Original Article

A comparison between the efficiency of the Xpert MTB/RIF assay

and nested PCR in identifying Mycobacterium tuberculosis during
routine clinical practice
Cheol-Hong Kim1,2*, Heungjeong Woo1*, In Gyu Hyun1,2, Changhwan Kim1,2, Jeong-Hee Choi1,2,
Seung-Hun Jang1,2, Sang Myeon Park1,2, Dong-Gyu Kim1,2, Myung Goo Lee1,2, Ki-Suck Jung1,2,
Jeongwon Hyun3, Hyun Soo Kim3
1

Department of Internal Medicine, 2Lung Research Institute, 3Department of Laboratory Medicine, Hallym University College of Medicine,

Chuncheon, Korea
*These authors contributed equally to this work.
Correspondence to: In Gyu Hyun. Department of Internal Medicine, Hallym Univeristy Dongtan Sacred Heart Hsopital, 7 Keunjaebong-gil,
Hwaseong-si, Gyeonggi-do 445-907, Korea. Email: ighyun@hallym.or.kr; Dong-Gyu Kim. Department of Internal Medicine, Hallym University
Kangnam Sacred Hospital, 1 Singil-ro, Yeongdengpo-gu, Seoul 150-950, Korea. Email: dongyu@hallym.or.kr.

Objectives: Polymerase chain reaction (PCR) for the detection of Mycobacterium tuberculosis (MTB) is more
sensitive, specific, and rapid than the conventional methods of acid-fast bacilli (AFB) smear and culture. The
aim of this study was to determine if the Xpert MTB/rifampicin (RIF) assay had additional advantages over
nested PCR for the detection of MTB in a geographical area with intermediate tuberculosis (TB) incidence.
Methods: Between February and December 2013, the Xpert MTB/RIF assay and MTB nested PCR, as
well as AFB smear and culture, were simultaneously performed on 198 clinical samples (160 pulmonary and
38 non-pulmonary specimens) collected from 171 patients hospitalized at Hallym University Medical Center
for possible TB. The accuracy of the diagnosis of MTB culture-positive TB and the turnaround time of
reporting laboratory results were calculated and compared. Rifampin resistance by the Xpert MTB/RIF assay
was reviewed with that of conventional drug susceptibility testing (DST).
Results: The sensitivity, specificity, and positive and negative predictive values of the Xpert MTB/RIF
assay and MTB nested PCR for diagnosis of MTB culture-positive pulmonary TB were 86.1% vs. 69.4%
(P=0.1563), 97.8% vs. 94.1% (P=0.2173), 91.2% vs. 75.8% (P=0.1695), and 96.4% vs. 92.0% (P=0.2032),
respectively. The median turnaround times of the Xpert MTB/RIF assay and MTB nested PCR were 0 [0-4]
days and 4 [1-11] days, respectively (P<0.001). Two cases of rifampin resistance, as determined by the Xpert
MTB/RIF assay, were found to be multi-drug resistant (MDR) pulmonary TB by DST.
Conclusions: The Xpert MTB/RIF assay seemed to be sensitive, specific, and comparable to nested PCR
for identifying MTB among clinically suspected TB patients, and the assay can be valuable in giving a timely
identification of resistance to rifampin.
Keywords: Mycobacterium tuberculosis (MTB); polymerase chain reaction (PCR); pulmonary tuberculosis
Submitted Jan 23, 2014. Accepted for publication Apr 02, 2014.
doi: 10.3978/j.issn.2072-1439.2014.04.12
View this article at: http://dx.doi.org/10.3978/j.issn.2072-1439.2014.04.12

Introduction

intermediate, the disease is an important public health issue.

