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

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 t...

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Bibliographic Details
Published in:Emerging infectious diseases Vol. 25; no. 3; pp. 482 - 488
Main Authors: Lipworth, Samuel, Jajou, Rana, de Neeling, Albert, Bradley, Phelim, van der Hoek, Wim, Maphalala, Gugu, Bonnet, Maryline, Sanchez-Padilla, Elizabeth, Diel, Roland, Niemann, Stefan, Iqbal, Zamin, Smith, Grace, Peto, Tim, Crook, Derrick, Walker, Timothy, van Soolingen, Dick
Format: Journal Article
Language:English
Published: United States U.S. National Center for Infectious Diseases 01.03.2019
Centers for Disease Control and Prevention
Subjects:
Animals
Antitubercular Agents - pharmacology
Complex
Computational Biology - methods
DNA, Bacterial
Drug Resistance, Bacterial
Genetic aspects
Genetic Markers
Genetic polymorphisms
Genomes
Genomics
Humans
Molecular Typing
Mycobacterium tuberculosis - classification
Mycobacterium tuberculosis - drug effects
Mycobacterium tuberculosis - genetics
Mycobacterium tuberculosis - isolation & purification
Phylogeny
Polymorphism, Single Nucleotide
Prevalence
single nucleotide polymorphism
Single nucleotide polymorphisms
SNP-IT
SNP-IT Tool for Identifying Subspecies and Associated Lineages of
Tuberculosis
Tuberculosis - epidemiology
Tuberculosis - microbiology
whole genome sequencing
Zoonoses
Zoonoses - epidemiology
Zoonoses - microbiology
United Kingdom
Netherlands
SNP-IT
Mycobacterium tuberculosis
bacteria
whole-genome sequencing
tuberculosis
United Kingdom
phylogeny
zoonoses
single-nucleotide polymorphism
TB
ISSN:1080-6040, 1080-6059, 1080-6059
Online Access:Get full text
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Summary: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 MTBC in greater detail.
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ISSN:1080-6040
1080-6059
1080-6059
DOI:10.3201/eid2503.180894