Spoligotyping of Mycobacterium tuberculosis complex isolates using hydrogel oligonucleotide microarrays

• Published in: Infection, genetics and evolution Vol. 26; pp. 41 - 46
• Main Authors: Bespyatykh, Julia A., Zimenkov, Danila V., Shitikov, Egor A., Kulagina, Elena V., Lapa, Sergey A., Gryadunov, Dmitry A., Ilina, Elena N., Govorun, Vadim M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2014
• Subjects: Biochips; DNA, Bacterial - genetics; Genotype; Genotyping; Humans; Hybridization; Molecular Typing - methods; Mycobacterium tuberculosis - classification; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - isolation & purification; Oligonucleotide Array Sequence Analysis; Spoligotyping; Tuberculosis; Tuberculosis - microbiology; Spoligotyping; Tuberculosis; Hybridization; Genotyping; Biochips
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2014.04.024

•We propose an adaptation of the spoligotyping approach on aplatform of three-dimensional hydrogel biochips.•We compared our results with a traditional spoligotyping method.•Our method shown a 99% sensitivity and 100% specificity vs. other spoligotyping approaches. 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.