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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