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ARTÍCULO ORIGINAL
Characterization of rpoB gene mutations in rifampicin
resistant Mycobacterium tuberculosis strains isolated
from pulmonary tuberculosis patients at
5 Mexican public hospitals
Cosme Alvarado-Esquivel,*,** Rudi Rossau,*** Sergio Martínez-García,** Jorge Arturo Cisneros-Martínez,****
Wouters Mijs,*** Adán Nevárez-Nájera,***** Roberto Fierro-Campa,******
Miguel Francisco Mercado-Suárez,******* Simón Hernández-Campos,***** Rosibeth Chacón-Arciniega,*
Justino Vázquez,******** Guillermina Saucedo-Martínez,**** Rosario Ruiz-Astorga*
* Departamento de Inmunología y Biología Molecular, Instituto de Investigación Científica, UJED, Durango, México.
** Departamento de Microbiología, Facultad de Medicina, UJED. *** Innogenetics NV, Zwijnaarde, Bélgica.
**** Hospital General “Santiago Ramón y Cajal”, ISSSTE, Durango, México. ***** Hospital General, Secretaría de Salud. Durango, México.
****** Centro de Salud 1, Secretaría de Salud. Durango, México. ******* Hospital “Dr. Ignacio Téllez” IMSS, Durango, México.
******** Hospital General del Centro Médico Nacional “La Raza” IMSS, México, D. F.
ABSTRACT
Objective. To characterize the rpoB gene mutations of the
rifampicin- resistant M. tuberculosis strains isolated in pulmonary tuberculosis patients from Mexico. Material and methods. Thirty-seven clinical M. tuberculosis isolates cultured on
Löwenstein-Jensen media and obtained from consecutive tuberculosis patients in 5 public hospitals were analyzed by PCR and
the INNO-LiPA Rif TB for amplification and detection of mutations associated with rifampicin resistance, respectively. Results. Twenty-three out of the 37 isolates (62.2%) were found to
be wild type (rifampicin susceptible), while 14 isolates (37.8%)
contained mutations associated with rifampicin resistance. Seven out of the 37 isolates (18.9%) had a ∆S1 mutation, in the nucleotide position number 511; one (2.7%) had a R4b mutation, in
nucleotide H526D; five (13.5%) contained a R5 mutation, in nucleotide S531L; and one (2.7%) showed a double mutation ∆S1/
R4b. Conclusion. According to the marker used (rifampicin resistance), at least five different strains of M. tuberculosis circulate among pulmonary tuberculosis patients in Mexico. rpoB
gene mutations associated with rifampicin resistance are common in Mexico. A single mutation in nucleotide 511 was the most
frequently observed, followed by single mutations in nucleotides
S531L and H526D.
Caracterización de las mutaciones del gen rpoB en cepas
Mycobacterium tuberculosis resistente a rifampicina
aislada de pacientes con tuberculosis pulmonar de
cinco hospitales públicos mexicanos.
RESUMEN
Objetivo. Caracterizar las mutaciones del gen rpoB de las cepas
de M. tuberculosis resistentes a rifampicina aisladas en pacientes
con tuberculosis pulmonar de México. Material y métodos. Se
analizaron 37 cepas de M. tuberculosis cultivadas en el medio de
Löwenstein-Jensen y aisladas de pacientes tuberculosos consecutivos de cinco hospitales públicos. Las cepas fueron analizadas
mediante PCR e INNO LiPA Rif TB para amplificación y detección de mutantes asociadas con resistencia a rifampicina, respectivamente. Resultados. Veintitrés de las 37 cepas (62.2%) resultaron ser de tipo salvaje (sensibles a rifampicina), y 14 cepas
(37.8%) contenían mutaciones asociadas con resistencia a rifampicina. Siete de las 37 cepas (18.9%) tenían una mutación ∆S1, en
la posición del nucleótido número 511; una (2.7%) tenía una mutación R4b, en el nucleótido H526D; cinco contenían una mutación R5, en el nucleótido S531L; y una (2.7%) mostró una doble
mutación ∆S1/R4b. Conclusión. De acuerdo con el marcador
usado (resistencia a rifampicina), por lo menos cinco cepas diferentes de M. tuberculosis circulan entre los pacientes con tuberculosis pulmonar en México. Las mutaciones del gen rpoB asociadas con resistencia a rifampicina son comunes en México. Una
526
Alvarado-Esquivel
al.The6rpoB
gene mutations in rifampicin
Mycobacterium tuberculosis. Rev Invest Clin 2001; 53 (6): 526-530
La
Revista de Investigación
Clínica / Vol.C,
53,etNúm.
