Single nucleotide polymorphism (SNP) analysis used for the phylogeny of the Mycobacterium tuberculosis complex based on a pyrosequencing assay.
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 katG(463), mgtC(182), Ag85C(103) 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.
Adriana
A
Cabal
Mark
M
Strunk
José
J
Domínguez
María Antonia
MA
Lezcano
María Asunción
MA
Vitoria
Miguel
M
Ferrero
Carlos
C
Martín
María José
MJ
Iglesias
IIS Aragón, Hopsital Universitario Miguel Servet, Zaragoza, Spain. ssamper.iacs@aragon.es.
Sofía
S
Samper
D016000:Cluster Analysis; D006801:Humans; D058889:Molecular Typing / Q000379:methods*; D060885:Multiplex Polymerase Chain Reaction; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013030:Spain; D014376:Tuberculosis / Q000382:microbiology