Open Access

BMC Genomics, volume 19, issue 1, publication number 762

New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe

Sinkov Viacheslav ¹

Ogarkov Oleg ^{1, 2}

Mokrousov I. V. ³

Bukin Yuri ^{4, 5}

Zhdanova Svetlana ¹

Heysell Scott K. ⁶

Hide authors affiliations Show authors affiliations: 6 affiliations

Department Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia |

Irkutsk State Medical Academy of Continuing Education, Irkutsk, Russia |

Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia |

⁴

Limnological Institute SB RAS, Irkutsk, Russia |

⁵

Irkutsk National Research technical University, Irkutsk, Russia |

⁶

Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA |

Publication type: Journal Article

Publication date: 2018-10-22

Springer Nature

Journal: BMC Genomics

Quartile SCImago

Quartile WOS

Impact factor: 4.4

ISSN: 14712164

DOI: 10.1186/s12864-018-5162-3

Copy DOI

PubMed ID: 30348088

Genetics

Biotechnology

Abstract

Ural genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and of low virulence, but recent studies reported an increasing circulation of the multidrug-resistant (MDR) and extensively drug-resistant (XDR) Ural strains. Here, we analyzed all publicly available whole genome sequence data of Ural genotype isolates, in order to elucidate their phylogenomic diversity with a special focus on MDR and potentially epidemic clones. A total of 149 M. tuberculosis genomes of Ural isolates from FSU countries were mined from the GMTV database and TB-ARC project. We identified 6002 variable amino acid positions that were assessed for functional significance and used to build ML, NJ trees and for Bayesian TMRCA estimation. Three robust monophyletic clades were identified: Clade A (31 isolates from Russia, Belarus, Moldova), Clade B (52 isolates from Russia), and Clade C (37 isolates from Moldova, 2 from Belarus). Clade C was significantly associated with XDR or pre-XDR status compared to the pooled Clades A and B (33/39 versus 5/83, P < 0.0001). Time of origin was estimated for Clade A at 77.7–137 years ago and for Clade B at 56.3–99.2 years ago compared to the significantly more recent origin for Clade C. in silico spoligotyping identified signatures specific of the Clade A (spoligotype SIT35), and Clades B and C (both SIT262). A genetically compact and evolutionarily young Ural Clade C, likely originated after collapse of the Soviet Union, and reached epidemic proportions in Moldova in the last 20 years. This epidemic pre-XDR clone (mostly rifampin, isoniazid and kanamycin resistant) is characterized by a specific combination of mutations: KatG Ser315Thr, fabG1 -15C > T, RpoB Ser450Leu, RpsL Lys88Arg, eis -12G > A and EmbB Ser297Ala/T > G. Its further dissemination may occur towards both Russia and European Union and should be taken into consideration by health authorities. The identified spoligotyping signatures can serve for rapid preliminary detection and surveillance of the more hazardous pre-XDR associated strains of the Ural family, both in populations from countries of their endemic circulation and migrant communities.

By date By citations

Citations by journals

	1 2 3 4 5
Infection, Genetics and Evolution	Infection, Genetics and Evolution, 5, 18.52% Infection, Genetics and Evolution 5 publications, 18.52%
International Journal of Antimicrobial Agents	International Journal of Antimicrobial Agents, 2, 7.41% International Journal of Antimicrobial Agents 2 publications, 7.41%
Acta Biomedica Scientifica (East Siberian Biomedical Journal)	Acta Biomedica Scientifica (East Siberian Biomedical Journal), 2, 7.41% Acta Biomedica Scientifica (East Siberian Biomedical Journal) 2 publications, 7.41%
Microbial genomics	Microbial genomics, 1, 3.7% Microbial genomics 1 publication, 3.7%
Antibiotics	Antibiotics, 1, 3.7% Antibiotics 1 publication, 3.7%
Frontiers in Cellular and Infection Microbiology	Frontiers in Cellular and Infection Microbiology, 1, 3.7% Frontiers in Cellular and Infection Microbiology 1 publication, 3.7%
Bulletin of Experimental Biology and Medicine	Bulletin of Experimental Biology and Medicine, 1, 3.7% Bulletin of Experimental Biology and Medicine 1 publication, 3.7%
PLoS Medicine	PLoS Medicine, 1, 3.7% PLoS Medicine 1 publication, 3.7%
Tuberculosis	Tuberculosis, 1, 3.7% Tuberculosis 1 publication, 3.7%
Data in Brief	Data in Brief, 1, 3.7% Data in Brief 1 publication, 3.7%
New Microbes and New Infections	New Microbes and New Infections, 1, 3.7% New Microbes and New Infections 1 publication, 3.7%
BMC Genomics	BMC Genomics, 1, 3.7% BMC Genomics 1 publication, 3.7%
Transboundary and Emerging Diseases	Transboundary and Emerging Diseases, 1, 3.7% Transboundary and Emerging Diseases 1 publication, 3.7%
Cardiovascular Therapy and Prevention (Russian Federation)	Cardiovascular Therapy and Prevention (Russian Federation), 1, 3.7% Cardiovascular Therapy and Prevention (Russian Federation) 1 publication, 3.7%
BMC Infectious Diseases	BMC Infectious Diseases, 1, 3.7% BMC Infectious Diseases 1 publication, 3.7%
Tuberculosis and Lung Diseases	Tuberculosis and Lung Diseases, 1, 3.7% Tuberculosis and Lung Diseases 1 publication, 3.7%
Vestnik KazNMU	Vestnik KazNMU, 1, 3.7% Vestnik KazNMU 1 publication, 3.7%
Journal of microbiology epidemiology immunobiology	Journal of microbiology epidemiology immunobiology, 1, 3.7% Journal of microbiology epidemiology immunobiology 1 publication, 3.7%
Epidemiology and Vaccinal Prevention (Epidemiologiya i Vaktsinoprofilaktika)	Epidemiology and Vaccinal Prevention (Epidemiologiya i Vaktsinoprofilaktika), 1, 3.7% Epidemiology and Vaccinal Prevention (Epidemiologiya i Vaktsinoprofilaktika) 1 publication, 3.7%
	1 2 3 4 5