/ Noviembre-Diciembre,
2001 resistant
/ pp 526-530
Versión completa de este artículo disponible en internet: www.imbiomed.com.mx
mutación única en el nucleótido 511 fue la más frecuentemente
observada, seguida por mutaciones únicas en los nucleótidos
S531L y H526D.
Key words. Rifampicin. Resistance. Mutations. Mexico.
INTRODUCTION
Worldwide reports indicate that tuberculosis cases
are increasing in spite of considerable control efforts.1,2 The emergence of Mycobacterium tuberculosis
mutants resistant to one or more anti-tuberculosis
drugs has even exacerbated this public health problem.3-5 Resistance to rifampicin (RMP), one of the
major anti-tuberculosis drugs, is frequently associated to resistance to other anti-tuberculosis drugs.6,7
RMP resistance of M. tuberculosis has been associated with mutations in the gene encoding the β-subunit of the RNA polymerase (rpoB).8 These mutations
can be identified by several molecular biology methods such as the polymerase chain reaction (PCR)
and the line probe assay (LiPA),9-11 restriction fragment length polymorphism,12,13 and sequencing.6,14
Molecular analysis of M. tuberculosis from culture or
clinical specimens has offered new opportunities for
the rapid identification of RMP-resistant mutants,
improving the diagnosis, and optimizing the treatment of tuberculosis patients.6-11 The frequency of infections by M. tuberculosis resistant to RMP and the
types of mutations associated with such a resistance
vary widely around the world.7,15-17 Nevertheless, there is little information concerning the molecular epidemiology of RMP-resistant M. tuberculosis infections in Mexico in general, and a lack of reports from
Durango state in particular. This study was designed
to characterize the rpoB gene mutations associated
with RMP resistance in M. tuberculosis strains obtained from pulmonary tuberculosis patients attending
5 public Mexican hospitals.
MATERIAL AND METHODS
Mycobacterium isolates. Thirty-seven M. tuberculosis isolates cultured on Löwenstein-Jensen media
and identified by biochemical tests were analyzed.
The samples were obtained from a similar number of
consecutive tuberculosis patients attending 5 public
hospitals of Mexico: 21 samples were collected from 4
hospitals in Durango City, and 16 samples from 1
hospital in Mexico City. The 37 isolates were cultured
from the following specimens: 31 sputa, 4 broncho-alveolar lavages, and 2 pleural fluids. The smears of all
specimens were positive for acid fast bacilli. Twenty-
Palabras clave. Rifampicina. Resistencia. Mutaciones. México.
two out of the 37 tuberculosis patients (59.5%) had
previously received anti-tuberculosis treatment,
whilst the remaining 15 patients had been recently
diagnosed and untreated for tuberculosis. The geographical distribution of the treated and untreated patients studied was as follows: of the 16 patients from
Mexico city, 11 were treated and 5 were untreated;
while of the 21 patients from Durango city, 11 were
treated and 10 were untreated. Only one out of the 37
patients was HIV-positive.
Sample preparation and PCR. From each positive Löwenstein-Jensen culture, a 10-µL loopful of
bacteria was obtained and suspended in 500 µl saline
solution, inactivated at 95 °C for 15 minutes, and frozen at -20 °C until analyzed. Amplification of the M.
tuberculosis rpoB gene was performed by using the
Rif. TB amplification assay (Innogenetics N.V., Zwijnaarde, Belgium) as described elsewhere.11 Briefly, 5
µL of the bacterial suspension was added to a 45-µL
master mixture containing biotinylated rpoB primers.
The amplification was performed in a GeneAmp PCR
System 9600 thermal cycler (Perkin-Elmer) under
the following conditions: initial denaturation at 95 °C
for 5 min and 30 cycles of 95 °C for 1 min, 62 °C for 1
min and 72 °C for 1 min, and terminal elongation at
72 °C for 10 min. PCR products were separated on
2.5% agarose gels, stained with ethidium bromide,
and visualized by UV illumination.
