Abstract
BackgroundDifferent polymorphisms have been described as markers to classify the lineages of the Mycobacterium tuberculosis complex. The analysis of nine single nucleotide polymorphisms (SNPs) was used to describe seven SNPs cluster groups (SCGs). We attempted to classify those strains that could not been categorized into lineages by the genotyping methods used in the routine testing.ResultsThe M. tuberculosis complex isolates collected in 2010 in our region were analysed. A new method based on multiplex-PCRs and pyrosequencing to analyse these SNPs was designed. For the pyrosequencing assay nine SNPs that defined the seven SCGs were selected from the literature: 1977, 74092, 105139, 232574, 311613, 913274, 2460626, 3352929 and gyrA95. In addition, SNPs in katG463, mgtC 182 , Ag85C103 and RDRio deletion were detected.ConclusionsThis work has permitted to achieve a better classification of Aragonian strains into SCGs and in some cases, to assign strains to its certain lineage. Besides, the description of a new pattern shared by two isolates “SCG-6c” reinforces the interest of SNPs to follow the evolution of M. tuberculosis complex.
Highlights
Different polymorphisms have been described as markers to classify the lineages of the Mycobacterium tuberculosis complex
Once tested for the presence of the nine single nucleotide polymorphisms (SNPs), we could confirm that those isolates with the same spoligopattern held into the same SNP cluster groups (SCG)
In conclusion, the current study shows that the polymorphisms selected have been quite useful to complement and enrich the characterization of all isolates, for those that would not have been classified by other routine techniques
Summary
Different polymorphisms have been described as markers to classify the lineages of the Mycobacterium tuberculosis complex. The species of the Mycobacterium tuberculosis complex (MTC) show a 99.9% of similarity in their nucleotide sequence and their 16SrRNA do not differ between members, only M. canetti does [1] Despite this identity in their genomes, a large number of long sequence polymorphisms (LSPs), a variation in repetitive elements in the genome, and single nucleotide polymorphisms (SNPs) have been detected [2,3]. Afterwards, Brudey et al based on the “Direct Repeat” locus (DR) diversity detected by Spoligotyping, classified thousands of MTC clinical strains isolated worldwide in different lineages or families [5] These families were named according with their main geographical origin; Latin AmericanMediterranean family (LAM) isolates, which are the cause of 15% of the new TB (tuberculosis) cases detected each year worldwide, are highly prevalent in Latin America and the Mediterranean area [6,7]. It includes over 600 shared international types (SITs) and it has been divided into 5 subgroups, from T1 to T5 [5,7]
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