Background
Genomics of M. tuberculosis
Methods
Result
Spoligotyping results of M. tuberculosis strains from Ethiopia
Author | Study Regiona | Type of Patientsb | No. isolates | Typing methodc | No. strains | Clustering rate (%) | Shared rated (%) | Predominant strains | Lineage/Clade |
---|---|---|---|---|---|---|---|---|---|
Agonafir et al., 2010 [28] | AA | MDR-TB | 107 | Spoligotyping | 81 | 80.43 | 82.61 | SIT149 | T, CAS |
Deribew et al., 2012 [29] | OR | PTB | 17 | Spoligotyping | 17 | 64.71 | 64.71 | SIT777 | T, H, CAS |
Mihret et al., 2012 [30] | AA | PTB | 192 | Spoligotyping | 192 | 82.81 | 88.02 | SIT149 | T, CAS, H |
Ameni et al., 2013 [31] | OR | PTB | 139 | Spoligotyping | 130 | 71.54 | 84.62 | SIT149, SIT53 | EA, EAI |
Diriba et al., 2013 [32] | AA | MDR-TB | 184 | Spoligotyping | 184 | 85.87 | 77.72 | SIT21, SIT149 | EA and IO |
Firdessa et al., 2013 [17] | AA, AM, OR, SNNPR | PTB, ETB | 950 | Spoligotyping, MIRU-VNTR, SNP | 950 | 62.21 | 81.79 | SIT149, SIT25 | EA, EAI |
Garedew et al., 2013a [33] | AM | PTB | 71 | Spoligotyping | 96 | 85.42 | 94.79 | SIT149, SIT53 | EA |
Garedew et al., 2013b [34] | AM | ETB | 44 | Spoligotyping | 44 | 79.54 | 95.45 | SIT54, SIT53 | EA, IO |
Workalemahu et al., 2013 [36] | OR | Child TB | 15 | Spoligotyping | 24 | 54.17 | 54.17 | SIT37 | EA |
Yimer et al., 2013 [37] | AM | PTB | 237 | Spoligotyping and MIRU-VNTR | 237 | 83.54 | 82.70 | SIT25, SIT910 | CAS_DELHI |
Belay et al., 2014 [38] | AM | PTB | 105 | Spoligotyping | 103 | 77.67 | 93.20 | SIT149, SIT37 | T3-ETH, T3 |
Debebe et al., 2014 [39] | AM | PTB | 118 | Spoligotyping | 118 | 83.89 | 89.83 | SIT25 and SIT53 | EA, CAS |
Disassa et al., 2015 [42] | BG | PTB | 33 | Spoligotyping | 33 | 45.45 | 75.76 | SIT53 | EA |
Gebrezgabiher et al., 2015 [43] | SNNPR | PTB, ETB | 31 | Spoligotyping | 31 | 38.71 | 61.29 | SIT53 | EA |
Getahun et al., 2015 [44] | ETH | PTB | 92 | Spoligotyping | 91 | 70.33 | 58.24 | SIT53, SIT149 | EA, EAI |
Korma et al., 2015 [45] | AA | ETB | 58 | Spoligotyping | 58 | 60.34 | 82.76 | SIT53, SIT149 | T |
Maru et al., 2015 [46] | AM | PTB | 118 | Spoligotyping | 118 | 73.73 | 90.68 | SIT25, SIT53 | H, T, CAS-DELHI |
Nuru et al., 2015 [47] | AM | PTB, ETB | 168 | Spoligotyping | 168 | 58.33 | 72.62 | SIT289, SIT134 | EA, EAI |
Zewudie et al., 2016 [51] | AA | PTB, ETB | 73 | Spoligotyping | 73 | 61.64 | 79.45 | SIT149, SIT53 | T, CASI-DELHI |
Nuru et al., 2017 [52] | AM | PTB, ETB | 38 | Spoligotyping | 38 | 36.84 | 68.42 | SIT53, SIT289 | EA, EAI |
Bedawi et al., 2017 [54] | OR & SNNPR | PTB | 281 | Spoligotyping | 281 | 79.36 | 79.72 | SIT53, SIT149 | EA |
Lineage | Clade/Sublineagea | Total strains | Percentage |
---|---|---|---|
Lineage 1 (Indo-Oceanic) | EAI | 22 | 0.9 |
EAI1-SOM | 5 | 0.2 | |
EAI5 or EAI3 | 4 | 0.15 | |
EAI6-BGD1 | 4 | 0.15 | |
F33 | 9 | 0.35 | |
MANU | 156 | 6.0 | |
Manu_ancestor | 41 | 1.6 | |
MANU2 | 115 | 4.5 | |
Lineage 2 (East Asian) | Beijing | 5 | 0.2 |
Lineage 3 (East African-Indian) | CAS | 598 | 23.1 |