Tuberculosis (TB) remains a serious public health

problem because of its high potential for person-to-person
transmission. In Korea, where the prevalence of TB is

In 2012 in Korea, the number of reported TB cases was

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49,532, and the estimated annual incidence was 108 per

100,000 people (1). Early diagnosis and rapid introduction

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626

of an anti-TB treatment are essential for successful patient

outcomes. However, there are shortcomings to the standard
diagnostic methods, which include the direct smear for
acid-fast bacilli (AFB), which has low sensitivity, and
mycobacterial culture, which is slow and usually requires
2-6 weeks to yield a final result (2).
During the last decade, a number of nucleic acid
amplification (NAA) methods have been developed for rapid
detection and identification of Mycobacterium tuberculosis
(MTB) in clinical specimens (3,4). These techniques are
attractive because they allow for the direct detection of low
MTB genomic copy numbers in specimens. Polymerase
chain reaction (PCR) is based on NAA methods and is
widely used for the rapid diagnosis of TB.
Our institution currently utilizes two commercial
standardized PCR procedures, the Xpert MTB/rifampicin
(RIF) assay and MTB nested PCR. MTB nested PCR was
developed in an effort to identify the members of the MTB
complex. The target is the IS6110 insertion sequence or the
mtp40 gene (5,6). The Xpert MTB/RIF assay, using real-time
PCR for the TB-specific rpoB gene, is a cartridge-based,
automated diagnostic test that can simultaneously identify
MTB and resistance to rifampin; it was recently introduced
for the rapid diagnosis of TB in Korea. The present study
compared the clinical efficiency of the Xpert MTB/RIF assay
with that of nested PCR for the detection of MTB among
patients with active TB in a newly opened university hospital.
Patients and methods
Study design and specimens
This study was approved by the local institutional review
board, with a waiver for obtaining consent from individual
patients. We retrospectively examined results from AFB
smears and cultures, the Xpert MTB/RIF assay, and MTB
nested PCR for 171 patients with suspected TB, in whom
those tests were performed at the Hallym University
Dongtan Sacred Heart Hospital between February and
December 2013. We evaluated the diagnostic accuracy and
turnaround time of the Xpert MTB/RIF assay and MTB
nested PCR and compared the efficacy of the Xpert MTB/
RIF assay with that of the conventional drug susceptibility
test (DST) in determining rifampin resistance.
A total of 160 pulmonary and 38 non-pulmonary
specimens from 171 suspected TB cases were analyzed in
this study. Pulmonary samples included sputum, bronchial
washing, and bronchoalveolar lavage fluid, whereas non-

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Kim et al. Comparison of Xpert MTB/RIF and nested PCR

pulmonary samples from normally sterile sites consisted

of pleural fluid, ascitic fluid, pericardial fluid, joint fluid,
cerebrospinal fluid, tissue, or lymph node. If multiple
specimens showed positive results from the same patient,
only one specimen was used for the analysis.
An initial treatment case of TB was defined as a new
patient who had never received treatment for TB or
who had taken anti-TB drugs for less than one month.
A retreatment case of TB was defined as a patient who
was treated after a failure, treated after having previously
defaulted, or newly diagnosed with active TB after being
previously declared cured or completing treatment (7).
AFB smear and mycobacterial culture
Pulmonary specimens were pretreated with N-acetyl-Lcystein-2% NaOH and centrifugation (3,000 g for 20 min at
4 ). AFB smears were performed using auramine-rhodamine
fluorescent staining and confirmed by Ziehl-Neelsen staining.
The sediments were inoculated into 3% Ogawa solid media
(Asan Pharmaceutical, Seoul, Korea) for eight weeks in 5-10%
CO2 incubators, as well as the BD BACTEC MGIT 960
system (Becton, Dickinson, and Company, Sparks, MD, USA),
automated liquid culture system, for 6 weeks. Non-pulmonary
specimens were cultured without prior pretreatment.
Once cultured, MTB was detected using BD MGIT TB
identification test, based-on rapid immunochromatography
(Becton, Dickinson, and Company).
Drug susceptibility testing (DST)
All positive cultures were tested for DST. It was performed
at the Korean Institute of Tuberculosis by the absolute
concentration method, considered the gold standard for
detection of isoniazid (INH) and RIF resistance, defined
as 1% bacterial growth in Lwenstein-Jensen medium at
concentrations of 0.2 g/mL for INH and 40.0 g/mL for
RIF, respectively (8).
MTB nested PCR
For nested PCR, the Seeplex MTB nested ACE Detection
assay (Seegene Inc., Seoul, Korea) was performed according
to the manufacturers instruction. The assay used multitarget (IS6110 and mpb64) PCR, instead of single target
PCR for specific detection of MTB. IS6100 is an insertion
sequence present in the MTB genome and mpb64 is a
conserved sequence present at a single copy in the MTB