Line probe assay (LiPA). M. tuberculosis mutations associated with RMP resistance were detected by
INNO-LiPA Rif. TB (Innogenetics N.V.) as previously
described.11 Briefly, 10 µL of biotin-labeled PCR products were hybridized with M. tuberculosis complex
(TB), wild-type (∆S1-∆S5), and specific rpoB mutation
probes (R2, R4a, R4b, R5) immobilized as parallel lines
on nitrocellulose paper strips. After hybridization, a
stringent washing was performed, and streptavidine
labeled with alkaline phosphatase was added. Strips
were then washed and incubated with BCIP/NBT
substrate. The reaction was stopped by adding distilled
water. A pattern of purple brown lines, as a result of
hybridization, was configured on the strips.
RESULTS
All 37 isolates analyzed yielded positive PCR results and hybridized with the M. tuberculosis com-
Alvarado-Esquivel C, et al.The rpoB gene mutations in rifampicin resistant Mycobacterium tuberculosis. Rev Invest Clin 2001; 53 (6): 526-530
527
Table 1. M. tuberculosis strains found in Mexican pulmonary tuberculosis patients.
LiPA profile
Treated patients
No. (%)
Untreated patients
No. (%)
All patients
No. (%)
12 (54.5)
4 (18.2)
1 (4.5)
4 (10.8)
1 (18.2)
22
11 (73.3)
3 (20.0)
23 (62.2)
7 (18.9)
1 (2.7)
5 (13.5)
1 (2.7)
37
wt
∆S1 (np 511)*
R4b (np 526)*
R5 (np 531)*
∆S1/R4b*
Total
wt = wild type; np = nucleotide position.
wt
∆S1 (np 511)*
R4b (np 526)*
R5 (np 531)*
∆S1/R4b
Total
Durango city
No. (%)
Mexico city
No. (%)
13 (61.9)
4 (19.0)
1 (4.8)
3 (14.3)
10 (62.5)
3 (18.8)
21 (100)
2 (12.5)
1 (6.2)
16 (100)
wt = wild type; np = nucleotide position.
* = mutations associated with rifampicin resistance.
plex probe on the LiPA strips confirming that all
isolates were indeed M. tuberculosis strains. Fourteen of the 37 isolates (37.8%) yielded RMP resistance mutation patterns, i.e., failed to hybridize to at
least one of the wild-type probes and/or hybridized
with specific rpoB mutation probes. The remaining
23 isolates (62.2%) hybridized only with wild-type
probes indicating their RMP susceptibility. Ten
(45.5%) out of the 22 previously treated patients
were infected by RMP-resistant strains of M. tuberculosis, while 4 (26.7%) of the 15 untreated patients
were infected by RMP-resistant strains. Table 1
summarizes the LiPA results and the distribution of
M. tuberculosis strains in treated and untreated tuberculosis patients. The geographical distribution of
M. tuberculosis strains in Durango and Mexico City
is shown in table 2. Both PCR and LiPA were performed following a quality control procedure, and no
contamination was observed.
DISCUSSION
In the present exploratory study, an alarmingly
high prevalence of 37.8% of RMP-resistant M. tuberculosis infection was found in Mexican tuberculosis
528
15
* = mutations associated with rifampicin resistance.
Table 2. Geographical distribution of the M. tuberculosis strains analyzed.
LiPA profile
1 (6.7)
patients. This prevalence rate is higher than that reported in the U.S., Europe, and in African countries,16,18-22 far higher than the mean worldwide prevalence,17 but just lower than that reported in the
countries of the former Soviet Union.6,23 In our study, 45.5% of the patients previously treated for tuberculosis and 26.7% of untreated patients were infected by RMP-resistant M. tuberculosis strains.
These frequencies are also higher than the mean
worldwide frequencies observed in treated and untreated tuberculosis patients, respectively.17,19,22,24
In a study performed in Mexico city in 1995,25 Sifuentes et al found prevalences of RMP resistance of
19% in treated patients and 6% in untreated patients.
