Rapid identification of Pseudallescheria and Scedosporium strains by using rolling circle amplification

Lackner, M. and Najafzadeh, M. J. and Sun, J. and Lu, Q. and de Hoog, G. S. (2012) Rapid identification of Pseudallescheria and Scedosporium strains by using rolling circle amplification. Applied and Environmental Microbiology, 78 (1). pp. 126-133.

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Abstract

The Pseudallescheria boydii complex, comprising environmental pathogens with Scedosporium anamorphs, has recently been subdivided into five main species: Scedosporium dehoogii, S. aurantiacum, Pseudallescheria minutispora, P. apiosperma, and P. boydii, while the validity of some other taxa is being debated. Several Pseudallescheria and Scedosporium species are indicator organisms of pollution in soil and water. Scedosporium dehoogii in particular is enriched in soils contaminated by aliphatic hydrocarbons. In addition, the fungi may cause life-threatening infections involving the central nervous system in severely impaired patients. For screening purposes, rapid and economic tools for species recognition are needed. Our aim is to establish rolling circle amplification (RCA) as a screening tool for species-specific identification of Pseudallescheria and Scedosporium. With this aim, a set of padlock probes was designed on the basis of the internal transcribed spacer (ITS) region, differing by up to 13 fixed mutations. Padlock probes were unique as judged from sequence comparison by BLAST search in GenBank and in dedicated research databases at CBS (Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre). RCA was applied as an in vitro tool, tested with pure DNA amplified from cultures. The species-specific padlock probes designed in this study yielded 100 specificity. The method presented here was found to be an attractive alternative to identification by restriction fragment length polymorphism (RFLP) or sequencing. The rapidity (<1 day), specificity, and low costs make RCA a promising screening tool for environmentally and clinically relevant fungi. © 2012, American Society for Microbiology.

Item Type: Article
Additional Information: Cited By :38 Export Date: 16 February 2020 CODEN: AEMID Correspondence Address: de Hoog, G.S.; CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands; email: s.hoog@cbs.knaw.nl
Uncontrolled Keywords: Aliphatic hydrocarbons Central nervous systems Fungal biodiversity GenBank In-vitro Indicator organisms Internal transcribed spacers Life-threatening infections Low costs Rapid identification Research database Restriction fragment length polymorphisms Rolling circle amplifications Screening tool Sequence comparisons Soil and water Species recognition Species-specific identification Biodiversity Fungi Hydrocarbons Locks (fasteners) Probes Soil pollution fungal DNA spacer DNA aliphatic hydrocarbon amplification bioindicator database fungus infectivity mutation pathogen article classification DNA probe evaluation genetics limit of detection methodology microbiological examination nucleic acid amplification phylogeny Pseudallescheria Scedosporium sensitivity and specificity DNA Probes DNA, Fungal DNA, Intergenic Mycological Typing Techniques Nucleic Acid Amplification Techniques Centraalbureau voor Pseudallescheria boydii Pseudallescheria minutispora Scedosporium aurantiacum
Subjects: WC Communicable Diseases
Divisions: Mashhad University of Medical Sciences
Depositing User: mr lib5 lib5
Date Deposited: 15 May 2020 12:51
Last Modified: 15 May 2020 12:51
URI: http://eprints.mums.ac.ir/id/eprint/18942

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