Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan
Asset Daniyarov,
Askhat Molkenov,
Saule Rakhimova,
Ainur Akhmetova,
Zhannur Nurkina,
Dauren Yerezhepov,
Lyailya Chingissova,
Venera Bismilda,
Bekzat Toxanbaeva,
Ainur Akilzhanova,
Ulan Kozhamkulov,
Ulykbek Kairov
Affiliations
Asset Daniyarov
Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; RSE National Center for Biotechnology, Nur-Sultan 010000, Kazakhstan
Askhat Molkenov
Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
Saule Rakhimova
Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
Ainur Akhmetova
Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; L.N.Gumilev Eurasian National University, Nur-Sultan 010000, Kazakhstan
Zhannur Nurkina
Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
Dauren Yerezhepov
Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
Lyailya Chingissova
National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
Venera Bismilda
National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
Bekzat Toxanbaeva
National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
Ainur Akilzhanova
Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
Ulan Kozhamkulov
Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan
Ulykbek Kairov
Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan 010000, Kazakhstan; Corresponding author.
Drug-resistant tuberculosis (TB) is a major public health problem. Clinical Mycobacterium tuberculosis (MTB) isolate with Extensively drug-resistant tuberculosis (MTB-XDR) profile was subjected to whole-genome sequencing using a next-generation sequencing platform (NGS) Roche 454 GS FLX+ followed by bioinformatics sequence analysis. Quality of read was checked by FastQC, paired-end reads were trimmed using Trimmomatic. De novo genome assembly was conducted using Velvet v.1.2.10. The assembled genome of XDR-TB-1599 strain was functionally annotated using the PATRIC platform. Analysis of de novo assembled genome was performed using ResFinder, CARD, CASTB and TB-Profiler tools. MIRU_VNTR genotyping on 12 loci and spoligotyping have been performed for XDR-TB-1599 isolate. M. tuberculosis XDR-TB-1599 strain yielded an average read depth of 21-fold with overall 4 199 325 bp. The assembled genome contains 5528 protein-coding genes, including key drug resistance and virulence-associated genes and GC content of 65.4%. We identified that all proteins encoded by this strain contain conserved domains associated with the first-line anti-tuberculosis drugs such as rifampicin, isoniazid, streptomycin and ethionamide. TB-Profiler had higher average concordance results with phenotypic DST (drug susceptibility testing) in comparison with ResFinder, CARD, CASTB profiling to first-line (75% vs 50%) and second-line (25% vs 0%) of anti-TB drugs, correspondingly. To our knowledge, this is the first report of a highly annotated and characterized whole-genome sequence and de novo assembled XDR-TB M.tuberculosis strain isolated from a sputum of new TB case-patient from Kazakhstan performed on Roche 454 GS FLX+ platform. This report highlights an important role of whole-genome sequencing technology and analysis as an advanced approach for drug-resistance investigations of circulated TB isolates.
