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Comparison of spoligotyping, mycobacterial interspersed repetitive units typing and IS6110-RFLP in a study of genotypic diversity of Mycobacterium tuberculosis in Delhi, North India
- Source :
- Memórias do Instituto Oswaldo Cruz, Memórias do Instituto Oswaldo Cruz, Instituto Oswaldo Cruz, Ministério da Saúde, 2011, 106 (5), pp.524-535. ⟨10.1590/S0074-02762011000500002⟩, Memórias do Instituto Oswaldo Cruz., Vol 106, Iss 5, Pp 524-535 (2011), Memórias do Instituto Oswaldo Cruz, Volume: 106, Issue: 5, Pages: 524-535, Published: AUG 2011
- Publication Year :
- 2011
- Publisher :
- FapUNIFESP (SciELO), 2011.
-
Abstract
- International audience; 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.
- Subjects :
- Male
MESH: Mycobacterium tuberculosis
lcsh:QR1-502
Minisatellite Repeats
Polymerase Chain Reaction
lcsh:Microbiology
law.invention
MESH: Genotype
law
Genotype
M. tuberculosis
IS6110-RFLP
Cluster Analysis
MESH: Genetic Variation
Polymerase chain reaction
Genetics
0303 health sciences
spoligotyping
biology
Bacterial Typing Techniques
3. Good health
tuberculosis
MESH: Young Adult
Female
Restriction fragment length polymorphism
Polymorphism, Restriction Fragment Length
Adult
DNA, Bacterial
Microbiology (medical)
lcsh:Arctic medicine. Tropical medicine
Tuberculosis
lcsh:RC955-962
India
MESH: Bacterial Typing Techniques
Microbiology
Mycobacterium tuberculosis
Young Adult
03 medical and health sciences
medicine
Humans
Typing
Genotyping
Repetitive Sequences, Nucleic Acid
030304 developmental biology
Genetic diversity
MESH: Humans
MESH: Repetitive Sequences, Nucleic Acid
MESH: Polymorphism, Restriction Fragment Length
030306 microbiology
Genetic Variation
MESH: Adult
MESH: Polymerase Chain Reaction
biology.organism_classification
medicine.disease
MESH: Cluster Analysis
MESH: DNA, Bacterial
[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
MESH: Male
genotyping
MESH: Minisatellite Repeats
MESH: India
MESH: Female
Subjects
Details
- ISSN :
- 00740276 and 16788060
- Volume :
- 106
- Database :
- OpenAIRE
- Journal :
- Memórias do Instituto Oswaldo Cruz
- Accession number :
- edsair.doi.dedup.....fd4456fd79766bc362029267422cd1b2