Unknown

Dataset Information

0

Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan.


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.

SUBMITTER: Daniyarov A 

PROVIDER: S-EPMC7578676 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

altmetric image

Publications

Whole genome sequence data of <i>Mycobacterium tuberculosis</i> XDR strain, isolated from patient in Kazakhstan.

Daniyarov Asset A   Molkenov Askhat A   Rakhimova Saule S   Akhmetova Ainur A   Nurkina Zhannur Z   Yerezhepov Dauren D   Chingissova Lyailya L   Bismilda Venera V   Toxanbaeva Bekzat B   Akilzhanova Ainur A   Kozhamkulov Ulan U   Kairov Ulykbek U  

Data in brief 20201017


Drug-resistant tuberculosis (TB) is a major public health problem. Clinical <i>Mycobacterium tuberculosis</i> (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. <i>De novo</i> genome assembly was conducted using Velvet v.1.2.10. Th  ...[more]

Similar Datasets

| S-EPMC7180286 | biostudies-literature
| S-EPMC10296843 | biostudies-literature
| S-EPMC6390763 | biostudies-literature
| S-EPMC4214991 | biostudies-literature
| S-EPMC6092779 | biostudies-literature
| S-EPMC3599118 | biostudies-literature
| S-EPMC7578197 | biostudies-literature
| S-EPMC5861094 | biostudies-literature
| S-EPMC7317096 | biostudies-literature
| S-EPMC5334602 | biostudies-literature