RT Journal Article SR Electronic T1 A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing JF bioRxiv FD Cold Spring Harbor Laboratory SP 213850 DO 10.1101/213850 A1 S Lipworth A1 R Jajou A1 H de Neeling A1 P Bradley A1 W van der Hoek A1 Z Iqbal A1 G Smith A1 T Peto A1 D Crook A1 T Walker A1 D van Soolingen YR 2017 UL http://biorxiv.org/content/early/2017/11/06/213850.abstract AB The clinical phenotype of zoonotic tuberculosis, its contribution to the global burden of disease and prevalence are poorly understood and probably underestimated. This is partly because currently available laboratory and in silico tools have not been calibrated to accurately distinguish between all subspecies of the Mycobacterium tuberculosis complex (Mtbc). We here present the first such tool, SNPs to Identify TB (‘SNP-IT’). Applying SNP-IT to a collection of clinical genomes from a UK reference laboratory, we demonstrate an unexpectedly high number of M. orygis isolates. These are seen at a similar rate to M. bovis which attracts much health protection resource and yet M. orygis cases have not been previously described in the UK. From an international perspective it is likely that M. orygis is an underestimated zoonosis. As whole genome sequencing is increasingly integrated into the clinical setting, accurate subspecies identification with SNP-IT will allow the clinical phenotype, host range and transmission mechanisms of subspecies of the Mtbc to be studied in greater detail.