title: Reliability of multilocus sequence typing of the Burkholderia cepacia complex in cystic fibrosis.
abstract: BACKGROUND
  Infection with the Burkholderia cepacia complex is an important cause of morbidity and mortality in cystic fibrosis (CF). We investigated the molecular clock speed of the seven genes used in the multilocus sequence typing (MLST) scheme for these bacteria.
  
  
  METHODS
  At least two isolates, separated by months to years, from each of 20 patients were typed using MLST. In total 41 isolates, providing 128 isolate-years, were analyzed. Mutation and recombination rates were estimated assuming a Poisson distribution.
  
  
  RESULTS
  Out of 20 patients, 15 had no change in sequence type over time (mean 7.07 years, range 1.09 to 14.24). One patient had strain replacement. Three patients had evidence of recombination involving one of the seven housekeeping genes, and one patient had evidence of recombination of two genes. The mutation rate was estimated as 2.36x10(-6) per nucleotide per year (50% confidence limit) and 1.02x10(-5) per nucleotide per year (upper 95% confidence limit). The rate of nucleotide changes due to recombination events was estimated as 0.676 to 0.839 per year (95% confidence limits).
  
  
  CONCLUSIONS
  B. cepacia complex housekeeping genes have a slow molecular clock speed and MLST provides a robust and reliable typing technique for isolates from this complex. A low rate of point mutation was found, with a higher rate of recombination events, in keeping with previous cross-sectional epidemiological data. The study also demonstrated, for the first time, recombination in a longitudinal in vivo study.
authors.affiliation: Department of Biological Sciences, Warwick University, Coventry, CV4 7AL, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Waine
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Henry
authors.forename: Adam
authors.initials: A
authors.lastname: Baldwin
authors.forename: David P
authors.initials: DP
authors.lastname: Speert
authors.forename: David
authors.initials: D
authors.lastname: Honeybourne
authors.forename: Eshwar
authors.initials: E
authors.lastname: Mahenthiralingam
authors.forename: Chris G
authors.initials: CG
authors.lastname: Dowson
mesh_terms: D015373:Bacterial Typing Techniques / Q000379:methods*; D019121:Burkholderia Infections / Q000235:genetics*; D042602:Burkholderia cepacia complex / Q000235:genetics*; D003550:Cystic Fibrosis / Q000382:microbiology*; D019143:Evolution, Molecular; D006801:Humans; D017354:Point Mutation; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*