Comparison of ITS and IGS1 regions for strain typing of clinical and non-clinical isolates of Pichia anomala

Pichia anomala is an emerging nosocomial pathogen and there is a need for methods that distinguish between different P. anomala strains. In the typing of several clinical as well as non-clinical P. anomala strains, the sequence variation of the internal transcribed spacer (ITS) was found to be inadequate for typing purposes. The intergenic spacer 1 (IGS1) region of the rDNA of several P. anomala strains was therefore investigated in detail. The IGS1 region (which varied from 1213 to 1231 bp in length) was interspersed with repeats and had more variation than the ITS regions. Comparative analysis in cases where analysis by the ITS was ambiguous clearly revealed the IGS1 region to be a more discriminatory tool in the typing of P. anomala strains.

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New insights into sequence variation in the IGS region of 21 cyathostomin species and the implication for molecular identification

Parasitology ◽

10.1017/s0031182012000467 ◽

2012 ◽

Vol 139 (8) ◽

pp. 1063-1073 ◽

Cited By ~ 15

Author(s):

K. CWIKLINSKI ◽

F. N. J. KOOYMAN ◽

D. C. K. VAN DOORN ◽

J. B. MATTHEWS ◽

J. E. HODGKINSON

Keyword(s):

Comparative Analysis ◽

Dna Sequences ◽

Sequence Variation ◽

Intergenic Spacer ◽

Parasitic Nematodes ◽

Sequence Information ◽

Detailed Knowledge ◽

Life Cycle Stages ◽

Third Stage ◽

Specific Variation

SUMMARYCyathostomins comprise a group of 50 species of parasitic nematodes that infect equids. Ribosomal DNA sequences, in particular the intergenic spacer (IGS) region, have been utilized via several methodologies to identify pre-parasitic stages of the commonest species that affect horses. These methods rely on the availability of accurate sequence information for each species, as well as detailed knowledge of the levels of intra- and inter-specific variation. Here, the IGS DNA region was amplified and sequenced from 10 cyathostomin species for which sequence was not previously available. Also, additional IGS DNA sequences were generated from individual worms of 8 species already studied. Comparative analysis of these sequences revealed a greater range of intra-specific variation than previously reported (up to 23%); whilst the level of inter-specific variation (3–62%) was similar to that identified in earlier studies. The reverse line blot (RLB) method has been used to exploit the cyathostomin IGS DNA region for species identification. Here, we report validation of novel and existing DNA probes for identification of cyathostomins using this method and highlight their application in differentiating life-cycle stages such as third-stage larvae that cannot be identified to species by morphological means†.

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Species identification and strain typing of Malassezia species stock strains and clinical isolates based on the DNA sequences of nuclear ribosomal internal transcribed spacer 1 regions

Journal of Medical Microbiology ◽

10.1099/0022-1317-49-1-29 ◽

2000 ◽

Vol 49 (1) ◽

pp. 29-35 ◽

Cited By ~ 81

Author(s):

KOICHI MAKIMURA ◽

YOSHIKO TAMURA ◽

MICHINARI KUDO ◽

KATSUHISA UCHIDA ◽

HIUGA SAITO ◽

...

Keyword(s):

Species Identification ◽

Dna Sequences ◽

Internal Transcribed Spacer ◽

Clinical Isolates ◽

Strain Typing ◽

Malassezia Species

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PCR-based identification and strain typing of Pichia anomala using the ribosomal intergenic spacer region IGS1

Journal of Medical Microbiology ◽

10.1099/jmm.0.46790-0 ◽

2007 ◽

Vol 56 (2) ◽

pp. 185-189 ◽

Cited By ~ 12

Author(s):

Sonia Bhardwaj ◽

Rajeshwari Sutar ◽

Anand K. Bachhawat ◽

Sunit Singhi ◽

Arunaloke Chakrabarti

Keyword(s):

