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Journal of Clinical Microbiology, March 2004, p. 1308-1312, Vol. 42, No. 3
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.3.1308-1312.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Differential Identification of Mycobacterium tuberculosis Complex and Nontuberculous Mycobacteria by Duplex PCR Assay Using the RNA Polymerase Gene (rpoB)
Bum-Joon Kim,1 Seong-Karp Hong,
Keun-Hwa Lee,1 Yeo-Jun Yun,1 Eui-Chong Kim,2 Young-Gil Park,3 Gil-Han Bai,3 and Yoon-Hoh Kook1*
Departmentof Microbiology and Cancer Research Institute, Institute of Endemic
Diseases, SNUMRC, Seoul National University College of Medicine, and
Clinical Research
Institute,1
Department of
Clinical Pathology, Seoul National University College of
Medicine, Seoul
110-799,2
The Korean
Institute of Tuberculosis, Korean National Tuberculosis
Association, Seoul 137-140,Korea3
Received 8 July 2003/
Returned for modification 20 August 2003/
Accepted 18 November 2003

ABSTRACT
A
novel duplex PCR method that can amplify the 235- and 136-bp
rpoB DNAs of
Mycobacterium tuberculosis
complex and nontuberculous
mycobacteria (NTM), respectively, with two
different sets of
primers was used to differentially identify 44
reference strains
and 379 clinical isolates of mycobacteria in a
single-step assay.
Showing 100% sensitivity and specificity, the
duplex PCR method
could clearly differentiate
M.
tuberculosis complex and NTM
strains. In addition, restriction
fragment length polymorphism
analysis and direct sequencing of the
amplicon of NTM could
be used to supplement species
identification.