CAS | 21 | 0.8 | |
CAS_DELHI | 472 | 18.3 | |
CAS1_KILI | 105 | 4.0 | |
Lineage 4 (Euro-American) | Haarlem | 281 | 10.1 |
H1 | 24 | 0.9 | |
H3 | 188 | 7.3 | |
H4 | 58 | 2.2 | |
H4/Ural-1 | 11 | 0.4 | |
LAM | 101 | 3.9 | |
LAM1 | 4 | 0.15 | |
LAM10 | 4 | 0.15 | |
LAM3 and S/Convergent | 24 | 0.9 | |
LAM5 | 6 | 0.2 | |
LAM7_TUR | 44 | 1.7 | |
LAM9 | 19 | 0.7 | |
S | 3 | 0.12 | |
T | 1247 | 48.3 | |
T | 10 | 0.4 | |
T1 | 502 | 19.4 | |
T1 (Tuscany variant) | 3 | 0.12 | |
T1/T3 | 5 | 0.2 | |
T2 | 85 | 3.3 | |
T2-T3 | 5 | 0.2 | |
T3 | 191 | 7.4 | |
T3-ETH | 434 | 16.8 | |
T4 | 12 | 0.5 | |
X | 45 | 1.8 | |
X1 | 40 | 1.6 | |
X2 | 5 | 0.2 | |
Lineage 7 (Ethiopian) | Ethiopian | 107 | 4.1 |
Unknown | Unknown | 19 | 0.7 |
U | 8 | 0.31 | |
U (likely H) | 8 | 0.31 | |
U (likely T3) | 3 | 0.12 |
SIT (Clade) Octal number | N. strains (%) in this study | N. in the data base | Distribution in regions with ≥3% of a given SITsa | Distribution in countries with ≥3% of a given SITsb |
---|---|---|---|---|
149 (T3_ETH) 777,000,377,760,771 | 420 (16.2) | 241 | EURO-N 33.2, AFRI-E 32.4, EURO-W 12.4, ASIA-W 10.8, AMER-N 8.7 | ETH 32.4, DNK 23.6, SAU 10.8, USA 8.7, NLD 7.1, GBR 5.8, FRA 3.7 |
53 (T1) 777,777,777,760,771 | 343 (13.2) | 3812 | AMER-N 21.7, EURO-W 16.1, AMER-S 9.8, EURO-S 9.2, ASIA-W 8.3, AFRI-S 6.3, EURO-N 5.5, AFRI-E 3.9 | USA 21.3, ZAF 6.1, ITA 5.9, AUT 5.6, BRA 5.1, TUR 4.3, FRA 3.9, SAU 3.4 |
25 (CAS_DELHI) 703,777,740,003,171 | 266 (10.2) | 254 | ASIA-W 34.3, ASIA-S 11.8, EURO-N 6.3, AFRI-N 9.8, EURO-W 9.1, AMER-N 19.3 | SAU 33.8, USA 19.3, IND 6.3, SDN 5.5, NLD 5.5, GBR 3.9, LIB 3.5 |
37 (T3) 777,737,777,760,771 | 162 (6.2) | 243 | EURO-W 18.9, AMER-N 17.3, ASIA-W 13.6, EURO-N 12.8,EURO-E 7, ASIA-S 6.2, EURO-S 4.5, AMER-S 4.1,AFRI-E 3.7, CARI 3.7 | USA 15.2, SAU 9.8, DNK 7.0, NLD 5.7, AUT 4.9, CZE 4.9, IND 4.5, BGR 3.9, ITA 3.7, FRA 3.3, TUR 3.3 |
21 (CAS1_KILI) 703,377,400,001,771 | 102 (4.0) | 243 | AFRI-E 61.3, AMER-N 9.1, EURO-W 8.6, EURO-N 7, AFRI-S 5.3, ASIA-W 4.9 | TZA 25.5, MDG 15.2, USA 9.0, ZMB 9.0, KEN 7.0, NLD 5.3, ZAF 5.3, SAU 4.9, GBR 4.1 |
54(MANU2) 777,777,777,763,771 | 87 (3.4) | 114 | ASIA-S 21.1, AMER-N 17.5, AFRI-S 14, ASIA-W 12.3, ASIA-N 8.8, AMER-S 3.5, EURO-N 3.5, EURO-W 3.5 | IND 19.3, USA 17.5, ZAF 14.0, SAU 9.6, RUS 8.8 |
26(CAS1_DELHI) 703,777,740,003,771 | 76 (3.0) | 896 | ASIA-S 48.4, AMER-N 23.7, EURO-N 8.6, ASIA-W 7.9, EURO-N 3 | USA 23.7, IND 23.4, PAK 16.1, BGD 8.0, SAU 7.8, NLD 4.8 |
52 (T2) 777,777,777,760,731 | 69 (2.7) | 526 | EURO-W 26, AMER-N 19.8, EURO-E 7.6, EURO-N 6.5, AFRI-M 6.3, ASIA-W 5.7, EURO-S 5.5, AFRI-S 3.8, AFRI-S 3.8, AFRI-E 3.2 | USA 19.0, BLG 8.4, FRA 7.6, NLD 5.1, AUS 4.4, CZE 4.7, ITA 4.7, CAM 4.5, ZAF 3.8 |
910 (ETH) 700,000,007,177,771 | 65 (2.5) | 5 | AMER-N 60, AFRI-E 40 | USA 60.0, ETH 40.0 |
289(CAS1_DELHI) 703,777,740,003,571 | 59 (2.3) | 9 | ASIA-S 44.4, EURO-W 22.2, ASIA-W 11.1, AUST 11.1, AMER-N 11.1 | NZD 22.2, PAK 22.2, AUS 11.1, BGD 11.1, IND 11.1, SAU 11.1, USA 11.1 |