Debaryomyces Hansenii ◽

Intergenic Spacer ◽

Rapid Identification ◽

Pichia Anomala ◽

Rrna Genes ◽

Identification System ◽

Rrna Gene ◽

Strain Typing ◽

Intergenic Spacer Region ◽

Specific Pcr

Frequent outbreaks of Pichia anomala fungaemia in paediatric patients have warranted the development of a rapid identification system for this organism. This study describes a specific PCR-based method targeting the rRNA gene intergenic spacer region 1 (IGS1) for rapid identification of Pichia anomala isolates and characterization at the strain level. These methods of species identification and strain typing were used on 106 isolates of Pichia anomala (77 from a previously described outbreak and 29 isolated post-outbreak from the same hospital). Using conventional morphological and biochemical methods, 11 strains isolated during the outbreak were misidentified as P. anomala. blast analysis of sequences of internal transcribed spacer (ITS) regions of rRNA genes confirmed that they were Pichia guilliermondii (eight isolates) and Debaryomyces hansenii (three isolates). Strain typing of Pichia anomala isolates confirmed the previous finding of a point-source outbreak. The results suggest that IGS sequences and their polymorphisms could be exploited for similar typing methods in other organisms.

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Typing of Histoplasma capsulatum Isolates Based on Nucleotide Sequence Variation in the Internal Transcribed Spacer Regions of rRNA Genes

Journal of Clinical Microbiology ◽

10.1128/jcm.38.1.241-245.2000 ◽

2000 ◽

Vol 38 (1) ◽

pp. 241-245

Author(s):

Bingdong Jiang ◽

Marilyn S. Bartlett ◽

Stephen D. Allen ◽

James W. Smith ◽

L. Joseph Wheat ◽

...

Keyword(s):

New York ◽

Internal Transcribed Spacer ◽

Sequence Variation ◽

Histoplasma Capsulatum ◽

Rrna Genes ◽

Sequence Variations ◽

Nucleotide Sequence Variation ◽

Sequence Patterns ◽

Its Regions ◽

Different Types

ABSTRACT The nucleotide sequences of internal transcribed spacer (ITS) regions of rRNA genes of 24 isolates of Histoplasma capsulatum were examined. The results indicate that the sequences of ITS regions in different isolates are not identical. Sequence variations were found at 20 positions in the 496 bp that were sequenced. Ten different sequence patterns, designated types A through H, were observed when the sequences from the 24 isolates were aligned. Twelve isolates from Indianapolis were classified into four different types. Two isolates from New York belonged to type G. Three isolates from different cities were type F. The remaining six isolates were of different types.

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Strain Typing of Trichosporon asahii Clinical Isolates by Random Amplification of Polymorphic DNA (RAPD) Analysis

Journal of Laboratory Physicians ◽

10.1055/s-0041-1731111 ◽

2021 ◽

Author(s):

Thayanidhi Premamalini ◽

Vijayaraman Rajyoganandh ◽

Ramaraj Vijayakumar ◽

Hemanth Veena ◽

Anupma Jyoti Kindo ◽

...

Keyword(s):

Genetic Relatedness ◽

Rapd Analysis ◽

Clinical Isolates ◽

Clinical Samples ◽

Strain Typing ◽

Trichosporon Asahii ◽

Pcr Fingerprinting ◽

Specific Pcr ◽

Rapd Primer ◽

Random Amplification

Abstract Objective The aim of this study was to identify and isolate Trichosporon asahii (T. asahii) from clinical samples and to assess the genetic relatedness of the most frequently isolated strains of T. asahii using random amplification of polymorphic DNA (RAPD) primers GAC-1 and M13. Methods All the clinical samples that grew Trichosporon species, identified and confirmed by polymerase chain reaction (PCR) using Trichosporon genus-specific primers, were considered for the study. Confirmation of the species T. asahii was carried out by T. asahii-specific PCR. Fingerprinting of the most frequently isolated T. asahii isolates was carried out by RAPD using random primers GAC-1 and M13. Results Among the 72 clinical isolates of Trichosporon sp. confirmed by Trichosporon-specific PCR, 65 were found to be T. asahii as identified by T. asahii-specific PCR. Fingerprinting of the 65 isolates confirmed as T. asahii using GAC-1 RAPD primer yielded 11 different patterns, whereas that of M13 primer produced only 5 patterns. The pattern I was found to be the most predominant type (29.2%) followed by pattern III (16.9%) by GAC-1 primer. Conclusions This study being the first of its kind in India on strain typing of T. asahii isolates by adopting RAPD analysis throws light on genetic diversity among the T. asahii isolates from clinical samples. Fingerprinting by RAPD primer GAC-1 identified more heterogeneity among the T. asahii isolates than M13.

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