Genetic diversity of Mycobacterium tuberculosis in south coastal Karnataka, India, using spoligotyping

Kiran Chawla, Ajay Kumar, Vishnu Prasad Shenoy, Devendra Singh Chauhan, Pragya Sharma

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1 Citation (Scopus)

Abstract

Background & objectives: Despite high occurrence of tuberculosis in India very little information is available about the genetic diversity of Mycobacterium tuberculosis isolates prevailing in coastal Karnataka, India. Thus, the present study was undertaken to explore the genetic biodiversity of M. tuberculosis isolates prevailing in south coastal region of Karnataka (Udupi District), India. Methods: A total of 111 Mycobacterial isolates were cultured in Lowenstein Jensen (LJ) medium and after obtaining growth, DNA was extracted and spoligotyping was performed. SITVIT WEB database was used to locate families of spoligotypes. Results: On analyzing the hybridization results of all 111 isolates on SITVIT WEB database 57 (51.35%) isolates were clustered into 11 Spoligotype International Types (SIT). The largest cluster of 14 (12.61%) isolates was SIT-48 (EAI1-SOM), followed by SIT-1942 (CAS1-Delhi) with 11 isolates (9.9%) and SIT-11 with seven (6.30%). Moreover, 23 isolates (20.72%) had unique spoligotypes and 31 (27.92%) were orphans. Spotclust analysis revealed that majority (67%) of orphan isolates were variants of CAS (37%) and EAI-5 (34%). Interpretation & conclusions: The present study revealed high biodiversity among the circulating isolates of M. tuberculosis in this region with the presence of mixed genotypes earlier reported from north and south India along with certain new genotypes with unique SITs. The study highlights the need for further longitudinal studies to explore the genetic diversity and to understand the transmission dynamics of prevailing isolates.

Original languageEnglish
Pages (from-to)278-286
Number of pages9
JournalIndian Journal of Medical Research
Volume147
Issue numberMarch
DOIs
Publication statusPublished - 01-03-2018

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Biodiversity
Mycobacterium tuberculosis
India
Genotype
Databases
DNA
Longitudinal Studies
Tuberculosis
Growth

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

@article{5d6b794beae04ea3acf443e17355d5de,
title = "Genetic diversity of Mycobacterium tuberculosis in south coastal Karnataka, India, using spoligotyping",
abstract = "Background & objectives: Despite high occurrence of tuberculosis in India very little information is available about the genetic diversity of Mycobacterium tuberculosis isolates prevailing in coastal Karnataka, India. Thus, the present study was undertaken to explore the genetic biodiversity of M. tuberculosis isolates prevailing in south coastal region of Karnataka (Udupi District), India. Methods: A total of 111 Mycobacterial isolates were cultured in Lowenstein Jensen (LJ) medium and after obtaining growth, DNA was extracted and spoligotyping was performed. SITVIT WEB database was used to locate families of spoligotypes. Results: On analyzing the hybridization results of all 111 isolates on SITVIT WEB database 57 (51.35{\%}) isolates were clustered into 11 Spoligotype International Types (SIT). The largest cluster of 14 (12.61{\%}) isolates was SIT-48 (EAI1-SOM), followed by SIT-1942 (CAS1-Delhi) with 11 isolates (9.9{\%}) and SIT-11 with seven (6.30{\%}). Moreover, 23 isolates (20.72{\%}) had unique spoligotypes and 31 (27.92{\%}) were orphans. Spotclust analysis revealed that majority (67{\%}) of orphan isolates were variants of CAS (37{\%}) and EAI-5 (34{\%}). Interpretation & conclusions: The present study revealed high biodiversity among the circulating isolates of M. tuberculosis in this region with the presence of mixed genotypes earlier reported from north and south India along with certain new genotypes with unique SITs. The study highlights the need for further longitudinal studies to explore the genetic diversity and to understand the transmission dynamics of prevailing isolates.",
author = "Kiran Chawla and Ajay Kumar and Shenoy, {Vishnu Prasad} and Chauhan, {Devendra Singh} and Pragya Sharma",
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Genetic diversity of Mycobacterium tuberculosis in south coastal Karnataka, India, using spoligotyping. / Chawla, Kiran; Kumar, Ajay; Shenoy, Vishnu Prasad; Chauhan, Devendra Singh; Sharma, Pragya.

In: Indian Journal of Medical Research, Vol. 147, No. March, 01.03.2018, p. 278-286.

Research output: Contribution to journalArticle

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AU - Kumar, Ajay

AU - Shenoy, Vishnu Prasad

AU - Chauhan, Devendra Singh

AU - Sharma, Pragya

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N2 - Background & objectives: Despite high occurrence of tuberculosis in India very little information is available about the genetic diversity of Mycobacterium tuberculosis isolates prevailing in coastal Karnataka, India. Thus, the present study was undertaken to explore the genetic biodiversity of M. tuberculosis isolates prevailing in south coastal region of Karnataka (Udupi District), India. Methods: A total of 111 Mycobacterial isolates were cultured in Lowenstein Jensen (LJ) medium and after obtaining growth, DNA was extracted and spoligotyping was performed. SITVIT WEB database was used to locate families of spoligotypes. Results: On analyzing the hybridization results of all 111 isolates on SITVIT WEB database 57 (51.35%) isolates were clustered into 11 Spoligotype International Types (SIT). The largest cluster of 14 (12.61%) isolates was SIT-48 (EAI1-SOM), followed by SIT-1942 (CAS1-Delhi) with 11 isolates (9.9%) and SIT-11 with seven (6.30%). Moreover, 23 isolates (20.72%) had unique spoligotypes and 31 (27.92%) were orphans. Spotclust analysis revealed that majority (67%) of orphan isolates were variants of CAS (37%) and EAI-5 (34%). Interpretation & conclusions: The present study revealed high biodiversity among the circulating isolates of M. tuberculosis in this region with the presence of mixed genotypes earlier reported from north and south India along with certain new genotypes with unique SITs. The study highlights the need for further longitudinal studies to explore the genetic diversity and to understand the transmission dynamics of prevailing isolates.

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