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Volume 19, Number 3—March 2013

Characterization of Mycobacterium orygis

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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 gyrBoryx 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 gyrBoryx 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.


Jakko van IngenComments to Author , Roland Brosch, and Dick van Soolingen
Author affiliations: Author affiliations: Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands (J. van Ingen, D. van Soolingen); Institut Pasteur, Paris, France (R. Brosch); National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands (D. van Soolingen)



  1. Gey van Pittius  NC, van Helden  PD, Warren  RM. Characterization of Mycobacterium orygis. Emerg Infect Dis. 2012;18:17089 .DOIPubMedGoogle Scholar
  2. Huard  RC, Fabre  M, de Haas  P, Oliveira Lazzarini  LC, van Soolingen  D, Cousins  D, Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex. J Bacteriol. 2006;188:427187. DOIPubMedGoogle Scholar
  3. Simons  SO, van Ingen  J, van der Laan  T, Mulder  A, Dekhuijzen  PN, Boeree  MJ, Validation of pncA gene sequencing in combination with the MGIT method to test susceptibility of Mycobacterium tuberculosis to pyrazinamide. J Clin Microbiol. 2012;50:42834. DOIPubMedGoogle Scholar
  4. van Ingen  J, Rahim  Z, Mulder  A, Boeree  MJ, Simeone  R, Brosch  R, Characterization of Mycobacterium orygis as M. tuberculosis complex subspecies. Emerg Infect Dis. 2012;18:6535. DOIPubMedGoogle Scholar
  5. Gey van Pittius  NC, Perrett  KD, Michel  AL, Keet  DF, Hlokwe  T, Streicher  EM, Infection of African buffalo (Syncerus caffer) by oryx bacillus, a rare member of the antelope clade of the Mycobacterium tuberculosis complex. J Wildl Dis. 2012;48:84957. DOIPubMedGoogle Scholar


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DOI: 10.3201/eid1903.121005

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Table of Contents – Volume 19, Number 3—March 2013


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Jakko van Ingen, Medical Microbiology, Radboud University Nijmegen Medical Center, PO Box 9101, Nijmegen 6500 HB, the Netherlands

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