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MTB genome sequencing activities in Russia
Igor MOKROUSOV, Ph.D., D.Sc.
Laboratory of Molecular MicrobiologySt. Petersburg Pasteur Institute, Russia
2nd NDWG workshop “Data sharing to improve management of drug resistant TB” Barcelona, 28.10.2014. 5:30-8:30 pm, AC Forum hotel
Current situation in Russia:
WGS/NGS and databasing, but not for routine drug resistance prediction
Genotypic detection of drug resistance, but not using WGS
No routineWGS of Mtb in Russia for epidemiology/diagnosis.
Regulations/Ministry of Health
No coordination, no special program for implementing WGS into practice
Concept of National register of all TB patients: unique ID for each TB patient, with all his/her information accessible from any location.
Implementation of WGS/NGS for routine DR‐Tb detection requires:
Mtb strains
WGS platform
Bioinformatics soft, incl. Databasing
Experts capable to interpret WGS data
Funding
St. Petersburg
Novosibirsk
Irkutsk
Collaborative (formal and informal) links and projects on Russian Mtb WGS
Mtb strainsMiseq (2)
Bioinformatics & DatabasingWGS analysis
Mtb strainsWGS: outsourceBioinformaticsWGS analysis
Mtb strainsSOLID™
BioinformaticsWGS analysis
London, UKWGS, bioinfo, Data analysis
SamaraMtb strains
MoscowMtb strainsMiseq, Hiseq,IonTorrent PGM, GS FLX+BioinformaticsWGS analysis
St Petersburg
Strains: TB reference lab at Institute of Phthisiopulmonology
Technical platform: Dobzhansky Center (19 strains), Pasteur Inst. (1 strain)
Bioinfo facilities: Dobzhansky Center (under implementation: Pasteur Inst)
WGS Databasing: Dobzhansky Center.
Publications on WGS: 3
Strain/patient databasing: Institute of Phthisiopulmonology
Expertise in molecular epidemiology (not only WGS): Pubmed papers in the last 5 years for Pasteur Institute - 38, Dobzhansky Center – 3.
Dobzhansky Center for Genome BioinformaticsSt. Petersburg State University
St. Petersburg Institute of Phthisiopulmonology
St. Petersburg Pasteur Institute
Moscow
Strains: Central Inst of Tuberculosis, City Center of Treatment of Tuberculosis
Technical platform: Inst of Physical-Chemical Medicine (54 strains)Central Inst of Epidemiology, Inst of Molecular Biology
Bioinfo facilities: Inst of Physical-Chemical Medicine,Central Inst of Epidemiology, Inst of Molecular Biology
Publications on WGS: 3 (Institute of Physical-Chemical Medicine)
Institute of Physical-Chemical MedicineCity Center of Treatment of Tuberculosis
Central Institute of Epidemiology
Central Institute of TuberculosisInstitute of Molecular Biology, Syntol Ltd
Irkutsk
Strains: TB dispensary
Technical platform: outsource (2 strains)
Bioinfo facilities: Institute of Epidemiology and Microbiology
Publications on WGS: 1 submitted
Strain/patient databasing: yes
Expertise in molecular epidemiology (not only WGS): Pubmed papers in the last 5 years: 3
Research Institute of Epidemiology and Microbiology
City TB dispensary
Novosibirsk
Strains: Res. Institute of Tuberculosis
Technical platform: Inst. of Chemical Biol. and Fundamental Medicine (11 strains)
Bioinfo facilities: Inst. of Chemical Biology and Fundamental Medicine
Publications on WGS: no
Strain/patient databasing: Research Institute of Tuberculosis
Expertise in molecular epidemiology (not only WGS): Pubmed papers in the last 5 years: 3
Institute of Chemical Biology and Fundamental MedicineResearch Institute of Tuberculosis
Samara
Strains: Regional TB dispensary
WGS and data analysis: Drobniewski lab,Sanger center, London, UK,
Outsource facilities for WGS: Moscow, St. Petersburg, Novosibirsk
Collaborative links and projects on Russian Mtb WGS, in Rissia
Project, finished (biochips and WGS), Moscow Inst of Physico Chem Med, Inst. of Mol Biol, Pasteur Inst, St. Petersburg Inst of Phthisiopulm.Support: Russian Ministry of Education and Science.
Project, ongoing (MTB genome diversity in Russia, databasing)Dobzhansky Center, Moscow Inst of Physico Chem Med, Pasteur Inst.St. Petersburg Inst of Phthisiopulm, Supported partly by Russian Ministry of Education and Science.
Project, ongoing (WGS and evolution of Mtb families) Pasteur Inst and St. Petersburg Inst of Phthisiopulmonology. Support: Russian Science Foundation
Project, ongoing (WGS, molepi and drug resistance genetics)Central Inst. of Epidemiology and Moscow Center of TB treatment
Project, ongoing (WGS, biochips): Central TB institute, Inst of Mol. Biology, Syntol Ltd
St. Petersburg
Novosibirsk
Irkutsk
Collaborative links and projects on Russian Mtb WGS
Mtb strainsMiseq (2)
Bioinformatics & DatabasingWGS analysis
Mtb strainsWGS: outsourceBioinformaticsWGS analysis
Mtb strainsSOLID™
BioinformaticsWGS analysis
London, UKWGS, bioinfo, Data analysis
SamaraMtb strains
MoscowMtb strainsMiseq, Hiseq,IonTorrent PGM, GS FLX+BioinformaticsWGS analysis
WGS done in St. Petersburg, Moscow (our labs) + published WGS on Samara (Casali et al., 2014)
http://mtb.dobzhanskycenter.org/
http://mtb.dobzhanskycenter.org/
WGS done in St. Petersburg, Moscow (our labs) + published WGS on Samara (Casali et al., 2014)
E. Chernyaeva: Dobzhansky Center for Genome Bioinformatics,St. Petersburg State University
V. Zhuravlev: St. Petersburg Institute of Phthisiopulmonology
I. Mokrousov, O. Narvskaya: St. Petersburg Pasteur Institute
E. Ilina, E. Shitikov: Research Institute of Physical-Chemical Medicine, MoscowMoscow Scientific-Practical Center of Treatment of Tuberculosis
M. Filipenko, M. Dymova: Institute of Chemical Biology and Fundamental Medicine, SB RAS, NovosibirskNovosibirsk Research Institute of Tuberculosis
O. Ogarkov, V. Sinkov: Research Institute of Epidemiology and Microbiology; TB dispensary, Irkutsk
CONTRIBUTORS TO THIS PRESENTATION
M. Alvares-Figueroa: Central Institute of Epidemiology, Moscow
Thank you!