover, the organizations that maintain each of the coding standards are independent and the standards themselves do not offer the ability to establish unique relational cross-references among them; the only place they ever come together is the LIMS. Vocabulary challenges require the LIMS to provide cross-referencing to multiple coding standards representing multiple LIMS entities (e.g., test names and analyte names) and the ability to accommodate updates from independent standards sets.

All STARLIMS public health systems provide integrated support for configuring, receiving, and sending HL7 messages. All STARLIMS systems allow each PHL to maintain its own test list and integrate independent configuration tools supporting SNOMED and LOINC code sets. The systems also enable integration of other code sets including CPT, ICD9 (and ICD10), and client-supplied code sets. This means that all STARLIMS systems can receive, process, assemble, and send PHIN-compliant HL7 messages as well as PHL-specific messages. In fact, a PHL using a STARLIMS system was the first to transmit a fully PHIN-compliant message to the CDC.

  • Work flow challenges: Modern LIMS can model any laboratory work flow. Even when analytical methodology is based on standardized procedures, other factors including physical parameters, laboratory culture, and historical behavior can combine to create unique work flows for common analyses. As a case in point, 20 state PHLs in the U.S have selected STARLIMS. All of them perform HIV screening according to published and accredited methodology, and all of them perform the analysis uniquely. Such wide variability in work flow requires the LIMS to allow virtually unlimited work flow definition.

In STARLIMS systems, work flows are infinitely variable. Many PHLs have taken advantage of this feature to create an environment precisely tailored to their unique processes and needs. STARLIMS work flows are also shareable between customers. Recently, three state PHLs worked together with STARLIMS to develop a common work flow for the H1N1 flu (reception, analysis, and reporting). The resultant work flow was made available to other PHLs.

Conclusion

LIMS is at the heart of the public health informatics environment. Compliance with APHL requirements ensures the LIMS will provide reliable specimen tracking, accurate analysis, and timely reporting all within a traceable QA/QC environment. Compliance with PHIN requirements ensures data can be exchanged unambiguously between public health partners. By implementing a LIMS designed to meet their exact requirements, public health organizations are more capable of promoting healthy outcomes, safeguarding the public good and containing threats.

Mr. Qualls is Senior Account Manager, STARLIMS Corp., 4000 Hollywood Blvd., #515S, Hollywood, FL 33021, U.S.A.; tel.: 954-964-8663; fax: 954-964-8113; e-mail: bill. [email protected].