SNP/RD typing of Mycobacterium tuberculosis beijing strains reveals local and worldwide disseminated clonal complexes

Anita Schürch; Kristin Kremer; Amber C.A. Hendriks; Benthe Freyee; Christopher R.E. McEvoy; Reinout van Crevel; Martin J. Boeree; Paul van Helden; Robin M. Warren; Roland J. Siezen; Dick van Soolingen

doi:10.1371/journal.pone.0028365

SNP/RD typing of Mycobacterium tuberculosis beijing strains reveals local and worldwide disseminated clonal complexes

Anita Schürch, Kristin Kremer, Amber C.A. Hendriks, Benthe Freyee, Christopher R.E. McEvoy, Reinout van Crevel, Martin J. Boeree, Paul van Helden, Robin M. Warren, Roland J. Siezen, Dick van Soolingen^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

The Beijing strain is one of the most successful genotypes of Mycobacterium tuberculosis worldwide and appears to be highly homogenous according to existing genotyping methods. To type Beijing strains reliably we developed a robust typing scheme using single nucleotide polymorphisms (SNPs) and regions of difference (RDs) derived from whole-genome sequencing data of eight Beijing strains. SNP/RD typing of 259 M. tuberculosis isolates originating from 45 countries worldwide discriminated 27 clonal complexes within the Beijing genotype family. A total of 16 Beijing clonal complexes contained more than one isolate of known origin, of which two clonal complexes were strongly associated with South African origin. The remaining 14 clonal complexes encompassed isolates from different countries. Even highly resolved clonal complexes comprised isolates from distinct geographical sites. Our results suggest that Beijing strains spread globally on multiple occasions and that the tuberculosis epidemic caused by the Beijing genotype is at least partially driven by modern migration patterns. The SNPs and RDs presented in this study will facilitate future molecular epidemiological and phylogenetic studies on Beijing strains.

Original language	English
Article number	e28365
Journal	PLoS ONE
Volume	6
Issue number	12
DOIs	https://doi.org/10.1371/journal.pone.0028365
Publication status	Published - 5 Dec 2011
Externally published	Yes

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Schürch, A., Kremer, K., Hendriks, A. C. A., Freyee, B., McEvoy, C. R. E., van Crevel, R., Boeree, M. J., van Helden, P., Warren, R. M., Siezen, R. J., & van Soolingen, D. (2011). SNP/RD typing of Mycobacterium tuberculosis beijing strains reveals local and worldwide disseminated clonal complexes. PLoS ONE, 6(12), Article e28365. https://doi.org/10.1371/journal.pone.0028365

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title = "SNP/RD typing of Mycobacterium tuberculosis beijing strains reveals local and worldwide disseminated clonal complexes",

abstract = "The Beijing strain is one of the most successful genotypes of Mycobacterium tuberculosis worldwide and appears to be highly homogenous according to existing genotyping methods. To type Beijing strains reliably we developed a robust typing scheme using single nucleotide polymorphisms (SNPs) and regions of difference (RDs) derived from whole-genome sequencing data of eight Beijing strains. SNP/RD typing of 259 M. tuberculosis isolates originating from 45 countries worldwide discriminated 27 clonal complexes within the Beijing genotype family. A total of 16 Beijing clonal complexes contained more than one isolate of known origin, of which two clonal complexes were strongly associated with South African origin. The remaining 14 clonal complexes encompassed isolates from different countries. Even highly resolved clonal complexes comprised isolates from distinct geographical sites. Our results suggest that Beijing strains spread globally on multiple occasions and that the tuberculosis epidemic caused by the Beijing genotype is at least partially driven by modern migration patterns. The SNPs and RDs presented in this study will facilitate future molecular epidemiological and phylogenetic studies on Beijing strains.",

author = "Anita Sch{\"u}rch and Kristin Kremer and Hendriks, {Amber C.A.} and Benthe Freyee and McEvoy, {Christopher R.E.} and {van Crevel}, Reinout and Boeree, {Martin J.} and {van Helden}, Paul and Warren, {Robin M.} and Siezen, {Roland J.} and {van Soolingen}, Dick",

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AU - van Crevel, Reinout

AU - Boeree, Martin J.

AU - van Helden, Paul

AU - Warren, Robin M.

AU - Siezen, Roland J.

AU - van Soolingen, Dick

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SNP/RD typing of Mycobacterium tuberculosis beijing strains reveals local and worldwide disseminated clonal complexes

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