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Characterization of Mycobacterium orygis.
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MedLine Citation:
PMID:  23017199     Owner:  NLM     Status:  MEDLINE    
Nicolaas C Gey van Pittius; Paul D van Helden; Robin M Warren
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Publication Detail:
Type:  Comment; Letter    
Journal Detail:
Title:  Emerging infectious diseases     Volume:  18     ISSN:  1080-6059     ISO Abbreviation:  Emerging Infect. Dis.     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-09-28     Completed Date:  2013-02-19     Revised Date:  2013-07-11    
Medline Journal Info:
Nlm Unique ID:  9508155     Medline TA:  Emerg Infect Dis     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1708-9     Citation Subset:  IM    
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MeSH Terms
Genes, Bacterial*
Mycobacterium tuberculosis / classification*
Tuberculosis / microbiology*
Comment On:
Emerg Infect Dis. 2012 Apr;18(4):653-5   [PMID:  22469053 ]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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Journal Information
Journal ID (nlm-ta): Emerg Infect Dis
Journal ID (iso-abbrev): Emerging Infect. Dis
Journal ID (publisher-id): EID
ISSN: 1080-6040
ISSN: 1080-6059
Publisher: Centers for Disease Control and Prevention
Article Information
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Print publication date: Month: 10 Year: 2012
Volume: 18 Issue: 10
First Page: 1708 Last Page: 1709
PubMed Id: 23017199
ID: 3471637
Publisher Id: 12-0569
DOI: 10.3201/eid1810.120569

Characterization of Mycobacterium orygis Alternate Title:Characterization of Mycobacterium orygis
Nicolaas C. Gey van Pittius
Paul D. van Helden
Robin M. Warren
Stellenbosch University Faculty of Medicine and Health Sciences, Tygerberg, South Africa
Correspondence: Address for correspondence: Nicolaas C. Gey van Pittius, DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology/Division of Molecular Biology and Human Genetics, Stellenbosch University Faculty of Medicine and Health Sciences, PO Box 19063, Tygerberg 7505, South Africa; email:

To the Editor: In a recently published study, van Ingen et al. (1) described the molecular characterization and phylogenetic position of the oryx bacillus, a member of the Mycobacterium tuberculosis complex, and proposed a long overdue name for the organism: Mycobacterium orygis. The authors described oryx bacillus as a separate taxon; the aim was for this description to be used in the future to identify the subspecies. Thus, we thought it pertinent to provide additional information that would be useful in speciating isolates of the oryx bacillus.

In a recent study, we genotyped an isolate of oryx bacillus obtained from an African buffalo in South Africa (2). This isolate was typed by using 16S rDNA, M. tuberculosis complex–specific multiplex-PCR, regions-of-difference analyses, gyrase B gene single nucleotide polymorphism (SNP) analysis, spoligotyping, and mycobacterial interspersed repetitive units–variable number tandem repeat typing. We showed that, in addition to the markers described by van Ingen et al. (1), regions of difference 701 and 702 were also intact in M. orygis.

In addition, van Ingen et al. identified the Rv204238 GGC mutation as a novel, useful genetic marker to identify M. orygis. However, such a marker already exists in the form of the very specific gyrBoryx G to A SNP at position 1113, which was described by Huard et al. (3). On its own, SNP detection in the gyrB gene allows differentiation of at least 6 of the 9 M. tuberculosis complex species from each other (M. canettii, M. tuberculosis, M. orygis, M. microti, M. caprae, and M. bovis) (3). Thus, the SNP at position 1113 is more useful than the Rv204238 mutation as a novel and distinct genetic marker to identify M. orygis.

Apart from this, we found that the sequence type (ST) 587 was not the only spoligotype specific for M. orygis. In our study, the variant type ST701 (annotated as M. africanum in the spolDB4 database) (4) is also an M. orygis–specific type and exactly matches that of a previous isolate of the oryx bacillus (SB0319) from the M. bovis spoligotype database (5). This spoligotype differs from ST587 by the presence of spacer 18, and the spoligotype was not found in the extensive sample set of van Ingen et al. (1).


Suggested citation for this article: Gey van Pittius NC, van Helden PD, Warren RM. Characterization of Mycobacterium orygis [letter]. Emerg Infect Dis [Internet]. 2012 Oct [date cited].

1. . van IngenJ, RahimZ, MulderA, BoereeMJ, SimeoneR, BroschR, et al. Characterization of Mycobacterium orygis as M. tuberculosis complex subspecies.Emerg Infect Dis. Year: 2012;18:653–510.3201/eid1804.11088822469053
2. . Gey van PittiusNC, PerrettKD, MichelAL, KeetDF, HlokweT, StreicherEM, et al. Infection of African buffalo (Syncerus caffer) by oryx bacillus, a rare member of the antelope clade of the Mycobacterium tuberculosis complex.J Wildl Dis. In press.
3. . HuardRC, FabreM, de HaasP, Oliveira LazzariniLC, van SoolingenD, CousinsD, et al. Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex.J Bacteriol. Year: 2006;188:4271–8710.1128/JB.01783-0516740934
4. . BrudeyK, DriscollJR, RigoutsL, ProdingerWM, GoriA, Al-HajojSA, et al. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.BMC Microbiol. Year: 2006;6:2310.1186/1471-2180-6-2316519816
5. . Mbovis.orgM. bovis spoligotype database. Year: 2008 [cited 2012 Jun 29].

Article Categories:
  • Letters to the Editor
Article Categories:
  • Letter

Keywords: Keywords: Mycobacterium tuberculosis complex, Mycobacterium orygis, oryx bacillus, genotyping, characterization, bacteria, tuberculosis and other mycobacteria.

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