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.
authors.affiliation: Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), Bilthoven, The Netherlands.
authors.forename: Anita C
authors.initials: AC
authors.lastname: Schürch
authors.forename: Kristin
authors.initials: K
authors.lastname: Kremer
authors.forename: Amber C A
authors.initials: AC
authors.lastname: Hendriks
authors.forename: Benthe
authors.initials: B
authors.lastname: Freyee
authors.forename: Christopher R E
authors.initials: CR
authors.lastname: McEvoy
authors.forename: Reinout
authors.initials: R
authors.lastname: van Crevel
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Boeree
authors.forename: Paul
authors.initials: P
authors.lastname: van Helden
authors.forename: Robin M
authors.initials: RM
authors.lastname: Warren
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
authors.forename: Dick
authors.initials: D
authors.lastname: van Soolingen
mesh_terms: D000465:Algorithms; D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D005838:Genotype; D016013:Likelihood Functions; D015233:Models, Statistical; D017720:Molecular Epidemiology; D009169:Mycobacterium tuberculosis / Q000378:metabolism*; D010802:Phylogeny; D058974:Phylogeography; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA