Table 2.
Relationship between single-nucleotide polymorphisms and mycobacterial interspersed repetitive units-variable number tandem repeat differences
| 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 |
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].
MIRU-VNTR mycobacterial interspersed repetitive units-variable number tandem repeats, SNP single-nucleotide polymorphisms
aIt was not possible to separate the mixed genotypes to precisely determine a SNP difference