Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India
The aim of the present study was to compare polymerase chain reaction (PCR)-based methods - spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing - with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculos...
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| Format: | Article |
| Language: | English |
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Fundação Oswaldo Cruz (FIOCRUZ)
2011-08-01
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| Series: | Memorias do Instituto Oswaldo Cruz |
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| Online Access: | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762011000500002&lng=en&tlng=en |
| _version_ | 1797758533208375296 |
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| author | Mandira Varma-Basil Sujeet Kumar Jyoti Arora Archana Angrup Thierry Zozio Jayant Nagesh Banavaliker Urvashi Balbir Singh Nalin Rastogi Mridula Bose |
| author_facet | Mandira Varma-Basil Sujeet Kumar Jyoti Arora Archana Angrup Thierry Zozio Jayant Nagesh Banavaliker Urvashi Balbir Singh Nalin Rastogi Mridula Bose |
| author_sort | Mandira Varma-Basil |
| collection | DOAJ |
| description | The aim of the present study was to compare polymerase chain reaction (PCR)-based methods - spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing - with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculosis to determine the genetic diversity of M. tuberculosis clinical isolates from Delhi, North India. Spoligotyping resulted in 49 patterns (14 clusters); the largest cluster was composed of Spoligotype International Types (SITs)26 [Central-Asian (CAS)1-Delhi lineage], followed by SIT11 [East-African-Indian (EAI) 3-Indian lineage]. A large number of isolates (75%) belonged to genotypic lineages, such as CAS, EAI and Manu, with a high specificity for the Indian subcontinent, emphasising the complex diversity of the phylogenetically coherent M. tuberculosis in North India. MIRU typing, using 11 discriminatory loci, was able to distinguish between all but two strains based on individual patterns. IS6110-RFLP analysis (n = 80 strains) resulted in 67 unique isolates and four clusters containing 13 strains. MIRUs discriminated all 13 strains, whereas spoligotyping discriminated 11 strains. Our results validate the use of PCR-based molecular typing of M. tuberculosis using repetitive elements in Indian isolates and demonstrate the usefulness of MIRUs for discriminating low-IS6110-copy isolates, which accounted for more than one-fifth of the strains in the present study. |
| first_indexed | 2024-03-12T18:30:22Z |
| format | Article |
| id | doaj.art-d41c71ef6152409fb210ab6c754044a6 |
| institution | Directory Open Access Journal |
| issn | 1678-8060 |
| language | English |
| last_indexed | 2024-03-12T18:30:22Z |
| publishDate | 2011-08-01 |
| publisher | Fundação Oswaldo Cruz (FIOCRUZ) |
| record_format | Article |
| series | Memorias do Instituto Oswaldo Cruz |
| spelling | doaj.art-d41c71ef6152409fb210ab6c754044a62023-08-02T08:19:25ZengFundação Oswaldo Cruz (FIOCRUZ)Memorias do Instituto Oswaldo Cruz1678-80602011-08-01106552453510.1590/S0074-02762011000500002S0074-02762011000500002Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North IndiaMandira Varma-Basil0Sujeet Kumar1Jyoti Arora2Archana Angrup3Thierry Zozio4Jayant Nagesh Banavaliker5Urvashi Balbir Singh6Nalin Rastogi7Mridula Bose8University of DelhiUniversity of DelhiAll India Institute of Medical SciencesUniversity of DelhiInstitut PasteurRajan Babu Tuberculosis HospitalAll India Institute of Medical SciencesInstitut PasteurUniversity of DelhiThe aim of the present study was to compare polymerase chain reaction (PCR)-based methods - spoligotyping and mycobacterial interspersed repetitive units (MIRU) typing - with the gold-standard IS6110 restriction fragment length polymorphism (RFLP) analysis in 101 isolates of Mycobacterium tuberculosis to determine the genetic diversity of M. tuberculosis clinical isolates from Delhi, North India. Spoligotyping resulted in 49 patterns (14 clusters); the largest cluster was composed of Spoligotype International Types (SITs)26 [Central-Asian (CAS)1-Delhi lineage], followed by SIT11 [East-African-Indian (EAI) 3-Indian lineage]. A large number of isolates (75%) belonged to genotypic lineages, such as CAS, EAI and Manu, with a high specificity for the Indian subcontinent, emphasising the complex diversity of the phylogenetically coherent M. tuberculosis in North India. MIRU typing, using 11 discriminatory loci, was able to distinguish between all but two strains based on individual patterns. IS6110-RFLP analysis (n = 80 strains) resulted in 67 unique isolates and four clusters containing 13 strains. MIRUs discriminated all 13 strains, whereas spoligotyping discriminated 11 strains. Our results validate the use of PCR-based molecular typing of M. tuberculosis using repetitive elements in Indian isolates and demonstrate the usefulness of MIRUs for discriminating low-IS6110-copy isolates, which accounted for more than one-fifth of the strains in the present study.http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762011000500002&lng=en&tlng=entuberculosisM. tuberculosisgenotypingspoligotypingIS6110-RFLP |
| spellingShingle | Mandira Varma-Basil Sujeet Kumar Jyoti Arora Archana Angrup Thierry Zozio Jayant Nagesh Banavaliker Urvashi Balbir Singh Nalin Rastogi Mridula Bose Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India Memorias do Instituto Oswaldo Cruz tuberculosis M. tuberculosis genotyping spoligotyping IS6110-RFLP |
| title | Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India |
| title_full | Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India |
| title_fullStr | Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India |
| title_full_unstemmed | Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India |
| title_short | Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India |
| title_sort | comparison of spoligotyping mycobacterial interspersed repetitive units typing and is6110 rflp in a study of genotypic diversity of mycobacterium tuberculosis in delhi north india |
| topic | tuberculosis M. tuberculosis genotyping spoligotyping IS6110-RFLP |
| url | http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0074-02762011000500002&lng=en&tlng=en |
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