TABLE 3.
Distribution of clustered isolates by the various typing methodsa
| Spoligotype | Spoligotyping alone
|
Subclustering by VNTR method
|
Subclustering by LM-PCR
|
||||
|---|---|---|---|---|---|---|---|
| No. of isolates | Frequency (%)b | Phylogenetic cladesc | Digit No. | Cluster (no. of isolates) | No. of bands in subclustered isolates | Subclusterd (no. of isolates) | |
| 50 | 12 | 4.71 | Haarlem | 32333 | A (9) | 6 | A1 (2) |
| 3 | A2 (2) | ||||||
| 32323 | C (3) | 3 | C1 (2) | ||||
| 2 | 11 | 0.95 | Haarlem | 32333 | L (6) | 6 | L (6) |
| 32323 | M (2) | 5 | M (2) | ||||
| 22333 | K (2) | 2 unrelated patterns | NAe | ||||
| 21333 | 1 | NA | NA | ||||
| 91 | 6 | 0.69 | Carib (X3) | 32333 | D (5) | 2 | D1 (4) |
| 32323 | 1 | NA | NA | ||||
| 42 | 6 | 3.11 | LAM | 21433 | F (4) | 4 | F (3) |
| 21233 | 1 | NA | NA | ||||
| 21234 | 1 | NA | NA | ||||
| 93 | 6 | 0.42 | LAM | 21433 | G (4) | 5 | G (4) |
| 21533 | H (2) | 5 | H (2) | ||||
| 17 | 5 | 0.94 | LAM | 22433 | J (3) | 3 unrelated patterns | NA |
| 12433 | 1 | NA | NA | ||||
| 22423 | 1 | NA | NA | ||||
| 70 | 4 | 0.31 | Carib (X3) | 32313 | 1 | NA | NA |
| 32323 | 1 | NA | NA | ||||
| 32333 | 1 | NA | NA | ||||
| 32433 | 1 | NA | NA | ||||
| 53 | 3 | 7.43 | Tf | 22432 | 1 | NA | NA |
| 22431 | 1 | NA | NA | ||||
| 22232 | 1 | NA | NA | ||||
| 20 | 3 | 1.32 | LAM | 22433 | 1 (3) | 6 | 1 (3) |
| 714 | 3 | 0.02 | LAM | 32333 | B (3) | 2 | B (3) |
| 295 | 2 | 0.05 | Haarlem | 32434 | E (2) | 2 unrelated patterns | NA |
| 193 | 2 | 0.07 | LAM | 22433 | 1 | NA | NA |
| 22423 | 1 | NA | NA | ||||
| 118 | 2 | 0.30 | Haarlem | 22333 | 1 | NA | NA |
| 22434 | 1 | NA | NA | ||||
| 34 | 2 | 0.72 | LAM | 32433 | 1 | NA | NA |
| 42442 | 1 | NA | NA | ||||
| Orphan | 29 | NA | NA | NA | NA | NA | NA |
Epidemiological observations and the links between patients are provided for each cluster in Table 4.
Major clades of the tubercle bacilli according to the wordwide spoligotyping database (14, 17). Note that the terms Carib and X3 have been used alternatively to designate the same major clade.
Subclusters defined by the VNTR method that were not further subdivided upon LM-PCR were designated with the same letter (e.g., clusters L, M, G, H, I, and B). On the other hand, if a cluster was further subdivided by LM-PCR, the original letter designation was followed by a number (e.g., clusters A1, A2, C1, D1, and F1).
NA, not applicable.
The T clade is highly ubiquitous and differs from the Haarlem type 50 by the presence of a single spacer (spacer 31).