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Journal of Thoracic Disease, Vol 6, No 6 Jun 2014

genome (5,6). The internal control (520 base pairs) a

DNA plasmid, was co-amplified with target DNA to
identify processed samples containing substances that
might interfere with PCR amplification. Amplified PCR
products (190 bp) were electrophoresed and visualized on
electrophoresis system.
Xpert MTB/RIF assay
The Xpert MTB/RIF assay (Cepheid Inc., Sunnyvale,
CA, USA) was performed according to the manufacturers
instruction. The assay is a fully automated NAA test (by
rapid, real-time PCR), was used for the detection of MTB
and rifampin resistance. The target was an MTB-specific
sequence of the rpoB gene, which was labeled with molecular
beacons for mutations within the rifampin resistance
determining region (9,10). The testing was carried out
on the GeneXpert test device platform, which simplifies
molecular testing by fully integrating and automating sample
preparation, amplification, and detection. A bacterial buffer
was added to the clinical specimens before a defined volume
was transferred to a cartridge containing all reagents. The
plastic cartridge was then introduced to the GeneXpert
device, which provided results in less than two hours.
Statistical analysis
The sensitivity, specificity, positive predictive value (PPV),
and negative predictive value (NPV) of the Xpert MTB/
RIF assay and nested TB PCR were calculated, and 95%
confidence intervals were estimated. The clinical data of the
included patients were described with means, medians, and
ranges. Continuous variables were compared by Students
t-test or Mann-Whitney U test (if the variables were not
normally distributed), whereas the categorical variables were
compared using the chi-square test or Fishers exact test.
A P value of <0.05 was considered significant. Statistical
analyses were performed using dBSTAT software version 4.0
(dBSTAT Inc., Chuncheon, Korea).
Results

627

patients were male. Hypertension, bronchiectasis, diabetes

mellitus, and malignancy were the co-morbidities found in
38 (22.2%), 27 (15.8%), 25 (14.6%), and 15 (8.8%) of the
patients, respectively. MTB culture-positive pulmonary TB
was finally diagnosed in 36 (21.1%). Seven patients (4.1%)
were diagnosed with MTB culture-negative pulmonary
TB, based on their clinical symptoms and radiographic
findings, even though their AFB smears showed positive
results. Extrapulmonary TB was diagnosed in six patients
(3.5%), TB pleurisy in three, TB meningitis in two, and TB
peritonitis in one (Table 1).
Comparison of the Xpert MTB/RIF assay and MTB nested
PCR
Of 43 pulmonary TB patients, the Xpert MTB/RIF assay
and nested PCR yielded positive results in 32 (94.1%) and
26 (78.8%) patients, respectively (P>0.05). Of the cases
of MTB culture-positive pulmonary TB, 31 (91.2%) and
25 (75.8%) were found positive by the Xpert MTB/RIF
assay and nested PCR, respectively (P>0.05). None of the
extrapulmonary TB patients had positive results in any
test. Among the patients with false positive results of the
Xpert MTB/RIF assay, non-tuberculous mycobacterial
(NTM) disease and bacterial pneumonia were identified in
each case (2.9%). Of the patients with false positive MTB
nested PCR results, bacterial pneumonia was found in three
patients (9.1%) and lung cancer, hemoptysis, sarcoidosis,
and empyema in one (3.0%) (Table 2).
No differences were observed between the results of the
Xpert MTB/RIF assay and MTB nested PCR in patients,
according to previous history of treatment for TB (P>0.05).
All six patients with extrapulmonary TB corresponded to
the initial treatment cases (Table 3). Among the 26 patients
available data from conventional DST, only two cases (7.7%)
showed resistance to RIF by the Xpert MTB/RIF assay
and were found to be multi-drug resistant (MDR) MTB by
DST on solid culture (Table 4).
The median turnaround times from the submission of
samples to obtaining results from the laboratory for the Xpert
MTB/RIF assay and MTB nested PCR were 0 day (0-4 days)
and 4 days (1-11 days), respectively (P<0.001) (Table 5).

