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Table 2 Relationship between single-nucleotide polymorphisms and mycobacterial interspersed repetitive units-variable number tandem repeat differences

From: Use of whole-genome sequencing to distinguish relapse from reinfection in a completed tuberculosis clinical trial

Study number Location Treatment arm SNPs MIRU-VNTR differences MIRU-VNTR loci amplified Prediction
001 Francistown 4 month 0 0 21 Relapse
003 Harare 4 month 0 0 14 Relapse
005 Harare 4 month 0 0 20 Relapse
007 Harare 4 month 0 0 7 Relapse
008 Harare 4 month 0 0 11 Relapse
013 Marondera 4 month 0 0 10 Relapse
014 Marondera 4 month 0 0 11 Relapse
016 Johannesburg 4 month 0 0 14 Relapse
020 Johannesburg 4 month 0 0 17 Relapse
023 Cape Town 4 month 0 0 15 Relapse
029 Cape Town 4 month 0 0 2 Relapse
030 Cape Town 4 month 0 0 15 Relapse
032 Cape Town 4 month 0 0 14 Relapse
017 Johannesburg 6 month 0 0 17 Relapse
034 Cape Town 6 month 0 0 21 Relapse
037 Cape Town Control 0 1 17 Relapse
011 Harare 4 month 0 1 16 Relapse
021 Johannesburg 4 month 0 1 16 Relapse
028 Cape Town 4 month 0 1 15 Relapse
024 Cape Town Control 1 0 18 Relapse
033 Cape Town Control 1 0 15 Relapse
010 Harare 4 month 1 0 18 Relapse
012 Harare 4 month 1 0 19 Relapse
025 Cape Town 4 month 1 0 11 Relapse
027 Cape Town 6 month 1 0 13 Relapse
019 Johannesburg Control 1 2 4 Relapse
026 Cape Town 4 month 2 0 18 Relapse
002 Harare 4 month 3 0 15 Relapse
006 Harare 4 month 3 0 12 Relapse
018 Johannesburg Control 5 0 5 Relapse
036 Cape Town 4 month 5 0 17 Relapse
031 Cape Town 6 month 5 0 16 Relapse
015 Johannesburg Control 1294 7 14 Reinfection
035 Cape Town 4 month 57a - - Relapse
004 Harare Control 737 6 6 Reinfection
009 Harare 4 month 1233 3 3 Reinfection
  1. The 36 isolates for which whole-genome sequencing was carried out are listed. With the mixed infection, although we concluded it to be a relapse, we could not precisely determine the SNP difference. For an explanation of the treatment arms, see the “Methods” section “RIFAQUIN trial” and Jindani et al. [17]. The table is sorted (in order) by number of SNPs, MIRU-VNTR differences, treatment arm and study number. Isolate 004-2 had previously been shown by Drug Susceptibility Testing (DST) to be resistant to isoniazid, rifampicin, ethambutol, streptomycin and pyrazinamide; however, all other isolates had been determined to be susceptible [17].
  2. MIRU-VNTR mycobacterial interspersed repetitive units-variable number tandem repeats, SNP single-nucleotide polymorphisms
  3. aIt was not possible to separate the mixed genotypes to precisely determine a SNP difference