Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae

Abstract

A group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as 'MCRO 33' (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S-23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68 T (=ATCC BAA-614 T =DSM 44648 T ). INTRODUCTIONSequence-based identification of non-tuberculous mycobacteria (NTM) has become a method of choice in several mycobacteriology laboratories and is accomplished by analysis of various targets, such as the 16S rRNA gene, 16S-23S spacer region (ITS1) and hsp65 gene. As a result, we are faced with the discovery of many novel species previously undifferentiable using other methods of identification. These cannot be ignored, since current studies show that the detection of novel species is a common occurrence that will only be compounded with an increase in use of automated sequencers in clinical laboratories, with some of these unusual isolates deemed clinically significant (Tortoli et al., 2001). The purpose of this study was to establish as a novel species a group of representative mycobacterial strains commonly found, not only in human clinical isolates obtained from our laboratory, but also in several past publications where evidence of its existence has been found. This species has shown similarities to several known NTM species using single identification methods, which may have been the cause for the delay in its establishment, but it is clearly a unique species as determined from a polyphasic approach. In one symptomatic patient, this organism was isolated in multiple respiratory samples, and associated computed tomography (CT) scan and chest X-ray showed evidence of respiratory disease, as described below.

Comparison of Sample Preparation Methods, Instrumentation Platforms, and Contemporary Commercial Databases for Identification of Clinically Relevant Mycobacteria by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

“…The maximal score for this isolate was 1.7 on Biotyper, while Saramis and Vitek MS v3.0 both reported a maximum confidence value of 99.9%. This isolate was confirmed by 16S rRNA and rpoB gene sequencing (14), suggesting that current MALDI-TOF MS methods may have difficulty distinguishing M. scrofulaceum and M. parascrofulaceum. Testing of additional related organisms is needed to further characterize this observation.…”

Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex

“…M. parascrofulaceum and the five strains described in this study, which constituted the second cluster (B), were characterized, in contrast, by HPLC profile similar to those of the Mycobacterium avium complex (Fig. 1) and susceptibility to most of the antimycobacterial drugs (Turenne et al, 2004b). The remaining six species, found on isolated branches, were more heterogeneous at the phenotypic level.…”

Revival and emended description of ‘Mycobacterium paraffinicum’ Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.

“…In contrast, the tightly clustered isolates of 'M. paraffinicum' were separated from M. scrofulaceum Davis et al (1956), Kent & Kubica (1985), Wayne et al (1991Wayne et al ( , 1996, Turenne et al (2004), Tsukamura (1984) and Mohamed et al (2004). +, Positive; 2, negative; V, variable; ND, no data available.…”