title: An evaluation of indices for quantifying tuberculosis transmission using genotypes of pathogen isolates.
abstract: BACKGROUND
  Infectious diseases are often studied by characterising the population structure of the pathogen using genetic markers. An unresolved problem is the effective quantification of the extent of transmission using genetic variation data from such pathogen isolates.
  
  
  METHODS
  It is important that transmission indices reflect the growth of the infectious population as well as account for the mutation rate of the marker and the effects of sampling. That is, while responding to this growth rate, indices should be unresponsive to the sample size and the mutation rate. We use simulation methods taking into account both the mutation and sampling processes to evaluate indices designed to quantify transmission of tuberculosis.
  
  
  RESULTS
  Previously proposed indices generally perform inadequately according to the above criteria, with the partial exception of the recently proposed Transmission-Mutation Index.
  
  
  CONCLUSIONS
  Any transmission index needs to take into account mutation of the marker and the effects of sampling. Simple indices are unlikely to capture the full complexity of the underlying processes.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Australia. m.tanaka@unsw.edu.au
authors.forename: Mark M
authors.initials: MM
authors.lastname: Tanaka
authors.forename: Renault
authors.initials: R
authors.lastname: Phong
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Francis
mesh_terms: D003198:Computer Simulation; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification; D014376:Tuberculosis / Q000382:microbiology / Q000635:transmission*
chemical_list: D005819:Genetic Markers