Table 2 Participant characteristics by Mycobacterium tuberculosis–complex (Mtbc) lineages in Botswana, 2012–2016.

From: Phylodynamic analysis reveals disparate transmission dynamics of Mycobacterium tuberculosis complex lineages in Botswana

 

Mtbc lineage

 

L1

n (%)

L2

n (%)

L3

n (%)

L4

n (%)

Total

n (%)

Sex

     

Female

35 (40.7)

38 (52.8)

6 (50.0)

522 (44.1)

601 (44.4)

Male

51 (59.3)

34 (47.2)

6 (50.0)

662 (55.9)

753 (55.6)

Age

<=15

2 (2.3)

3 (4.2)

1 (8.3)

21 (1.8)

27 (2.0)

16–24

10 (11.6)

9 (12.5)

1 (8.3)

226 (19.1)

246 (18.2)

25–40

47 (54.7)

46 (63.9)

7 (58.3)

632 (53.4)

732 (54.1)

41–64

24 (27.9)

14 (19.4)

3 (25.0)

280 (23.6)

321 (23.7)

>=65

3 (3.5)

0

0

25 (2.1)

28 (2.1)

Previous TB

No

63 (73.3)

57 (79.2)

10 (83.3)

967 (81.7)

1097 (81.0)

Yes

23 (26.7)

15 (20.8)

2 (16.7)

217 (18.3)

257 (19.0)

Isoniazid preventive therapy

No

83 (96.5)

64 (88.9)

12 (100.0)

1127 (95.2)

1286 (95.0)

Yes

2 (2.3)

5 (6.9)

0

42 (3.5)

49 (3.6)

Unknown

1 (1.2)

3 (4.2)

0

15 (1.3)

19 (1.4)

AFB smear results

Negative

5 (5.8)

7 (9.7)

3 (25.0)

76 (6.4)

91 (6.7)

Positive

61 (70.9)

46 (63.9)

8 (66.7)

752 (63.5)

867 (64.0)

Not done

20 (23.3)

19 (26.4)

1 (8.3)

356 (30.1)

396 (29.2)

TB type

Pulmonary

79 (91.9)

65 (90.3)

11 (91.7)

1075 (90.8)

1230 (90.8)

Extrapulmonary

7 (8.1)

6 (8.3)

0

105 (8.9)

118 (8.7)

Unknown

0

1 (1.4)

1 (8.3)

4 (0.3)

6 (0.4)

HIV status

Negative

27 (31.4)

27 (37.5)

5 (41.7)

533 (45.0)

592 (43.7)

Positive

56 (65.1)

42 (58.3)

7 (58.3)

616 (52.0)

721 (53.2)

Unknown

3 (3.5)

3 (4.2)

0

35 (3.0)

41 (3.0)

ART status1

Never taken ART

26 (46.4)

17 (40.5)

1 (14.3)

278 (45.1)

322 (44.7)

Taking ART

25 (44.6)

20 (47.6)

3 (42.9)

277 (45.0)

325 (45.1)

Took ART but stopped

1 (1.8)

1 (2.4)

2 (28.6)

11 (1.8)

15 (2.1)

Unknown

4 (7.1)

4 (9.5)

1 (14.3)

50 (8.1)

59 (8.2)

Phenotypic drug-resistance2

INH-resistant

13 (15.1)

11 (15.3)

1 (8.3)

78 (6.6)

103 (7.6)

RIF-resistant

10 (11.6)

7 (9.7)

2 (16.7)

53 (4.5)

72 (5.3)

EMB-resistant

9 (10.5)

5 (6.9)

2 (16.7)

41 (3.5)

57 (4.2)

PZA-resistant

5 (5.8)

1 (1.4)

0

21 (1.8)

27 (2.0)

MDR-TB3

7 (8.1)

7 (9.7)

1 (8.3)

35 (3.0)

50 (3.7)

Genotypic drug-resistance4

INH-resistant

17 (19.8)

14 (19.4)

0

77 (6.5)

108 (8.0)

RIF-resistant

19 (22.1)

13 (18.1)

2 (16.7)

90 (7.6)

124 (9.2)

EMB-resistant

10 (11.6)

2 (2.8)

0

27 (2.3)

39 (2.9)

PZA-resistant

11 (12.8)

2 (2.8)

0

89 (7.5)

102 (7.5)

MDR-TB3

13 (15.1)

10 (13.9)

0

50 (4.2)

73 (5.4)

  1. AFB acid-fast bacilli. ART antiretroviral therapy. INH Isoniazid. RIF Rifampin. EMB Ethambutol. PZA Pyrazinamide. MDR-TB Multidrug-resistant TB.
  2. 1Among HIV-positive individuals only.
  3. 2Culture-based phenotypic drug susceptibility testing for first-line anti-tuberculous drugs was performed with MGIT 960 system. The critical concentrations for INH, RIF, ethambutol (EMB), and pyrazinamide (PZA) using MGIT DST were 0.1 µg/ml, 1.0 µg/ml, 5.0 µg/ml, and 100 µg/ml, respectively.
  4. 3Mycobacterium tuberculosis complex that are resistant to both isoniazid and rifampin.
  5. 4Mycobacterium tuberculosis complex genomes were annotated with known association to antibiotic resistance by MTBseq.
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