Patient characteristics
The Xpert MTB/RIF assay and MTB nested PCR using
pulmonary and non-pulmonary clinical specimens were
requested for 171 patients with suspicion of TB. The
age of these patients was 58.617.58, and 104 (60.8%)

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Diagnostic accuracy of the Xpert MTB/RIF assay and

MTB nested PCR for mycobacterial culture positive
pulmonary TB
The overall sensitivity, specificity, PPV, and NPV of the

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Kim et al. Comparison of Xpert MTB/RIF and nested PCR

628

Table 1 Characteristics of the 171 patients in whom the Xpert

Table 2 Comparison of the results of Xpert MTB/RIF assay and

MTB/RIF assay and MTB nested PCR were performed

MTB nested PCR

Characteristics
Age, years

Number of positive with

58.617.58

Xpert MTB/RIF

Male

104 (60.8)

Number of clinical specimens

198

Pulmonary TB

160 (80.8)

(n=43)

Pulmonary
Non pulmonary

38 (19.2)

Co-morbidites

MTB culture

MTB nested

assay

PCR

32 (94.1)

26 (78.8)

0.08

31 (91.2)

25 (75.8)

0.63

1 (2.9)

1 (3.0)

1 (2.9)

positive (n=36)

Hypertension

38 (22.2)

MTB culture

Bronchiectasis

27 (15.8)

negative (n=7)

Diabetes mellitus

25 (14.6)

Extrapulmonary TB

Malignancy

15 (8.8)

(n=6)

Cardiovascular disease

13 (7.6)

Nontuberculous

Stroke

6 (3.5)

mycobacterial

Bronchial asthma

5 (2.9)

disease

Dementia

4 (2.3)

Bacterial pneumonia

1 (2.9)

3 (9.1)

Chronic liver disease

3 (1.8)

Lung cancer

1 (3.0)

Chronic kidney disease

3 (1.8)

Hemoptysis

1 (3.0)

Taking immunosuppressive drugs

2 (1.2)

HIV/AIDS

1 (0.6)

Sarcoidosis

1 (3.0)

Empyema

1 (3.0)

33 [100]

Final diagnosis
Pulmonary TB

43 (25.1)

MTB culture positive

36 (21.1)

MTB culture negative

7 (4.1)

Extrapulmonary TB

Total

34 [100]

Abbreviations: MTB, Mycobacterium tuberculosis; RIF,

rifampin; PCR, polymerase chain reaction.

6 (3.5)

Bacterial pneumonia

45 (26.3)

Table 3 Comparison of the results of Xpert MTB/RIF assay

Lung cancer

13 (7.6)

and MTB nested PCR in patients with tuberculosis according

Nontuberculous mycobacterial lung disease

8 (4.7)

Hemoptysis

8 (4.7)

Number of positive with

Lung abscess

7 (4.1)

Xpert MTB/ MTB nested

Transudative pleural effusion

6 (3.5)

RIF assay

PCR

Inactive TB sequalae

4 (2.3)

Malignant pleural effusion

4 (2.3)

24

17

0.132

Empyema

4 (2.3)

Influenza

4 (2.3)

Pulmonary edema

3 (1.8)

Atelectasis

3 (1.8)

Others*

13 (7.6)

*, Fungus ball, 2; interstitial pneumonitis, 2; eosinophilic

pneumonia, 2; anthracofibrosis, 2; bronchiectasis, 1;
sarcoidosis, 1; pyogenic pericarditis, 1; norcardiosis, 1; chronic
respiratory failure, 1. Abbreviations: MTB, Mycobacterium
tuberculosis; RIF, rifampin; PCR, polymerase chain reaction.

