Lab Matters Fall 2023 | Page 52

APHL 2023 POSTER ABSTRACTS

be an impressive contrast of impressions compared to sending lab staff to a college fair or career fair for the same amount of time . Therefore , to appropriately respond to the staffing needs of public health laboratories , especially in matters of public health emergencies , the identified barriers need to be addressed by a cross-divisional team within each jurisdiction to better promote career opportunities at public health laboratories .

Presenter : Amanda Berlon , aberlon @ health . in . gov

DATA AND ANALYTICS

Automating Data Processing and Data Management in a High-throughput Public Health Laboratory using Google Colaboratory

S . Baird , M . Hetherington-Rauth , A . Rossheim , N . Pysnack , L . Bankers , S . Matzinger ; Colorado Department of Public Health and Environment

High-throughput biotechnology allows public health laboratories to sequence large numbers of pathogen genomes , but it also increases the burden of data processing and data management tasks on laboratory and bioinformatics staff . Python is a versatile programming language with rich data science libraries , like Pandas , that can fully automate such tasks . Python code can be executed in Jupyter notebooks , which are interactive documents for incorporating code and text in one place . Jupyter notebooks can be created , shared , and run in Google Colaboratory ( Colab ), a secure cloud-based web platform within Google Drive . Colab has advantages over other Jupyter notebook platforms because , like Google Docs , it requires no software installation except a web browser , and different users can access the same Colab notebook , ensuring all users can see all edits . Colab can also directly read and write files from and to Google Cloud Platform and Google Drive , allowing for automatic data transfer . Sequencing and bioinformatics staff in the Colorado State Laboratory at the Colorado Department of Public Health and Environment use Colab to automate multiple tasks , saving time and reducing human error . In the Sequencing Unit , we developed a Colab notebook that reads a set of COVID-19 PCR result files , then generates files used by a liquid handling robot to select and consolidate positive samples for sequencing . Generating these files using a previous method was often an hours-long and error-prone process of manually copying and pasting between multiple spreadsheets for each batch of samples . Now , using Colab , this process takes less than five minutes . In the Bioinformatics Unit , we implemented a Colab notebook that reads COVID-19 sequencing result files from Google Cloud Platform and flags variants of concern and quality control failures . Then , it writes the sequencing result files directly to Google Drive . Using this notebook , we re-analyzed initially manually inspected sequencing result data . This automated analysis revealed previously unnoted SARS-CoV-2 lineages within our laboratory , and it also revealed cases where sequencing coverage was missing in a key area of the genome , demonstrating improvements in the depth and speed of analysis . While Colab is a powerful platform , Python programming is an unfamiliar skill to many staff who would benefit from the ability to create and edit code in Colab notebooks . To help develop this skill at our laboratory , we are using APHL ’ s DataCamp training program . Such workforce training programs will aid in the development of automation tools to keep up with the increasingly high-throughput world of laboratory technology .

Presenter : Samuel Baird , sam . baird @ state . co . us

Biotin Supplement Use in the United States , January 2017 – March 2020

J . R . Leachman 1 , S . Mishra 1 , J . Gahche 2 , B . Kit 1 , R . Storandt1 ; 1US Centers for Disease Control and Prevention , 2National Institutes of Health

Background : Biotin is an essential water-soluble vitamin that is naturally occurring in food and available in dietary supplements commonly used for hair , skin and nail health . In 2017 , the Food and Drug Administration issued a communication to alert the public of the possibility that biotin-containing dietary supplement use ( BDSU ) can interfere with clinical lab tests and mask serious clinical conditions . For example , high biotin blood levels can yield falsely low troponin results , which could lead to missed diagnoses of heart attacks . Biotin interference is of particular concern with BDSU≥1mg . We assessed BDSU by sociodemographic characteristics among US children , adolescents and adults . Methods : Prevalence of any BDSU and BDSU ≥1mg / day and ≥5mg / day were analyzed from 15,548 participants in the January 2017 – March 2020 pre-pandemic National Health and Nutrition Examination Survey using the 30-Day Dietary Supplement Questionnaire data . Interview survey weights and Taylor series linearization were used to produce nationally representative estimates and to account for the complex survey design . Sociodemographic differences were tested with t-tests . Results : Approximately 29 % of US children , adolescents and adults reported any BDSU in the past 30 days . Females had higher BDSU than males ( 31.6 % vs 26.2 %, P <. 001 ). BDSU was highest among adults 60 + years and lowest among adolescents 12 – 19 years ( 41.4 % vs 15.7 %, P <. 001 ). Non-Hispanic ( NH ) white ( 33.6 %) had higher BDSU compared to NH Asian ( 28.7 %), NH black ( 21.3 %), and Hispanic people ( 19.5 %) ( each P <. 01 ). BDSU ≥1mg / day and ≥5mg / day in the past 30 days overall was 2.9 % and 0.8 %, respectively , and increased with age ( 4.8 % ≥1mg and 1.7 % ≥5mg among adults 60 + years ) ( linear P trend <. 0001 ). Conclusions : Overall , these results warrant detailed history-taking of supplement use especially among older adults who have the highest prevalence of BDSU , particularly given the increased rates of evaluation for heart disease in this group .

Presenter : Jacqueline Leachman , tqd0 @ cdc . gov

COVID-19 Variant Dynamics Among Individuals with Repeat Whole Genome Sequencing Tests in South Carolina

S . Sarkar , J . Scott , G . Goodwin , D . Drociuk ; South Carolina Department of Health & Environmental Control

Abstract : With the rapid development of whole genome sequencing ( WGS ) for COVID-19 variant identification , the use of these results by public health is also in development . In order to evaluate the ability and functionality of using WGS results , an exploratory analysis of a public health surveillance system , the South Carolina Infectious Disease and Outbreak Reporting Network ( SCION ), was performed . This analysis evaluated WGS reporting dynamics , including repeat WGS testing , time between WGS testing , and proportion of individuals with WGS results indicating multiple COVID-19 variants among the SC population . Methods : Laboratories from across