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Volume 25, Number 3—March 2019

SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex

Samuel Lipworth1Comments to Author , 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
Author affiliations: University of Oxford, Oxford, UK (S. Lipworth, T. Peto, D. Crook, T. Walker); National Institute for Public Health and the Environment, Bilthoven, the Netherlands (R. Jajou, A. de Neeling, W. van der Hoek, D. van Soolingen); Wellcome Trust Centre for Human Genetics, Oxford (P. Bradley); National Reference Laboratory, Ministry of Health, Mbabane, Swaziland (G. Maphalala); Epicentre, Paris, France (M. Bonnet, E. Sanchez-Padilla); University of Kiel, Kiel, Germany (R. Diel); Borstel Research Centre, Borstel, Germany (S. Niemann); European Bioinformatics Institute, Cambridge, UK (Z. Iqbal); Public Health England, Birmingham, UK (G. Smith)

Main Article

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 ( 266 (213)
Ural (4.2.1) 43 (34)
Tur ( 41 (36)
LAM (4.3) 213 (159)
S-type ( 60 (45)
Uganda (4.6.1) 13 (12)
Cameroon (
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.

Main Article

1These authors contributed equally to this article.

2Joint senior authors.

Page created: February 19, 2019
Page updated: February 19, 2019
Page reviewed: February 19, 2019
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