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Clinical

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Newsletter
Vol. 30, No. 23 www.cmnewsletter.com December 1, 2008

GeneXpert Testing: Applications for Clinical Microbiology, Part I*


Elizabeth M. Marlowe, Ph.D., D(ABMM),1 and Donna M. Wolk, Ph.D., D(ABMM),2 1Southern California Permanente Medical
Group, Regional Reference Laboratories, North Hollywood, California, 2Department of Pathology, University of Arizona, College
of Medicine, BIO5 Institute, Tucson, Arizona
Abstract
The impact of rapid polymerase chain reaction (PCR) technology on infectious disease testing is continuing to evolve outside
the realm of a centralized laboratory. The GeneXpert Dx system is the first unit dose, near-point-of-care molecular device com-
mercially available. To date, there are five FDA-cleared assays available for the GeneXpert System: group B Streptococcus (GBS)
from vaginal-rectal swabs, enterovirus from cerebrospinal fluid, methicillin-resistant Staphylococcus aureus (MRSA) from nares
swabs, MRSA and methicillin-susceptible S. aureus (MSSA) from skin and soft tissue infection swabs, and MRSA and MSSA
from positive blood cultures. Advantages of the GeneXpert assays include ease of use, random access, rapid results, and the ability
to run the assay without the need for pre- and post-analytical rooms. Limitations include a currently limited menu with few speci-
men types and potential delay of results due to indeterminate results. Part I of this article presents a review of this technology and
its application for the detection of GBS, enterovirus, and MRSA from various clinical specimens.

Introduction practiced, after 2 decades, the practice the cartridge. Once the sample and
When Kary Mullis first tested the of molecular diagnostics remains tied accompanying dispensable reagents are
concept of polymerase chain reaction to a highly skilled laboratory staff and added to the cartridge, no additional
(PCR), the initial experiments were per- batch processing. Emerging technology manual intervention is required. Controls
formed using water baths monitored by has the potential to change the reference include probe checks, pressure checks,
a simple laboratory timer. This manual laboratory-centric model of molecular and specimen-processing controls. Inter-
cycling of temperatures quickly evolved diagnostics. The future of molecular nal controls are incorporated into each
to automated cycling in thermocyclers, diagnostics is changing and is focused run to ensure that the cartridge and
followed by detection of PCR amplicons on producing rapid results in a general chemistry are functioning properly. The
with gel electrophoresis. Real-time PCR hospital setting. The concept of point- cartridges are placed in an independently
is now used in many clinical laboratories of-care molecular diagnostics is evolv- controlled GeneXpert module, which
because it allows the rapid detection of ing and is closer than was ever thought is a configuration of the independent
PCR products by the use of specific possible. heating and cooling optical reaction
fluorescent chemistries in a closed sys- The technology that has transformed (ICORE) module found in the Cepheid
tem. It has become a mainstay of core molecular testing from “batch” to SmartCycler instrument. Accompany-
molecular laboratory technologies. “STAT” is Cepheid’s GeneXpert system
While molecular diagnostics has (Sunnyvale, CA), which can offer near-
revolutionized the way medicine is point-of-care results in 1 to 2.5 h. The
system consists of an instrument and a
personal computer with preloaded soft-
*Editor’s Note: Part II of this article will
ware for running the tests and interpret-
be published in the December 15, 2008
issue of CMN (Vol. 30, No. 24). ing the results. The assays are simple to
run and utilize a single-unit disposable
Mailing Address: Elizabeth M. Marlowe, cartridge. The cartridge automates and
Ph.D., D(ABMM), Southern California
Permanente Medical Group, Regional Ref-
combines specimen processing, nucleic
erence Laboratories, North Hollywood, CA acid extraction, amplification, and
91605. Tel.: 818-503-7067. Fax: 818-503- detection. The PCR reagents are lyophi-
6713. E-mail: Elizabeth.M.Marlowe@kp.org lized and held in various chambers in

