title: Spoligotyping of Mycobacterium tuberculosis complex isolates using hydrogel oligonucleotide microarrays.
abstract: Mycobacterium tuberculosis remains a leading cause of morbidity and mortality worldwide. This circumstance underscores the relevance of population studies of tuberculosis for transmission dynamics control. In this study, we describe a conversion of the spoligotyping of M.tuberculosis complex isolates on a platform of custom designed hydrogel microarrays (biochips). An algorithm of automated data processing and interpretation of hybridization results using online database was proposed. In total, the 445 samples were tested. Initially, 97 samples representing multiple species of M.tuberculosis complex and nontuberculous mycobacteria were used for protocol optimization and cut-off settings. The developed assay was further evaluated on the out-group of the 348 mycobacterial samples. Results showed high concordance with the conventional membrane-based spoligotyping method. Diagnostic sensitivity and diagnostic specificity of the spoligo-biochip assay were 99.1% and 100%, respectively. The analytical sensitivity was determined to be 500 genomic equivalents of mycobacterial DNA. The high sensitivity and specificity, ease of operation procedures, and the automatic processing of measured data make the developed assay a useful tool for the rapid and accurate genotyping of M. tuberculosis.
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation. Electronic address: JuliaBespyatykh@gmail.com.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Bespyatykh
authors.affiliation: Engelhardt Institute of Molecular Biology, Moscow, Russian Federation.
authors.forename: Danila V
authors.initials: DV
authors.lastname: Zimenkov
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Egor A
authors.initials: EA
authors.lastname: Shitikov
authors.affiliation: Engelhardt Institute of Molecular Biology, Moscow, Russian Federation.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Kulagina
authors.affiliation: Engelhardt Institute of Molecular Biology, Moscow, Russian Federation.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Lapa
authors.affiliation: Engelhardt Institute of Molecular Biology, Moscow, Russian Federation.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Gryadunov
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Elena N
authors.initials: EN
authors.lastname: Ilina
authors.affiliation: Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation.
authors.forename: Vadim M
authors.initials: VM
authors.lastname: Govorun
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D005838:Genotype; D006801:Humans; D058889:Molecular Typing / Q000379:methods; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D020411:Oligonucleotide Array Sequence Analysis; D014376:Tuberculosis / Q000382:microbiology
chemical_list: D004269:DNA, Bacterial
keywords: Biochips; Genotyping; Hybridization; Spoligotyping; Tuberculosis