Lab Matters Fall 2023 | Page 81

APHL 2023 POSTER ABSTRACTS

Whole Genome Sequencing of Mpox : Assessment of Different Library Preparation Protocols

A . Alford 1 , A . Rossheim 1 , S . Baird 1 , D . Mallal 1 , N . Downey 2 , S . Matzinger 1 ; 1 Colorado Department of Public Health and Environment , 2 Integrated DNA Technologies , Inc

Onboarding a streamlined , scalable whole-genome sequencing ( WGS ) workflow for viral pathogens is important when piecing together transmission networks and tracking genetic mutations that might impact pathogenicity . Efficient and consistent WGS surveillance is dependent on the ability to onboard an adaptable and robust workflow that capitalizes on the strengths of the different available sequencing platforms . However , when onboarding new protocols , it is important to compare the efficacy of the available options . That can be achieved by testing whether or not there is a measurable difference in genome percent coverage , mean depth of coverage , total number of reads ( raw and filtered ), total number of reads mapped to the reference genome and lineage designation . In response to the 2022 mpox outbreak , multiple WGS and next-generation sequencing ( NGS ) options have been developed . To assess the usefulness of a subset of these newly available approaches for public health response on Colorado mpox clinical specimens , we participated in an early access trial of a tiled amplicon approach from Integrated DNA Technologies ( IDT ) and assessed the feasibility of using different library preparation protocols for use on the Miseq Illumina platform . Specifically , we compared an mpox amplicon panel from IDT that can be used in combination with either the IDT xGen library preparation or the Illumina DNA library preparation . In order to compare the two different workflows for clinical samples , we ran each workflow on seven clinical samples with Ct values 400 , increased total number of raw reads by > 1,000,000 , and filtered reads by > 400,000 , with comparable percent reads mapped to the reference genome of > 99 %, and equivalent NextClade lineage designation . Future plans include assessing hybrid capture as an additional / alternative approach for sequencing mpox clinical samples and wastewater detection . Overall , this comparison highlights diversity in library preparation strategies for WGS and NGS workflows .

Presenter : Alexis Alford , lexi . alford @ state . co . us

ONE HEALTH APPROACHES

Survey of Abscess-Forming Pathogens Found in Cervid Retropharyngeal Lymph Nodes

E . Palise , Montana Veterinary Diagnostic Laboratory

Caseous Lymphadenitis ( CL ) is an economically important chronic infection of sheep and goats . The disease occurs when the bacterium Corynebacterium pseudotuberculosis ( C . pseudoTB ) enters the body through breaks in the skin or contact with mucous membranes . The bacteria then travel to the lymph nodes via the lymphatic system and form encapsulated abscesses over an incubation period of one to three months . Although less commonly described in scientific literature , CL can also be found in wild ruminants including deer and other cervids . In previous years , the Montana Veterinary Diagnostic Lab ( MVDL ) observed a large number of abscessed cervid lymph nodes among hunter-harvested samples that were submitted for chronic wasting disease ( CWD ) testing . During the 2021 CWD testing season , most of the abscesses observed in these lymph nodes were found to be caused by C . pseudoTB , and additional work was completed to phylogenetically characterize the C . pseudoTB isolates . The present project aims to continue and expand upon this preliminary work using hunterharvested cervid lymph node samples submitted to MVDL during the 2022 CWD testing season . The first goal of this project is to catalog and characterize which bacteria , in addition to C . pseudoTB , may be contributing to the observed lymph node abscesses in wild cervid specimens . This information will aid in understanding what types of abscess-forming bacteria may be circulating through wild cervid populations . Since recreational hunting of wild cervids is widely enjoyed amongst the people of Montana , the second goal of this project is to assess the potential threat of zoonotic transmission of bacterial pathogens to hunters and other personnel that may be handling biological material from these animals , given that over 60 % of emerging infectious diseases are zoonotic . Ultimately , the work completed during this project serves a One Health purpose , by gathering information that can be used to inform decisions and recommendations for managing human and animal health .

Presenter : Erica Palise , enp102799 @ gmail . com

PANDEMIC PREPAREDNESS , DISEASE FORECASTING AND EMERGENCY RESPONSE

A Nationwide Survey of Clinical Laboratories ’ Capabilities , Capacity , and Willingness to Support Emergency Response Surge Testing

S . Courtney 1 , C . Meyer 2 , K . Kryda 2 , B . Bowzard 2 , J . Chaitram 2 ; 1 US Centers for Disease Control and Prevention , 2 Gryphon Scientific

Clinical laboratories are often the first line of defense in a public health response as they conduct testing at the request of physicians to diagnose , monitor or treat disease . As part of these functions , many clinical laboratories are responsible for referring suspicious or unusual specimens to public health reference laboratories for further characterization and analysis . More recently , select clinical laboratories with high-throughput testing capacity ensured timely diagnostic testing to inform medical care follow-up for individuals in a large-scale outbreak . As such , clinical laboratories serve as a critical gateway between every day medical care of individuals and public health . Although CDC has considerable information on the capabilities of public health laboratories , the same level of information is not available for the clinical laboratory sector , which includes small , medium and large organizations in hospital , independent and other private sector healthcare settings . To collect this information , the CDC conducted a three-year , multi-faceted study to assess the capabilities , factors that influence capacity , and willingness of the nation ’ s clinical laboratories to support large-scale response to chemical , biological , radiological and / or emerging threats . The outcome of this study resulted in a significant yield of information from 1,295 laboratories spread out across the 10 HHS regions that will inform CDC and its state and local public health stakeholders how to better leverage and integrate clinical