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. 2020 Aug 25;6(3):146.
doi: 10.3390/jof6030146.

Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris

Affiliations

Evaluation of Microsatellite Typing, ITS Sequencing, AFLP Fingerprinting, MALDI-TOF MS, and Fourier-Transform Infrared Spectroscopy Analysis of Candida auris

Mansoureh Vatanshenassan et al. J Fungi (Basel). .

Abstract

Candida auris is an emerging opportunistic yeast species causing nosocomial outbreaks at a global scale. A few studies have focused on the C. auris genotypic structure. Here, we compared five epidemiological typing tools using a set of 96 C. auris isolates from 14 geographical areas. Isolates were analyzed by microsatellite typing, ITS sequencing, amplified fragment length polymorphism (AFLP) fingerprint analysis, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and Fourier-transform infrared (FTIR) spectroscopy methods. Microsatellite typing grouped the isolates into four main clusters, corresponding to the four known clades in concordance with whole genome sequencing studies. The other investigated typing tools showed poor performance compared with microsatellite typing. A comparison between the five methods showed the highest agreement between microsatellite typing and ITS sequencing with 45% similarity, followed by microsatellite typing and the FTIR method with 33% similarity. The lowest agreement was observed between FTIR spectroscopy, MALDI-TOF MS, and ITS sequencing. This study indicates that microsatellite typing is the tool of choice for C. auris outbreak investigations. Additionally, FTIR spectroscopy requires further optimization and evaluation before it can be used as an epidemiological typing method, comparable with microsatellite typing, as a rapid method for tracing nosocomial fungal outbreaks.

Keywords: Candida auris; epidemiological typing; molecular epidemiology; nosocomial outbreak.

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Conflict of interest statement

M.K., N.M., T.M., and M.V. are employees of the mass spectrometry company Bruker Daltonik GmbH. All authors declare that they have no competing interests. V.R. is an employee of the WI and CEO of BioAware and has no competing interest.

Figures

Figure 1
Figure 1
A UPGMA dendrogram was generated with BioloMICS v12 based on microsatellite analysis. Four main geographically linked clusters, namely South Asia/Middle East, East Asia, South Africa/Europe, and South America/Israel were created using 96 isolates. Microsatellite abbreviation (MS) was used for sub-clusters. The color coding used for this dendrogram was the same as follows: Austria (turquoise), Belgium (dark green), Japan (blue), India (light green), Israel (rose), Korea (light blue), Malaysia (dark blue), Oman (red), Pakistan (light pink), Saudi Arabia (chartreuse), Spain (yellow), South Africa (brown), Switzerland (green), and Venezuela (purple).
Figure 2
Figure 2
A UPGMA dendrogram generated with BioloMICS v12 made three clusters based on ITS sequences. ITS I included isolates from South Asia/Middle East and South Africa/Europe, ITS II and III included isolates from East Asia and South America/Israel, respectively. The color coding used for this dendrogram was the same as Figure 1.
Figure 3
Figure 3
A UPGMA dendrogram was generated with BioloMICS v12 based on AFLP genotyping results. Two main clusters, namely, AFLP I and AFLP II, were created and each was divided into four sub-clusters, AFLP Ia-Id and AFLP IIa-IId. The color coding used for this dendrogram was the same as Figure 1.
Figure 4
Figure 4
A UPGMA dendrogram was generated with BioloMICS v12 for 96 C. auris isolates by MALDI-TOF MS. Two main clusters were made, namely, MALDI I and MALDI II, with eight isolates forming basal lineages without assignment to a cluster. The color coding used for this dendrogram was the same as Figure 1.
Figure 5
Figure 5
A UPGMA dendrogram generated with BioloMICS v12 of spectra generated by IR Biotyper. Two major clusters were created, namely, IR I and IR II, and among them, cluster IR I was divided into four sub-clusters, IR Ia-Id. IR Biotyper abbreviation (IR) was used for sub-clusters. The colur coding used for this dendrogram was the same as Figure 1.

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