Volume 25, Number 3—March 2019
Research
SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex
Samuel Lipworth1
, Rana Jajou1, Albert de Neeling, Phelim Bradley, Wim van der Hoek, Gugu Maphalala, Maryline Bonnet, Elizabeth Sanchez-Padilla, Roland Diel, Stefan Niemann, Zamin Iqbal, Grace Smith, Tim Peto, Derrick Crook, Timothy Walker2, and Dick van Soolingen2
, Rana Jajou1, Albert de Neeling, Phelim Bradley, Wim van der Hoek, Gugu Maphalala, Maryline Bonnet, Elizabeth Sanchez-Padilla, Roland Diel, Stefan Niemann, Zamin Iqbal, Grace Smith, Tim Peto, Derrick Crook, Timothy Walker2, and Dick van Soolingen2
Table 2
Speciation predictions for collection of 3,128 clinical MTBC isolates from 2,106 patients using SNP-IT*
| Species and subspecies (lineage) |
No. isolates
(no. patients) |
| Mycobacterium tuberculosis |
|
| Indo-Oceanic (lineage 1) | 240 (208) |
| Beijing/East Asian (lineage 2) | 242 (175) |
| East African Indian (lineage 3) |
775 (644) |
| European American (lineage 4); no sublineage call made† | 512 (+ 368 H37Rv‡) (336) |
| Lineage 4 sublineages | |
| Ghana (4.1) | 5 (4) |
| X-type (4.1.1) | 197 (159) |
| Haarlem (4.1.2.1) | 266 (213) |
| Ural (4.2.1) | 43 (34) |
| Tur (4.2.2.1) | 41 (36) |
| LAM (4.3) | 213 (159) |
| S-type (4.4.1.1) | 60 (45) |
| Uganda (4.6.1) | 13 (12) |
| Cameroon (4.6.2.2) |
40 (32) |
| West African 1 (lineage 5) | 4 (2) |
| West African 2 (lineage 6) |
11 (9) |
| No call made |
10 (10) |
| M. bovis BCG | 26 (20) |
| M. bovis | 34 (28) |
| M. orygis | 24 (19) |
| M. microti | 3 (2) |
| M. caprae |
1 (1) |
| Total | 3,128 (2,106) |
*Numbers in parentheses represent the lineage numbering scheme of Coll for the major lineages 1–7 and Stucki for the lineage 4 sublineages. BCG, bacillus Calmette-Guérin; MTBC, Mycobacterium tuberculosis complex; SNP, single-nucleotide polymorphism; SNP-IT, SNPs to Identify TB.
†These samples belong to lineage 4 but not to one of the named sublineages.
‡SNP-IT correctly identified 880 isolates as being lineage 4; however, 368 of these were identified as being H37Rv when we unblinded ourselves to their laboratory records.
1These authors contributed equally to this article.
2Joint senior authors.
Page created: February 19, 2019
Page updated: February 19, 2019
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