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 nextgeneration 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 virulenceassociated 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.
