2298. Identifying and Addressing Implementation Barriers to Whole Genome Sequencing (WGS) in State Public Health Laboratories
Session: Poster Abstract Session: Molecular & Sequence Based Diagnostics
Saturday, October 6, 2018
Room: S Poster Hall
Background: The past decade has witnessed revolutionary advances in DNA sequencing, bioinformatics, and related technologies. The Advanced Molecular Detection (AMD) program at the Centers for Disease Control and Prevention (CDC) is a catalyst for bringing advanced DNA sequencing and related technologies to the forefront for combatting a wide range of infectious disease threats by the US public health system, resulting in quicker detection of outbreaks and more effective public health responses. Bacterial whole genome sequencing (WGS) has many applications in public health and is now being implemented in several areas both at the CDC and in state public health laboratories (SPHLs). While SPHLs have overcome a variety barriers to the implementation of WGS technology, only a small percentage of SPHLs using bacterial WGS (3 out have 51) have validated workflows that comply with regulations set forth by the Clinical Laboratory Improvement Amendments of 1988 (CLIA). If a piece of data has the potential to make it back to a patient’s record, then the laboratory that generated it must be compliant with CLIA. CLIA validation of WGS methods is critical to ensuring safety with regard to patient clinical care.

Methods: As a way to help facilitate WGS implementation, we sought to identify the challenges for the establishment and use of CLIA-compliant WGS workflows in SPHLs. An environmental scan was performed in which we assessed materials produced at CDC, by the Association of Public Health Laboratories (APHL), by a Next Generation Sequencing Tri-agency workgroup, as well as published papers and guidance. We also engaged stakeholders through conversations with SPHL partners, APHL, and several groups within CDC.

Results: Our analysis revealed relevant resources and key WGS validation materials were dispersed and difficult to locate. To address this, we developed a CDC Next-generation Sequencing Resource Roadmap, to house key materials. After we reviewed, selected, and collated the resources, our web developer created a visual roadmap webpage to guide the user through the resources. This roadmap was then reviewed and tested for initial use internally at CDC.

Conclusion: This communication tool has the potential to provide critical resources needed to develop functional WGS validation strategies.

Angela Oliver, JD, Ana Lauer, PhD, Rebecca Lindsey, PhD, Alexandra Mercante, PhD, Amanda Raziano, MPH and Luciann Draper, BA, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA


A. Oliver, None

A. Lauer, None

R. Lindsey, None

A. Mercante, None

A. Raziano, None

L. Draper, None

Findings in the abstracts are embargoed until 12:01 a.m. PDT, Wednesday Oct. 3rd with the exception of research findings presented at the IDWeek press conferences.