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to previous history of treatment for tuberculosis

P

Pulmonary TB (n=43)
Initial treatment (n=34)
Retreatment (n=9)

Abbreviations: MTB, Mycobacterium tuberculosis; RIF, rifampin;

PCR, polymerase chain reaction.

Xpert MTB/RIF assay and nested PCR for diagnosis of

MTB culture positive pulmonary TB were 86.1% (70.49,
95.28) vs. 69.4% (51.89, 83.63), 97.8% (93.63, 99.51) vs.
94.1% (88.65, 97.40), 91.2% (76.30, 98.04) vs. 75.8% (57.74,
88.88), and 96.4% (91.68, 98.79) vs. 92.0% (86.18, 95.95),
respectively. No differences were seen among diagnostic

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629

accuracies of the Xpert MTB/RIF assay and nested PCR

(Table 6).
Discussion
TB remains a major challenge to public health worldwide,
especially in endemic areas, despite global efforts to control
the disease. Early identification of MTB is very important, as
it can help in the initiation of adequate treatment for patients
(11-13). PCR is currently the most promising applicative
method in the diagnosis of TB. The technique is based on
Table 4 Comparison of the Xpert MTB/RIF assay and conventional
DST results among mycobacterial culture positive MTB
Conventional DST

Resistance to RIF by Xpert

MTB/RIF assay

Susceptible (n=23)

INH mono-resistant (n=1)

MDR (n=2)

Contaminated (n=2)

Not done* (n=8)

*, Fail to grow on solid culture. Abbreviations: MTB,

Mycobacterium tuberculosis; RIF, rifampin; INH, isoniazid; PCR,
polymerase chain reaction; DST, drug susceptibility test; MDR,
multi-drug resistant.

Table 5 Turnaround time of the Xpert MTB/RIF assay and

MTB nested PCR (n=171)
From submission of samples to obtaining results from
laboratory, days, median [range]
Xpert MTB/RIF assay
0 [0-4]

MTB nested PCR

4 [1-11]

0.000

Abbreviations: MTB, Mycobacterium tuberculosis; RIF,

rifampin; PCR, polymerase chain reaction.

the amplification of a specific genomic sequence of MTB,

which is theoretically highly specific and can be useful
in giving a rapid diagnosis. However, variable sensitivity
(73-80%) and specificity (80-100%) are obtained with
different PCR methods, depending on the area of the
genome that is amplified and the techniques used for DNA
extraction among different laboratories (14-16). Recently,
the Xpert MTB/RIF assay, based on real-time PCR, has
been developed in an effort to detect MTB, as well as RIFresistance TB. Its clinical application, however, is limited in
Korea, as it has been introduced relatively recently. Because
conventional methods, such as AFB smear and culture, can
fail due to the paucibacillary nature of TB and presently
used PCR methods often show questionable reliability, an
evaluation of newer diagnostic methods for TB is important.
Therefore, this study evaluated the efficiency of the Xpert
MTB/RIF assay compared to preexisting IS6110- and mtp40nested PCR to detect MTB in clinical specimens.
In our study, the sensitivity, specificity, PPV, and NPP
of the Xpert MTB/RIF assay for diagnosis of MTB
culture-positive TB were 86.1%, 97.8%, 91.2%, and
96.4%, respectively, whereas those of nested PCR were
69.4%, 94.1%, 75.8%, and 92.0%, respectively. Out of
43 pulmonary TB patients, no differences were observed
between the results of the two tests (P>0.05). Although
the sensitivity (86.1%) of the Xpert MTB/RIF assay was
higher than that of nested PCR (69.4%), our value was
slightly lower than that (90.4%) of a recent study (17). In
addition, the turnaround time of the Xpert MTB/RIF assay
was shorter than that of the nested PCR, median 0 [0-4] vs.
4 [1-11] days, respectively (P<0.001). These findings suggest
that the Xpert MTB/RIF assay is comparable to nested
PCR for detection of a case of mycobacterial culturepositive TB among clinical TB suspects; in addition, the
shorter turnaround time of the assay may help us to initiate
anti-TB therapy promptly.
The number of genomic copies in a specimen can affect a

