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Volume 25, Number 3—March 2019
Research

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 1

Comparison between speciation calls for 614 MTBC samples in validation set made by SNP-IT and position on maximum-likelihood phylogenetic tree*

Species (lineage)
 SNP-IT typing calls
 Maximum-likelihood calls
 % Correct
Mycobacterium bovis BCG 22 22 100%
M. bovis 15 15 100%
M. orygis† 31 31 100%
M. microti† 18 18 100%
M. canettii† 34 34 100%
M. pinnipedii† 8 8 100%
M. caprae† 15 15 100%
Dassie bacillus† 2 2 100%
M. suricattae†
 2
 2
 100%
M. tuberculosis
Indo Oceanic (lineage 1) 44 44 100%
Beijing/East Asian (lineage 2) 42 42 100%
East African Indian (lineage 3) 46 46 100%
European American (lineage 4)‡ 18 18 100%
Lineage 4 sublineages
Ghana (4.1) 12 12 100%
X-type (4.1.1) 45 45 100%
Haarlem (4.1.2.1) 45 45 100%
Ural (4.2.1) 19 19 100%
Tur (4.2.2.1) 25 25 100%
LAM (4.3) 37 37 100%
S-type (4.4.1.1) 45 45 100%
Uganda (4.6.1) 18 18 100%
Cameroon (4.6.2.2) 32 32 100%
West African 1 (lineage 5) 13 13 100%
West African 2 (lineage 6) 11 11 100%
M. aethiops vetus ( lineage 7) 15 15 100%

*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.
†Validation set for subspecies augmented with published strains.
‡No sublineage call made.

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
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
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