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J Clin Microbiol. 2006 May; 44(5): 1763–1768.
PMCID: PMC1479214

Spoligotyping of Mycobacterium tuberculosis Isolates from Pakistan Reveals Predominance of Central Asian Strain 1 and Beijing Isolates


The estimated incidence of tuberculosis in Pakistan is 181 per 100,000; however, there is limited information on Mycobacterium tuberculosis genotypes circulating in the country. We studied 314 M. tuberculosis clinical isolates; of these, 197 (63%) isolates grouped into 22 different clusters, while 119 (37%) had unique spoligotypes. Eighty-nine percent of the isolates were pulmonary (Pul), and 11% were extrapulmonary (E-Pul). We identified Central Asian Strain (CAS), Beijing, T1, Latin American-Mediterranean, and East African-Indian genogroups. Beijing strains, reportedly the most prevalent spoligotype worldwide, constituted 6% of our strain population. The CAS1 strain comprised 121 (39%) of the study isolates. No difference was observed between clustered isolates from cases of Pul and E-Pul tuberculosis. However, E-Pul isolates included a greater number of unique spoligotypes than Pul isolates (P = 0.005). The overall percentage of drug resistance was 54%, and that of MDR strains was 40%. While CAS1 strains were not associated with drug resistance, the relative risk of MDR was significant in Beijing strains compared to the non-Beijing groups (95% confidence interval, 1.2 to 8.9). The fact that the predominant strain, CAS1, is not associated with drug resistance is encouraging and suggests that an effective tuberculosis control program should be able to limit the high incidence of disease in this region.

Globally, Pakistan ranks sixth in terms of tuberculosis (TB) burden, with a World Health Organization-estimated incidence rate of 181 cases per 100,000 persons or 272,000 new cases annually (32). Pakistan shares geographical borders with four countries where TB is endemic, i.e., Afghanistan, Iran, China, and India. In addition, it is closely associated with other South Asian countries where TB is highly endemic, i.e., Bangladesh, Sri Lanka, and Nepal. Despite the high TB burden in the South Asian region, there are currently very limited data available pertaining to strains circulating in the country. Both treatment and detection of TB are significant problems; it is estimated that 4/5 TB cases in Pakistan remain untreated (7). The situation is further confounded by a lack of availability of genotypic epidemiological tools that would allow contact tracing and identification of transmission patterns within the country.

The most commonly used methods of genotyping employ the IS6110 element to fingerprint strains (24). In addition, spacer oligotyping (spoligotyping) based on the variation of spacers (36 to 41 bp) in the direct-repeat region of the Mycobacterium tuberculosis chromosome has been used with great efficiency to define predominant clades worldwide (18). Although less discriminatory than IS6110 typing, spoligotyping is a rapid, quick, and robust method of genotyping M. tuberculosis and is particularly useful in the study of South Asian M. tuberculosis strains, which commonly have few copies of IS6110 elements (8, 14). Recently, data from international spoligotyping studies have identified a growing number of important clades or genogroups (11, 28).

Beijing strains are an aggressively expanding clone that has been identified in a number of populations across the world (13). This family is characterized by a highly similar multibanded IS6110 pattern and a common spoligotype pattern with the absence of spacers 1 to 34 and the presence of only the last nine spacers (30). It includes the M. tuberculosis W strain associated with multidrug resistance (MDR) in New York (1, 5, 15). The Beijing family is reportedly the most prevalent spoligotype worldwide and constitutes 90 to 92% of the M. tuberculosis strains in China (25, 30). High rates of infection with Beijing strains in the countries neighboring China suggest that this particular strain may have radiated from Beijing to other regions. The prevalence of Beijing strains in Southeast Asia has been reported to be 30 to 100% in different studies. A lower prevalence is reported in South Asia and the Middle East, 8% in Delhi (27), 10% from one region of Iran (10), and 31% in a study in Dhaka (3).

A second predominant cluster in the South Asian region is the Central Asian strain 1 type (CAS1) or Delhi type genogroup, which is characterized by the absence of spacers 4 to 7 and 23 to 34 (4). The presence of CAS1 strains in his region is supported by recent studies of M. tuberculosis isolates from India (27) and Bangladesh (3).

To date, there is very limited genotypic information on M. tuberculosis strains circulating in Pakistan. The World Spoligotyping Database SpolDB3.0 describes an update on the global distribution of M. tuberculosis complex spoligotypes but shows little information about Pakistan (11). In this study, we have typed M. tuberculosis isolates from specimens received at the clinical laboratory of The Aga Khan University Hospital, Karachi, Pakistan, in 2003 and 2004 in order to detect the presence of Beijing strains within the country. We have also investigated the association between predominant spoligotypes and drug resistance among our isolates.


