Table 1 Genotypes associated with drug resistant TB across Africa

Angola

Luanda (22/89)

MDR-TB (13.5%) mono-resistant TB (55%), poly-resistant (31.5%)

Reported, but not specified for DR cases.

LAM1 (36%), T1 (23.5%), LAM9 (18%), LAM2 (9%), LAM6 (4.5%), T2 (4.5%), orphan (4.5%)

MIRU-VNTR, Spoligotyping

[17]

Benin

Countrywide (40/100)

Pre-XDR-TB (5%), MDR-TB (25%), S mono resistant-TB (35%), poly-resistant-TB (22.5%), other mono-resistant TB (12.5%)

Reported, but not specified for DR cases

L1 (3%), L2 (22.5%), L3 (3%), L4 (55%), L5 (13%), M. bovis (3%)

Spoligotyping

[18] [19]

Cotonou (17/194)

S mono resistant (100%)

35%

Beijing (100%)

MIRU-VNTR

Burkina Faso

Ouagadougou (3/58)

MDR-TB (33%), mono-resistant TB (67%)

33%

T (67%), Haarlem (33%)

MIRU-VNTR, Spoligotyping

[20]

CAR

Bangui (53/318)

MDR-TB (100%)

26%

T (47%), proportion of Cameroon, H, EAI not specified

Spoligotyping

[21]

Cameroon

Adamaoua (35/437)

MDR (16%), mono-(71%) & poly-resistant (13%)

Reported, but not specified for DR cases

Cameroon (68.5%), T1 (17%), U (8.5%), H (3%), T2 (3%)

MIRU-VNTR, Spoligotyping

[22]

Chad

Countrywide

MDR-TB (19%) mono-resistant TB (81%)

Not reported

T (5%), Cameroon (60%), H (25%), X (4%), EAI (2%), S (2%), undefined (2%)

MIRU-VNTR, Spoligotyping

[23]

N’djamena (13/33)

Mono-resistant TB (77%), poly-resistant TB (23%)

Not reported

T (46%), H (31%), H37Rv (8%), EAI (8%), Orphan (7%)

Spoligotyping

[24]

Congo Brazzaville

Brazzavile & Pointe Noire (21/46)

MDR-TB (71%), I mono-resistant (19%), S mono- resistant (5%), IS poly resistant TB (5%)

Not reported

T (67%), Beijing (20%), LAM (13%)

DNA sequencing, MIRU-VNTR

[25]

Djibouti

Countrywide (15/435)

MDR-TB

Not reported

Beijing (73%), T (27%)

MLVA, Spoligotyping, WGS

[26]

Djibouti city (29/32)

XDR-TB (14%), MDR-TB (79%), mono-resistant TB (7%)

Not reported

CAS (24%), LAM (21%), Orphan (21%), EAI (17%), T (10%), Beijing (3.5%), X (3.5%)

IS6110-RFLP, MIRU-VNTR, Spoligotyping

[27]

Egypt

Countrywide (16/67)

Mono-resistant TB (69%), poly-resistant TB (31%)

Not reported

T, LAM, M. bovis, CAS, S, undefined

IS6110-RFLP, Spoligotyping

[28]

Assiut (11/25)

MDR-TB (100%)

Not reported

Not defined

IS6110-RFLP

[29]

Ethiopia

North-West (116/244)

MDR-TB (10%), mono- & poly- resistant TB (90%),

Reported, but not specified for DR cases

H (32%), T3_ETH (32%), CAS (28%), TUR (2.5%), H37Rv like (2.5%), X (1.5%), Orphan (1.5%)

MIRU-VNTR, Spoligotyping

[30]

Butajura (95/106)

^aPoly- (98%), mono-resistant TB (2%)

Reported, but not specified for DR cases

Haarlem (37%), other unspecified

MLPA

[31]

Jimma (1/15)

I mono resistant (100%)

Reported, but not specified for DR case

T3_ETH

Spoligotyping, DNA sequencing

[32]

Oromia, SNNRPS, Harari

MDR-TB (15%), mono- & poly-resistant TB (85%)

Not reported

Ethiopia_3 (34%), Lineage 7 (22%), CAS (11%), EA (11%), H37Rv like (7%), H (7%), X (4%), EAI (4%)

Spoligotyping

[33]

Ghana

South-west, Southern and Northern Ghana (71/130)

MDR-TB (6%), mono- & poly-resistant TB (94%)

Not reported

Cameroon (47%), MAF (22%), undefined (31%)

DNA sequencing, IS6110-RFLP, Spoligotyping

[34] [35] [36]

