Single nucleotide polymorphism (SNP) analysis used for the phylogeny of the Mycobacterium tuberculosis complex based on a pyrosequencing assay

BMC Microbiology

Sofía Samper¹  María José Iglesias⁵  Carlos Martín⁵  Miguel Ferrero⁶  María Asunción Vitoria²  María Antonia Lezcano⁷  José Domínguez⁷  Mark Strunk³  Adriana Cabal⁴ 

[1] Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain;Hospital Universitario Lozano Blesa, CIBER de Enfermedades Respiratorias, Zaragoza, Spain;IIS Aragón, CIBER de Enfermedades Hepáticas y Digestivas, Zaragoza, Spain;IIS Aragón, Hopsital Universitario Miguel Servet, Zaragoza, Spain;Universidad de Zaragoza, CIBER de Enfermedades Respiratorias, Zaragoza, Spain;Hospital San Jorge, Huesca, Spain;CIBER de Enfermedades Respiratorias, Madrid, Spain

关键词: Cluster;    Lineages;    SCG;    Pyrosequencing;    SNP;    M. tuberculosis;   

Others  :  1142094
DOI  :  10.1186/1471-2180-14-21

 received in 2013-06-12, accepted in 2014-01-27,  发布年份 2014

【 摘 要 】

Background

Different 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.

Results

The 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, mgtC¹⁸², Ag85C¹⁰³ and RD^Rio deletion were detected.

Conclusions

This 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.

【 授权许可】

   
2014 Cabal et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

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