Table 1.
Characteristics and risk factor analysis of large genomic clusters resulting from a threshold of 10 SNPs.
| Number | WGS cluster code | Number of cases in cluster | Number of variable fixed SNPs | Median pairwise SNP (IQR) | Lineage (sub-lineagea) | Lineage classification by Stucki/Coll | Any drug resistanceb | Gender, male:female | Median age (IQR) |
|---|---|---|---|---|---|---|---|---|---|
| 1 | WGSC-5 | 78 | 138 | 7 (6–9) | L4 (Cameroon) | L4.6.2/L4.6.2.2 | 2 | 59:17 | 34 (24–43) |
| 2 | WGSC-28 | 15 | 39 | 7 (5–7) | L4 (Ghana) | L4.10/L4.8 | ND | 11:4 | 39 (32–51) |
| 3 | WGSC-6 | 12 | 18 | 5 (3–6) | L4 (Haarlem) | NA/L4.6 | ND | 11:1 | 38 (28–48) |
| 4 | WGSC-13 | 10 | 23 | 5 (5–6) | L4 (Cameroon) | L4.6.2/L4.6.2.2 | ND | 8:2 | 42.5 (32–49) |
| 5 | WGSC-11 | 8 | 22 | 8 (6.5–8.5) | L4 (Ghana) | NA/L4.6.2 | 5 | 5:3 | 32.5 (28–41.5) |
| 6 | WGSC-42 | 8 | 6 | 3 (1–3.5) | L4 (Cameroon) | L4.6.2/L4.6.2.2 | ND | 8:0 | 25.5 (22.5–28.5) |
| 7 | WGSC-49 | 8 | 13 | 4 (1–7.5) | L4 (LAM) | L4.3/L4.3.1 | ND | 6:2 | 42 (32–54) |
| 8 | WGSC-25 | 7 | 16 | 4 (3–9) | L4 (Cameroon) | L4.6.2/L4.6.2.2 | ND | 7:0 | 39 (28–50) |
WGS, Whole genome sequencing; L4, lineage 4; ND, none determined; IQR, interquartile range.
a
Sub-lineage defined using spoligotyping.
b
Number of participants carrying strains with drug resistance to either isoniazid or rifampicin.