Citations by publishers

	2 4 6 8 10
Elsevier	Elsevier, 10, 37.04% Elsevier 10 publications, 37.04%
Springer Nature	Springer Nature, 3, 11.11% Springer Nature 3 publications, 11.11%
Scientific Centre for Family Health and Human Reproduction Problems	Scientific Centre for Family Health and Human Reproduction Problems, 2, 7.41% Scientific Centre for Family Health and Human Reproduction Problems 2 publications, 7.41%
Microbiology Society	Microbiology Society, 1, 3.7% Microbiology Society 1 publication, 3.7%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 1, 3.7% Multidisciplinary Digital Publishing Institute (MDPI) 1 publication, 3.7%
Frontiers Media S.A.	Frontiers Media S.A., 1, 3.7% Frontiers Media S.A. 1 publication, 3.7%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 1, 3.7% Public Library of Science (PLoS) 1 publication, 3.7%
Wiley	Wiley, 1, 3.7% Wiley 1 publication, 3.7%
Russian Society of Cardiology	Russian Society of Cardiology, 1, 3.7% Russian Society of Cardiology 1 publication, 3.7%
Russian Phthisiologists’ Society	Russian Phthisiologists’ Society, 1, 3.7% Russian Phthisiologists’ Society 1 publication, 3.7%
Asfendiyarov Kazakh National Medical University	Asfendiyarov Kazakh National Medical University, 1, 3.7% Asfendiyarov Kazakh National Medical University 1 publication, 3.7%
Central Research Institute for Epidemiology	Central Research Institute for Epidemiology, 1, 3.7% Central Research Institute for Epidemiology 1 publication, 3.7%
National Association of the Specialists in Control of Health Care-Associated Infections	National Association of the Specialists in Control of Health Care-Associated Infections, 1, 3.7% National Association of the Specialists in Control of Health Care-Associated Infections 1 publication, 3.7%
	2 4 6 8 10

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Sinkov V. et al. New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe // BMC Genomics. 2018. Vol. 19. No. 1. 762

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Sinkov V., Ogarkov O., Mokrousov I. V., Bukin Y., Zhdanova S., Heysell S. K. New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe // BMC Genomics. 2018. Vol. 19. No. 1. 762

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TY - JOUR

DO - 10.1186/s12864-018-5162-3

UR - https://doi.org/10.1186%2Fs12864-018-5162-3

TI - New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe

T2 - BMC Genomics

AU - Sinkov, Viacheslav

AU - Ogarkov, Oleg

AU - Mokrousov, I. V.

AU - Bukin, Yuri

AU - Zhdanova, Svetlana

AU - Heysell, Scott K.

PY - 2018

DA - 2018/10/22 00:00:00

PB - Springer Nature

IS - 1

VL - 19

PMID - 30348088

SN - 1471-2164

ER -

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BibTex Copy

@article{2018_Sinkov,

author = {Viacheslav Sinkov and Oleg Ogarkov and I. V. Mokrousov and Yuri Bukin and Svetlana Zhdanova and Scott K. Heysell},

title = {New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe},

journal = {BMC Genomics},

year = {2018},

volume = {19},

publisher = {Springer Nature},

month = {oct},

url = {https://doi.org/10.1186%2Fs12864-018-5162-3},

number = {1},

doi = {10.1186/s12864-018-5162-3}

}

Found error?

Publisher

Springer Nature

Journal

BMC Genomics

Quartile SCImago

Quartile WOS

Impact factor

4.4

ISSN

14712164 (Print)

Labs

Laboratory of Epidemiologically and Socially Significant Infections

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