scholarly journals Identification of Medically RelevantTrichosporon Species Based on Sequences of Internal Transcribed Spacer Regions and Construction of a Database forTrichosporon Identification

1999 ◽  
Vol 37 (6) ◽  
pp. 1985-1993 ◽  
Author(s):  
Takashi Sugita ◽  
Akemi Nishikawa ◽  
Reiko Ikeda ◽  
Takako Shinoda
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Comparative Sequence Analysis ◽  
Nucleotide Sequences ◽  
Its Sequences ◽  
Rrna Gene ◽  
Comparative Sequence ◽  
Internal Transcribed Spacer Regions ◽  
Molecular Phylogenetic

The nucleotide sequences of the internal transcribed spacer (ITS) 1 and 2 regions in the rRNA gene were determined by directly sequencing PCR-amplified fragments for all of the species (17 species and five varieties) in the genus Trichosporon. Comparative sequence analysis suggests that six medically relevant species, T. asahii, T. asteroides, T. cutaneum,T. inkin, T. mucoides, and T. ovoides, can be readily identified by their ITS sequences. In addition, the sequence analysis showed that conspecific strains have fewer than 1% nucleotide differences in the ITS 1 and 2 regions overall. Molecular phylogenetic trees are also presented.

scholarly journals Differentiation of Phylogenetically Related Slowly Growing Mycobacteria Based on 16S-23S rRNA Gene Internal Transcribed Spacer Sequences

1998 ◽  
Vol 36 (1) ◽  
pp. 139-147 ◽  
Author(s):  
Andreas Roth ◽  
Marga Fischer ◽  
Mohamed E. Hamid ◽  
Sabine Michalke ◽  
Wolfgang Ludwig ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Internal Transcribed Spacer ◽  
Sequence Divergence ◽  
Comparative Sequence Analysis ◽  
Its Sequences ◽  
23S Rrna ◽  
Rrna Gene ◽  
Its Sequencing

Interspecific polymorphisms of the 16S rRNA gene (rDNA) are widely used for species identification of mycobacteria. 16S rDNA sequences, however, do not vary greatly within a species, and they are either indistinguishable in some species, for example, in Mycobacterium kansasii and M. gastri, or highly similar, for example, in M. malmoense and M. szulgai. We determined 16S-23S rDNA internal transcribed spacer (ITS) sequences of 60 strains in the genus Mycobacterium representing 13 species (M. avium, M. conspicuum, M. gastri, M. genavense, M. kansasii,M. malmoense, M. marinum, M. shimoidei, M. simiae, M. szulgai,M. triplex, M. ulcerans, and M. xenopi). An alignment of these sequences together with additional sequences available in the EMBL database (for M. intracellulare, M. phlei, M. smegmatis, and M. tuberculosis) was established according to primary- and secondary-structure similarities. Comparative sequence analysis applying different treeing methods grouped the strains into species-specific clusters with low sequence divergence between strains belonging to the same species (0 to 2%). The ITS-based tree topology only partially correlated to that based on 16S rDNA, but the main branching orders were preserved, notably, the division of fast-growing from slowly growing mycobacteria, separate branching for M. simiae, M. genavense, and M. triplex, and distinct branches for M. xenopi and M. shimoidei. Comparisons of M. gastri with M. kansasii and M. malmoense with M. szulgairevealed ITS sequence similarities of 93 and 88%, respectively.M. marinum and M. ulcerans possessed identical ITS sequences. Our results show that ITS sequencing represents a supplement to 16S rRNA gene sequences for the differentiation of closely related species. Slowly growing mycobacteria show a high sequence variation in the ITS; this variation has the potential to be used for the development of probes as a rapid approach to mycobacterial identification.

Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species

2006 ◽  
Vol 29 (4) ◽  
pp. 265-275 ◽  
Author(s):  
Michael Lebuhn ◽  
Stephan Bathe ◽  
Wafa Achouak ◽  
Anton Hartmann ◽  
Thierry Heulin ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Comparative Sequence Analysis ◽  
Comparative Sequence

Ribosomal internal transcribed spacer regions are not suitable for intra- or inter-specific phylogeny reconstruction in haplosclerid sponges (Porifera: Demospongiae)

2009 ◽  
Vol 89 (6) ◽  
pp. 1251-1256 ◽  
Author(s):  
Niamh E. Redmond ◽  
Grace P. McCormack
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Population Level ◽  
Single Species ◽  
Its Sequences ◽  
Closely Related Species ◽  
Internal Transcribed Spacer Regions ◽  
Species Specific ◽  
Close Relatives ◽  
Number Of Individuals

Sequences of the ribosomal internal transcribed spacer regions 1 and 2 (ITS-1 and ITS-2) were employed to investigate relationships between putatively very closely related species of marine haplosclerids and to investigate the species status of Haliclona cinerea. Results indicate that intra-genomic and intra-specific levels of diversity are equivalent, and sequences from multiple clones from a number of individuals of a single species could not be separated on phylogenetic trees. As a result, the ITS regions are not suitable markers for population level studies in marine haplosclerids. Sequences of these regions were highly species specific, and large differences were found between species. ITS sequences from three Callyspongia and three Haliclona species could not be aligned successfully and therefore this locus could not be used to investigate relationships between these putative close relatives. However, ITS sequences retrieved from one H. cinerea were very different from sequences generated from other H. cinerea individuals indicating that this species comprises more than one taxon.

Comparative sequence analysis of 5·8S rRNA genes and internal transcribed spacer (ITS) regions of trichomonadid protozoa

Parasitology ◽  
1997 ◽  
Vol 115 (2) ◽  
pp. 111-119 ◽  
Author(s):  
R. S. J. FELLEISEN
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Trichomonas Vaginalis ◽  
Comparative Sequence Analysis ◽  
Rrna Genes ◽  
Its2 Region ◽  
Rrna Gene ◽  
Molecular Biological Analysis ◽  
Future Revision ◽  
High Degree

The taxonomic situation in the genus Tritrichomonas is the subject of controversial discussion: potentially T. foetus and T. suis, the tritrichomonads from cattle and swine, respectively, could belong to the same species. In order to shed some light on this question, a molecular biological analysis was performed. The 5·8S rRNA gene and the flanking internal transcribed spacer regions (ITS1 and ITS2) of 12 different isolates of 3 Tritrichomonas species T. foetus, T. suis and T. mobilensis were enzymatically amplified by PCR and subcloned. Also, the corresponding regions of the trichomonads Trichomonas vaginalis, T. tenax, T. gallinae and Pentatrichomonas hominis were included in this study. Sequence analysis of cloned fragments was used to compare the parasite isolates. The genus Tritrichomonas exhibited an extremely high degree of homogeneity. All T. foetus and T. suis isolates had identical sequences, and only 1 substitution was found in the ITS2 region of T. mobilensis. In contrast, the genus Trichomonas shared more diversity. The results obtained in this study support a possible future revision of the taxonomic classification of tritrichomonads.

scholarly journals Identification of Mycobacterial Species by Comparative Sequence Analysis of the RNA Polymerase Gene (rpoB)

1999 ◽  
Vol 37 (6) ◽  
pp. 1714-1720 ◽  
Author(s):  
Bum-Joon Kim ◽  
Seung-Hyun Lee ◽  
Mi-Ae Lyu ◽  
Seo-Jeong Kim ◽  
Gill-Han Bai ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Rna Polymerase ◽  
Phylogenetic Tree ◽  
Comparative Sequence Analysis ◽  
Clinical Isolates ◽  
Species Differentiation ◽  
Rrna Gene ◽  
Alignment Algorithm ◽  
Mycobacterial Species ◽  
Comparative Sequence

