To the Editor: We thank Gey van Pittius and colleagues for their addition to the markers that identify Mycobacterium orygis as a distinct subspecies in the M. tuberculosis complex (1). Its isolation from a wild buffalo broadens the host range of M. orygis. Gey van Pittius and colleagues raise 3 issues: the utility of the gyrB^oryx single-nucleotide polymorphism (SNP) being equally specific as the reported SNP in Rv2042³⁸, the presence of genomic regions RD701 and RD702 in M. orygis, and the addition of the sequence type (ST) 701 spoligotype to M. orygis–specific spoligotypes.

We agree that use of the gyrB^oryx mutation is more practical for routine daily use because this gene helps identify several subspecies of the M. tuberculosis complex. However, use of the partial Rv2042 sequencing is similarly practical because it can be combined with sequencing of the adjacent pncA gene, which enables identification of several M. tuberculosis complex species and some subspecies (i.e., M. orygis, M. bovis, M. canettii) (2), to identify the CAS genotype of M. tuberculosis (J. van Ingen, unpub. data) and, to some degree, assess susceptibility to pyrazinamide (3).

With the added data, we can conclude that M. orygis is an M. tuberculosis complex subspecies defined by the presence of genomic regions RD1, RD2, RD4, RD5a, RD6, RD13–RD16, RD701, and RD702, by the C-to-G SNP in mmpL6⁵⁵¹, and by the deletion of regions RD3, RD5b, RD7-RD12, RDoryx_1, RDoryx_4, and RDoryx_wag22. Subspecies-specific SNPs are present in gyrB and Rv2042. Spoligotypes ST587, ST701, and closely related types are characteristic of M. orygis, and this subspecies yields 17–20 copies of insertion sequence 6110 and a distinct 24-locus variable number tandem repeats pattern (4,5). Given the rapid progress in genome sequencing, additional markers specific for the different subspecies will further enrich this panel of differences.