Clinical Microbiology Newsletter 30:23,2008 © 2008 Elsevier 0196-4399/00 (see frontmatter) 175
ing software automates data interpreta- In 2002, the CDC issued revised incubated for 18 to 24 h, and then plated
tion. The GeneXpert instrument is avail- guidelines in collaboration with the onto sheep blood agar. After 24 h, the
able in random-access 1-bay, 4-bay, and American College of Obstetrics and plates are examined for GBS; if nega-
16-bay module, and more automated Gynecology and the American Academy tive, the plates are incubated another
48-bay configurations. A more auto- of Pediatrics recommending universal 24 h and re-examined. Suspicious colo-
mated 72-bay configuration is due to prenatal screening of all pregnant women nies can be confirmed as GBS by latex
be released soon. between 35 and 37 weeks of gestations agglutination methods (8).
Cepheid has received FDA clearance to determine their vaginal-rectal GBS For an assay to have maximum
for their GeneXpert device for a variety colonization status. Since GBS is easily impact when used for intrapartum test-
of pathogens, including group B Strep- treated with antibiotics, intrapartum ing, the CDC suggested that it would
tococcus (GBS) from vaginal-rectal antibiotic prophylaxis (IAP) can be have to be rapid, sensitive, a minimum
swabs (1,2), enterovirus (EV) from provided during labor and delivery if of 85% accurate compared to culture,
cerebrospinal fluid (CSF) (3,4), and a woman is GBS positive (8). In 2005, and fit easily into the clinical labora-
methicillin-resistant Staphylococcus the CDC examined the impact of these tory’s routine (8). Routine PCR meets
aureus (MRSA) from nares swabs (5). guidelines and found that overall EOD some of these requirements; however,
The Xpert methods are rapid and rela- had decreased more than 30% (11). the simplicity of the GeneXpert makes
tively easy to perform; the GBS and Despite these preventative measures, it a good fit for around-the-clock testing
MRSA methods are rated as “moderate disparities still remain among certain scenarios. GBS testing could potentially
complexity,” and the EV method is rated ethnic groups and those with a lower occur in STAT laboratories to support
as a “high complexity” test according socioeconomic status (11). A 2007 labor and delivery suites as testing is
to Clinical Laboratory Improvement report from the CDC highlighted that needed.
Act (CLIA) categorization. Recently, among African Americans the incidence PCR for GBS from vaginal-rectal
a GeneXpert assay that simultaneously of EOD had risen 70% to pre-recom- swabs is available. Only FDA-cleared
detects MRSA and S. aureus (SA) from mendation levels (12). Furthermore, PCR methods will be discussed, since
skin and soft tissue specimens was FDA the majority of EOD cases arise from full discussion of alternate PCR methods
cleared. A similar MRSA-S. aureus women with negative GBS cultures is not within the scope of this review.
assay has also been FDA approved for and no risk factors (13). Maternal GBS GBS-PCR has the ability to both
use in blood culture bottles. colonization may be transient, chronic, decrease turnaround time (TAT) and
or intermittent (14). Thus, antepartum increase sensitivity (17). The BD
Applications of the Technology
screening may not provide the most GeneOhm Strep B PCR (BDGO) assay
GBS accurate determination of GBS colo- (BD Diagnostics, San Diego, CA) was
GBS emerged as a leading cause of nization status at the time of delivery the first FDA-cleared test on the market
neonatal morbidity and mortality in the (15). Preterm deliveries can also miss for testing on the Cepheid SmartCycler
1970s. As GBS is an inhabitant of the the 35- to 37-week GBS culture. These DX system (Cepheid, Sunnyvale, CA),
gastrointestinal tract, transmission from births make up 7 to 11% of deliveries with results available within 2 h. A
mother to infants can occur at the time but comprise 32 to 38% of EOD (13). multi-center study demonstrated that
of delivery. Early-onset disease (EOD) The solution to these problems would the BDGO Strep B PCR had a sensi-
occurs within 7 days of birth and be to screen these women at delivery, tivity and a specificity of 94% and
accounts for about 80% of GBS infec- since IAP given early enough (≥2 to 95.5%, respectively (17).
tions in infants. Late-onset disease 4 h) to GBS positive mothers at the Cepheid also has two FDA-cleared
appears after 7 days of age (6,7). Colo- time of delivery significantly diminishes GBS assays: the Smart GBS, which is
nization of pregnant women is approx- GBS transmission to newborns (16). run on their SmartCycler platform, and
imately 10 to 30% depending on the The CDC recommends the use of the Xpert GBS assay that is run on the
patient population (8,9). Higher rates antepartum GBS screening, primarily GeneXpert Dx System. The Smart GBS
of colonization have been noted among with culture from vaginal-rectal swabs. is FDA cleared for testing directly from
African Americans, non-smokers, and Swabs are placed in selective media, swabs or from LIM broth-enriched spec-
those with a high body mass index (10). typically Todd-Hewitt or LIM broth, imens. The direct method demonstrated

