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

Emerging Infectious Diseases
Samuel LipworthDick van Soolingen

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.

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Citations

Jun 20, 2019·Frontiers in Genetics·Abigail C ShockeyCaitlin S Pepperell
Dec 19, 2019·Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin·Rana JajouDick van Soolingen
May 24, 2019·The Journal of Antimicrobial Chemotherapy·Rana JajouDick van Soolingen
Jun 19, 2019·Nature Reviews. Microbiology·Conor J MeehanAnnelies Van Rie
Oct 6, 2020·Frontiers in Microbiology·Frédéric J VeyrierMarcel A Behr
Dec 16, 2020·Database : the Journal of Biological Databases and Curation·David CouvinNalin Rastogi
Jan 8, 2021·Frontiers in Genetics·Alexander Stephen ByrneKapil Tahlan
Oct 18, 2020·Trends in Parasitology·Paul CapewellWilliam Weir
Jul 10, 2021·Frontiers in Cellular and Infection Microbiology·Amol O BajajAdam P Barker
Sep 27, 2020·Nature Communications·Roberto ColangeliDavid Alland
Jan 15, 2022·Database : the Journal of Biological Databases and Curation·David CouvinNalin Rastogi

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Software Mentioned

IT
KvarQ
Colored Bloom Graph ( CBG )
Mesquite
predictor
Mykrobe
Profiler
SNPs to Identify TB ( SNP - IT
SNP
TB

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