Whole Genome Sequencing (WGS)

Whole Genome Sequencing (WGS...
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Whole Genome Sequencing (WGS)
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What is whole genome sequencing

(WGS)?
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The genome, or genetic material, of an organism

(bacteria, virus, potato, human) is made up of DNA.
Each organism has a unique DNA sequence which is
composed of bases (A, T, C, and G). If you know the
sequence of the bases in an organism, you have
identied its unique DNA ngerprint, or pattern.
Determining the order of bases is called sequencing.
Whole genome sequencing is a laboratory procedure
that determines the order of bases in the genome of
an organism in one process.
How does whole genome sequencing

work?
Scientists conduct whole genome sequencing by
following these four main steps:
1. D N A s h e a r i n g : Scientists begin by using
molecular scissors to cut the DNA, which is
composed of millions of bases: As, Cs, Ts and Gs,
into pieces that are small enough for the
sequencing machine to read.
2. D N A b a r - c o d i n g : Scientists add small pieces of
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DNA tags, or bar codes, to identify which piece of

sheared DNA belongs to which bacteria. This is
similar to how a bar code identies a product at a
grocery store.
3. W h o l e g e n o m e s e q u e n c i n g : The bar-coded DNA
from multiple bacteria are combined and put in the
whole genome sequencer. The sequencer
identies the As, Cs, Ts, and Gs, or bases, that
make up each bacterial sequence. The sequencer
uses the bar code to keep track of which bases
belong to which bacteria.
4. D a t a a n a l y s i s : Scientists use computer analysis
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tools to compare bacterial sequences and identify

differences. The number of differences can tell the
scientists how closely related the bacteria are, and
how likely it is that they are part of the same
outbreak.
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How will whole genome sequencing

transform disease detection?
Whole genome sequencing provides more detailed
and precise data for identifying outbreaks than the
current standard technique that PulseNet uses,
pulsed-eld gel electrophoresis (PFGE). Instead of
only having the ability to compare bacterial genomes
using 15-30 bands that appear in a PFGE pattern, we
now have millions of bases to compare. That is like
comparing all of the words in a book (WGS), instead of
just the number of chapters (PFGE), to see if the books
are the same or different. Using whole genome
sequencing, we have found that some bacteria that
appeared to be different using PFGE are actually from
the same source. This has helped solve some
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outbreaks sooner.
Whole genome sequencing is a fast and affordable
way to obtain high-level information about the
bacteria using just one test. Currently, the process to
fully characterize bacteria requires two or more
scientists to perform four or more separate tests
including PFGE. WGS will greatly improve the
efciency of how PulseNet conducts surveillance.
PulseNet is actively validating next-generation
sequencing (NGS) technology as well as developing,
evaluating, and implementing the tools needed to
analyze the data.
Meeting the challenges of whole

genome sequencing.
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In 2013, CDC began using whole genome sequencing

to detect outbreaks caused by the deadly bacteria
Listeria. Since then, this method has allowed scientists

to:
Detect more clusters of Listeria illnesses
Solve more Listeria outbreaks while they are still
small
Link ill patients to likely food sources
Identify new food sources of Listeria, such as
caramel apples and ice cream
Learn more about how the Listeria Whole Genome
Sequencing Project has improved the detection and
investigation of foodborne outbreaks.
CDC is quickly expanding the use of whole genome
sequencing in state laboratories, and scientists will
soon begin using whole genome sequencing for
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outbreak investigations of other foodborne

pathogens, such as Campylobacter, Shiga toxinproducing E. coli (STEC), and Salmonella. CDCs
Advanced Molecular Detection (http://www.cdc.gov
/amd/) (AMD) initiative partially funded the expansion
of real-time WGS for food safety.
Through collaboration with CDCs AMD initiative and
the food safety program, PulseNet is establishing the
structure to support a switch to whole genome
sequencing, including training of public health
microbiologists to perform sequencing, purchasing
sequencing supplies, and updating systems for data
analysis. These activities are critical to launching
whole genome sequencing in public health
laboratories and improving surveillance for foodborne
disease outbreaks and trends in foodborne infections
and antibiotic resistance.
As the use of whole genome sequencing expands,
CDCs national surveillance systems and laboratory
infrastructure must keep pace with the changing
technology. With modernization, CDC and its public
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health partners can continue to successfully detect,

respond, and stop infectious diseases. Together, we
can ensure rapid and less costly diagnoses for
individuals and the evidence needed to quickly solve
and prevent foodborne outbreaks.
WGS Protocols
Standard operating procedure for Illumina Miseq
data quality control
[PDF - 9 pages]
Laboratory standard operating procedure for

PulseNet Nextera XT library prep and run setup
for Illumina Miseq
[PDF - 44 pages]
R
Reellaatteedd LLiinnkkss
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Advanced Molecular Detection (AMD)

The Listeria Whole Genome Sequencing Project
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F i l e Fo r m a t s H e l p :
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PPT, MPEG) on this site? (//www.cdc.gov/Other
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Page last reviewed: February 11, 2016
Page last updated: February 11, 2016
Content source: National Center for Emerging and Zoonotic
Infectious Diseases (NCEZID) (http://www.cdc.gov/ncezid/)
, Division of Foodborne, Waterborne, and Environmental
Diseases (DFWED) (http://www.cdc.gov/ncezid/dfwed
/index.html)
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Whole Genome Sequencing (WGS) - PulseNet Methods - PulseNet - CDC

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What is whole genome sequencing