INTRODUCTION
With the recent global resurgence of mycobacterial infections,
especially
of tuberculosis, attributed to increased human
immunodeficiency
virus infection, there is an increasing demand for
rapid, sensitive,
and specific diagnostic methods for the
detection and identification
of
Mycobacterium
tuberculosis and nontuberculous mycobacteria
(NTM) in a
clinical setting (
2,
3,
4). NTM infection can
cause
clinical problems, as its pathogenic potential and
susceptibilities
to antituberculosis treatments vary
(
22). In addition, mixed
infections
of
M. tuberculosis and NTM have been
reported (
16). Therefore,
it
has become important to be able to differentiate between the
two
during the early stage of the diagnostic procedure.
The diagnosis
of mycobacterial infection is accomplished by culture-based
identification. Primary culture of slowly growing mycobacteria, without
using the BACTEC culture system, usually takes 4 to 6 weeks or longer
(10). However, recent
methodological advances in molecular biology have provided alternative
rapid approaches, e.g., the PCR and PCR-linked methods. For the rapid
detection or identification of M. tuberculosis,
target genes specific to mycobacteria are used in a PCR
(7,
8,
17,
19).
Because the
incidence of NTM infection is increasing, any methods capable of
simultaneously determining the presence of M.
tuberculosis and/or NTM would be useful. For this purpose,
multiplex PCR, which simultaneously uses two or three different genes,
has been frequently used, as the technique can specifically detect and
identify different species of the genus Mycobacterium
(6,
15,
18) and differentiate
members of the M. tuberculosis complex
(6,
9) in the routine
diagnostic laboratory by using Mycobacterium genus- and
species-specific genes. However, some of these genes have been found to
lack specificity for M. tuberculosis. In addition,
IS6110 PCR has been reported to produce false-negative
(23) and false-positive
(11) results, and the
mtp40 gene is not present in all M.
tuberculosis strains
(21). These reports
suggest that the multiplex PCR targeting of these genes has associated
problems.
In the present study, we used a simplified multiplex
PCR assay, basically a duplex PCR (DPCR) assay, to differentiate
M. tuberculosis complex and NTM by using a single
gene, the RNA polymerase ß-subunit-encoding gene
(rpoB). To demonstrate the efficiency and usefulness of the
DPCR assay in this context, we used it to identify
reference strains and clinical isolates of
mycobacteria.
Forty-four mycobacteria and 17 non-mycobacteria
were used as reference strains (Table
1). Three hundred seventy-nine clinical isolates (193 M.
tuberculosis complex [183 M.
tuberculosis and 10 M. bovis] and 186
NTM isolates), which had been isolated by the Korean Institute of
Tuberculosis and the Seoul National University Hospital, were
identified by conventional biochemical tests and provided for blind
testing. An IS6110 PCR assay and analysis of partial 16S rRNA
gene (rDNA) sequences were performed separately, and the
results were compared with those of the DPCR assay.
Two different
kinds of DNA extraction protocols were used for
type strains and
clinical isolates. The DNAs of the reference
strains were purified by
using the bead beater-phenol extraction
method as previously described
(
12,
13). The DNAs of clinical
isolates
were prepared by the boiling method without a purification
step
to reduce the DNA preparation time and to minimize the risk
of
cross contamination (
1). A
loopful culture of each sample
was suspended in a screw-cap tube with
50 µl of TEN buffer
(10 mM Tris-HCl, 1 mM EDTA, 100 mM NaCl
[pH 8.0]), and the tube
contents were then boiled on a hot
plate for 10 min. Without
further purification, 5 µl of the
boiled mycobacterial
suspension was used directly as a template for the
DPCR assay.
For construction of the two DPCR primer sets,
rpoB sequences of 44 mycobacteria (GenBank accession no.
AF057449
to
AF057493)
were aligned by using the multiple alignment algorithm in the MegAlign
package (Windows, version 3.12e; DNASTAR, Madison, Wis.). The specific
nucleotides of the M. tuberculosis or NTM strains
were located at the 3'-hydroxyl end of each primer, as
previously reported (12).
The developed Tbc1 (5'-CGT ACG GTC GGC GAG CTG ATC
CAA-3')-TbcR5 (5'-C CAC CAG TCG
GCG CTT GTG GGT CAA-3') and M5
(5'-G GAG CGG ATG ACC ACC CAG GAC
GTC-3')-RM3 (5'-CAG CGG
GTT GTT CTG GTC CAT GAA C-3') primer sets amplify a
235-bp DNA sequence from the M. tuberculosis complex
and a 136-bp DNA sequence from NTM, respectively (Fig.
1A). Primers (10 pmol of Tbc1-TbR5 and 20 pmol of M5-RM3) and 5 µl
of bacterial DNA were added to a PCR mixture tube (AccuPower PCR
PreMix; Bioneer, Daejeon, Korea) containing 2 U of Taq
polymerase, 250 µM each deoxynucleoside triphosphate, 10 mM
Tris-HCl (pH 8.3), and 1.5 mM MgCl2, and water was added to
a final volume of 20 µl per reaction mixture. PCR was performed
with an initial denaturation of 95°C for 5 min, 30 cycles of
amplification (30 s at 95°C, 60 s at 72°C),
and a final elongation at 72°C for 5 min (model 9600
thermocycler; Perkin-Elmer Cetus). Denaturation was extended to 15 min
for the clinical isolates. Escherichia coli DNA was
used as a negative control. The PCR products were analyzed by agarose
gel (1.5%) electrophoresis.
After completion of the DPCR
assay, all 186 NTM isolates showing
a 136-bp DNA amplicon were further
analyzed by restriction fragment
length polymorphism (RFLP) and by
direct sequencing for species
identification. On the basis of the
rpoB sequences of mycobacteria
(GenBank accession no.
AF057449
to
AF057493),
two restriction
enzymes,
MspI and
HaeIII
were selected by using MapDraw (version
3.14; DNASTAR). Two
enzymes,
MspI (TaKaRa, Shiga, Japan) and
HaeIII
(TaKaRa) were independently applied to the PCR
products. Ten
microliters of the PCR products, 2 U of each enzyme, and
restriction
buffer were transferred to a fresh microcentrifuge tube,
