Development of an Oligonucleotide Array for Direct Detection of Fungi in Sputum Samples from Patients with Cystic Fibrosis
- 1 January 2009
- journal article
- research article
- Published by American Society for Microbiology in Journal of Clinical Microbiology
- Vol. 47 (1), 142-152
- https://doi.org/10.1128/jcm.01668-08
Abstract
Cystic fibrosis (CF) is the most common inherited genetic disease in Caucasian populations. Besides bacteria, many species of fungi may colonize the respiratory tract of these patients, sometimes leading to true respiratory infections. In this study, an oligonucleotide array capable of identifying 20 fungal species was developed to directly detect fungi in the sputum samples of CF patients. Species-specific oligonucleotide probes were designed from the internal transcribed spacer (ITS) regions of the rRNA operon and immobilized on a nylon membrane. The fungal ITS regions were amplified by PCR and hybridized to the array for species identification. The array was validated by testing 182 target strains (strains which we aimed to identify) and 141 nontarget strains (135 species), and a sensitivity of 100% and a specificity of 99.2% were obtained. The validated array was then used for direct detection of fungi in 57 sputum samples from 39 CF patients, and the results were compared to those obtained by culture. For 16 sputum samples, the results obtained by the array corresponded with those obtained by culture. For 33 samples, the array detected more fungal species than culture did, while the reverse was found for eight samples. The accuracy of the array for fungal detection in sputum samples was confirmed (or partially confirmed) in some samples by cloning and resequencing the amplified ITS fragments. The present array is a useful tool for both the simultaneous detection of multiple fungal species present in the sputa of CF patients and the identification of fungi isolated from these patients.Keywords
This publication has 43 references indexed in Scilit:
- Molecular and Phenotypic Data Supporting Distinct Species Statuses for Scedosporium apiospermum and Pseudallescheria boydii and the Proposed New Species Scedosporium dehoogiiJournal of Clinical Microbiology, 2008
- Identification of Medically Important Candida and Non- Candida Yeast Species by an Oligonucleotide ArrayJournal of Clinical Microbiology, 2007
- Microbial ecology of the cystic fibrosis lungMicrobiology, 2007
- Airway Colonization by Acrophialophora fusispora in Patients with Cystic FibrosisJournal of Clinical Microbiology, 2005
- Isolation of Fungi, Especially Exophiala dermatitidis, in Patients Suffering from Cystic FibrosisRespiration, 2004
- Acrophialophora fusispora Misidentified as Scedosporium prolificansJournal of Clinical Microbiology, 2002
- Case Reports. Transient colonization with Scedosporium prolificans. Report of four cases in MadridMycoses, 2001
- The addition of low numbers of 3′ thymine bases can be used to improve the hybridization signal of oligonucleotides for use within arrays on nylon supportsJournal of Microbiological Methods, 2000
- Chronic airway colonization by Penicillium emersonii in a patient with cystic fibrosisMedical Mycology, 1999
- Exophiala dermatitidis infection in cystic fibrosisThe Lancet, 1990