Lab Matters Fall 2023 | Page 104

APHL 2023 POSTER ABSTRACTS

be challenging , resource intense and time consuming , SPE is deemed necessary in this instance . In our lab , SPE is performed online system . A major limitation of this approach is that sample preparation occurs sequentially before sample injection , therefore limiting throughput . The main goal of this project is to improve the sample throughput of the SPE system by offline automation , where samples are prepared concurrently using a 96 well plate format using a Janus automated liquid handler . The proposed off-line SPE has been successfully deployed by others on various platforms . Sample pre-treatment was deemed the most crucial in eliminating analyte recoveries . The SPE will be conducted on weak anion extraction ( WAX ) stationary phase . The automated procedure includes sample pre-treatment : Combine 50 µ l , 150 µ l Acetonitrile and internal standard , load the supernatant to the SPE plate after conditioning and washing before sample elution . The new automated offline SPE sample preparation method is expected to enable the lab to prepare PFAS samples from 48 aliquot of 50 μl human serum in less than two hours for analysis of the 18 PFAS . Meanwhile , the accuracy of the further LC-MS / MS analysis must be within ± 30 % of nominal value or 3 times of STD value .

Presenter : Zhijin Xu , zjxu234 @ yahoo . com

Next Generation Sequencing at Texas Department of State Health Services

M . Rahman , B . Oh , Y . Sun ; Texas Department of State Health Services

The Texas DSHS Laboratory has been successfully performing next generation sequencing ( NGS ) since 2015 . DSHS routinely sequences clinical and non-clinical enteric bacterial pathogens as part of the US Centers for Disease Control and Prevention ( CDC ) and the US Food and Drug Administration ( FDA ) PulseNet and GenomeTrakr programs to track outbreaks related to human disease , in addition to other microorganisms including Cyclospora and SARS-CoV-2 . DSHS uses Illumina DNA Prep kits and Illumina sequencing platforms for performing Whole Genome Sequencing ( WGS ) for bacterial pathogens and amplicon-based sequencing for Cyclospora and SARS-CoV-2 samples . DSHS has been using BioNumerics 7.6 for enteric bacterial WGS data analysis and inhouse Cecret pipeline to analyze SARS-CoV-2 sequence data . As of January 2023 , 18,587 clinical foodborne bacterial pathogens including 15,252 Salmonella , 2,477 STEC E . coli , 249 Listeria , 137 Vibrio , 234 Shigella , and 238 Campylobacter isolates have been sequenced . A total of 2,450 non-clinical environmental and food isolates were sequenced as well , including 1,222 Salmonella , 606 STEC E . coli , 241 Listeria , and 381 Campylobacter . DSHS also sequenced 750 Cyclospora and 3,583 Neisseria gonorrhoeae samples . Since June 2020 , DSHS sequenced 18,520 clinical SARS- CoV-2 samples for variant identification and tracking . DSHS also participated in an FDA SARS-CoV-2 wastewater sequencing pilot project in 2022 and are continuing to sequence wastewater from nursing homes and correctional facilities . Two new NGS tests , WGS for Mpox and carbapenem-resistant bacteria , were implemented in December 2022 . SHS is in the process of implementing WGS for Mycobacterium tuberculosis and Candida auris in 2023 , and newborn screening ( NBS ) in 2024 . In order to act as a sequencing core laboratory for the state , DSHS is expanding testing capacity with automation and robust sequencers to meet that need . NGS for infectious diseases are critical for our epidemiologists to investigate outbreaks , ensuring precise patient care and improving the public health and well-being of Texans .

Presenter : Yan Sun , yan . sun @ dshs . texas . gov

NIH / RADx Collaboration for Pandemic Surveillance using the TaqMan SARS-CoV-2 Mutation Research Panel

K . Hayashibara 1 , J . Lozach 2 , P . Brzoska 1 , Q . Zhou 1 , C . Clark 3 , J . Galanter 3 , A . Greninger 4 , P . Roychoudhury 4 , P . Hajian 4 , T . Cassens 5 , D . Becker 5 , M . Ghandi 1 , T . Wesselman 2 , S . Williams 1 , E . Lai 6 ; 1 Thermo Fisher Scientific , 2 ROSALIND , 3 Aegis Labs , 4 University of Washington Medical Center , 5 Helix OpCo , 6 Personalized Science

Surveillance testing demonstrated its importance in driving public health decisions during the COVID-19 pandemic . Whole genome sequencing ( WGS ) served as the primary method for surveillance to monitor spread of known variants and detect new variants . However , WGS is expensive and can take weeks before sequence data is available in public repositories . We describe an alternate , low-cost genotyping-based approach that enables broad-based surveillance and identifies potential new variants using the TaqMan SARS-CoV-2 Mutation Research Panel . s part of the NIH Rapid Acceleration of Diagnostics ( RADx ) initiative , we developed methodology for selecting a small number of highly specific mutations for variant identification . Genotyping results from a panel of these mutations were used to identify variants associated with each positive sample at a pace roughly 10 days earlier than sequencing when put in practice . Variant identification by genotyping was compared with sequencing to verify accuracy . Furthermore , we demonstrate that these panels are capable of detecting SARS-CoV-2 variant co-infection and recombination that are frequently assigned by sequencing to incorrect subtypes , and we show that these panels can be used to analyze low-input mixed samples at levels found in wastewater .

Presenter : Kathleen Hayashibara , kathleen . hayashibara @ thermofisher . com

Onsite SARS-CoV-2 Sequencing Procedures Following Ongoing Workplace CLIA Surveillance

K . Pinet , M . Angel , B . Langhorst , Z . Li , J . Bruce , R . Moncion , C . Carlow , K . Krishnan , N . Nichols ; New England Biolabs

Viral pathogen transmission within workplace environments has negatively impacted employee health and business continuity throughout modern history . The SARS-CoV-2 pandemic is an extreme example of this issue . Common workplace responses to the SARS-CoV-2 pandemic have been to promote social distancing , mask usage , and vaccinations . However , the efficacy of these safety precautions within a work environment are rarely confirmed through viral-sequencing-based contact tracing . Here we report on a proactive workplace SARS-CoV-2 surveillance system established at a private biotech company in MA with 500-1,000 local employees and contractors ( New England Biolabs , NEB ). NEB ’ s viral surveillance strategy tracks SARS-CoV-2 positivity rates amongst the employee population through RT-LAMP based testing and then identifies variant genomes present through targeted sequencing . Central to this viral surveillance strategy was the establishment of an on-site CLIA certified lab to perform rapid-turnaround testing of