Table 6 Diagnostic accuracy of the Xpert MTB/RIF assay and MTB nested PCR for the diagnosis of MTB culture positive pulmonary tuberculosis
Xpert MTB/RIF assay (n=171)

MTB nested PCR (n=171)

Sensitivity, % (95% CI)

86.11 (31/36) (70.49, 95.28)

69.44 (25/36) (51.89, 83.63)

0.1563

Specificity, % (95% CI)

97.78 (132/135) (93.63, 99.51)

94.07 (127/135) (88.65, 97.40)

0.2173

PPV, % (95% CI)

91.18 (31/34) (76.3, 98.04)

75.76 (25/33) (57.74, 88.88)

0.1695

NPV, % (95% CI)

96.35 (132/137) (91.68, 98.79)

92.03 (135/138) (86.18, 95.95)

0.2032

Abbreviations: MTB, Mycobacterium tuberculosis; RIF, rifampin; PCR, polymerase chain reaction; CI, confidence interval; PPV,
positive predictive value; NPV, negative predictive value.

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positive PCR result (18). Among 36 pulmonary TB patients

with a positive mycobacterial culture, 31 (86.1%) and
25 (69.4%) were found positive with the Xpert MTB/RIF
assay and nested PCR, respectively (P>0.05). On the other
hand, out of 13 patients, including seven patients with
mycobacterial culture-negative pulmonary TB and six
patients with extrapulmonary TB, only one patient (7.7%)
showed positive results with both tests. These results may
come from paucibacillary specimens, such as with TB
pleurisy, TB meningitis, and TB peritonitis (19-21). False
negative results, however, remain a problem with any test.
Among 36 pulmonary MTB culture-positive TB patients,
5 (16.1%) and 11 (30.6%) showed negative results with
the Xpert MTB/RIF assay and nested PCR, respectively
(P>0.05). A likely reason for the false negative PCR result
was the absence of MTB targets (the rpoB gene for the
Xpert MTB/RIF assay and the IS6110 or mtp40 gene for
nested PCR) in the requested specimens (22,23). Another
possible reason was the number of samples submitted for
detection of MTB. More than two sets of sputum samples
from patients suspected to have TB are normally requested
for AFB cultures. However, the cost and labor of PCR
often limits the assay to be performed on one specimen
because of sampling difficulties, such as bronchial washing,
bronchoalveolar lavage fluid, and body fluid from sterile
sites. For these reasons, the sensitivity and PPV of the
Xpert MTB/RIF assay and nested PCR in our study (86.1%
vs. 69.4% and 91.2% vs. 75.8%, respectively) were relatively
low compared those in other studies (14-16,21,24).
Compared to the Xpert MTB/RIF assay, nested PCR
is time consuming and requires manual labor for sample
manipulations, which reduce proteins and enzymes that
may inhibit the amplification reactions of specimens. This
may cause unintentional errors, such as inappropriate
specimen dilution and cross-contamination. In our study,
among non-TB patients (n=122), excluding 43 pulmonary
TB patents and six extrapulmonary TB patients, two (1.6%)
and seven patients (5.7%) were positive with the Xpert
MTB/RIF assay and nested PCR, respectively (P>0.05).
Indeed, nested PCR required multiple user-dependent
steps for manipulations, which may give rise to a crosscontamination. In contrast, the Xpert MTB/RIF assay was
automatically and simply performed on the GeneXpert
device, thus limiting the carryover contamination.
In Korea, MDR-TB strains cause 2.7-3.9% of new TB
and 14.0-27.2% of retreatment cases (8,25). In this study,
two cases of RIF resistance by the Xpert MTB/RIF assay
were found to be MDR-TB patients, one new and one

