A new identification service for filamentous fungi

Infections caused by fungi have an increased prevalence resulting from the growing population of patients undergoing a weakened immunity (neutropenia, chemotherapy, transplants, AIDS, etc.). Moreover, a high mortality can be associated with such infections and the susceptibility to antifungal drugs varies among fungal pathogens. A fast and reliable identification of yeasts and moulds is therefore essential in order to provide an effective treatment. For filamentous fungi, the identification is traditionally based on the observation of morphological characteristics of the strains. However, this method displays several limits including the time required for the analysis, the need for trained technicians and experienced mycologists, the impossibility to differentiate between species showing the same morphology or the difficulty to identify strains lacking typical features. Identifications based on DNA sequencing are considered as the gold-standard but are time-consuming, expensive and labour-intensive.

In this context, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) has arisen as a powerful, reproducible and accurate tool to identify fungal agents. It analyses the protein content of an unknown strain under the form of a species-specific spectrum which is then identified by comparison with the reference spectra of a database. This technology uses a simple, fast and cost-effective protocol allowing the identification of any species, provided that it is properly represented in the library.

MALDI-TOF MS identification was initially intended for bacteria and yeasts. Consequently, commercially available databases dedicated to filamentous fungi are still poorly developed and generally limited to the most common species. Additionally, they were built using a protocol based on liquid cultures which is particularly cumbersome and inconvenient. It also prevents comparison with spectra acquired using the more practical solid media culture, as spectral profiles depend on the growing conditions.

BCCM/IHEM holds a collection of more than 16000 fungal strains of medical interest. In collaboration with the University Hospital of Marseille, selected strains of this collection were used to build the most diverse, extended and comprehensible MALDI-TOF MS database to date. While being continuously upgraded, it now comprises the reference spectra of more than 1200 strains, representing almost 600 different species. The database has been validated on 500 clinical isolates and showed an accuracy of more than 95% of correct identification at species level.

The BCCM/IHEM collection intends to make its MALDI-TOF MS reference database available to the scientific community and the clinical laboratories. In this aim, an online identification application is being created in which customers will be able to upload their spectra for identification. The protein extraction and the spectra acquisition will first be carried out by the customer using its own mass spectrometer and a standard protocol compatible with the database. The spectra will then be uploaded on the online application and the identification will be provided as an answer within a few seconds. A soon as the website will be ready, a special prepaid subscription will offer an easy access to this service while guaranteeing the best expertise in moulds identification.


The application is currently the subject of a validation process and will be available soon!