title: Identification and genotyping of Mycobacterium tuberculosis complex species by use of a SNaPshot Minisequencing-based assay.
abstract: The aim of the present study was to investigate the use of the SNaPshot minisequencing method for the identification of Mycobacterium tuberculosis complex (MTBC) isolates to the species level and for further genotyping of M. tuberculosis isolates. We developed an innovative strategy based on two multiplex allele-specific minisequencing assays that allowed detection of eight species-specific and eight lineage-specific single nucleotide polymorphisms (SNPs). Each assay consisted of an eightplex PCR amplification, followed by an eightplex minisequencing reaction with the SNaPshot multiplex kit (Applied Biosystems) and, finally, analysis of the extension products by capillary electrophoresis. The whole strategy was developed with a panel of 56 MTBC strains and 15 negative controls. All MTBC strains tested except one M. africanum clinical isolate were accurately identified to the species level, and all M. tuberculosis isolates were successfully further genotyped. This two-step strategy based on SNaPshot minisequencing allows the simultaneous differentiation of closely related members of the MTBC, the distinction between principal genetic groups, and the characterization of M. tuberculosis isolates into one of the seven prominent SNP cluster groups (SCGs) and could be a useful tool for diagnostic and epidemiological purposes.
authors.affiliation: EA4438 Physiopathologie et Médecine Translationnelle, Université de Strasbourg, Institut de Médecine Légale, 11 rue Humann, Strasbourg 67 085, France. caroline.bouakaze@etu.unistra.fr
authors.forename: C
authors.initials: C
authors.lastname: Bouakaze
authors.forename: C
authors.initials: C
authors.lastname: Keyser
authors.forename: S J
authors.initials: SJ
authors.lastname: de Martino
authors.forename: W
authors.initials: W
authors.lastname: Sougakoff
authors.forename: N
authors.initials: N
authors.lastname: Veziris
authors.forename: H
authors.initials: H
authors.lastname: Dabernat
authors.forename: B
authors.initials: B
authors.lastname: Ludes
mesh_terms: D015373:Bacterial Typing Techniques; D001431:Bacteriological Techniques / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D019075:Electrophoresis, Capillary / Q000379:methods; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers