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!