title: Genetic stability of pneumococcal isolates during 35 days of human experimental carriage.
abstract: BACKGROUND
  Pneumococcal carriage is a reservoir for transmission and a precursor to pneumococcal disease. The experimental human pneumococcal carriage model provides a useful tool to aid vaccine licensure through the measurement of vaccine efficacy against carriage (VEcol). Documentation of the genetic stability of the experimental human pneumococcal carriage model is important to further strengthen confidence in its safety and conclusions, enabling it to further facilitate vaccine licensure through providing evidence of VEcol.
  
  
  METHODS
  229 isolates were sequenced from 10 volunteers in whom experimental human pneumococcal carriage was established, sampled over a period of 35 days. Multiple isolates from within a single volunteer at a single time provided a deep resolution for detecting variation. HiSeq data from the isolates were mapped against a PacBio reference of the inoculum to call variable sites.
  
  
  RESULTS
  The observed variation between experimental carriage isolates was minimal with the maximum SNP distance between any isolate and the reference being 3 SNPs.
  
  
  CONCLUSIONS
  The low-level variation described provides evidence for the stability of the experimental human pneumococcal carriage model over 35 days, which can be reliably and confidently used to measure VEcol and aid future progression of pneumococcal vaccination.
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: R A
authors.initials: RA
authors.lastname: Gladstone
authors.affiliation: Respiratory Infection Group, Liverpool School of Tropical Medicine, Liverpool, UK.
authors.forename: J F
authors.initials: JF
authors.lastname: Gritzfeld
authors.affiliation: Sequencing R&D Group, Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: P
authors.initials: P
authors.lastname: Coupland
authors.affiliation: Respiratory Infection Group, Liverpool School of Tropical Medicine, Liverpool, UK.
authors.forename: S B
authors.initials: SB
authors.lastname: Gordon
authors.affiliation: Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge, UK. Electronic address: sdb@sanger.ac.uk.
authors.forename: S D
authors.initials: SD
authors.lastname: Bentley
mesh_terms: D000293:Adolescent; D000328:Adult; D002353:Carrier State / Q000382:microbiology*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D064368:Healthy Volunteers; D006801:Humans; D008875:Middle Aged; D011008:Pneumococcal Infections / Q000382:microbiology*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D013296:Streptococcus pneumoniae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D055815:Young Adult
chemical_list: D004269:DNA, Bacterial
keywords: Experimental human pneumococcal carriage; Pneumococcal vaccines; Streptococcus pneumoniae; Vaccine efficacy against carriage (VEcol)