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. 2024 Oct 26;12(11):2153.
doi: 10.3390/microorganisms12112153.

"CLADE-FINDER": Candida auris Lineage Analysis Determination by Fourier Transform Infrared Spectroscopy and Artificial Neural Networks

Carlotta Magrì  1 , Elena De Carolis  1 , Vittorio Ivagnes  1 , Vincenzo Di Pilato  2   3 , Bram Spruijtenburg  4   5 , Anna Marchese  2   3 , Eelco F J Meijer  4   5 , Anuradha Chowdhary  6 , Maurizio Sanguinetti  1
Affiliations

"CLADE-FINDER": Candida auris Lineage Analysis Determination by Fourier Transform Infrared Spectroscopy and Artificial Neural Networks

Carlotta Magrì et al. Microorganisms. .

Abstract

In 2019, Candida auris became the first fungal pathogen included in the list of the urgent antimicrobial threats by the Centers for Disease Control (CDC). Short tandem repeat (STR) analysis and whole-genome sequencing (WGS) are considered the gold standard, and can be complemented by other molecular methods, for the genomic surveillance and clade classification of this multidrug-resistant yeast. However, these methods can be expensive and require time and expertise that are not always available. The long turnaround time is especially not compatible with the speed needed to manage clonal transmission in healthcare settings. Fourier transform infrared (FTIR) spectroscopy, a biochemical fingerprint approach, has been applied in this study to a set of 74 C. auris isolates belonging to the five clades of C. auris (I-V) in combination with an artificial neural network (ANN) algorithm to create and validate "CLADE-FINDER", a tool for C. auris clade determination. The CLADE-FINDER classifier allowed us to discriminate the four primary C. auris clades (I-IV) with a correct classification for 96% of the samples in the validation set. This newly developed genotyping scheme can be reasonably applied for the effective epidemiological monitoring and management of C. auris cases in real time.

Keywords: C. auris; CLADE-FINDER; FTIR; clades; outbreak management.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
A 2D scatter plot based on the training spectra included in the model. Each point on the plot corresponds to an individual spectrum, colored and grouped by clade: clade I (gray), clade II (blue), clade III (red), and clade IV (green).
Figure 2
Figure 2
Classification results for FTIR profiles of the validation set of C. auris isolates, visualized as a scatter plot, with LDA used for dimensionality reduction. Isolates are colored and grouped by clade: clade I (gray), clade II (turquoise), clade III (green), clade IV (violet), and clade V (red).
See this image and copyright information in PMC

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