176 0196-4399/00 (see frontmatter) © 2008 Elsevier Clinical Microbiology Newsletter 30:23,2008
a sensitivity of 85% and a specificity of children recover from EV meningitis 12-member proficiency panel and up
97% compared to culture among intra- without sequelae. However, the clinical to 138 CSF specimens. The Xpert EV,
partum specimens tested in a clinical diagnosis of EV is often one of exclu- NASBA, and TaqMan assays correctly
trial, while the enriched method demon- sion, so that a bacterial etiology cannot identified 10/12, 8/12, and 7/12 profi-
strated a sensitivity and specificity of be excluded. Without actual EV diag- ciency panel members, respectively. For
98.7% and 90.4%, respectively, com- nostic confirmation, patients may be detection of EV RNA in CSF, the sensi-
pared to culture among anetpartum spec- hospitalized for further diagnostic test- tivities of the Xpert EV, NASBA, and
imens (18). One limitation of the PCR ing and the administration of antibiotics. TaqMan were 100%, 87.5%, and 96%,
assays performed on the SmartCycler is This practice leads to extended length respectively.
that they require a laboratory with suffi- of stay and increased hospital costs. In a prospective, unblinded compara-
cient space to house the instrument and Isolation of EV from CSF in cell tive study of the Xpert EV to the Argene
a medical technologist to perform the culture requires multiple cell lines and EV consensus kit (Argene SA, Varilhes,
test. These tests are rated high com- 3 to 8 days of incubation before cyto- France) and an in-house real-time PCR,
plexity by CLIA. pathic effect appears. This time frame the initial and resolved sensitivities of
Clinical-trial data demonstrated that is typically not rapid enough to affect the Xpert EV assay were 90.45% and
the Xpert GBS assay has a sensitivity therapy or the duration of hospitaliza- 98.8%, respectively (40). QCMD pro-
and a specificity of 88.6% and 96.7%, tion. Additionally, the sensitivity of cell ficiency panel results were comparable
respectively, for both antepartum and culture for recovery of EVs from CSF is to those of Marlowe et al. (4).
intrapartum specimens compared to cul- approximately 50 to 75% depending on A limitation of the Xpert EV assay
ture (1). In the intrapartum arm of the the serotype causing infection and the is the ability to test alternative specimen
study, the sensitivity and specificity concentration of virus in the CSF types, as the assay is FDA cleared only
were 91.3% and 95.6%, respectively. (23,24). for CSF. While customers are indepen-
The mean TAT was 1.84 h. During It is no surprise that nucleic acid dently examining the off-label ability
the clinical trials, the FDA required amplification methods have replaced of the cartridge to detect EV from alter-
that nurses perform the testing on the traditional culture-based methods as native specimens, data are limited and
GeneXpert System. The assay was the gold standard for detecting EV in have yet to be validated in multiple
FDA cleared in July 2006 as the first CSF, as PCR supports a considerable laboratories (41).
molecular test given a moderate-com- increase in sensitivity and a shorter The ease of use and software inter-
plexity rating by CLIA. In a prospective time to result (23,25-31). Depending pretation make the Xpert EV assay a
study, Gavino and Wang (2) reported on when results are available and how very attractive alternative for molecular
the Xpert GBS assay to have a sensi- they are used in the discharge plan, EV testing from CSF. Random-access
tivity and a specificity of 95.5% and significant health care-associated cost testing makes it particularly useful for
64.5%, respectively. savings have been coupled with PCR a low-volume assay and a short-staffed
Because of its sensitivity and perfor- diagnosis of EV meningitis (21,32-37). laboratory. Testing can be performed as
mance simplicity, the Xpert GBS assay While many laboratories have specimens are received with less than 5
has the potential to decrease EOD, par- employed laboratory-developed assays minutes hands-on time. Random access
ticularly among populations for which (LDAs) for the detection of EV for and decreased TAT, compared to the
there are marked disparities. However, years, LDAs require that each labora- batch mode of testing have the potential
culture techniques will remain, as PCR- tory independently verify its assays. to significantly decrease hospital costs.
based tests, as yet, do not provide In 2001, a multi-center study found A cost analysis study demonstrating the
susceptibility results for the pencillin- only 66% of laboratories performed use of the Xpert EV assay in emergency
allergic populations. Antepartum cul- adequately on EV proficiency testing, rooms and laboratories would be of
tures would still need to be performed highlighting the need for more interest.
to ensure GBS remains susceptible to standardized testing (38). MRSA
first line antibiotics. Another potential The Xpert EV cartridge is currently The spread of drug-resistant bacteria,
limitation of the Xpert GBS assay is the only FDA-cleared molecular assay such as MRSA, is a major concern for
that unresolved results, due to failed for the detection of EV from CSF. The healthcare and communities in which
controls or inhibition, require repeat Xpert EV assay is able to detect 63 dif- aggressive infections have caused deaths
testing, thus delaying results and IAP, ferent serotypes of EV with a limit of in both hospitalized patients and other-
as well as adding to the cost of testing. detection range of 0.0002 to 200 tissue wise healthy individuals (42). A known
Enterovirus culture infective doses/ml (3,39). A colonizer, MRSA is often harbored in the
EV is composed of positive-sense, multi-center beta trial study demon- human nares, skin, throat, and mucosa
single-stranded RNA viruses. The genus strated that the performance character- of the vagina and rectum. Human “car-
is in the family Picornaviridae and cur- istics of the Xpert EV assay were riers” can spread MRSA to others in
rently consists of 68 distinct serotypes comparable to those of assays currently health care settings, who can fall victim
(19). In the United States, an estimated being used in clinical laboratories (3). to potential infections. Since 2003,
75,000 cases of aseptic meningitis Marlowe et al. (4) compared it to real- MRSA has accounted for more than 60%
occur annually, and approximately 80 time NASBA and a Taq-Man reverse of all S. aureus health care-associated
to 90% of these are caused by EVs (20- transcription-PCR and found similar infections (HAIs) reported in U.S. hos-
22). Typically, most infants and young results. Assays were evaluated using a pitals (43). At last report, the National

Clinical Microbiology Newsletter 30:23,2008 © 2008 Elsevier 0196-4399/00 (see frontmatter) 177
Health and Safety Network estimated based comparison of strategies to pre- Parker. 1986. Temporal and geographic
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