and
water was added to a final volume of 20 µl per reaction
mixture.
Digestion was performed for 2 h at 37°C.
Following digestion,
the mixtures were electrophoresed in a 3%
agarose gel.
NTM isolates were separately identified by
determining 87-bp amplicon sequences, which excluded the primer
sequences, and by comparing these with sequences in the GenBank
database. Sequencing reactions with primers M5 and RM3 were performed
as previously described
(13). Analysis of the
partial 16S rDNA sequence was performed separately to identify the NTM
strains, and the results were compared with the results of the
rpoB sequence analysis. Briefly, 16S rDNA fragments were
amplified by using forward primer 285 and reverse primer 264 and then
directly sequenced by using sequencing primer 244, as previously
described (14).
The
specificity of each primer set was assessed by a separate PCR. When a
PCR using each specific primer set (Tbc1-TbcR5 or M5-RM3) was applied
to the 44 reference strains at the same annealing temperature, an
amplicon of either 235 or 136 bp of DNA was observed from the
M. tuberculosis complex or NTM, respectively. When
this method was applied to 17 non-mycobacteria, only 10 strains of
Tuskamurella, Rhodococcus, and Nocardia
species, which are phylogenetically close to mycobacteria, produced a
136-bp DNA amplicon (Table
1). Finally, a DPCR assay
with a mixture of the two primer sets was performed on the reference
strains. While the 235-bp DNAs were amplified from only four strains of
M. tuberculosis complex, the 136-bp DNAs were
amplified from all of the 40 NTM strains (Fig.
2). Nothing was amplified from the negative control, E.
coli DNA. Therefore, DPCR assay allowed the differential
identification of M. tuberculosis complex and NTM in
a single reaction. Despite the mismatching of several nucleotides with
those of the M5 or RM3 primer in the rpoB sequences of NTM
(Fig. 1B), all of the NTM
strains tested produced 136-bp amplicons.
In order to determine
the lower limit of the sensitivity of
the DPCR method,
rpoB
DNAs were amplified from the serially
diluted DNAs (10 ng to 10 fg) of
M. tuberculosis and
M. avium.
The
amplification product was obtained from 10 pg of
M.
tuberculosis DNA, whereas in the case of
M.
avium DNA, as little as 1 pg
was detected on an ethidium
bromide-stained gel (data not shown).
Taking 5 fg of DNA as a
mycobacterial cell equivalent
(
5), this
method could
detect 2,000 bacillus equivalents.
The usefulness of the DPCR
assay was demonstrated by applying the technique to the identification
of 379 clinical isolates. Of the 379 culture isolates examined, 193
strains were identified as M. tuberculosis complex
and the other 186 strains were identified as NTM (Table
1). These results were
completely concordant with those obtained by conventional culture
testing (Table
2). Although primer TbcR5 is located in the
rifr region
(20) (Fig.
1A), in which mutations
are related to the rifampin resistance of M.
tuberculosis, all of the 40 rifampin-resistant M.
tuberculosis isolates produced 235-bp amplicons without PCR
interference.
View this table:
[in this window]
[in a new window]
|
TABLE 2. Differentiation
of M. tuberculosis complex and NTM clinical isolates by DPCR
and conventional biochemical testing
|
Since DPCR produces only one (136-bp)
rpoB
DNA from NTM, restriction
analysis and sequencing could be used for
further species identification.
An algorithm for species identification
by DPCR-linked restriction
analysis with
MspI and
HaeIII was developed (Fig.
3). All of
the 186 NTM isolates analyzed in this study were tentatively
identified
in accordance with this scheme. However, NTM isolates,
except
M. abscessus and
M.
chelonae, which have identical sequences
in the 87-bp
rpoB region, could be exactly identified by comparing
their
determined
rpoB sequences to those of reference strains.
These
results are concordant with those obtained by 16S rDNA analysis
and
culture-based biochemical testing.
In the present study, we
developed a novel DPCR assay based
on
rpoB sequences. Unlike
previous methods, two differently
sized DNAs were amplified from a
single target gene of
M. tuberculosis and NTM. The
advantages of this DPCR assay over other multiplex
PCRs are as follows.
(i)
rpoB nucleotides specific for
M.
tuberculosis complex or NTM are invariably constant.
Therefore, false-positive
or -negative results due to sequence
variations do not occur.
(ii) DPCR yields only one product,
irrespective of the
Mycobacterium species tested. Even the
coexistence of
M. tuberculosis and
NTM can be
detected by the presence of two different PCR products
in a single
reaction mixture. (iii) Moreover, the (136-bp)
rpoB DNAs of
NTM can be further analyzed by RFLP or by direct sequencing
to
supplement species identification.
In conclusion, the DPCR assay
based on rpoB provides a rapid and reliable means for the
differential identification of M. tuberculosis and
NTM in culture with a single reaction.

ACKNOWLEDGMENTS
B.-J. Kim and S.-K. Hong contributed equally to
this work.
This study was supported by a grant from the Korean
Health 21 R&D Project, Ministry of Health & Welfare, Republic
of Korea (01-PJ10-PG6-01GM03-0002), and in part by the BK21 project for
Medicine, Dentistry, and
Pharmacy.

FOOTNOTES
* Corresponding
author. Mailing address: Department of Microbiology, Seoul National
University College of Medicine, 28 Yongon-Dong, Chongno-Gu, Seoul
110-799, Korea. Phone: 82-2-740-8306. Fax: 82-2-743-0881. E-mail:
yhkook{at}plaza.snu.ac.kr.

Present
address: Department of Microbiology, College of Medicine, The Catholic
University of Korea, Seoul 137-701, Korea. 

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Journal of Clinical Microbiology, March 2004, p. 1308-1312, Vol. 42, No. 3
0095-1137/04/$08.00+0 DOI: 10.1128/JCM.42.3.1308-1312.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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