Characterization of Mycobacterium orygis

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).


Characterization of Mycobacterium orygis
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 complexspecifi c multiplex-PCR, regions-ofdifference 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. identifi ed the Rv2042 38 GGC mutation as a novel, useful genetic marker to identify M. orygis. However, such a marker already exists in the form of the very specifi c gyrB oryx G to A SNP at position 1113, which was described by Huard et al. Apart from this, we found that the sequence type (ST) 587 was not the only spoligotype specifi c for M. orygis. In our study, the variant type ST701 (annotated as M. africanum in the spolDB4 database) (4) is also an M. orygis-specifi c 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).  (2), the authors concluded that C. ureolyticus species "are unlikely causes of diarrhea," an assertion with which we take issue.

Nicolaas C. Gey van
This interpretation does not take into account that our screening involved 7,194 symptomatic patients: a sample size 40× greater than that of Cornelius et al. In this context, the likely carriage rate for C. ureolyticus is 1.15%. Also, our assay, which has a limit of detection in the picomolar range, is likely comparable with, if not greater than, that of Cornelius et al. (1).
Accounting for variations in geographic location and detection methods, a detection rate of 24.5% in healthy volunteers (overall detection rate 14.7%) is high in contrast to our reported rate of 1.15%. One possible explanation for this discrepancy is that Cornelius et al. "did not specifi cally exclude volunteers who had had gastrointestinal disturbances in the 10 days before sampling," Campylobacter can be shed in feces for <4 weeks after infection. Also, Cornelius et al. (1) noted the possibility of "genetically distinct but phenotypically indistinguishable genomospecies differing in their pathogenic potential" to account for the presence of the emerging pathogen C. concisus in healthy volunteers and patients with diarrheal illness. This may also apply for C. ureolyticus.
We reported a strong seasonal prevalence of C. ureolytcius and a bimodal age distribution (2). The lack of any related details from Cornelius et al. may undermine their reported detection rates. These factors strongly suggest that the statement, "these species are unlikely causes of diarrhea," should, at the very least, be taken under advisement.