Identification of moulds in the diagnostic laboratory—an algorithm implementing molecular and phenotypic methods

Ciardo, Diana; Schär, G.; Altwegg, Martin; Böttger, Erik C.; Bosshard, Philipp P.

doi:10.1016/j.diagmicrobio.2007.04.020

Cited by 38 publications

(41 citation statements)

References 22 publications

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“…Mold isolates were subjected to DNA extraction using the InstaGene matrix (Bio-Rad, Reinach BL, Switzerland), as described previously (7). For DNA extraction, a fungal mycelium with a surface area of 2 to 4 cm 2 was obtained from Mycosel or Sabouraud dextrose agar plates.…”

Section: Conventional Identificationmentioning

confidence: 99%

“…PCR of the ITS regions was performed as described before using the LightCycler FastStart DNA Master SYBR green I kit (LightCycler reagents; Roche, Rotkreuz, Switzerland) and a PerkinElmer GeneAmp PCR System 9600 or 9700 (Applied Biosystems, Rotkreuz, Switzerland) (7). The amplified ITS regions were sequenced with primer ITS1 or, in case of failure, with primer ITS4, ITS3, or ITS2 (37) (Fig.…”

Section: Conventional Identificationmentioning

confidence: 99%

“…The SmartGene ITS database is a curated database which is designed to include most of the clinically relevant fungi and which contains some ITS sequences that are missing in GenBank. Sequence assignment to species and genus level was done according to guidelines published previously (7). A sequence was assigned to a species if the best matching reference sequence showed Ն98% homology and the next best matching reference species showed at least 0.8% less sequence homology.…”

Section: Conventional Identificationmentioning

confidence: 99%

“…A sequence was assigned to genus level on the basis of 95 to 98% homology to the best matching sequence or of Ն98% homology with sequence entries for several species from the same genus. "No identification" was defined as Ͻ95% homology with the best matching reference sequence or as sequence homology of Ͼ95% with various genera present (7).…”

Section: Conventional Identificationmentioning

confidence: 99%

“…According to these criteria, mold isolates of clinical relevance that cannot readily be identified by standard conventional characteristics are subjected to ITS sequence-based identification (7). Analysis of the ITS regions is the most commonly used molecular method for identification of molds (3,4,29).…”

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confidence: 99%

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Systematic Internal Transcribed Spacer Sequence Analysis for Identification of Clinical Mold Isolates in Diagnostic Mycology: a 5-Year Study

et al. 2010

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The implementation of internal transcribed spacer (ITS) sequencing for routine identification of molds in the diagnostic mycology laboratory was analyzed in a 5-year study. All mold isolates (n ‫؍‬ 6,900) recovered in our laboratory from 2005 to 2009 were included in this study. According to a defined work flow, which in addition to troublesome phenotypic identification takes clinical relevance into account, 233 isolates were subjected to ITS sequence analysis. Sequencing resulted in successful identification for 78.6% of the analyzed isolates (57.1% at species level, 21.5% at genus level). In comparison, extended in-depth phenotypic characterization of the isolates subjected to sequencing achieved taxonomic assignment for 47.6% of these, with a mere 13.3% at species level. Optimization of DNA extraction further improved the efficacy of molecular identification. This study is the first of its kind to testify to the systematic implementation of sequence-based identification procedures in the routine workup of mold isolates in the diagnostic mycology laboratory.

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Section: Conventional Identificationmentioning

confidence: 99%

Section: Conventional Identificationmentioning

confidence: 99%

Section: Conventional Identificationmentioning

confidence: 99%

Section: Conventional Identificationmentioning

confidence: 99%

mentioning

confidence: 99%

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Systematic Internal Transcribed Spacer Sequence Analysis for Identification of Clinical Mold Isolates in Diagnostic Mycology: a 5-Year Study

et al. 2010

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Molecular Microbial Biodiversity Assessment in the Mycorrhizosphere

Nadarajah

Kumar

2019

Mycorrhizosphere and Pedogenesis

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Advances in molecular detection of Aspergillus: an update

2010

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Filamentous cosmopolitan fungi of the genus Aspergillus can be harmful in two ways, directly they can be opportunistic pathogens causing aspergillosis and indirectly due to aflatoxin production on food products which can lead to aflatoxicosis. Therefore, a number of methods have been proposed so far for detection of the fungi with lowest possible concentration at the earliest. Molecular methods such as PCR and/or in combination with certain techniques have been found to be useful for Aspergillus detection. We discuss here various technologies that have emerged in recent years and can possibly be used for the molecular detection of Aspergillus in an efficient way. These methods like RSIC, C-probe, and inversion probe with pyrosequencing or direct ss/dsDNA detection have been used for the identification of fungal or bacterial pathogens and thus formulate a 'gold standard' for Aspergillus detection.

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Identification of moulds in the diagnostic laboratory—an algorithm implementing molecular and phenotypic methods

Cited by 38 publications

References 22 publications

Systematic Internal Transcribed Spacer Sequence Analysis for Identification of Clinical Mold Isolates in Diagnostic Mycology: a 5-Year Study

Systematic Internal Transcribed Spacer Sequence Analysis for Identification of Clinical Mold Isolates in Diagnostic Mycology: a 5-Year Study

Molecular Microbial Biodiversity Assessment in the Mycorrhizosphere

Advances in molecular detection of Aspergillus: an update

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