title: Phylogeny of Mycobacterium tuberculosis Beijing strains constructed from polymorphisms in genes involved in DNA replication, recombination and repair.
abstract: BACKGROUND
  The Beijing family is a successful group of M. tuberculosis strains, often associated with drug resistance and widely distributed throughout the world. Polymorphic genetic markers have been used to type particular M. tuberculosis strains. We recently identified a group of polymorphic DNA repair replication and recombination (3R) genes. It was shown that evolution of M. tuberculosis complex strains can be studied using 3R SNPs and a high-resolution tool for strain discrimination was developed. Here we investigated the genetic diversity and propose a phylogeny for Beijing strains by analyzing polymorphisms in 3R genes.
  
  
  RESULTS
  A group of 3R genes was sequenced in a collection of Beijing strains from different geographic origins. Sequence analysis and comparison with the ones of non-Beijing strains identified several SNPs. These SNPs were used to type a larger collection of Beijing strains and allowed identification of 26 different sequence types for which a phylogeny was constructed. Phylogenetic relationships established by sequence types were in agreement with evolutionary pathways suggested by other genetic markers, such as Large Sequence Polymorphisms (LSPs). A recent Beijing genotype (Bmyc10), which included 60% of strains from distinct parts of the world, appeared to be predominant.
  
  
  CONCLUSIONS
  We found SNPs in 3R genes associated with the Beijing family, which enabled discrimination of different groups and the proposal of a phylogeny. The Beijing family can be divided into different groups characterized by particular genetic polymorphisms that may reflect pathogenic features. These SNPs are new, potential genetic markers that may contribute to better understand the success of the Beijing family.
authors.affiliation: Unité de Génétique Mycobactérienne, Institut Pasteur, Paris, France.
authors.forename: Olga
authors.initials: O
authors.lastname: Mestre
authors.forename: Tao
authors.initials: T
authors.lastname: Luo
authors.forename: Tiago
authors.initials: T
authors.lastname: Dos Vultos
authors.forename: Kristin
authors.initials: K
authors.lastname: Kremer
authors.forename: Alan
authors.initials: A
authors.lastname: Murray
authors.forename: Amine
authors.initials: A
authors.lastname: Namouchi
authors.forename: Céline
authors.initials: C
authors.lastname: Jackson
authors.forename: Jean
authors.initials: J
authors.lastname: Rauzier
authors.forename: Pablo
authors.initials: P
authors.lastname: Bifani
authors.forename: Rob
authors.initials: R
authors.lastname: Warren
authors.forename: Voahangy
authors.initials: V
authors.lastname: Rasolofo
authors.forename: Jian
authors.initials: J
authors.lastname: Mei
authors.forename: Qian
authors.initials: Q
authors.lastname: Gao
authors.forename: Brigitte
authors.initials: B
authors.lastname: Gicquel
mesh_terms: D004260:DNA Repair / Q000235:genetics; D004261:DNA Replication / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D055614:Genetic Phenomena / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic / Q000235:genetics
chemical_list: D004269:DNA, Bacterial