SNP-IT Tool for Identifying Subspecies and Associated Lineages of Mycobacterium tuberculosis Complex
Year: 2019
Type: article
Abstract: 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.
Source: Emerging infectious diseases
Institutions: European Bioinformatics Institute, Centre for Human Genetics, Christian-Albrechts-Universität zu Kiel, Public Health England, University of Oxford, National Institute for Public Health and the Environment, Research Center Borstel - Leibniz Lung Center, Ministry of Health, Epicentre, Médecins Sans Frontières, Institut de Recherche pour le Développement, Recherches Translationnelles sur le VIH et les Maladies Infectieuses
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: diamond
OpenAlex ID: W2915026237