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Kim et al. Comparison of Xpert MTB/RIF and nested PCR

retreatment case of TB. The WHO recommends that

the test should be used as the initial diagnostic method in
individuals at risk of having MDR-TB or HIV-associated
TB and could be used as a follow-up test to sputum
microscopy in areas with a low prevalence of MDR-TB
or HIV (1). Likewise, the Xpert MTB/RIF assay is likely
to play an additional role in detecting MDR-TB strains,
regardless of the past history of therapy for TB, after the
increase in notification rate of MDR-TB in Korea (1,24).
However, we should consider the false negative aspect of
the assay, as it may neither detect MTB nor identify RIF
resistance in some MDR-TB strains (21,24).
The limitations of our study include a small sample size,
as well as the fact that the submitted specimen was not
aliquoted into two portions (one for the Xpert MTB/RIF
and the other for nested PCR), because of the small amount
of volume and sampling difficulties, such as bronchoscopy
and body fluid aspiration. Furthermore, both tests were
not performed on the same day, in a blind manner by one
technician, and independently. This fact may yield some
variations in diagnostic accuracy between the Xpert MTB/
RIF and nested PCR. We also must consider the costeffectiveness of PCR techniques, which limits the number
times the test can be repeated.
In conclusion, the Xpert MTB/RIF assay appears to
have comparable sensitivity and specificity to the nested
PCR technique for the routine diagnosis of mycobacterial
culture-positive TB. In addition, the assay provides results
in a relatively short period, allowing for faster initiation of
anti-TB treatment.
Acknowledgements
Disclosure: The authors declare no conflict of interest.
References
1. WHO. Estimates of TB and MDR-TB burden are
produced by WHO in consultation with countries.
Available online: https://extranet.who.int/sree/
Reports?op=Replet&name=%2FWHO_HQ_Reports%2F
G2%2FPROD%2FEXT%2FTBCountryProfile&ISO2=
KR&LAN=EN&outtype=html
2. Centers for Disease Control and Prevention (CDC).
Updated guidelines for the use of nucleic acid amplification
tests in the diagnosis of tuberculosis. MMWR Morb
Mortal Wkly Rep 2009;58:7-10.
3. Jouveshomme S, Cambau E, Trystram D, et al. Clinical

www.jthoracdis.com

J Thorac Dis 2014;6(6):625-631

Journal of Thoracic Disease, Vol 6, No 6 Jun 2014

4.

5.

6.

7.
8.

9.

10.
11.

12.

13.

14.

15.

utility of an amplification test based on ligase chain

reaction in pulmonary tuberculosis. Am J Respir Crit Care
Med 1998;158:1096-101.
Piersimoni C, Scarparo C, Piccoli P, et al. Performance
assessment of two commercial amplification assays for
direct detection of Mycobacterium tuberculosis complex
from respiratory and extrapulmonary specimens. J Clin
Microbiol 2002;40:4138-42.
Hasegawa N, Miura T, Ishii K, et al. New simple and
rapid test for culture confirmation of Mycobacterium
tuberculosis complex: a multicenter study. J Clin Microbiol
2002;40:908-12.
Magdalena J, Vachee A, Supply P, et al. Identification of a
new DNA region specific for members of Mycobacterium
tuberculosis complex. J Clin Microbiol 1998;36:937-43.
WHO (2013). Global tuberculosis report.
Bai GH, Park YK, Choi YW, et al. Trend of antituberculosis drug resistance in Korea, 1994-2004. Int J
Tuberc Lung Dis 2007;11:571-6.
El-Hajj HH, Marras SA, Tyagi S, et al. Detection of
rifampin resistance in Mycobacterium tuberculosis in
a single tube with molecular beacons. J Clin Microbiol
2001;39:4131-7.
Tyagi S, Kramer FR. Molecular beacons in diagnostics.
F1000 Med Rep 2012;4:10.
Pai M, Minion J, Sohn H, et al. Novel and improved
technologies for tuberculosis diagnosis: progress and
challenges. Clin Chest Med 2009;30:701-16, viii.
Van Deun A, Martin A, Palomino JC. Diagnosis of drugresistant tuberculosis: reliability and rapidity of detection.
Int J Tuberc Lung Dis 2010;14:131-40.
Yang XY, Li YP, Mei YW, et al. Time and spatial
distribution of multidrug-resistant tuberculosis among
Chinese people, 1981-2006: a systematic review. Int J
Infect Dis 2010;14:e828-37.
Aryan E, Makvandi M, Farajzadeh A, et al. Clinical value
of IS6110-based loop-mediated isothermal amplification
for detection of Mycobacterium tuberculosis complex in
respiratory specimens. J Infect 2013;66:487-93.
Aryan E, Makvandi M, Farajzadeh A, et al. A novel and

