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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

CountryRegion (No. of DR samples/total in study)DST phenotype (% of isolates)HIV/TB coinfection in DR-TB cases %Genotype (%)Genotyping methodRef.
AngolaLuanda (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]
BeninCountrywide (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 casesL1 (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 FasoOuagadougou (3/58)MDR-TB (33%), mono-resistant TB (67%)33%T (67%), Haarlem (33%)MIRU-VNTR, Spoligotyping[20]
CARBangui (53/318)MDR-TB (100%)26%T (47%), proportion of Cameroon, H, EAI not specifiedSpoligotyping[21]
CameroonAdamaoua (35/437)MDR (16%), mono-(71%) & poly-resistant (13%)Reported, but not specified for DR casesCameroon (68.5%), T1 (17%), U (8.5%), H (3%), T2 (3%)MIRU-VNTR, Spoligotyping[22]
ChadCountrywideMDR-TB (19%) mono-resistant TB (81%)Not reportedT (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 reportedT (46%), H (31%), H37Rv (8%), EAI (8%), Orphan (7%)Spoligotyping[24]
Congo BrazzavilleBrazzavile & Pointe Noire (21/46)MDR-TB (71%), I mono-resistant (19%), S mono- resistant (5%), IS poly resistant TB (5%)Not reportedT (67%), Beijing (20%), LAM (13%)DNA sequencing, MIRU-VNTR[25]
DjiboutiCountrywide (15/435)MDR-TBNot reportedBeijing (73%), T (27%)MLVA, Spoligotyping, WGS[26]
Djibouti city (29/32)XDR-TB (14%), MDR-TB (79%), mono-resistant TB (7%)Not reportedCAS (24%), LAM (21%), Orphan (21%), EAI (17%), T (10%), Beijing (3.5%), X (3.5%)IS6110-RFLP, MIRU-VNTR, Spoligotyping[27]
EgyptCountrywide (16/67)Mono-resistant TB (69%), poly-resistant TB (31%)Not reportedT, LAM, M. bovis, CAS, S, undefinedIS6110-RFLP, Spoligotyping[28]
Assiut (11/25)MDR-TB (100%)Not reportedNot definedIS6110-RFLP[29]
EthiopiaNorth-West (116/244)MDR-TB (10%), mono- & poly- resistant TB (90%),Reported, but not specified for DR casesH (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 casesHaarlem (37%), other unspecifiedMLPA[31]
Jimma (1/15)I mono resistant (100%)Reported, but not specified for DR caseT3_ETHSpoligotyping, DNA sequencing[32]
Oromia, SNNRPS, HarariMDR-TB (15%), mono- & poly-resistant TB (85%)Not reportedEthiopia_3 (34%), Lineage 7 (22%), CAS (11%), EA (11%), H37Rv like (7%), H (7%), X (4%), EAI (4%)Spoligotyping[33]
GhanaSouth-west, Southern and Northern Ghana (71/130)MDR-TB (6%), mono- & poly-resistant TB (94%)Not reportedCameroon (47%), MAF (22%), undefined (31%)DNA sequencing, IS6110-RFLP, Spoligotyping[34] [35] [36]
GuineaConakry (154/359)MDR-TB (6%), mono- (41%), poly-resistant TB (53%)Not reportedT (35%), H (20%), CAS (25%), Beijing (10%), S (5%), Orphan (5%)Spoligotyping[37]
KenyaNairobi (33/73)MDR-TB (45.5%), poly- (15%), mono-resistant TB (39%)Not reportedCAS (45.5%), Orphan (30.5%), S (9%), Beijing (6%), LAM (6%), T (3%)DNA sequencing, Spoligotyping[38] [39]
North-EasternMDR-TB (14.5%), Mono- (73%), poly resistant TB (12.5%)Not reportedNot definedIS6110-RFLP, Spoligotyping
MalawiKaronga district (116/16870I resistant (100%)Reported, but not specified for DR casesL1 (17%), L3 (18%), L4 (65%)WGS[40]
MaliBamako (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 casesT (64%), MAF2 (11%), LAM (5%), H (5%), EAI (4%), M. bovis (3.5%), Beijing (3.5%), other (2%)Spoligotyping[41]
MoroccoCasablanca (53/147)MDR-TB (56%), mono-resistant TB (22%) & poly-resistant (22%)Not reportedEAI, LAM, H, Beijing, otherMIRU-VNTR[42]
Countrywide (19/198)MDR-TB (37%), Mono- (7%), poly resistant (56%)Not reportedLAM9 (42%), H (22%), other (21%), Beijing (5%), T (5%), U (5%)MIRU-VNTR, Spoligotyping[43]
MozambiqueCountrywide (1/543)1 MDR-TB case1 HIV positive caseBeijingIS6110-RFLP, MIRU-VNTR, Spoligotyping[44]
NigeriaCross river state (6/58)6 MDR-TB cases33%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 reportedCameroon (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]
RwandaCountrywide (67/151)MDR-TB (96%), mono-resistant TB (4%)48%T2 (72%), Undefined (28%)RD analysis, Spoligotyping[48]
Sierra LeoneWestern area & kenema district (50/97)MDR-TB (22%), mono- (48%), poly-resistant TB (30%)Not reportedSierra Leone1/2 (26%), LAM (16%), H (16%), MAF (14%), Beijing (8%), S (8%)IS6110-RFLP, MIRU-VNTR, Spoligotyping[49]
South AfricaEastern Cape (342/651)XDR-TB (25%)Not reportedBeijing (93%), LAM (3%), MANU (3%), S (1%)DNA sequencing, IS6110-RFLP, Spoligotyping[50] [51]
Pre- XDR TB (31%)Not reportedBeijing (92%), LAM (6%), H (1%), Orphan (1%)
MDR-TB (44%)Not reportedBeijing (39%), LAM (30%), T (12%), S (5%), X (2%), H (1%), U (1%), Orphan (10%)
Gauteng (672/984)XDR-TB (9%)Not reportedBeijing (45%), LAM (41%), T (5%), H (5%), EAI (2%), X (2%)MIRU-VNTR, Spoligotyping[52] [53] [54] [55]
Pre-XDR-TB (5%)Not reportedLAM (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 reportedLAM4 (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 reportedBeijing (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 reportedEAIMIRU-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%)
SudanOmdurman, Khartoum & Port Sudan (108/235)MDR-TB (24%), mono resistant TB (76%)Not reportedCAS1(49%), Beijing (2%), undefined (49%)MIRU-VNTR, Spoligotyping[63]
TanzaniaChagga 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]
TunisiaBizerte 2121 MDR-TB cases0%Haarlem3 (95%), undefined (5%)MIRU-VNTR, Spoligotyping, PCR typing[65]
UgandaMubende district (13/67)MDR-TB (15%), mono- (69%), poly-resistant TB (16%)Reported, but not specified for DR caseT (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 caseUganda (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 caseT (27%), T2-Uganda (18%), CAS (20%), LAM (15%), orphan (12%), undefined (6%)Spoligotyping[68]
Kampala districtMDR-TB (54%), I mono-resistant TB (46%)29%T (71%), LAM9 (11%), Uganda (3.5%), Beijing (3.5%), orphan (11%)Spoligotyping[69]
ZimbabweCountrywide (58/86)Pre-XDR (27%), MDR-TB (73%)Not reportedLAM11_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
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