Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology.
BACKGROUND
Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome.


METHODS
Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes.


CONCLUSIONS
Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains.
St, Petersburg State University, Theodosius Dobzhansky Center for Genome Bioinformatics, 41 Sredniy prospect, St, Petersburg, Russia. echernya@gmail.com.
Ekaterina N
EN
Chernyaeva
Marina V
MV
Shulgina
Mikhail S
MS
Rotkevich
Pavel V
PV
Dobrynin
Serguei A
SA
Simonov
Egor A
EA
Shitikov
Dmitry S
DS
Ischenko
Irina Y
IY
Karpova
Elena S
ES
Kostryukova
Elena N
EN
Ilina
Vadim M
VM
Govorun
Vyacheslav Y
VY
Zhuravlev
Olga A
OA
Manicheva
Peter K
PK
Yablonsky
Yulia D
YD
Isaeva
Elena Y
EY
Nosova
Igor V
IV
Mokrousov
Anna A
AA
Vyazovaya
Olga V
OV
Narvskaya
Alla L
AL
Lapidus
Stephen J
SJ
O'Brien
D030541:Databases, Genetic; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D014376:Tuberculosis / Q000453:epidemiology* / Q000382:microbiology