This study was conducted with M. tuberculosis strains isolated at the clinical laboratory of The Aga Khan University Hospital between January 2003 and June 2004. During this period, 2,890 samples from suspected TB cases were cultured and 666 M. tuberculosis strains were isolated. Only one isolate was included per patient. Samples included in this study were from patients presenting to our laboratory units across the country; therefore, treatment history was not available. Representative samples from different geographical locations across the country were selected by using the stratified random sampling method. Fifty percent of the strains from each location were selected for inclusion in the study; a total of 314 strains (only one isolate per patient) were included. Of these, the largest proportion (135 strains [43%]) was from 14 different locations across Karachi. A further 179 strains were from the four different provinces of the country, i.e., 89 from the Punjab Province, 58 from the Sindh Province (excluding Karachi), 30 from Northwest Frontier Province, and 3 from the Balouchistan Province.

Two hundred eighty-four isolates were from pulmonary sites, i.e., sputum (n = 269), pleural exudate (n = 6), and bronchoalveolar lavage fluid (n = 9), while 30 isolates were from extrapulmonary sites.

Mycobacterial culture and antibiotic susceptibility.

Mycobacterial cultures were performed with both liquid and solid media. Respiratory samples were decontaminated by using N-acetyl-l-cysteine sodium hydroxide prior to culture. Samples from sterile sites were processed without decontamination (23). All specimens were concentrated by centrifugation (3,000 × g) for 30 min, and sediments were cultured at 37°C with BACTEC 460 (Becton Dickinson Diagnostic Instruments Systems) and Lowenstein-Jensen medium. The growth index of inoculated BACTEC vials was checked for 4 weeks; Lowenstein-Jensen slants were incubated for up to 8 weeks. M. tuberculosis was identified by the BACTEC NAP TB differentiation test (Becton Dickinson).

Susceptibility testing was performed by the standard agar proportion method with enriched Middlebrook 7H10 medium (BBL) at the following final drug concentrations: rifampin, 1 μg/ml and 5 μg/ml; isoniazid, 0.2 μg/ml and 1 μg/ml; streptomycin, 2 μg/ml and 10 μg/ml; ethambutol, 5 μg/ml and 10 μg/ml (17, 22, 31). Pyrazinamide sensitivity was tested with BACTEC 7H12 medium, pH 6.0, at 100 μg/ml (BACTEC PZA test medium; Becton Dickinson) in accordance with the manufacturer's instructions. To ensure the selection of strains with high-level resistance for this study, however, only resistance to the higher concentrations was used for analysis. MDR was defined in accordance with standard criteria of resistance to at least isoniazid and rifampin.

DNA methods.

Mycobacteria were cultured on Middlebrook 7H10 agar. DNA extraction from mycobacterial colonies was carried out by the cetyltrimethylammonium bromide method (16). Spoligotyping was carried out with a commercially available kit from Isogen Bioscience BV, Maarssen, The Netherlands, according to the manufacturer's instructions. Spoligotyping based on the 43 spacers of the direct-repeat region of the M. tuberculosis complex was carried out with primers DRa (5′GGTTTTGGGTCTGACGAC 3′) and DRb (5′CCGAGAGGGGACGGAAAC 3′) as originally described by Kamerbeek et al. (18).

Data analysis.

Spoligotyping results were analyzed with the Bionumerics software program (BioSystematica). Dendrograms were generated by the unweighted-pair group method using average linkages. A cluster was defined as two or more isolates from different patients with identical spoligotype patterns. We defined unique spoligotypes as those which did not cluster with any other sample in our study. The spoligotypes were compared with the 36 most prevalent M. tuberculosis subfamilies as identified by the World Spoligotyping Database SpolDB3.0 of the Pasteur Institute of Guadeloupe (www.cdc.gov/ncidod/EID/vol8no11/02-0125-Table.htm) (12). In addition, all clusters obtained were compared with the shared types (STs) present in SpolDB3.0 (http://www.pasteur-guadeloupe.fr/tb/spoldb3) (11). This database contains information on the prevalence of spoligotypes in different countries and their relative occurrence.

Pearson's chi-square test was used to determine statistical associations between strain types and specific parameters with SPSS software. Odds ratios were calculated with 95% confidence intervals. A P value of <0.05 was considered evidence of a significant difference.


Study population.

The demographic information for patients whose M. tuberculosis isolates were studied showed that the majority of 314 M. tuberculosis isolates were from patients in the 15- to 30-year age group, with 73.4% in the 15- to 45-year age group, compared with 24% in the >45-year age group. There were no differences in terms of gender distribution. The majority (n = 284) of isolates were from patients with pulmonary disease, of which 92% were smear positive. The 30 remaining isolates were from patients with extrapulmonary TB, of which 66.6% were smear positive.


