WHOLE GENOME SEQUENCE DATA OF MYCOBACTERIUM TUBERCULOSIS XDR STRAIN, ISOLATED FROM PATIENT IN KAZAKHSTAN
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Date
2020-12
Authors
Daniyarov, Asset
Molkenov, Askhat
Rakhimova, Saule
Akhmetova, Ainur
Nurkina, Zhannur
Yerezhepov, Dauren
Chingissova, Lyailya
Bismilda, Venera
Toxanbaeva, Bekzat
Akilzhanova, Ainur
Journal Title
Journal ISSN
Volume Title
Publisher
Elsevier
Abstract
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.
Description
Keywords
Mycobacterium, Whole genome sequence, Draft genome, Extensively drug-resistance, Tuberculosis, Kazakhstan, Research Subject Categories::NATURAL SCIENCES, Research Subject Categories::NATURAL SCIENCES::Biology
Citation
Daniyarov, A., Molkenov, A., Rakhimova, S., Akhmetova, A., Nurkina, Z., Yerezhepov, D., Chingissova, L., Bismilda, V., Toxanbaeva, B., Akilzhanova, A., Kozhamkulov, U., & Kairov, U. (2020). Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan. Data in Brief, 33, 106416. https://doi.org/10.1016/j.dib.2020.106416