Thirteen out of the 14 isolates with rpoB mutations contained single mutations; in only one case was
a double mutation ∆S1/R4b observed. In total, three
different mutations - either single or in combination
- were observed among our Mexican isolates: the ∆S1
mutation (nucleotide position number 511) was present in 8 out of 14 RMP-resistant isolates (57.1%),
the R5 mutation (nucleotide position number 531) in
5 (35.7%), and the R4b mutation (nucleotide position
number 526) in 2 isolates (14.3%). The ∆S1 mutation
frequency found in Mexican RMP-resistant isolates
is considerably higher than that reported in Asian
countries, Greece, and the U.S.15, 18, 26 The R5 mutation frequency was found to be similar to the one reported in the U.S.18 and slightly lower than that reported in Asian countries, Greece, and Rwanda.10, 15,
26 Concerning the R4b mutation, our frequency was
similar to that reported in Asian countries,15, 26 but
slightly higher than that observed in the U.S.18 On
the other hand, in the present study there were not
cases of the R2, R4a, ∆S4, ∆S5 mutations which are
generally found in Asian, European, and African
countries as well as in the U.S.10,11,18 With respect to
the geographical distribution of M. tuberc ulosis
strains in the two Mexican cities explored, we obser-
Alvarado-Esquivel C, et al.The rpoB gene mutations in rifampicin resistant Mycobacterium tuberculosis. Rev Invest Clin 2001; 53 (6): 526-530
ved approximately the same distribution of strains
in the northern city of Durango than in the central
city of Mexico, suggesting that M. tuberculosis strains may circulate to similar extents in northern and
central Mexico. In addition, results indicate that at
least 5 different strains of M. tuberculosis circulate
in Mexico.
We were able to identified all 37 M. tuberculosis
isolates by the LiPA. The INNO-LiPA Rif. TB has
been widely tested and been shown to be a highly
sensitive method for detection of RMP-resistant mutants.11,18,27 It is easy to perform and the equipment
needed is more likely to be available in laboratories
of developing countries, where tuberculosis is a major public health problem, than that needed for other
molecular methods such as sequencing. In this study, no traditional bacteriological methods for drug
susceptibility were used. It is well know that the
great majority of RMP-resistant strains are successfully identified by current molecular methods.
Approximately 95% of RMP-resistant isolates have a
mutation in the 69-bp region corresponding to codons 511 to 533 of the rpoB gene.28 Current molecular
methods to identify RMP resistance rely on detection of mutations in this region. The remaining 5%
of resistant isolates may have additional mutations
at codons 381,29 481,30 505, 508,26 and 509.30 Therefore, the frequency of RMP resistance found in the
present study may be slightly higher if any RMP-resistant strain with a mutation beyond the 511 to 533
region was present. Nevertheless, even traditional
bacteriological methods may also fail to detect RMP
resistance.28
It is estimated that 90% of RMP-resistant isolates
are also resistant to isoniazid.28 Therefore, identification of RMP resistance serves as a useful surrogate marker for the detection of multidrug resistance.
In addition, RMP resistance means that a short
course therapy is useless and that second- and thirdline antituberculosis drugs must be tested for susceptibility for alternative therapy.31 In a study preformed in the southern Mexican State of Chiapas, a
66.7% of resistance to RMP and isoniazid together
was found.32 While in a study performed in 3 Mexican states in 1997,33 Granich et al found a prevalence of resistance to one or more drugs of 12.9% and
50.5%, respectively.
Since resistance to anti-tuberculosis drugs is believed to result from inadequate treatment, i.e., irregular drug intake, insufficient time, and poor compliance, results of the present study indicate sub-optimal
performance of current Mexican anti- tuberculosis
therapy programs, and suggest that stronger efforts
are urgently needed to provide efficient treatment in
Mexico. Indeed, infections by M. tuberculosis strains
resistant to anti-tuberculosis drugs have increased
lately in Mexico when compared to previously reported frequencies.25,33,34 We conclude that RMP-resistant M. tuberculosis infections are common in Mexico, and RMP-resistant M. tuberculosis strains circulating in Mexico are mainly those containing single ∆S1
(511), R5 (531) or R4b (526) mutations.
ACKNOWLEDGEMENTS
This study was supported by Innogenetics NV,
Zwijnaarde, Belgium; and Sistema de Investigación
“Francisco Villa”, CONACYT. We thank Fred Shapiro for critical reading of the text.
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Correspondence and reprint requests:
Dr. Cosme Alvarado Esquivel.
Departamento de Inmunología y Biología Molecular.
Instituto de Investigación Científica.
Av. Universidad y Fanny Anitua.
34000 Durango, Dgo. México.
Tel: (18) 12 29 21. Fax: (18) 11 62 26.
E-mail: [email protected]
[email protected]
Recibido el 30 de octubre de 2000.
Aceptado el 14 de agosto de 2001.
Alvarado-Esquivel C, et al.The rpoB gene mutations in rifampicin resistant Mycobacterium tuberculosis. Rev Invest Clin 2001; 53 (6): 526-530