APHL 2021 Poster Abstracts of current submitters and during this time , we observed an almost 50 % reduction in problem specimen rejection rates . The use of an electronic ordering system reduced the probability of data entry errors , thus reducing the likelihood of receiving problem specimens or having to reject submissions . Specimens that were considered unacceptable or untestable ( e . g . leaky container , hemolyzed specimen , improper storage , improper transport ) were excluded from this comparison . A marked reduction in ordering errors was observed following the implementation of eOrder . The most common reasons for a problem specimen , included “ No submission form received ,” “ Patient gender missing ” and “ Missing specimen source ,” account for approximately 70 % of the errors observed . This decreased to 24 % following the implementation of eOrder . Similarly , specimen rejection rates decreased from 60 % to 10 % following the implementation of eOrder ; among the highest reported reasons , “ Specimen Mislabeled-Name ” and “ Specimen Mislabeled- DOB ” ( date of birth ). In fact , when comparing specimen turnaround time prior to and following eOrder implementation , we observed a 4-hour improvement , suggesting that eOrder is a contributing factor to improving TAT . Overall , the use of eOrder has had a positive impact on reducing errors , improving TAT and facilitated specimen accessioning workflow at PHL .
Presenter : Sharifah Suleiman , New York City Public Health Laboratory , ssuleiman @ health . nyc . gov
Strengthening Electronic Laboratory Reporting for the Laboratory Response Network
T . Wolford and S . Abrams , Association of Public Health Laboratories , Silver Spring , MD
Responding to a potential biological or chemical threat requires coordinated efforts among public health stakeholders . As members of the Laboratory Response Network ( LRN ), public health laboratories utilize electronic information systems to collect testing data and provide results to sample submitters and other external partners . These data are used to determine appropriate treatment options for individuals and , on a population basis , may be used as part of a surveillance program . The COVID-19 pandemic and past outbreaks illustrated the importance of timely laboratory results . Today , an urgent need still exists for modernized electronic data systems , including Electronic Laboratory Reporting ( ELR ). APHL and CDC have partnered to strengthen the public health system by assisting laboratories with the implementation of ELR to ensure that important testing information is sent quickly and securely to partner agencies . Via funding from CDC , APHL is supporting public health laboratories with enhancing electronic data exchange of biological and chemical threat agents and metabolites , which include anthrax and nerve agents , among others . The implementation of ELR represent significant advancements for electronic data exchange over current generation technology used for LRN data messaging . These include improving the speed and accuracy of data transmission to CDC while ensuring consistent report formatting despite originating from different sources . This approach enables both CDC and state and local public health agencies to mount a more effective response , providing appropriate intervention measures . Successful implementation of ELR hinges on the utilization of Health Level 7 ( HL7 ), which provides standards and guidelines to ensure that individual laboratories across the country can communicate to CDC uniformly . Although LRN laboratories employ a range of electronic information systems , maintaining HL7
APHL . org standards guarantees that critical information will be accurately received by CDC . Public health laboratory staff are working closely with informatics vendors and the CDC Informatics and Data Science Branch LRN Data Integration Team to complete updates to their systems . ELR integration into laboratory information systems provides a significant step in advancing public health laboratory data reporting capabilities . In supporting public health laboratories , both APHL and CDC are strengthening the nation ’ s laboratories ’ ability to mount effective response measures for a range of biological and chemical threats .
Presenter : Tyler Wolford , Association of Public Health Laboratories , tyler . wolford @ aphl . org
State and Regional Implementation and Support of Bioinformatics Resources Using the Terra Google Cloud Computing Platform
L . Bankers 1 , D . Ir 1 , M . Hetherington-Rauth 1 , J . Sevisky 2 , D . Park 3 , A . Lang 4 , K . Libuit 2 , S . Matzinger 1 , S . E . Totten 1 , E . Travanty 1 ; 1 Colorado Department of Public Health and Environment , Denver , CO ,
2
Theiagen Genomics , Highland Ranch , CO , 3 Broad Institute of MIT and Harvard , Cambridge , MA , 4 Massachusetts Department of Public Health , Boston , MA
The bioinformatic analysis of high-throughput sequencing data provides important insights for the public health field , including the identification , investigation , and surveillance of pathogens . For example , throughout the SARS-CoV-2 pandemic , bioinformatic analysis of whole genome sequencing data has played an integral role in improving our understanding of the biology of SARS- CoV-2 and has helped the scientific community identify emerging genetic variants of the virus . However , large-scale bioinformatics requires sophisticated computational infrastructure . The Colorado Department of Public Health and Environment ( CDPHE ) is an important resource for bioinformatics infrastructure and support in the Rocky Mountain region . Specifically , we aim to provide sustainable and affordable cloud computing resources for the region , develop bioinformatics workflows and make them available to the public , make bioinformatics accessible to epidemiologists and facilitate collaboration between bioinformaticians and epidemiologists , as well as provide training courses . Here , we will describe the bioinformatics resources we are providing to Colorado and the Rocky Mountain region as a whole . We will also discuss the rapid national expansion of Terra cloud computing in the public health field and how such resources facilitate collaboration within and among public health labs . Using the Terra Google Cloud computing platform , we provide the necessary computational infrastructure for performing large-scale bioinformatics analysis in several states , such as WY , NM , and TX . Furthermore , we have written and made freely available analytical workflows to increase the efficiency and reproducibility of analyses performed within and among public health laboratories . In the coming months , we will expand the use of Terra Google Cloud computing across the region , and develop training modules on the setup and use of these resources , as well as aid in training others to perform bioinformatic and genomic analyses . More broadly , cloud computing resources such as Terra have not only been important for outbreak detection and response during the current pandemic , but will be widely useful in monitoring other pathogens of public health concern and future emerging infectious diseases .
Presenter : Shannon Matzinger , Colorado Department of Health and Environment , shannon . matzinger @ state . co . us
Summer 2021 LAB MATTERS 65
Informatics