Genomic analysis of Latin American-Mediterranean family of  Mycobacterium tuberculosis  clinical strains from Kazakhstan

There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

Abstract

The human-adapted strains of the Mycobacterium tuberculosis complex (MTBC) comprise seven phylogenetic lineages originally associated with their geographical distribution. Here, we report the genomes of three drug-resistant clinical isolates of the Latin American-Mediterranean (LAM) family collected in Kazakhstan. We utilised whole-genome sequencing to study the distribution and drug resistance of these isolates. Phylogenetic analysis grouped the genomes described in this study with the sequences from Russia, Uzbekistan, and Kazakhstan belonging to the LAM family. One isolate has acquired extensive drug resistance to seven antituberculosis drugs. Our results suggest at least two multi-drug resistant (MDR)/extensively drug-resistant (XDR)-associated genotypes of the LAM family circulate in Kazakhstan.

Related collections

Most cited references 25

Record: found
Abstract: found
Article: not found

Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis.

D. Van Soolingen, P. Hermans, P. E. W. de Haas … (1991)

In this study we established the usefulness of DNA fingerprinting for the epidemiology of tuberculosis on the basis of the DNA polymorphism generated by the insertion sequence (IS) IS986. Although clinical isolates of Mycobacterium tuberculosis displayed a remarkably high degree of restriction fragment length polymorphism, we showed that transposition of this IS element is an extremely rare event in M. tuberculosis complex strains grown either in vitro or in vivo for long periods of time. The M. tuberculosis and Mycobacterium africanum strains tested in this study contained 6 to 17 IS copies. In the Mycobacterium bovis strains, the copy numbers ranged between 1 and 5, and all 27 M. bovis BCG strains investigated invariably contained a single IS copy. This copy was located at a unique chromosomal position, reinforcing the idea that the frequency of IS transposition is very low in M. tuberculosis complex strains. Various microepidemics are described in which each microepidemic corresponds to a particular fingerprint type. The extent of similarity between Dutch and African strains was quantitatively assessed by computer-assisted analysis of DNA fingerprints. The results indicate that M. tuberculosis strains from regions in central Africa, where tuberculosis is highly prevalent, are generally more related to each other than isolates from the Netherlands, where the transmission rate is low and where the majority of the tuberculosis cases are presumed to be the result of reactivation of previously contracted M. tuberculosis infections.

0 comments Cited 214 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

Mycobacterium tuberculosis Lineage 4 comprises globally distributed and geographically restricted sublineages

David Stucki, Daniela Brites, Leïla Jeljeli … (2016)

Generalist and specialist species differ in the breadth of their ecological niche. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis Lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that Lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that while the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of Lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.

0 comments Cited 210 times – based on 0 reviews      Review now

Bookmark

Record: found
Abstract: found
Article: not found

PhyResSE: a Web Tool Delineating Mycobacterium tuberculosis Antibiotic Resistance and Lineage from Whole-Genome Sequencing Data.

Silke Feuerriegel, Viola Schleusener, Patrick Beckert … (2015)

Antibiotic-resistant tuberculosis poses a global threat, causing the deaths of hundreds of thousands of people annually. While whole-genome sequencing (WGS), with its unprecedented level of detail, promises to play an increasingly important role in diagnosis, data analysis is a daunting challenge. Here, we present a simple-to-use web service (free for academic use at http://phyresse.org). Delineating both lineage and resistance, it provides state-of-the-art methodology to life scientists and physicians untrained in bioinformatics. It combines elaborate data processing and quality control, as befits human diagnostics, with a treasure trove of validated resistance data collected from well-characterized samples in-house and worldwide.

0 comments Cited 146 times – based on 0 reviews      Review now

Bookmark

All references

Author and article information

Journal

Journal ID (nlm-ta): Mem Inst Oswaldo Cruz

Journal ID (iso-abbrev): Mem. Inst. Oswaldo Cruz

Journal ID (publisher-id): mioc

Title: Memórias do Instituto Oswaldo Cruz

Publisher: Instituto Oswaldo Cruz, Ministério da Saúde

ISSN (Print): 0074-0276

ISSN (Electronic): 1678-8060

Publication date (Electronic): 18 September 2020

Publication date Collection: 2020

Volume: 115

Electronic Location Identifier: e200215

Affiliations

[1 ]National Center for Biotechnology, Nur-Sultan, Kazakhstan

[2 ]National Scientific Center for Phthisiopulmonology, Almaty, Kazakhstan

Author notes

+ Corresponding author: tarlykov@ 123456biocenter.kz

PT and YR conceived the study; PT and AA designed the study protocol; AA assisted in the culture work; SA and PT performed the sequencing; PT and SA analysed the data; PT and SA wrote the manuscript. The authors declare no conflict of interest, financial, or other.

Author information

Pavel Tarlykov http://orcid.org/0000-0003-2075-307X

Article

Other ID: 00417

DOI: 10.1590/0074-02760200215

PMC ID: 7508292

PubMed ID: 32965331

SO-VID: beab971c-1ffa-4a2e-860f-2983d8725d85

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License

History

Date received : 06 May 2020

Date accepted : 20 August 2020

Page count

Figures: 1, Tables: 3, References: 38

Comments

Comment on this article

scite_

Smart Citations

Citing PublicationsSupportingMentioningContrasting

View Citations

See how this article has been cited at scite.ai

scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.