Guinea

Conakry (154/359)

MDR-TB (6%), mono- (41%), poly-resistant TB (53%)

Not reported

T (35%), H (20%), CAS (25%), Beijing (10%), S (5%), Orphan (5%)

Spoligotyping

[37]

Kenya

Nairobi (33/73)

MDR-TB (45.5%), poly- (15%), mono-resistant TB (39%)

Not reported

CAS (45.5%), Orphan (30.5%), S (9%), Beijing (6%), LAM (6%), T (3%)

DNA sequencing, Spoligotyping

[38] [39]

North-Eastern

MDR-TB (14.5%), Mono- (73%), poly resistant TB (12.5%)

Not reported

Not defined

IS6110-RFLP, Spoligotyping

Malawi

Karonga district (116/16870

I resistant (100%)

Reported, but not specified for DR cases

L1 (17%), L3 (18%), L4 (65%)

WGS

[40]

Mali

Bamako (3/20)

XDR (100%)

50%

L4 (100%)

MIRU-VNTR, Spoligotyping

[10]

Bamako (45/126)

MDR-TB (71%), mono- & poly-resistant (29%)

Reported, but not specified for DR cases

T (64%), MAF2 (11%), LAM (5%), H (5%), EAI (4%), M. bovis (3.5%), Beijing (3.5%), other (2%)

Spoligotyping

[41]

Morocco

Casablanca (53/147)

MDR-TB (56%), mono-resistant TB (22%) & poly-resistant (22%)

Not reported

EAI, LAM, H, Beijing, other

MIRU-VNTR

[42]

Countrywide (19/198)

MDR-TB (37%), Mono- (7%), poly resistant (56%)

Not reported

LAM9 (42%), H (22%), other (21%), Beijing (5%), T (5%), U (5%)

MIRU-VNTR, Spoligotyping

[43]

Mozambique

Countrywide (1/543)

1 MDR-TB case

1 HIV positive case

Beijing

IS6110-RFLP, MIRU-VNTR, Spoligotyping

[44]

Nigeria

Cross river state (6/58)

6 MDR-TB cases

33%

LAM10-CAM (83%), T/orphan (17%)

MIRU-VNTR, Spoligotyping

[45]

Ibadan, Nnewi and Abuja, South-West (29/407)

MDR-TB (76%), mono- & poly-resistant (24%)

Not reported

Cameroon (79%), T (10%), MAF (5%), LAM (3%), U (3%)

MIRU-VNTR, Spoligotyping

[46]

South-West (36/63)

Pre-XDR- (14%), MDR-TB (86%)

25%

Cameroon (47%), MAF (14%), Ghana (8%), H (8%), LAM (6%), Uganda (6%), H37Rv (6%), X (6%), Orphan (6%)

WGS

[47]

Rwanda

Countrywide (67/151)

MDR-TB (96%), mono-resistant TB (4%)

48%

T2 (72%), Undefined (28%)

RD analysis, Spoligotyping

[48]

Sierra Leone

Western area & kenema district (50/97)

MDR-TB (22%), mono- (48%), poly-resistant TB (30%)

Not reported

Sierra Leone1/2 (26%), LAM (16%), H (16%), MAF (14%), Beijing (8%), S (8%)

IS6110-RFLP, MIRU-VNTR, Spoligotyping

[49]

South Africa

Eastern Cape (342/651)

XDR-TB (25%)

Not reported

Beijing (93%), LAM (3%), MANU (3%), S (1%)

DNA sequencing, IS6110-RFLP, Spoligotyping

[50] [51]

Pre- XDR TB (31%)

Not reported

Beijing (92%), LAM (6%), H (1%), Orphan (1%)

MDR-TB (44%)

Not reported

Beijing (39%), LAM (30%), T (12%), S (5%), X (2%), H (1%), U (1%), Orphan (10%)

Gauteng (672/984)

XDR-TB (9%)

Not reported

Beijing (45%), LAM (41%), T (5%), H (5%), EAI (2%), X (2%)

MIRU-VNTR, Spoligotyping

[52] [53] [54] [55]

Pre-XDR-TB (5%)

Not reported

LAM (41%), Beijing (27%), H (14%), EAI (14%), S (4%)

MDR-TB (73%)

LAM (29%), S (15%), T (14%), H (13%), EAI (12%), Beijing (11%), X (6%)

Mono-resistant TB (13%)

Beijing (37%), S (20%), T (16%), EAI (10%), LAM (8%), X (5%), H (4%)

KZN (1051/1139)

