IS6110 restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, South India

Das, Sulochana D.; Paramasivan, C. N.; Lowrie, Douglas B.; Prabhakar, R; Narayanan, P R

doi:10.1016/0962-8479(95)90533-2

Cited by 173 publications

(122 citation statements)

References 19 publications

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“…There have also been studies from this region describing the prevalence of low copy IS6110 strains in the past (Das et al 1995) In spite of the presence of all the 9 clades in this region the only lineage which has been predominating in this region is the EAI clade. Recently there have been reports on the notion that M. tuberculosis has adapted to human population.…”

Section: Discussionmentioning

confidence: 99%

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

Narayanan

Gagneux

Hari

et al. 2008

Infection, Genetics and Evolution

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Mycobacterium tuberculosis is a very important global pathogen. One quarter of the world's TB cases occur in India. The tuberculosis strains isolated from south Indian patients exhibit certain phenotypic characteristics like low virulence in guinea-pigs, resistance to isoniazid, thiophene-2-carboxylic acid hydrazide (TCH) and para-amino salicylic acid (PAS) enhanced susceptibility to H 2 O 2 . Besides this, a large percentage of the isolates harbor only a single copy of IS 6110 which makes these strains distinct. Hence we have studied the genotypic characteristics of these strains by using advanced techniques like Deletion Micro array, deletion PCR, allelic discrimination RT-PCR using several lineage specific markers and KatG G13887 (non synonymous) polymorphism along with spoligotyping. The analysis of 1,215 tuberculosis patient isolates from South India revealed that 85.2% belonged to the ancestral lineage of Mycobacterium tuberculosis.Comparative whole-genome hybridization identified six new genomic regions within this lineage that were variably deleted.

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Section: Discussionmentioning

confidence: 99%

Genomic interrogation of ancestral Mycobacterium tuberculosis from south India

Narayanan

Gagneux

Hari

et al. 2008

Infection, Genetics and Evolution

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“…IS6110 low-copy-number strains, though not all belonging to the EAI family, are also prevalent in South India (9) and in other countries of Southeast Asia (8,19,32 (4). Fully consistent with this, we found that all of the isolates assigned to the EAI family by MIRU-VNTR analysis (group I) were positive for the TbD1 region and that all of the remaining isolates, including those assigned to known modern M. tuberculosis genotype families (group II), were negative for the TbD1 region.…”

Section: Discussionmentioning

confidence: 99%

Use of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing To Examine Genetic Diversity ofMycobacterium tuberculosisin Singapore

et al. 2004

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Strain typing using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) is a powerful tool for studying the epidemiology and genetic relationships of Mycobacterium tuberculosis isolates. For this study, isolates from 291 patients in Singapore were genotyped by this method. One hundred sixty-six distinct MIRU-VNTR patterns were detected. One hundred sixty-two strains were grouped into 1 of 35 different MIRU-VNTR clusters and 131 isolates were unique. In this sample collection, 9 of the 12 MIRU-VNTR loci were moderately or highly discriminative according to their allelic diversities. The HunterGaston discriminatory index was 0.975, indicating the high power of discrimination of MIRU-VNTR typing. By direct comparisons with previously typed MIRU-VNTR patterns and by genetic relationship analyses, we could identify and clearly define four epidemic groups of M. tuberculosis in our sample, corresponding to the W/Beijing, East-Africa-Indian, Haarlem, and Delhi genotype families. Furthermore, MIRU-VNTR typing was able to clearly distinguish ancestral and modern M. tuberculosis strains as defined by TbD1 genomic deletion analysis. These results indicate that MIRU-VNTR typing can be a useful first-line tool for studying the genetic diversity of M. tuberculosis isolates in a large urban setting such as Singapore.Tuberculosis remains a major infectious disease and causes high morbidity and mortality worldwide. Mycobacterium tuberculosis genotyping is a useful tool for the epidemiological surveillance and control of disease transmission. Although a large number of DNA-fingerprinting methods for typing M. tuberculosis isolates have been developed (15), only IS6110 restriction fragment length polymorphism (RFLP) typing (5) and spacer oligonucleotide typing (spoligotyping) (14) have gained wide acceptance.IS6110 typing is the most commonly used strain-typing method for M. tuberculosis. This method is based on variations among IS6110 insertion elements between strains. IS6110 typing has been shown to be reproducible and highly discriminatory (15). However, there are several drawbacks of IS6110 typing. Firstly, it has poor discriminatory power for M. tuberculosis strains with low copy numbers of IS6110 (7,15,17). Secondly, it requires relatively large quantities of purified DNA. Thirdly, it is time-consuming to perform and analyze. Finally, although a standardized methodology has been recommended (29), it is difficult to compare IS6110 RFLP results between laboratories. This hinders global studies of M. tuberculosis epidemiology and transmission. Spoligotyping is a PCRbased method which detects the presence or absence of 43 spacers in the direct repeat locus of the M. tuberculosis genome. This has advantages over IS6110 typing in that it is faster and easier to perform, it is reproducible, and it requires only small quantities of DNA. However, the major drawback of spoligotyping is that it has a lower discriminatory power than IS6110 typing. In particular, this method is not informative in are...

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“…Note that number of copies > 9 is shown by a letter (10 = A, 11 = B, 12 = C etc. significant number of M. tuberculosis isolates with low copy numbers (15, 67%) or zero copies (1, 24%) of IS6110 bands (Das et al 1995, Mathuria et al 2008, Narayanan et al 2008, Radhakrishnan et al 2001). We did not find any zero-copy strains in the present study.…”

Section: Discussionmentioning

confidence: 99%

“…IS6110 restriction fragment length polymorphism (RFLP)-based fingerprinting has been used to study the mycobacterial population structure in Southern India, Northern India and the Delhi region (Das et al 1995, Radhakrishnan et al 2001, Siddiqi et al 2001, Bhanu et al 2002. However, IS6110 fingerprinting is of limited use because a significant proportion (40-44%) of M. tuberculosis isolates from several regions of India have been reported to either lack or have low copy numbers of IS6110 (Das et al 1995, Radhakrishnan et al 2001, Narayanan et al 2002, Chauhan et al 2004, Mathuria et al 2008. Furthermore, IS6110 typing is labour intensive and requires several weeks for culturing the M. tuberculosis isolates.…”

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confidence: 99%