title: Evidence for positive selection on Mycobacterium tuberculosis within patients.
abstract: BACKGROUND
  While the pathogenesis and epidemiology of tuberculosis are well studied, relatively little is known about the evolution of the infectious agent Mycobacterium tuberculosis, especially at the within-host level. The insertion sequence IS6110 is a genetic marker that is widely used to track the transmission of tuberculosis between individuals. This and other markers may also facilitate our understanding of the disease within patients.
  
  
  RESULTS
  This article presents three lines of evidence supporting the action of positive selection on M. tuberculosis within patients. The arguments are based on a comparison between empirical findings from molecular epidemiology, and population genetic models of evolution. Under the hypothesis of neutrality of genotypes, 1) the mutation rate of the marker IS6110 is unusually high, 2) the time it takes for substitutions to occur within patients is too short, and 3) the amount of polymorphism within patients is too low.
  
  
  CONCLUSIONS
  Empirical observations are explained by the action of positive selection during infection, or alternatively by very low effective population sizes. I discuss the possible roles of antibiotic treatment, the host immune system and extrapulmonary dissemination in creating opportunities for positive selection.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, NSW 2052, Australia. m.tanaka@unsw.edu.au
authors.forename: Mark M
authors.initials: MM
authors.lastname: Tanaka
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D036262:Empirical Research; D005819:Genetic Markers / Q000235:genetics; D016680:Genome, Bacterial; D042822:Genomic Instability / Q000235:genetics; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D017720:Molecular Epidemiology / Q000379:methods; D016296:Mutagenesis / Q000235:genetics; D009169:Mycobacterium tuberculosis / Q000302:isolation & purification*; D011110:Polymorphism, Genetic / Q000235:genetics; D014376:Tuberculosis / Q000175:diagnosis* / Q000453:epidemiology
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers