SNP-IT tool for identifying subspecies and associated lineages of Mycobacterium tuberculosis complex

Samuel Lipworth*, Rana Jajou, 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 Walker, Dick Van Soolingen

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)


The clinical phenotype of zoonotic tuberculosis and its contribution to the global burden of disease are poorly understood and probably underestimated. This shortcoming is partly because of the inability of currently available laboratory and in silico tools to accurately identify all subspecies of the Mycobacterium tuberculosis complex (MTBC). We present SNPs to Identify TB (SNP-IT), a single-nucleotide polymorphism-based tool to identify all members of MTBC, including animal clades. By applying SNP-IT to a collection of clinical genomes from a UK reference laboratory, we detected an unexpectedly high number of M. orygis isolates. M. orygis is seen at a similar rate to M. bovis, yet M. orygis cases have not been previously described in the United Kingdom. From an international perspective, it is possible that M. orygis is an underestimated zoonosis. Accurate identification will enable study of the clinical phenotype, host range, and transmission mechanisms of all subspecies of MTBCin greater detail.

Original languageEnglish
Pages (from-to)482-488
Number of pages7
JournalEmerging Infectious Diseases
Issue number3
Publication statusPublished - Mar 2019

Bibliographical note

Funding Information:
This research was supported by the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at the University of Oxford in partnership with Public Health England (PHE) and by Oxford NIHR Biomedical Research Centre. T.P. is a NIHR senior investigator. The report presents independent research funded by NIHR. The views expressed in this publication are those of the authors and not necessarily those of the National Health Service, NIHR, the Department of Health, or PHE. Z.I. is a Sir Henry Dale Fellow jointly funded by the Wellcome Trust and the Royal Society (grant no. 102541/Z/13/Z).

Publisher Copyright:
© 2019, Centers for Disease Control and Prevention (CDC). All rights reserved.


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