Lab Matters Fall 2020 - Page 35

APHL 2020 POSTER ABSTRACTS medical staff and patients to address these exposures early and improve health outcomes for their babies .
Presenter : Andrew Steffens , New Jersey Department of Health , Ewing , NJ , andrew . steffens @ doh . nj . gov
The Importance of Investing in Robust Chemical Testing Capabilities in the Environmental Health Laboratories
N . Ancona , J . Liebreich , E . Moran and S . Wright , Association of Public Health Laboratories , Silver Spring , MD
Recent public health emergencies and community concerns have been the result of harmful chemical exposures . Building upon the expertise , experience and relationships developed through laboratory networks such as the Laboratory Response Network for Chemical Threats ( LRN-C ), the National Biomonitoring Network ( NBN ) and the nascent Opioids Biosurveillance System , public health and environmental laboratories were poised to respond efficiently and effectively to events involving electronic cigarettes and vaping ( EVALI ), per- and poly-fluorinated substances ( PFAS ), lead and opioids overdoses . Investments in specialized analytical instrumentation , technical training , quality systems and partnering with public health and clinical partners were critical in identifying sources and extent of exposures , and prevention and treatment of disease .
Presenter : Julianne Nassif , Association of Public Health Laboratories , Silver Spring , MD , julianne . nassif @ aphl . org
FOOD SAFETY
Tinsel — An RShiny Application for Annotating Outbreak Trees
J . Hamlin and A . J . Williams , Centers for Disease Control and Prevention , Atlanta , GA
Across the United States , PulseNet member public health laboratories now perform isolate whole genome sequencing for foodborne pathogen surveillance , a milestone for protecting our food supply , by providing higher resolution genomic data for identifying common sources of contamination . This genomic data is analyzed to determine relationships between pathogen isolates , and the analysis endpoint is often a phylogenetic (“ outbreak ”) tree , which allow scientists to visualize the evolutionary relationships of organisms . During a foodborne outbreak , additional sample and epidemiology data can be represented on trees to help identify potential sources . The importance of visualization and annotation cannot be understated , as these trees are often the basis for discussions between the lab scientists , epidemiologists , and bioinformaticians investigating known and potential outbreaks . However , there is no widely available , user-friendly tool available to create these visualizations . Our goal is the development of an opensource phylogenetic tree visualization and annotation tool , which will be available online or hosted locally . To accomplish this goal , we built Tinsel , an interactive web application , using the R programming language and the R package Shiny . In addition to the free and open source nature of R , R has powerful graphic capabilities along with additional phylogenetic packages that are the gold standard for phylogenetic applications . The input requirements for Tinsel include a tab-delimited genetic distance matrix file based on high quality single nucleotide polymorphism ( SNP ) or allele counts , a Newick formatted tree file generated from the matrix data , and a tab-delimited file containing sample metadata . Once the base tree image has been displayed , visualization changes can be performed via user inputs . One of the main annotation features is the ability to easily display the genetic distance between isolates or clades on the phylogenetic tree . This annotated phylogenetic tree can then be downloaded in various formats for presentations or publications . Broadly , these images are helpful for epidemiologists , laboratorians , public health officials , and stakeholders when discussing the genetic differences and evolutionary relatedness between isolates and / or clades in response to foodborne outbreaks . A completed version of Tinsel will be available through the CDC OAMD Portal and also as a R package via the Comprehensive R Archive Network ( CRAN ) with documentation that describes basic usage and sample datasets for labs that require local data analysis . Currently the Tinsel source code , documentation , and datasets are available here : https :// github . com / jennahamlin / Tinsel .
Presenter : Jenna Hamlin , Centers for Disease Control and Prevention , Atlanta , GA , jennahamlin @ gmail . com
Enhancing National Foodborne Outbreak Response and Surveillance By Building Whole Genome Sequencing Capacity in Public Health Laboratories Through Standardized , Hands-on Training
A . Poates 1 , J . Truong 2 , A . Sabol 1 , J . Concepcion-Acevedo 1 , K . Hise 1 , S . Stroika 1 , J . Adams 3 , P . Lafon 4 , K . Kubota 3 , P . Smith 1 , E . Trees 3 , R . Lindsey 1 ; 1 Centers for Disease Control and Prevention , Atlanta , GA , 2 ORISE , Atlanta , GA , 3 Association of Public Health Laboratories , Silver Spring , MD , 4 IHRC , Inc ., Atlanta , GA
Eighty-three federal , state , and local public health laboratories ( PHLs ) from across the country make up PulseNet , the national network that conducts surveillance and detection of foodborne outbreaks by using bacterial DNA fingerprints . PulseNet detects and investigates approximately 280 foodborne illness clusters annually . In 2019 , PulseNet transitioned away from using Pulsed Field Gel Electrophoresis ( PFGE ) and instead implemented whole genome sequencing ( WGS ) technology for laboratory-based surveillance . To build and implement WGS capacity effectively across this broad network , it is imperative to have a trained and competent laboratory workforce performing standardized protocols . To achieve this goal , PulseNet has been collaborating with the Association of Public Health Laboratories ( APHL ) to host WGS training workshops since 2014 . During the week-long , hands-on workshop , public health professionals learn to perform DNA extraction , prepare genomic libraries , set up and perform sequencing runs , and perform maintenance of sequencing equipment . Attendees are trained on WGS analysis using Applied Maths BioNumerics software and participate in associated hands-on analysis exercises . This customized combination of wet and dry lab training provides the knowledge and skills required to perform and troubleshoot whole genome sequencing and analysis , to interpret data critically and then to utilize this data to detect and investigate foodborne outbreaks . Trainees return to their home laboratories prepared with the skills necessary to pass PulseNet ’ s certification program . Subsequently they are able to generate , analyze and share sequencing data from enteric pathogens and are capable of training other public health professionals in their laboratories .
Food Safety
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