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GeneQuence™
Novel Rapid Pathogen Detection – Sensitive, Simple, and
Scalable - AOAC Official Method Approved

GeneQuence utilizes a novel DNA hybridization technology

which assays for Salmonella, Listeria spp., Listeria
monocytogenes, and E.coli O157:H7* Each test kit uses two
specific DNA elements ensuring the highest of specificity,
thereby increasing your confidence of the rapid results. This
web portal is designed to provide you with all of the technical
and product related information on the GeneQuence and
GENE-TRAK rapid pathogen detection platforms. Each kit has
been developed to detect 1-5 CFU/25g sample in less than 2
hours. By coupling this easy to use technology with an
automated plate handling unit , it is possible test more than 700
samples in an 8 hour work day with very little hands on time.
Contact us if you are ready to simplify your pathogen testing
program.

Technology that performs

GeneQuence is based upon the DNA-probe technology that
lead to broad adoption of the classic GENE-TRAK Pathogen
Assays. Each test kit contains capture and detector DNA probes
specific to ribosomal RNA (rRNA) of the target organism and a
coated solid phase (dipstick or microwell). To achieve a positive
result both the capture probe AND the detector probe must
bind. This dual selectivity ensures that only the organism of
interest is detected during the assay.

Protocol Overview:
First, a portion of the enrichment culture is placed into a test
tube. A lysis reagent is added, which disrupts the cell and
releases the nucleic acid target molecules. A portion of the
lysed sample is then transferred to a microwell and the probe
reagents are added. (In the GENE-TRAK® DLP format, the
probe reagents are added to the tube with the lysed sample,
followed by introduction of the coated dipstick to the tube.)

The probe reagents consist of: 1) an oligonucleotide capture

probe specific to rRNA sequences of the target organism
and labeled at the 3’ end with polydeoxyadenylic acid (poly
dA); and 2) an oligonucleotide detector probe also specific to
rRNA sequences of the target organism and labeled at the 5’

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end with the enzyme horseradish peroxidase (HRP). The

hybridization reaction is then allowed to proceed for one
hour. If target rRNA is present in the sample, both probes will
hybridize to their complementary sequences on the target
molecule.

The resulting complex is captured onto the solid phase

coated with polydeoxythymidylic acid (poly dT), which is
complementary to the poly dA portion of the capture probe.
Unbound probe is then washed away, and a substrate of
HRP is added.

Following a short incubation, blue color indicates the

presence of hybridized detector probe in the complex and
thus the presence of rRNA from the target organism. Stop
solution is added to convert blue to yellow color and results
are determined spectrophotometrically at 450 nm. An
absorbance value in excess of a predetermined threshold
indicates a positive test result.

The GeneQuence Advantage

GeneQuence DNA Hybridization Method versus
PCR-based Methods

Point of Benefit of
Comparison GeneQuence PCR GeneQuence
Assay time 1 hr, 50 min 3 hrs, 30 Faster results.
min GeneQuence also
(average) has at least 25%
less off-line labor
time (instrument
set-up, manual
reagent addition,
etc.) than PCR
methods.
Commodities Good Some Published data
performance food documents
across foods types problems PCR in
difficult certain food
commodities.
Flexibility 4 pathogens 1 GeneQuence, due
at same time pathogen to its superior
per run automation,
allows 4
pathogens to be
assayed

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concurrently. To
do this by PCR,
more than one
instrument would
be needed (at a
higher capital
cost).
Processing 4 96-well 1 set of As soon as one
plates 96 plate is finished,
concurrently samples GeneQuence can
at a time accept another
sample set. PCR
systems must wait
until the entire run
is complete before
loading another
set. GeneQuence
can provide
uninterrupted,
continuous
operation.
Technology Nucleic acid PCR The thermostable
hybridization polymerase used
in PCR has
documented
inhibition
problems that
lead to false
negatives with
several matrices.
GeneQuence
avoids this issue
entirely by using
nucleic acid
hybridization.
GeneQuence also
probes the target
directly, rather
than an
intermediate
amplified from the
original target.
Throughput 1.32 samples 0.46 187% more
per minute samples throughput on
per GeneQuence will
minute minimize retention
time of inventory.
References:
Optimal polymerase varies per food type
Abu Al-Soud, W. and Radstrom, P. 1998. Appl. Environ.
Microbiol. 64: 3748-3753.

High false negatives (vs. ELISA and semi-solid medium)

Uyttendaele, M. et al. 2003. Lett. Appl. Microbiol. 37: 386-391.

Biological samples affect sensitivity and kinetics of PCR

Radstrom, P. et al. 2004. Mol. Biotechnol. 26: 133-146.

Lower sensitivity (than ELISA) in seafood

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Thompson, S. et al. 2003. ASM General Meeting Abstracts.

Evaluation of PCR versus culture based detection of E.coli

0157:H7 in Ground Beef
Arthur, T.M. et al. 2005. J. of Food Protect. 68(8): 1566-1574.

GeneQuence DNA Hybridization Method versus

Antibody-Microwell Based Methods

Point of Benefit of
Comparison GeneQuence ELISA GeneQuence
Detection rRNA Protein 1,000 to 10,000
copies of rRNA per
cell give
GeneQuence its
high level of
sensitivity.
Inclusivity DNA Sandwich Allows detection of
Hybridization ELISA all serovars of
Salmonella
enteritidis
Pathogen rRNA Protein RNA is very
Target short-lived as it is
constantly broken
down by ubiquitous
RNases. Couple
that with dilutions
from enrichment,
GeneQuence will
not detect dead
bacteria.
Procedure Manual or Varies Some ELISA
Automated systems can only
be run on an
instrument. Others
specify only a
manual method that
may be adapted by
the user into an
automated system.
Only GeneQuence
allows the user to
perform the test
manually or in a
company-supported
automated format.
Specificity DNA:rRNA Antibody: Two levels of
Protein stringency (binding
of target rRNA to
capture probe, and
rRNA to detector
probe) decrease
false positive rates
with GeneQuence.

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Throughput DSX Other The DSX can

platforms process more than
744 samples in an
8-hour shift, at least
double that of any
ELISA system on
the market. This will
reduce labor and
equipment costs.

GENE-TRAK® Assays
GENE-TRAK is the classic version of our GeneQuence
technology, where instead of being performed in a microtiter
plate, the assay utilized small ‘dipstick’ paddles to which the
capture probe is bound. The DLP (direct labeled probe)
employs specific DNA probes which are directly labeled with
horseradish peroxidase, thereby decreasing the time by ~20
minutes.

GENE-TRAK demonstrates the same high specificity found in

our GeneQuence microwell assay but is perfect for those who
test less than 15 samples per evaluation. GENE-TRAK is highly
referenced in the industry and has additional target organisms
such as Staphylococcus aureus, Campylobacter spp. and E.coli
(contact food safety customer service for more information)
GENE-TRAK pathogen detection products:
GENE-TRAK Listeria Assay
GENE-TRAK Listeria DLP Assay
GENE-TRAK Listeria monocytogenes Assay
GENE-TRAK Salmonella Assay
GENE-TRAK Salmonella DLP Assay
GENE-TRAK Staphylococcus aureus Assay
GENE-TRAK E. coli Assay

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800/234-5333 (USA/Canada) or 517/372-9200
Fax: 517/372-2006 • foodsafety@neogen.com

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