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Table 1 Genotypes associated with drug resistant TB across Africa

From: Molecular epidemiology of drug resistant Mycobacterium tuberculosis in Africa: a systematic review

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 [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]
  1. aBased on genotyping. Abbreviations: XDR-TB Extensively drug resistant tuberculosis, MDR-TB Multidrug resistant tuberculosis, R Rifampicin, H Isoniazid, E Ethambutol, S Streptomycin, WGS Whole genome sequencing, MLVA Multiple loci VNTR analysis, IS6110-RFLP Insertion Sequence 6110-Restriction Fragment Length Polymorphism, Spoligotyping Spacer oligonucleotide typing, MIRU-VNTR Mycobacterial interspaced repeat units-variable number of tandem repeats, PCR Polymerase Chain Reaction, CAS Central Asian, EAI_SOM East African Indian_Somalia, KZN KwaZulu-Natal, LAM Latin American Mediterranean, MAF Mycobacterium africanum, H Haarlem, ETH Ethiopia, SNNRPS Southern Nations Nationalists and Peoples Regional State‚ ref reference