For the differentiation and identification of mycobacterial species, the rpoB gene, encoding the β subunit of RNA polymerase, was investigated. rpoB DNAs (342 bp) were amplified from 44 reference strains of mycobacteria and clinical isolates (107 strains) by PCR. The nucleotide sequences were directly determined (306 bp) and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method. Comparative sequence analysis of rpoB DNAs provided the basis for species differentiation within the genusMycobacterium. Slowly and rapidly growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. Pathogenic Mycobacterium kansasii was easily differentiated from nonpathogenic M. gastri; this differentiation cannot be achieved by using 16S rRNA gene (rDNA) sequences. By being grouped into species-specific clusters with low-level sequence divergence among strains of the same species, all of the clinical isolates could be easily identified. These results suggest that comparative sequence analysis of amplified rpoB DNAs can be used efficiently to identify clinical isolates of mycobacteria in parallel with traditional culture methods and as a supplement to 16S rDNA gene analysis. Furthermore, in the case of M. tuberculosis, rifampin resistance can be simultaneously determined.

scholarly journals First Report of Klebsiella oxytoca Strain Simultaneously Producing NDM-1, IMP-4, and KPC-2 Carbapenemases

2017 ◽  
Vol 61 (9) ◽  
Author(s):  
Juan Wang ◽  
Min Yuan ◽  
Hai Chen ◽  
Xia Chen ◽  
Yuanchun Jia ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Klebsiella Oxytoca ◽  
Comparative Sequence Analysis ◽  
Nucleotide Sequences ◽  
Content Type ◽  
First Report ◽  
Comparative Sequence ◽  
Pacbio Rs Ii ◽  
Plasmid Analysis ◽  
First Time

ABSTRACT The nucleotide sequences of five plasmids from one Klebsiella oxytoca isolate were determined using the PacBio RS II system. Plasmid analysis revealed that bla NDM-1 was carried on an IncX3 plasmid. The bla IMP-4 and bla KPC-2 genes were located on IncN and IncP-6 plasmids, respectively. Comparative sequence analysis highlighted the successful spread of carbapenemase-harboring plasmids among different enterobacterial species. We report for the first time, to our knowledge, coproducing NDM-1, KPC-2, and IMP-4 carbapenemases on a K. oxytoca isolate.

scholarly journals Comparison of the 5.8S rRNA Gene and Internal Transcribed Spacer Regions of Trichomonadid Protozoa Recovered from the Bovine Preputial Cavity

2003 ◽  
Vol 15 (1) ◽  
pp. 14-20 ◽  
Author(s):  
R. L. Walker ◽  
D. C. Hayes ◽  
S. J. Sawyer ◽  
R. W. Nordhausen ◽  
K. A. Van Hoosear ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Rrna Gene ◽  
Tritrichomonas Foetus ◽  
Similarity Matrix ◽  
Multiple Sequence ◽  
Internal Transcribed Spacer Regions ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
High Degree

Sequence analysis of the 5.8S rRNA gene and the internal transcribed spacer regions (ITSRs) was used to compare trichomonadid protozoa ( n = 39) of varying morphologies isolated from the bovine preputial cavity. A multiple sequence alignment was performed with bovine isolate sequences and other trichomonadid protozoa sequences available in GenBank. As a group, Tritrichomonas foetus isolates ( n = 7) had nearly complete homology. A similarity matrix showed low homology between the T. foetus isolates and other trichomonads recovered from cattle (<70%). Two clusters of trichomonads other than T. foetus were identified. Eighteen isolates comprised 1 group. These isolates shared >99% homology among themselves and with Pen-tatrichomonas hominis. The other non– T. foetus cluster ( n = 14) did not exhibit a high degree of homology (<87%) with other bovine isolates or any of the trichomonad sequences available in GenBank. The sequence homology among isolates in that cluster was >99%, except for 1 isolate that varied from the others in both ITSRs (∼2% dissimilarity). Sequence analysis of the 5.8S rRNA gene and ITSRs was useful for comparing trichomonadid protozoa isolated from the bovine preputial cavity and demonstrated that 2 distinct types of trichomonads constituted the non– T. foetus isolates recovered from the bovine preputial cavity.

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