Volume 16, Number 2—February 2010
Research
Associations between Mycobacterium tuberculosis Strains and Phenotypes
Table 1
Analysis of associations between Mycobacterium tuberculosis phylogenetic lineages defined by SNP analysis and spoligotyping families in the group of isolates not classified using VNTR codes, UK*
| Spoligotypes | Lineages (6,7) and relevant MIRU codes (12) |
||||
|---|---|---|---|---|---|
| M. tuberculosis |
M. bovis; 10–2, 40–2, C–5 | ||||
| I/East Asian; 39–3, A–4, C–4 | II/European American; 16–1,2,3, 39–2, B–1,2 | III/EAI; 23–5, C–2 | IV/Indo-Oceanic; 24–2, 26–2 | ||
| H37Rv, n = 2 | 0 | 2 | 0 | 0 | 0 |
| Beijing, n = 13 | 13 | 0 | 0 | 0 | 0 |
| LAM, n = 17 | 0 | 17 | 0 | 0 | 0 |
| T, n = 53 | 1 600740007764671† | 51 | 0 | 1 777200007403371† | 0 |
| Haarlem, n = 21 | 0 | 20 | 0 | 1 777777774000731† | 0 |
| EAI, n = 61 | 2 777777770003331† 477777377413771† | 1 777734000000031† | 0 | 58 | 0 |
| CAS, n = 18 | 0 | 0 | 18 | 0 | 0 |
| X, n = 9 | 0 | 9 | 0 | 0 | 0 |
| S, n = 2 | 0 | 2 | 0 | 0 | 0 |
| Family 33, n = 4 | 1 | 1 | 0 | 2 | 0 |
| Family 35, n = 7 | 7 | 0 | 0 | 0 | 0 |
| Family 36, n = 5 | 0 | 5 | 0 | 0 | 0 |
| M. bovis BCG, n = 4 | 0 | 0 | 0 | 0 | 4 |
| M. africanum, n = 35 | 34 | 1 710044706302261* | 0 | 0 | 0 |
*SNP, single nucleotide polymorphism; VNTR, variable number tandem repeat; MIRU, mycobacterial interspersed repetitive unit; EAI, East African–Indian; LAM Latin American; CAS, Central Asian; BCG, bacillus Calmette-Guérin. European American includes the X, T, LAM, S, and Haarlem families.
†Octal codes indicate spoligotyping patterns for isolates with disagreements between SNP- and spoligotype-defined lineages. Dominant families within each lineage are in boldface.
