The Use of Whole Genome Sequencing for Surveillance of Enteric Organisms by United States Public Health Laboratories

Abstract

In the United States, surveillance by public health laboratories of enteric organisms is undergoing a technological revolution. The advent of affordable, massively parallel DNA sequencing technology and leadership from the FDA and CDC has put these laboratories at the forefront of this new era of whole genome sequence based surveillance. Pulsed-Field Gel Electrophoresis has been the gold standard for enteric pathogen subtyping in the United State over the past two decades. Numerous studies have shown that bacterial typing based on genomic sequence data has greater discriminatory power and better able to assist in the identification of the source of an outbreak compared to PFGE. The data is so compelling that PulseNet, the national enteric disease subtyping method in the United States, expects to transition entirely to these technologies in the next few years.

As the United States of America (US) enteric surveillance network transitions to a new technology, many uncertainties and challenges exist for the public health laboratories. Challenges familiar to public health laboratories include optimizing workflows, quality assurance and quality control, and funding. But there are also unfamiliar challenges that relate to the sequencing technology itself such as the need for highly specialized bioinformatics interpretation of the data and how to communicate the complex, new information to partners. This chapter examines current practices, benefits, and challenges in the United States public health laboratory as the next generation of surveillance technologies are implemented.