Background
Burden of drug resistant tuberculosis in Africa
Treatment regimens implemented
Diagnosis of drug resistant tuberculosis
Drug resistance tuberculosis surveillance
Molecular typing tools in epidemiological investigations
Methods
Search strategy and selection criteria
Country | Region (No. of DR samples/total in study) | DST phenotype (% of isolates) | HIV/TB coinfection in DR-TB cases % | Genotype (%) | Genotyping method | Ref. |
---|---|---|---|---|---|---|
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 | |
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 | |
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 | |
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 | |
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 | ||
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 | ||
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 | ||
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] |
Results
Overview of drug resistant Mycobacterium tuberculosis strain types in Africa
Molecular epidemiological data
Population structure of drug resistant TB genotypes in Africa
Application of molecular methods to describe transmission dynamics of drug resistant tuberculosis in Africa
Acquired MDR- and XDR-TB
Outbreaks
Country (region) | MTB phenotype (number of cases) | MTB lineage (clustered/total isolates) | Transmission dynamics (nosocomial and/or outbreak) | HIV/TB coinfectiona (%) | Genotyping method | Ref. |
---|---|---|---|---|---|---|
Benin (Cotonou) | S mono-resistant TB (17) | Lineage 2/Beijing (17/194) | Community outbreak | 6/17 (35%) | MIRU-VNTR | [19] |
Mali (Bamako) | XDR-TB(3) | Lineage 4 (3) | Nosocomial transmission | 1/2 (50%) | MIRU-VNTR, Spoligotyping | [15] |
South Africa (KZN) | XDR-TB (148) | Lineage 4 (53/148) | Nosocomial transmission | 123/126 (98%) | DNA sequencing, IS6110-RFLP, Spoligotyping | [88] |
South Africa (KZN) | MDR-TB (3) | Lineage 4 /F15/LAM4/KZN (3/3) | Nosocomial transmission | HIV status of clustered isolates not defined | IS6110-RFLP | [89] |
South Africa (North-Western) | I mono-resistant TB (13/128) Poly-resistant TB (7/128) MDR-TB (108/128) Pre-XDR-TB (26/108) XDR-TB (5/108) | Lineage Not specified (74/128) | Community outbreak and nosocomial transmission | 84/91 (92%) | DNA sequencing, IS6110-RFLP, MIRU-VNTR, Spoligotyping | [82] |
South Africa (Western Cape) | MDR-TB (209) | L2/Beijing (62/209) | Community outbreak | Not specified | DNA sequencing, IS6110-RFLP, MIRU-VNTR, Spoligotyping | [59] |
South Africa (Western Cape) | MDR-TB (21) | L2/Beijing (16/21) | Community outbreak | 0% | IS6110-RFLP | [60] |
Tunisia | MDR-TB (21) | Lineage 4/Haarlem3 (19/21) | Community outbreak | 0% | IS6110-RFLP, Spoligotyping | [65] |