631

16.

17.

18.

19.
20.

21.

22.

23.

24.

25.

more sensitive loop-mediated isothermal amplification

assay targeting IS6110 for detection of Mycobacterium
tuberculosis complex. Microbiol Res 2010;165:211-20.
Singh A, Kashyap VK. Specific and Rapid Detection of
Mycobacterium tuberculosis Complex in Clinical Samples
by Polymerase Chain Reaction. Interdiscip Perspect Infect
Dis 2012;2012:654694.
Chang K, Lu W, Wang J, et al. Rapid and effective
diagnosis of tuberculosis and rifampicin resistance
with Xpert MTB/RIF assay: a meta-analysis. J Infect
2012;64:580-8.
Helb D, Jones M, Story E, et al. Rapid detection of
Mycobacterium tuberculosis and rifampin resistance
by use of on-demand, near-patient technology. J Clin
Microbiol;48:229-37.
Morehead RS. Tuberculosis of the pleura. South Med J
1998;91:630-6.
Bastian I, Rigouts L, Van Deun A, et al. Directly observed
treatment, short-course strategy and multidrug-resistant
tuberculosis: are any modifications required? Bull World
Health Organ 2000;78:238-51.
Bunsow E, Ruiz-Serrano MJ, Lpez Roa P, et al.
Evaluation of GeneXpert MTB/RIF for the detection of
Mycobacterium tuberculosis and resistance to rifampin in
clinical specimens. J Infect 2014;68:338-43.
Das S, Paramasivan CN, Lowrie DB, et al. IS6110
restriction fragment length polymorphism typing of
clinical isolates of Mycobacterium tuberculosis from
patients with pulmonary tuberculosis in Madras, south
India. Tuber Lung Dis 1995;76:550-4.
Kent L, McHugh TD, Billington O, et al. Demonstration
of homology between IS6110 of Mycobacterium
tuberculosis and DNAs of other Mycobacterium spp.? J
Clin Microbiol 1995;33:2290-3.
Kwak N, Choi SM, Lee J, et al. Diagnostic Accuracy
and Turnaround Time of the Xpert MTB/RIF Assay in
Routine Clinical Practice. PLoS One 2013;8:e77456.
Choi JC, Lim SY, Suh GY, et al. Drug resistance rates of
Mycobacterium tuberculosis at a private referral center in
Korea. J Korean Med Sci 2007;22:677-81.

Cite this article as: Kim CH, Woo H, Hyun IG, Kim C, Choi
JH, Jang SH, Park SM, Kim DG, Lee MG, Jung KS, Hyun
J, Kim HS. A comparison between the efficiency of the Xpert
MTB/RIF assay and nested PCR in identifying Mycobacterium
tuberculosis during routine clinical practice. J Thorac Dis
2014;6(6):625-631. doi: 10.3978/j.issn.2072-1439.2014.04.12

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J Thorac Dis 2014;6(6):625-631