All 314 isolates were spoligotyped and analyzed (Fig. (Fig.1).1). A total of 197 (63%) isolates were grouped into 22 different clusters, while 119 (37%) isolates had unique spoligotypes. Previously, 18 different STs had been identified as having geographic specificity to Pakistan as listed in SpolDB3.0 (11). We compared our 22 clusters with this list and found them to include six of the spoligotypes attributed to Pakistan in SpolDB3.0. These six spoligotypes included ST1 (Beijing strain), ST26 (CAS1), ST53 (T1), ST11 (East African Indian strain 3), ST25, and ST486 (11). Our isolates did not include ST27, ST37, ST48, ST50, ST52, ST172, ST236, ST281, ST381, ST428, ST520, and ST794, which have previous been identified by SpolDB3.0 as being present in Pakistan.

FIG. 1.
Dendrogram of Pakistani isolates (Pearson correlation). All isolates were spoligotyped, and data were analyzed with the Bionumerics software program. A dendrogram was calculated on the basis of the Jacquard index for pairwise analysis of strains by the ...

Six further clusters were also identified with homology to ST357, ST288 (CAS2), ST142, ST203, ST289, and ST127 (Table (Table1).1). Of these, only ST127 was identified as ubiquitous while the others had all previously been reported as rare or localized to regions of North America, Europe, and Australia, with the exception of ST288 (also in India and Iran) and ST357 (identified in Iran). Clusters Pak1 to -10 were unique and not homologous to STs within SpolDB3.0. We also compared our strains with the 36 most common STs in SpolDB3.0 (12) and found one isolate homologous with ST64 or Latin American-Mediterranean strain 6.

Spoligotypes shared by M. tuberculosis isolates evaluated in this study

Overall, 18 Beijing strains (ST1) were identified, making up 6% of the isolates studied. These strains were from different locations in Pakistan; 9 were from the city of Karachi, 6 were from the Punjab Province, and 3 were from the Northwest Frontier Province.

The most prevalent shared spoligotype in our population, however, was ST26 or CAS1, also known as the Delhi strain (27); 39% (n = 121) of the strains analyzed belonged to this spoligotype. In addition, differing levels of homology with CAS1 was also shown by other strains in the study population; 13 strains showed 96% homology, 24 strains showed 92% homology, and 31 strains showed 80% homology. The related CAS2 strain was also present. The CAS clade included a total of 174 isolates.

Analysis of agewise clustering of M. tuberculosis spoligotypes indicated that of the 228 isolates, 145 (64.4%) were clustered in the 15- to 45-year age group, compared with 45 (59%) out of a total of 76 isolates that clustered in the >45-year age group. The difference was not significant (odds ratio, 1.6; 95% confidence interval [95% CI], 0.953 to 2.716). Similarly, there was no association between patient age groups and the occurrence of the CAS1 or Beijing strain.

Pulmonary versus extrapulmonary isolates.

We analyzed the association between clustered and nonclustered (unique) spoligotypes and the source (pulmonary or extrapulmonary) of the M. tuberculosis isolates (Table (Table2).2). There was no statistically significant difference in the distribution of clustered spoligotypes (CAS1, Beijing, or others) between the pulmonary and extrapulmonary groups. However, 60% of the isolates from extrapulmonary sources were unique, compared with 43% of the pulmonary isolates. This difference was statistically significant (P = 0.005; 95% CI, 8.8 to 43.1).

Cluster distribution among pulmonary and extrapulmonary M. tuberculosis isolates

Drug resistance patterns.

Of the 314 strains included in this study, 45.9% were sensitive to all five of the first-line agents tested. Among the 170 drug-resistant isolates, 74% were MDR (Table (Table3).3). Analysis of the association of MDR with cluster type showed that the Beijing strains in this population were highly associated with MDR (P = 0.017 [Pearson's chi-square test]). The relative risk of MDR in the Beijing strains at 3.024 is significantly higher than in the non-Beijing groups (95% CI, 1.182 to 8.872). In addition, ST Pak6 (Table (Table1)1) was also classified as MDR.

Association of antimicrobial resistance with spoligotypes

The MDR rate in the predominant CAS1 cluster, on the other hand, was not significantly different from that in other circulating clustered and unique spoligotypes (P = 0.844 [Pearson's chi-square test]).


This report presents the largest amount of epidemiological data on M. tuberculosis isolates from Pakistan to date. Previously, the limited data available from this area were those based on the IS6110 restriction fragment length polymorphism genotyping method (21, 26) or were from studies of immigrant Pakistanis carried out in Europe (19). In this region where TB is endemic, it is critical to identify predominant strain types in order to study transmission patterns within the country and to understand the epidemiology of the disease in Pakistan. This is all the more important as Pakistan is host to a very large number of immigrant populations and migrant workers from neighboring countries where TB is endemic (Afghanistan and Bangladesh), and the movement of these populations would influence strain distribution in the entire region.