XDR-TB & Pre-XDR-TB (30)

88%

LAM4 (F15/LAM/KZN) (44%), X (20%), Beijing (11%), EAI (9%), T (6%), LAM3 (3%), S (3%)

DNA sequencing, IS6110-RFLP, Spoligotyping, WGS

[14] [56] [57] [55]

MDR-TB (56%)

LAM4 (F15/LAM/KZN) (40%), S (35%), T (10%), Beijing (6%), CAS (2%), EAI (2%)

Mono- & poly- resistant (14%)

LAM (35%), Beijing (30%), T (16%), EAI (8%), X (7%), S (2%), CAS (2%)

Limpopo (20/336)

XDR-TB (10%)

Not reported

LAM4 (50%), X1 (50%)

MIRU-VNTR, Spoligotyping

[52]

Pre-XDR (5%)

Orphan

MDR-TB (85%)

Beijing (35%), LAM (18%), EAI1_SOM (12%), S (12%), Orphan (11%), X (6%), T (6%)

Mpumalanga (235/336)

XDR-TB (9%)

Not reported

Beijing (29%), EAI (24%), T (14%), S (10%), X (10%), LAM9 (5%), LAM11 (5%), H (3%)

MIRU-VNTR, Spoligotyping

[52]

Pre-XDR (10%)

EAI (22%), T (18%), Beijing (13%), LAM11 (9%), X (9%), S (4%), LAM9 (4%), LAM4 (4%), H (4%), Orphan (13%)

MDR-TB (81%)

EAI (22%), T (20%), Beijing (16%), S (11%), H (5%), LAM9 (5%), LAM11 (3%), LAM3 (3%), X (4%), MANU (2%), LAM4 (1%), Orphan (8%)

North-West (31/336)

XDR-TB (3%)

Not reported

EAI

MIRU-VNTR, Spoligotyping

[52]

Pre-XDR (10%)

EAI1_SOM (67%), Orphan (33%)

MDR-TB (87%)

Beijing (37%), T (19%), S (11%), EAI1_SOM (7%), LAM3 (7%), LAM11 (7%), Orphan (18%)

Western Cape (611/1682)

XDR-TB (9%)

18%

Beijing (45%), LAM (27%), H (8%), X (6%), other (14%)

DNA sequencing, IS6110-RFLP, Spoligotyping

[58] [59] [60] [61] [62]

Pre- XDR-TB (5%)

MDR-TB (35%)

Mono- & poly-resistant TB (51%)

Sudan

Omdurman, Khartoum & Port Sudan (108/235)

MDR-TB (24%), mono resistant TB (76%)

Not reported

CAS1(49%), Beijing (2%), undefined (49%)

MIRU-VNTR, Spoligotyping

[63]

Tanzania

Chagga and Masai tribes (12/111)

MDR-TB (25%), mono- (67%) & poly-resistant TB (8%)

42%

LAM (42%), CAS (17%), T (17%), EAI (8%), MANU (8%), orphan (8%)

Spoligotyping

[64]

Tunisia

Bizerte 21

21 MDR-TB cases

0%

Haarlem3 (95%), undefined (5%)

MIRU-VNTR, Spoligotyping, PCR typing

[65]

Uganda

Mubende district (13/67)

MDR-TB (15%), mono- (69%), poly-resistant TB (16%)

Reported, but not specified for DR case

T (38%), CAS (23%), U (8%), LAM (8%), undefined (23%)

MIRU-VNTR, Spoligotyping, RD analysis

[66]

Mbabara district (20/125)

MDR-TB (10%), mono- (40%), poly-resistant TB (50%)

Reported, but not specified for DR case

Uganda (45%), CAS (25%), LAM (20%), undefined (10%)

Spoligotyping, RD analysis

[67]

Kampala district (75/497)

MDR-TB (16%), mono- & poly-resistant TB (84%)

Reported, but not specified for DR case

T (27%), T2-Uganda (18%), CAS (20%), LAM (15%), orphan (12%), undefined (6%)

Spoligotyping

[68]

Kampala district

MDR-TB (54%), I mono-resistant TB (46%)

29%

T (71%), LAM9 (11%), Uganda (3.5%), Beijing (3.5%), orphan (11%)

Spoligotyping

[69]

Zimbabwe

Countrywide (58/86)

Pre-XDR (27%), MDR-TB (73%)

Not reported

LAM11_ZWE (28%), LAM other (29%), T (16%), Beijing (13%), CAS (5.5%), S (5.5%), MANU (3%)

Spoligotyping

[70]