Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North India
Objective/background: Molecular epidemiology methods are very useful for differentiating between strains, assessing their diversity, and measuring the prevalence of the most circulating strain in an area. Various molecular typing methods using different molecular markers have been utilized worldwide...
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| Format: | Article |
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Wolters Kluwer Medknow Publications
2016-01-01
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| Series: | International Journal of Mycobacteriology |
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| Online Access: | http://www.ijmyco.org/article.asp?issn=2212-5531;year=2016;volume=5;issue=5;spage=174;epage=175;aulast=Mathuria |
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| author | Jitendra Prasad Mathuria Pragya Sharma Pradyot Prakash Jai Kumar Samaria Vishwa Mohan Katoch Shampa Anupurba |
| author_facet | Jitendra Prasad Mathuria Pragya Sharma Pradyot Prakash Jai Kumar Samaria Vishwa Mohan Katoch Shampa Anupurba |
| author_sort | Jitendra Prasad Mathuria |
| collection | DOAJ |
| description | Objective/background: Molecular epidemiology methods are very useful for differentiating between strains, assessing their diversity, and measuring the prevalence of the most circulating strain in an area. Various molecular typing methods using different molecular markers have been utilized worldwide, such as restriction fragment length polymorphism (RFLP), spoligotyping, Mycobacterial Interspersed Repetitive Unit – Variable Number of Tandem Repeat (MIRU-VNTR), and Double repetitive element-PCR (DRE-PCR) typing, for simultaneous detection and epidemiologic typing of Mycobacterium tuberculosis. The present study is conducted to assess the genetic diversity of M. tuberculosis by IS6110-RFLP and spoligotyping in patients attending a tertiary care hospital in eastern Uttar Pradesh, North India.
Methods: A total of 83 representative isolates of M. tuberculosis were included in this study. These isolates were subjected to spoligotyping and IS6110-RFLP DNA fingerprinting techniques as described previously.
Results: The spoligotype patterns were compared with SpolDB4.0; patterns of 64 out of 83 M. tuberculosis isolates were matched with the available data, while 19 isolates were found to be orphan, that is, absent in the SpolDB4.0 database. The majority of the M. tuberculosis strains (56.5%) belong to central Asian (32.5%), ill defined T (13.2%), and Beijing (10.8%) families. On IS6110-RFLP analysis, in 19.2% (16/83) of these isolates, IS6110 element was not found (0 copy number strains). Further, 15.6% (13/83) isolates were found to be low-copy-number strains having less than six copies of IS6110 element, and the remaining 65.0% (54/83) were multiple-copy-number strains with six or more copies of the element. On comparing the results of spoligotyping and IS-6110-RFLP, a total of 47 isolates were clustered by spoligotyping; out of these isolates, 40 were found to be unique by IS6110-RFLP.
Conclusion: Spoligotype analysis resulted in the grouping of a much larger number of isolates within apparently identical clusters compared with IS6110-RFLP typing, while IS6110-RFLP was not found to effectively distinguish between zero- and low-copy-number isolates. Therefore, we concluded that, in India, the use of both the techniques simultaneously for DNA fingerprinting of M. tuberculosis could be a better approach. |
| first_indexed | 2024-12-10T23:58:28Z |
| format | Article |
| id | doaj.art-7d65c84db36b45a58c5d3ca8b0ebc3e4 |
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| issn | 2212-5531 2212-554X |
| language | English |
| last_indexed | 2024-12-10T23:58:28Z |
| publishDate | 2016-01-01 |
| publisher | Wolters Kluwer Medknow Publications |
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| series | International Journal of Mycobacteriology |
| spelling | doaj.art-7d65c84db36b45a58c5d3ca8b0ebc3e42022-12-22T01:28:32ZengWolters Kluwer Medknow PublicationsInternational Journal of Mycobacteriology2212-55312212-554X2016-01-015517417510.1016/j.ijmyco.2016.11.015Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North IndiaJitendra Prasad MathuriaPragya SharmaPradyot PrakashJai Kumar SamariaVishwa Mohan KatochShampa AnupurbaObjective/background: Molecular epidemiology methods are very useful for differentiating between strains, assessing their diversity, and measuring the prevalence of the most circulating strain in an area. Various molecular typing methods using different molecular markers have been utilized worldwide, such as restriction fragment length polymorphism (RFLP), spoligotyping, Mycobacterial Interspersed Repetitive Unit – Variable Number of Tandem Repeat (MIRU-VNTR), and Double repetitive element-PCR (DRE-PCR) typing, for simultaneous detection and epidemiologic typing of Mycobacterium tuberculosis. The present study is conducted to assess the genetic diversity of M. tuberculosis by IS6110-RFLP and spoligotyping in patients attending a tertiary care hospital in eastern Uttar Pradesh, North India. Methods: A total of 83 representative isolates of M. tuberculosis were included in this study. These isolates were subjected to spoligotyping and IS6110-RFLP DNA fingerprinting techniques as described previously. Results: The spoligotype patterns were compared with SpolDB4.0; patterns of 64 out of 83 M. tuberculosis isolates were matched with the available data, while 19 isolates were found to be orphan, that is, absent in the SpolDB4.0 database. The majority of the M. tuberculosis strains (56.5%) belong to central Asian (32.5%), ill defined T (13.2%), and Beijing (10.8%) families. On IS6110-RFLP analysis, in 19.2% (16/83) of these isolates, IS6110 element was not found (0 copy number strains). Further, 15.6% (13/83) isolates were found to be low-copy-number strains having less than six copies of IS6110 element, and the remaining 65.0% (54/83) were multiple-copy-number strains with six or more copies of the element. On comparing the results of spoligotyping and IS-6110-RFLP, a total of 47 isolates were clustered by spoligotyping; out of these isolates, 40 were found to be unique by IS6110-RFLP. Conclusion: Spoligotype analysis resulted in the grouping of a much larger number of isolates within apparently identical clusters compared with IS6110-RFLP typing, while IS6110-RFLP was not found to effectively distinguish between zero- and low-copy-number isolates. Therefore, we concluded that, in India, the use of both the techniques simultaneously for DNA fingerprinting of M. tuberculosis could be a better approach.http://www.ijmyco.org/article.asp?issn=2212-5531;year=2016;volume=5;issue=5;spage=174;epage=175;aulast=MathuriaGenetic diversityIS6110-based restriction fragment length polymorphismSpoligotypingTuberculosis |
| spellingShingle | Jitendra Prasad Mathuria Pragya Sharma Pradyot Prakash Jai Kumar Samaria Vishwa Mohan Katoch Shampa Anupurba Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North India International Journal of Mycobacteriology Genetic diversity IS6110-based restriction fragment length polymorphism Spoligotyping Tuberculosis |
| title | Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North India |
| title_full | Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North India |
| title_fullStr | Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North India |
| title_full_unstemmed | Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North India |
| title_short | Assessing genetic diversity of Mycobacterium tuberculosis by spoligotyping and IS6110-based restriction fragment length polymorphism in North India |
| title_sort | assessing genetic diversity of mycobacterium tuberculosis by spoligotyping and is6110 based restriction fragment length polymorphism in north india |
| topic | Genetic diversity IS6110-based restriction fragment length polymorphism Spoligotyping Tuberculosis |
| url | http://www.ijmyco.org/article.asp?issn=2212-5531;year=2016;volume=5;issue=5;spage=174;epage=175;aulast=Mathuria |
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