We found the CAS1 or type 26 strain (14) to be predominant (39%) among the 314 isolates tested, followed by Beijing isolates (6%). CAS1 has been also identified as a predominant strain in Delhi (27) and Mumbai, India (2). Furthermore, our results also compare well to data from Delhi, India, where 22% of 105 isolates were of the CAS1 strain and 8% were Beijing isolates (27). Another Delhi-based study showed that 75% of the strains belonged to the Delhi genogroup (4), while a study carried out in Dhaka, Bangladesh, identified Beijing strains as the most common type in that population (3). Geographically speaking, India provides us with the closest comparison. Additional clustered spoligotypes identified in Indian studies were ST18, ST23, ST31, ST21, ST13 (4), ST26, ST54, and ST1 (27). Of these, we identified ST26 (n = 121), ST1 (n = 18), and ST21 (n = 1) among our Pakistani isolates. The identification of a dominant spoligotype common to India and Bangladesh illustrates an important trend in the M. tuberculosis infection pattern in the South Asian region.

Recent transmission of TB is indicated by the increased incidence observed in the younger age group (15 to 45 years). However, we did not find any significant clustering between age groups and spoligotypes in our study. This is in contrast to other studies, which have indicated significant clustering in younger and also in older age groups (27). Our data further confirm that the predominant genogroups CAS and Beijing are well established in the region and are not a result of recent introduction.

We found CAS1 to be equally associated with drug sensitivity or drug resistance and did not find it to be associated with MDR TB (P = 0.844). This correlates with a report by Singh et al. (27) but does not correlate with a study of 65 isolates from Bombay, India, reporting an association of CAS1 with MDR (20). The difference may be attributed to the smaller sample size in the earlier study (20) and also to the fact the study in Bombay had only included strains from one hospital in an urban setting and was therefore likely to include a larger proportion of resistant strains.

As our study was based on referred patients presenting at a clinical laboratory, we were unable to determine any epidemiological associations between patients and strains. However, it was clear that the predominant clusters—CAS1 and Beijing—were present in locations dispersed throughout the country and were therefore not associated with a recent or epidemic strain.

We found that the extrapulmonary isolates were significantly associated with unique spoligotypes. There is little information as to the pathogen dynamics that result in dissemination to extrapulmonary sites in the host. A recent study by de Viedma et al. (9) suggests increased infectivity of strains which are found at extrapulmonary locations. Given that the predominant TB site is pulmonary and that extrapulmonary disease may be associated with more-virulent isolates, it is not surprising to observe less genetic variation in pulmonary compared to extrapulmonary isolates.

In our study population, we noted a higher relative risk of MDR among Beijing strains. Association between Beijing strains and MDR varies worldwide; whereas such an association is reported in studies in the United States, Estonia, and Vietnam (6), it has not been noted in countries such as China and Indonesia, where the representation of the Beijing strains in the population is greater (29). However, a recent study in Mumbai, India, also showed a high frequency of Beijing strains (35%) among the MDR isolates (2).

The diversity of global TB clinical isolates has been illustrated by the major spoligotype families and patterns identified by the World Spoligotyping Database at the Pasteur Institute, Guadeloupe. SpolDB3.0 shows that the 24 most prevalent isolates represent 53% of the strains present worldwide (11). We did not compare all of our strains against SpolDB3.0. However, we ran comparisons of all of the clusters identified in our study (Table (Table1)1) with SpolDB3.0 and also of the 36 most common spoligotypes identified by the database. By using this methodology, in addition to the CAS and Beijing strains, we identified the East African-Indian family, the T group, and the Latin American-Mediterranean family of M. tuberculosis in our population.

In addition to the predominant groups identified, we also were able to identify the occurrence of clusters of rare or localized STs listed in SpolDB3.0 that have previously been found in North America, Australia, and Europe in addition to those found in neighboring Iran and India. While more community-based data are required in order to understand transmission patterns and to monitor strain resistance, our study provides essential information about M. tuberculosis strains circulating in Pakistan. Strain analysis, together with virulence studies, will also help in pinpointing isolates associated with higher morbidity and mortality, with the aim of directing efforts to limit the spread of those strains within the region. In addition, knowledge of prevalent strains will help evaluate the efficacy of commonly used TB vaccines in the region.


This study was supported by a University Research Council grant; The Aga Khan University, Karachi, Pakistan; and a guest scholarship program award from the Swedish Institute, Stockholm, Sweden.

Thanks to Gunilla Kallenius and Ramona Petersson for guidance. Thanks also to Amin Kabani and Meenu Sharma of the National Reference Centre for Mycobacteriology, Winnipeg, Manitoba, Canada, for support in the initial phase of this study.


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