Lab Matters Fall 2024 | Page 88

APHL 2024 POSTER ABSTRACTS

establish one connection with our system and can gain access to reporting to all disease surveillance systems that are connected to the platform . Agencies can focus onboarding efforts on the content of the data files and spend very little time on the integration of electronic data streams or validation of CSV files . Manual “ clean up ” of data is handled by an automated system and not by an individual which saves more staff hours .

This poster will describe the collaborative effort to develop a modernized process to report and receive mandatory data from laboratories and the repeatable process which resulted from this collaboration . We will share how the process creates one standard format for laboratory reporting ensuring the highest quality data no matter which laboratory reports and which public health department receives the data , the efficiencies gained , how laboratories can benefit from a more modernized method to report laboratory data and lessons learned from laboratories using the system today .

Presenter : Millie Malai , millie . malai @ aphl . org

Novel Informatics Deployment Using a Pilot Process B . Lewis Van 1 , S . Chorlton 2 , J Michael Consulting 1 , BugSeq 2

The public health informatics infrastructure must modernize detection and reporting technology to continue to rapidly detect and accurately characterize public health infectious diseases to guide critical decisions . One tool that has been targeted for inclusion in the Data Modernization Initiative ( DMI ) effort is next generation sequencing ( NGS ). Instrumentation for NGS analytical approaches are now widespread in PHLs , but approaches to integration of this technology into the larger laboratory is not . A standardized , systematic and effective approach to integrate these new methodologies into the laboratory systems and processes are lacking . The JMC team created support , training and procedure documentation and provided those materials together with the software to support the preparation , sequencing and analysis to three volunteer pilot laboratories as a pilot project for CDC to explore deployment of NGS to the Laboratory Response Network ( LRN ). This session will cover the following topics related to that project : Details on the project context and goals . Discussion of the challenges , opportunities and lessons learned in this pilot .

At the conclusion of this breakout session attendees will be able to :

• Describe the systematic approach used in the LRN pilot project .

• Transfer the lessons learned from the LRN pilot project for their own informatics projects .

Presenter : Tim Longo , tlongo @ jmichael-consulting . com

Open-source Software Platform to Integrate Next Generation Sequencing Capabilities

M . Kumar 1 , T . Moore 2 , V . Reeb 3 , J Michael Consulting 1 , Maryland Department of Health 2 , Iowa Department of Public Health 3

The LIMS Lite software platform has been built on contract for the CDC to present an open source software option to support nextgeneration sequencing in public health laboratories . The software platform will be described , along with experience and impressions from two laboratories that have used the platform in pilot projects for SARS-CoV-2 sequencing . The LIMS Lite platform is a set of discrete , well-integrated software modules that can be configured to collate , analyze and report against infectious disease isolate characterization and genetic sequence . The tools combine data accessioning , processing , quality assurance and reporting . While the components can be used in an integrated fashion , there is also the flexibility of selecting and plugging a certain set of components or modules across an existing NGS landscape to help achieve consistent and standardized laboratory processes .

Presenter : Tim Longo , tlongo @ jmichael-consulting . com

Past , Present and Future of Public Health Laboratory Information Systems

A . Harvey , C . Duffy , R . McNall , M . Light Mueller , M . Hoover , T . Jue , A . Shultz , A . Ganim , T . Aden , Centers for Disease Control and Prevention

Background : The Epidemiology and Laboratory Capacity ( ELC ) Cooperative Agreement provides epidemiology , laboratory and health information systems ( HIS ) support to 64 health departments across the United States . ELC / Project C1 includes activities to maintain , improve and modernize HIS infrastructure . Modernizing public health laboratories ( PHLs ) and enhancing laboratory information management systems ( LIMS ) are critical for data management and automation to support patient care and public health action . COVID-19 emphasized the need for modernization with a massive increase in test volume and new data flows . Guiding strategies were developed for PHLs to progress toward building a modernized technical architecture and improving interoperability which includes implementing electronic test ordering and results ( ETOR ) with one or more partners , enhancing LIMS processing and configuration capabilities and reducing point-to-point connections using intermediaries .

Methods : To maintain ELC funding , recipients are required to submit data quarterly through the ELC / HIS Monitoring REDCap portal . Key variables from Budget Period ( BP ) 2 ( August 2020 - July 2021 ), BP 3 ( August 2021 - July 2022 ), BP 4 ( August 2022 - July 2023 ) and the first two months of BP 5 ( August 2023 – October 2023 ) include ETOR and LIMS . These were compared to examine the dynamic nature of the PHL information systems landscape .

Results : From BP2 through the beginning of BP5 , several improvements were made across ELC recipients . This includes : 1 ) The percentage of laboratories sending updated HL7 2.5.1 PHLIP messages increased from 61 % to 70 % and HL7 2.5.1 LRN messages being sent increased from 27 % to 44 %. 2 ) The number of PHLs that implemented direct or indirect ETOR has increased from 37 to 49 PHLs . 3 ) Electronic ordering and reporting increased from 27 to 32 PHLs and the use of web portals to support ETOR increased from 37 to 46 PHLs . 4 ) The percentage of total PHL orders submitted via ETOR increased from 34.3 % ( BP2 ) to 62.8 % ( BP3 ) but decreased slightly from BP3 to BP4 to 61.1 %. A similar pattern was observed for proportion of results submitted via ETOR , increasing from 55.5 % ( BP2 ) to 69.6 % ( BP3 ) and decreasing to 63.4 % in BP4 . And 5 ) The predominant LIMS software used by jurisdictions was STARLIMS followed by Horizon and the ability for PHLs to generate HL7 messages remained constant at 89 %.

Discussion : While PHL systems are improving , modernization efforts must continue . Funding availability will impact the maintenance and