What is Whole Genome Sequencing (WGS)?

All organisms (bacteria, plants, mammals) have a unique genetic code, or genome, made up of nucleotide bases (A, T, C and G). If you know the base sequence of an organism, you have identified its unique genetic fingerprint, or pattern. Determining the order of bases is called sequencing. Whole genome sequencing is a laboratory procedure that determines the order of bases in an organism’s genome in a single process.

How does whole genome sequencing work?

Scientists perform whole genome sequencing by following these four main steps:

DNA Shear

Scientists begin by using molecular scissors to cut DNA, which is made up of millions of bases (A, C, T and G), into pieces small enough to be read by the sequencing machine.

DNA Barcoding

Scientists add small pieces of DNA tags, or barcodes, to identify which piece of sheared DNA belongs to which bacteria. This is similar to how a barcode identifies a product in a grocery store.

DNA Sequencing

Barcoded DNA from multiple bacteria is combined and placed into a DNA sequencer. The sequencer identifies the A, C, T and G, or bases, that make up each bacterial sequence. The sequencer uses the barcode to find out which bases belong to which bacteria.

Data Analysis

Scientists use computer analysis tools to compare the sequences of several bacteria and identify differences. The number of differences can tell scientists how closely related the bacteria are and how likely they are to be part of the same epidemic.

How has whole genome sequencing improved disease detection?

As of 2019, whole genome sequencing has been the standard PulseNet method for detecting and investigating foodborne outbreaks associated with bacteria such as Campylobacter, Shiga toxin-producing E. coli (STEC), Salmonella, Vibrio, and Listeria. Since its inception, whole genome sequencing of pathogens in public health laboratories has improved surveillance of foodborne illness outbreaks and enhanced our ability to detect trends in foodborne infections and antimicrobial resistance. .

Whole genome sequencing provides detailed and accurate data to identify outbreaks earlier. Additionally, whole genome sequencing is used to characterize bacteria as well as to track disease outbreaks; this greatly improves the monitoring efficiency of PulseNet.

PulseNet has established the framework to support whole genome sequencing in state public health laboratories through:

As the use of whole genome sequencing expands, national surveillance systems and CDC laboratory infrastructure must keep pace with the evolving technology. With modernization, the CDC and its public health partners can continue to successfully detect, respond to, and stop infectious diseases. Whole genome sequencing is a fast and affordable way to get detailed information about bacteria using a single test. Together, we can ensure rapid, less costly diagnoses for individuals and collect the evidence needed to quickly resolve and prevent foodborne outbreaks.

The implementation of whole genome sequencing of pathogens to detect and track foodborne outbreaks has been made possible through collaborations with the CDC’s Office of Advanced Molecular Detection (DMA), Office of Food Safety and Antimicrobial Resistance Solutions Initiative.