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

2004 ◽  
Vol 54 (5) ◽  
pp. 1543-1551 ◽  
Author(s):  
C. Y. Turenne ◽  
V. J. Cook ◽  
T. V. Burdz ◽  
R. J. Pauls ◽  
L. Thibert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Great Part ◽  
16S Rrna Gene Sequencing ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Culture Collections ◽  
Clinical Specimens ◽  
Mycobacterium Simiae ◽  
Reference Strains

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 HSC68T (=ATCC BAA-614T=DSM 44648T).

scholarly journals Identification of Atypical Rhodococcus-Like Clinical Isolates as Dietzia spp. by 16S rRNA Gene Sequencing

2010 ◽  
Vol 48 (5) ◽  
pp. 1904-1907 ◽  
Author(s):  
L. Pilares ◽  
J. Aguero ◽  
J. A. Vazquez-Boland ◽  
L. Martinez-Martinez ◽  
J. Navas
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Identification of non-tuberculous mycobacteria: utility of the GenoType Mycobacterium CM/AS assay compared with HPLC and 16S rRNA gene sequencing

2009 ◽  
Vol 58 (7) ◽  
pp. 900-904 ◽  
Author(s):  
Andie S. Lee ◽  
Peter Jelfs ◽  
Vitali Sintchenko ◽  
Gwendolyn L. Gilbert
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Rapid Identification ◽  
Mycobacterium Abscessus ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Specific Pcr ◽  
Clinically Significant ◽  
Species Specific

Non-tuberculous mycobacteria (NTM) causing clinical disease have become increasingly common and more diverse. A new reverse line probe assay, GenoType Mycobacterium CM/AS (Hain Lifescience), was evaluated for identification of a broad range of NTM. It was compared with phenotypic (HPLC) and molecular (DNA probes, in-house real-time multiplex species-specific PCR, 16S rRNA gene PCR and sequencing) identification techniques, which together provided the reference ‘gold standard’. A total of 131 clinical isolates belonging to 31 Mycobacterium species and 19 controls, including 5 non-Mycobacterium species, was used. Concordant results between the GenoType Mycobacterium assay and the reference identification were obtained in 119/131 clinical isolates (90.8 %). Identification of Mycobacterium abscessus and Mycobacterium lentiflavum by the assay was problematic. The GenoType Mycobacterium assay enables rapid identification of a broad range of potentially clinically significant Mycobacterium species, but some species require further testing to differentiate or confirm ambiguous results.

scholarly journals Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens

2006 ◽  
Vol 56 (6) ◽  
pp. 1413-1418 ◽  
Author(s):  
Joann L. Cloud ◽  
Jay J. Meyer ◽  
June I. Pounder ◽  
Kenneth C. Jost ◽  
Amy Sweeney ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Several Mycobacterium-like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99.6 % to Mycobacterium nonchromogenicum ATCC 19530T. Sequencing of the nearly full-length 16S rRNA gene, the 16S–23S internal transcribed spacer region and the hsp65 gene did not reveal genotypic identity with the type strains of M. nonchromogenicum, M. terrae or Mycobacterium triviale. Although sequence analysis suggested that these clinical isolates represented a novel species, mycolic acid analysis by HPLC failed to distinguish them from M. nonchromogenicum. Therefore, phenotypic analysis including growth characterization, antibiotic susceptibility testing and biochemical testing was performed. These strains from clinical samples should be recognized as representing a novel species of the genus Mycobacterium, for which the name Mycobacterium arupense sp. nov. is proposed. The type strain is AR30097T (=ATCC BAA-1242T=DSM 44942T).

scholarly journals Hafnia paralvei sp. nov., formerly known as Hafnia alvei hybridization group 2

2010 ◽  
Vol 60 (8) ◽  
pp. 1725-1728 ◽  
Author(s):  
Geert Huys ◽  
Margo Cnockaert ◽  
Sharon L. Abbott ◽  
J. Michael Janda ◽  
Peter Vandamme
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
Reference Strains ◽  
Sequence Similarities

It has been shown previously, based largely on DNA–DNA hybridizations and partial 16S rRNA gene sequencing, that Hafnia alvei is genotypically heterogeneous and consists of at least two DNA hybridization groups (HGs). In the present study, the taxonomic status of H. alvei HGs 1 and 2 was reassessed. A panel of 24 reference strains and isolates previously assigned to one of the two HGs in H. alvei was subjected to (GTG)5-PCR fingerprinting; this resulted in the delineation of two (GTG)5-PCR clusters in perfect accordance with the respective HG designations. Based on full 16S rRNA gene sequencing of a selection of reference strains, H. alvei HGs 1 and 2 showed internal sequence similarities of 99.8 and 99.5 %, respectively. Between the two groups, sequence similarities ranged from 98.8 to 99.1 %. Mean DNA–DNA hybridization values of 74.7–99.9 % were obtained within each of the two HGs, whereas cross-hybridizations between members of H. alvei HG 1 (including ATCC 13337T) and HG 2 revealed only 32.7–48.7 % DNA–DNA hybridization. Previously published and new phenotypic data revealed that a combination of malonate assimilation and β-glucosidase activity enabled correct assignment of Hafnia isolates to one of the two HGs. Collectively, taxonomic data from this study confirm that H. alvei comprises at least two taxa at the species level, of which HG 1 corresponds to H. alvei sensu stricto because it includes the type strain ATCC 13337T. Strains formerly classified as members of H. alvei HG 2 represent a novel species, for which the name Hafnia paralvei sp. nov. is proposed; ATCC 29927T (=CDC 4510-73T =LMG 24706T), the former reference strain of H. alvei HG 2, is designated the type strain.

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