Draft Genome Sequence of an Extensively Drug-Resistant
Mycobacterium tuberculosis Clinical Isolate of the Ural Strain
Shamsudheen Karuthedath Vellarikkal,a Ajay Vir Singh,c Pravin Kumar Singh,c Parul Garg,c Viswa Mohan Katoch,c Kiran Katoch,c
Open Source Drug Discovery Consortium,d D. S. Chauhan,c Vinod Scaria,b Sridhar Sivasubbua
Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Delhi, Indiaa; GN Ramachandran Knowledge Center for Genome Informatics, CSIR
Institute of Genomics and Integrative Biology, Delhi, Indiab; National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, Indiac; CSIR Open Source
Drug Discovery Unit, Anusandhan Bhavan, New Delhi, Indiad
We describe the genome sequencing and analysis of a clinical isolate of Mycobacterium tuberculosis belonging to the Ural strain
OSDD493 from India.
2 October 2013 Accepted
4 October 2013 Published
7 November 2013
Karuthedath Vellarikkal S, Vir Singh A, Kumar Singh P, Garg P, Mohan Katoch V, Katoch K, Open Source Drug Discovery Consortium, Chauhan DS, Scaria V, Sivasubbu S.
2013. Draft genome sequence of an extensively drug-resistant Mycobacterium tuberculosis
clinical isolate of the Ural strain OSDD493. Genome Announc. 1(6):e00928-13. doi:
2013 Karuthedath Vellarikkal et al. This is an open-access article distributed under the terms of
Address correspondence to Sridhar Sivasubbu, firstname.lastname@example.org, or Vinod Scaria, email@example.com.
uberculosis is caused by a closely related group of pathogenic CLCGenomicsWorkbench6.Theassemblyresultedin193contigsat
organisms known as the Mycobacterium tuberculosis
50 values of 42,650 bp and a total assembly of 4,227,747 bp. Further,
Distinct lineages of Mycobacterium tuberculosis
have been reported
automated gene prediction on the draft genomes was performed us-
and have been characterized and classified based on spoligotype pat-
ing the RAST server Analysis revealed 4,223 genes, including 42
terns. The six major distinct lineages are the Indo-Oceanic (EAI), East
Asian (Beijing), East African-Indian (CAS), Euro-American (Haar-
Nucleotide sequence accession numbers.
lem, LAM, T, X), West African I (AFRI1), and West African lineage II
shotgun project has been deposited at DDBJ/EMBL/GenBank un-
(AFRI2) lineages The Ural spoligotype was initially identified
der the accession number The version described
from the Ural region in Russia, which has one of the highest inci-
in this paper is version AVQJ01000000.
dences of tuberculosis in the country. Nevertheless, the Ural spoligo-type forms a minority of genotypes of M. tuberculosis
from this region The genotype has also been reported from across
We thank Swati Subodh (TCGA) and Nupur Mehrotra (Premas Biotech)
Eurasia and Central Asia and forms a significant proportion of geno-
for scientific discussions and help in maintaining the strains. We also
types observed in some of these regions. The Ural genotype is thought
acknowledge S. Ramachandran for valuable input.
to be associated with significantly low transmissibility, pathogenicity,
The project was funded by CSIR India through the Open Source Drug
Discovery Programme (HCP001). The sequencing facility is supported
Understanding the genome sequence of the Ural strain of Myco-
through grants SIP006 and FAC002 from CSIR, India, and the computa-
would provide immense insights into the
tional analysis was performed at the CSIR Center for In Silico
genomic architecture associated with low pathogenicity. In this pa-
per, we describe the draft genome sequence of an extensively drug-resistant clinical isolate of Mycobacterium tuberculosis
a novel spoligotype clustering within the Ural spoligotype. The clini-
1. Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA,
Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi
cal isolate OSDD493 was obtained from the strain repository main-
A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Fer-
tained at the National JALMA Institute of Leprosy and other Myco-
dinand S, Garcia de Viedma D, Garzelli C, Gazzola L, Gomes HM,
bacterial Diseases, which is part of the Open Source Drug Discovery
Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN,
Open Access Repository. Spoligotyping was performed and drug sen-
Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ho ML, Martin
sitivity was evaluated per standard protocols Drug sensitivity
C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L,
Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Ra-
analysis revealed the isolate to be resistant to streptomycin, rifampin,
solonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S,
isoniazid, ethambutol, ofloxacin, kanamycin, and ethionamide and
Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D,
sensitive to amikacin, pyrazinamide, capreomycin, cycloserine, and
Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC,
-aminosalicylate sodium (PAS). DNA was isolated per standard
Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C.
complex genetic diversity: mining the fourth
protocols. The raw sequence data were generated after library prepa-
international spoligotyping database (SpolDB4) for classification, popula-
ration on Ion Torrent PGM according to protocols recommended by
tion genetics and epidemiology. BMC Microbiol. 6:
the manufacturers. Draft genomes were assembled de novo using
2. Kovalev SY, Kamaev EY, Kravchenko MA, Kurepina NE, Skorniakov SN.
November/December 2013 Volume 1 Issue 6 e00928-13
2005. Genetic analysis of Mycobacterium tuberculosis
strains isolated in Ural
6. National Committee for Clinical Laboratory Standards.
region, Russian Federation, by MIRU-VNTR genotyping. Int. J. Tuberc.
bility testing of mycobacteria, Nocardia
, and other aerobic actinomycetes.
Lung Dis. 9:
Tentative standard M24T2, 2nd ed. National Committee for Clinical Lab-
3. Mokrousov I.
2012. The quiet and controversial: Ural family of Mycobac-
. Infect. Genet. Evol. 12:
619 – 629.
7. Canetti G, Fox W, Khomenko A, Mahler HT, Menon NK, Mitchison DA,
4. Mokrousov I, Vyazovaya A, Otten T, Zhuravlev V, Pavlova E, Tarash-
Rist N, Smelev NA.
1969. Advances in techniques of testing mycobacterial
kevich L, Krishevich V, Vishnevsky B, Narvskaya O.
drug sensitivity, and the use of sensitivity tests in tuberculosis control pro-
population in northwestern Russia: an update from Russian-
grammes. Bull. World Health Organ. 41:
EU/Latvian border region. PLoS One 7:
8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma
5. Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D,
K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman
Kuijper S, Bunschoten A, Molhuizen H, Shaw R, Goyal M, van
AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch
1997. Simultaneous detection and strain differentiation of
GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.
for diagnosis and epidemiology. J. Clin. Mi-
2008. The RAST server: rapid annotations using subsystems technology.
BMC Genomics 9:
November/December 2013 Volume 1 Issue 6 e00928-13
Monthly Newsletter of National Centre for Disease Control, Directorate General of Health Services, Government of India May - July 2009 Vol. 13 : No. 1 SCRUB TYPHUS & OTHER RICKETTSIOSES it lacks lipopolysaccharide and peptidoglycan RICKETTSIAL DISEASES and does not have an outer slime layer. It isThese are the diseases caused by rickettsiaeendowed with a major surface prote
N E W S L E T T E R 2 patients of Dr. Steinhouser are being treated in the Calming Zone. The Calming Zone effect of the Infratonic reduces their vibration is so helpful in preparing decreasing overall tension and is used extensively by our massage therapists. “ When a patient comes into the office with such severe pain and emotional such wide applications in our office, from