title: Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data.
abstract: BACKGROUND
  Mycobacterium tuberculosis is characterised by limited genomic diversity, which makes the application of whole genome sequencing particularly attractive for clinical and epidemiological investigation. However, in order to confidently infer transmission events, an accurate knowledge of the rate of change in the genome over relevant timescales is required.
  
  
  METHODS
  We attempted to estimate a molecular clock by sequencing 199 isolates from epidemiologically linked tuberculosis cases, collected in the Netherlands spanning almost 16 years.
  
  
  RESULTS
  Multiple analyses support an average mutation rate of ~0.3 SNPs per genome per year. However, all analyses revealed a very high degree of variation around this mean, making the confirmation of links proposed by epidemiology, and inference of novel links, difficult. Despite this, in some cases, the phylogenetic context of other strains provided evidence supporting the confident exclusion of previously inferred epidemiological links.
  
  
  CONCLUSIONS
  This in-depth analysis of the molecular clock revealed that it is slow and variable over short time scales, which limits its usefulness in transmission studies. However, the superior resolution of whole genome sequencing can provide the phylogenetic context to allow the confident exclusion of possible transmission events previously inferred via traditional DNA fingerprinting techniques and epidemiological cluster investigation. Despite the slow generation of variation even at the whole genome level we conclude that the investigation of tuberculosis transmission will benefit greatly from routine whole genome sequencing.
authors: Josephine M
authors: JM
authors: Bryant
authors: Anita C
authors: AC
authors: Schürch
authors: Henk
authors: H
authors: van Deutekom
authors: Simon R
authors: SR
authors: Harris
authors: Jessica L
authors: JL
authors: de Beer
authors: Victor
authors: V
authors: de Jager
authors: Kristin
authors: K
authors: Kremer
authors: Sacha A F T
authors: SA
authors: van Hijum
authors: Roland J
authors: RJ
authors: Siezen
authors: Martien
authors: M
authors: Borgdorff
authors: Stephen D
authors: SD
authors: Bentley
authors: Julian
authors: J
authors: Parkhill
authors: Dick
authors: D
authors: van Soolingen
mesh_terms: D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D059645:Mutation Rate; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D009426:Netherlands / Q000453:epidemiology; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013997:Time Factors; D014397:Tuberculosis, Pulmonary / Q000453:epidemiology / Q000382:microbiology / Q000635:transmission*