What exactly is whole genome sequencing?
All organisms (bacteria, plants, and mammals) have a unique genetic code, or genome, made up of nucleotide bases (A, T, C, and G).If you know the sequence of an organism’s bases, you have identified its unique DNA fingerprint, or pattern. Sequencing refers to the process of determining the order of bases. Whole genome sequencing is a laboratory procedure that determines the order of bases in the genome of an organism in a single step.
What is the procedure for whole-genome sequencing?
Whole genome sequencing is carried out by scientists in four steps:
DNA shearing: Scientists begin by cutting the DNA, which is made up of millions of bases (A’s, C’s, T’s, and G’s), into pieces small enough for the sequencing machine to read.
DNA bar coding: To identify which piece of sheared DNA belongs to which bacteria, scientists add small pieces of DNA tags, or bar codes. This is similar to how a bar code at a grocery store identifies a product.
DNA sequencing involves combining bar-coded DNA from multiple bacteria and running it through a DNA sequencer . The sequencer identifies the A, C, T, and G bases that comprise each bacterial sequence. The bar code is used by the sequencer to keep track of which bases belong to which bacteria.
Data analysis: Computer analysis tools are used by scientists to compare sequences from different bacteria and identify differences. The number of differences between the bacteria can tell scientists how closely related they are and how likely it is that they are part of the same outbreak.
What role has whole genome sequencing played in disease detection?
Whole genome sequencing has been the standard PulseNet method for detecting and investigating foodborne outbreaks caused by bacteria like Campylobacter, Shiga toxin-producing E. coli (STEC), Salmonella, Vibrio, and Listeria since 2019. Whole genome sequencing of pathogens in public health laboratories has improved surveillance for foodborne disease outbreaks and our ability to detect trends in foodborne infections and antimicrobial resistance since its inception.
Whole genome sequencing provides detailed and precise data that can be used to identify outbreaks sooner. Furthermore, whole genome sequencing is used to characterise bacteria and track outbreaks, greatly improving the efficiency with which PulseNet conducts surveillance.
The PulseNet structure was established to support whole genome sequencing at state public health laboratories by:
• Educating public health laboratory scientists in whole genome sequencing
• Purchasing supplies and equipment
• System and software updates for data analysis
As the use of whole genome sequencing grows, the CDC’s national surveillance systems and laboratory infrastructure must evolve to keep up. With modernization, the CDC and its public health partners will be able to detect, respond to, and prevent infectious diseases in the future. Whole genome sequencing is a quick and inexpensive way to obtain detailed information about bacteria with a single test. Together, we can provide individuals with faster and less expensive diagnoses, as well as collect the evidence needed to quickly solve and prevent foodborne outbreaks.