title: Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains.
abstract: Several human pathogens (e.g., Bacillus anthracis, Yersinia pestis, Bordetella pertussis, Plasmodium falciparum, and Mycobacterium tuberculosis) have very restricted unselected allelic variation in structural genes, which hinders study of the genetic relationships among strains and strain-trait correlations. To address this problem in a representative pathogen, 432 M. tuberculosis complex strains from global sources were genotyped on the basis of 230 synonymous (silent) single nucleotide polymorphisms (sSNPs) identified by comparison of four genome sequences. Eight major clusters of related genotypes were identified in M. tuberculosis sensu stricto, including a single cluster representing organisms responsible for several large outbreaks in the United States and Asia. All M. tuberculosis sensu stricto isolates of previously unknown phylogenetic position could be rapidly and unambiguously assigned to one of the eight major clusters, thus providing a facile strategy for identifying organisms that are clonally related by descent. Common clones of M. tuberculosis sensu stricto and M. bovis are distinct, deeply branching genotypic complexes whose extant members did not emerge directly from one another in the recent past. sSNP genotyping rapidly delineates relationships among closely related strains of pathogenic microbes and allows construction of genetic frameworks for examining the distribution of biomedically relevant traits such as virulence, transmissibility, and host range.
authors.affiliation: Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana 59840, USA.
authors.forename: Michaela M
authors.initials: MM
authors.lastname: Gutacker
authors.forename: James C
authors.initials: JC
authors.lastname: Smoot
authors.forename: Cristi A Lux
authors.initials: CA
authors.lastname: Migliaccio
authors.forename: Stacy M
authors.initials: SM
authors.lastname: Ricklefs
authors.forename: Su
authors.initials: S
authors.lastname: Hua
authors.forename: Debby V
authors.initials: DV
authors.lastname: Cousins
authors.forename: Edward A
authors.initials: EA
authors.lastname: Graviss
authors.forename: Elena
authors.initials: E
authors.lastname: Shashkina
authors.forename: Barry N
authors.initials: BN
authors.lastname: Kreiswirth
authors.forename: James M
authors.initials: JM
authors.lastname: Musser
mesh_terms: D000483:Alleles; D000818:Animals; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D017720:Molecular Epidemiology; D009163:Mycobacterium bovis / Q000235:genetics / Q000302:isolation & purification; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D014774:Virulence / Q000235:genetics