title: Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial.
abstract: RIFAQUIN was a tuberculosis chemotherapy trial in southern Africa including regimens with high-dose rifapentine with moxifloxacin. Here, the application of whole-genome sequencing (WGS) is evaluated within RIFAQUIN for identifying new infections in treated patients as either relapses or reinfections. WGS is further compared with mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) typing. This is the first report of WGS being used to evaluate new infections in a completed clinical trial for which all treatment and epidemiological data are available for analysis.
  
  
  
  DNA from 36 paired samples of Mycobacterium tuberculosis cultured from patients before and after treatment was typed using 24-loci MIRU-VNTR, in silico spoligotyping and WGS. Following WGS, the sequences were mapped against the reference strain H37Rv, the single-nucleotide polymorphism (SNP) differences between pairs were identified, and a phylogenetic reconstruction was performed.
  
  
  
  WGS indicated that 32 of the paired samples had a very low number of SNP differences (0-5; likely relapses). One pair had an intermediate number of SNP differences, and was likely the result of a mixed infection with a pre-treatment minor genotype that was highly related to the post-treatment genotype; this was reclassified as a relapse, in contrast to the MIRU-VNTR result. The remaining three pairs had very high SNP differences (>750; likely reinfections).
  
  
  
  WGS and MIRU-VNTR both similarly differentiated relapses and reinfections, but WGS provided significant extra information. The low proportion of reinfections seen suggests that in standard chemotherapy trials with up to 24 months of follow-up, typing the strains brings little benefit to an analysis of the trial outcome in terms of differentiating relapse and reinfection. However, there is a benefit to using WGS as compared to MIRU-VNTR in terms of the additional genotype information obtained, in particular for defining the presence of mixed infections and the potential to identify known and novel drug-resistance markers.
authors.affiliation: Institute for Infection and Immunity, St George's University of London, London, UK. awitney@sgul.ac.uk.
authors.forename: Adam A
authors.initials: AA
authors.lastname: Witney
authors.affiliation: UCL Centre for Clinical Microbiology, Royal Free Campus, UCL, London, UK.
authors.forename: Anna L E
authors.initials: AL
authors.lastname: Bateson
authors.affiliation: Institute for Infection and Immunity, St George's University of London, London, UK.
authors.forename: Amina
authors.initials: A
authors.lastname: Jindani
authors.affiliation: MRC Clinical Trials Unit at UCL, London, UK.
authors.forename: Patrick P J
authors.initials: PP
authors.lastname: Phillips
authors.affiliation: Institute for Infection and Immunity, St George's University of London, London, UK.
authors.forename: David
authors.initials: D
authors.lastname: Coleman
authors.affiliation: Institute for Infection and Immunity, St George's University of London, London, UK.
authors.forename: Neil G
authors.initials: NG
authors.lastname: Stoker
authors.affiliation: Institute for Infection and Immunity, St George's University of London, London, UK.
authors.forename: Philip D
authors.initials: PD
authors.lastname: Butcher
authors.affiliation: UCL Centre for Clinical Microbiology, Royal Free Campus, UCL, London, UK.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: McHugh
mesh_terms: D000904:Antibiotics, Antitubercular / Q000627:therapeutic use; D015373:Bacterial Typing Techniques; D004269:DNA, Bacterial / Q000032:analysis*; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D018598:Minisatellite Repeats; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D012008:Recurrence; D017422:Sequence Analysis, DNA / Q000379:methods*; D014376:Tuberculosis / Q000175:diagnosis* / Q000188:drug therapy / Q000382:microbiology
chemical_list: D000904:Antibiotics, Antitubercular; D004269:DNA, Bacterial
keywords: Clinical trial; Tuberculosis; Whole genome sequencing