Whole-genome sequencing in PulseNet foodborne molecular surveillance systems

Abstract

Whole-genome sequencing (WGS) technologies have revolutionized how public health and regulatory agencies respond to foodborne, waterborne, and one-health related surveillance, detection, and response activities. PulseNet — the national molecular surveillance network of over 80 public health labs in the United States, connects food, water, and one-health related illnesses that may be part of an outbreak —fully implemented WGS in 2019. WGS data is comprehensive: antimicrobial resistance, virulence markers, serotype markers, plasmids, and core and accessory genes are all characterized as part of the WGS workflow. Additionally, sequence data is portable and is shared between United States federal agencies, over 80 PulseNet International member countries, and public repositories, including the National Center for Biotechnology Information (NCBI). Currently, PulseNet USA sequences approximately 65,000 Salmonella, Escherichia, Listeria, Vibrio, Campylobacter, and Shigella isolates annually. For sequence data to be submitted to PulseNet, data must meet a series of minimum quality thresholds that have been extensively validated. To be able to use the data is core and whole-genome multilocus sequence typing methods for outbreak detection. During this session, we will discuss the validation of sequence data generated from Oxford Nanopore Technologies for use in the PulseNet USA and PulseNet International network, and future applications of this technology.

Biography

Dr. Heather Carleton, MPH, PhD is the chief of the Enteric Diseases Laboratory Branch (EDLB) in the Division of Foodborne, Waterborne and Environmental Diseases at the National Centre for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), USA. The mission of EDLB is to provide and use quality data, expertise, and effective tools to improve the control and prevention of enteric diseases in the USA and around the world. Dr. Carleton joined the CDC in 2012 as a microbiologist and led the development of whole-genome sequence-based analysis tools for the transition of the foodborne molecular surveillance network, PulseNet, from pulsed-field gel electrophoresis (PFGE) to whole-genome sequencing (WGS). She serves as chair of PulseNet USA and co-chair of PulseNet International steering committees. Dr. Carleton leads activities in prevention of enteric diseases, bioinformatics, metagenomics, and next generation sequencing in EDLB.