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

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.

Antifungal Activity of Minocycline and Azoles Against Fluconazole-Resistant Candida Species

“…In our in vitro analyses, MIN and POS showed 100% in vitro synergy effect in C. albicans , C. parapsilosis , C. tropicalis , C. glabrata group, functioning against 94% (29/31) of tested strains, whereas combinations of MIN+ITC, MIN+FLU, and MIN+VOR exhibited synergistic activity against 84 (26/31), 65 (20/31), and 45% (14/31) of tested strains, respectively. The C. auris strains used in this study belonged to four different clusters, with AR382, AR387, AR388, AR389, and AR390 belonging in cluster I, AR381 belonging in cluster II, AR383 and AR384 belonging in cluster III, and AR385 and AR386 belonging in cluster IV ( Vatanshenassan et al, 2020 ). No differences among these clusters were detected in our in vitro analyses.…”

Candida auris: An Overview of How to Screen, Detect, Test and Control This Emerging Pathogen

“…In a recent study, Vatanshenassan and colleagues compared different typing techniques (i.e., microsatellite typing, AFLP fingerprinting, ITS sequencing, MALDI-TOF MS and IR Biotyper FTIR spectroscopy) to evaluate their application in typing C. auris [57]. Results indicated microsatellite typing as the tool of choice for C. auris outbreak investigations because only this technique grouped the isolates into four main clusters, in accordance with WGS data.…”

“…VITEK 2 MIC distributions can vary substantially for C. auris isolates from different clades [28] MBT ASTRA MBT ASTRA has a potential to detect echinocandin nonsusceptible C. auris isolates within 6 h. [57] Molecular methods Echinocandin resistance is mediated through limited mutations S639P or S639F in FKS1, and azole resistance through F126L, Y132F, and K143R in ERG11 * [2,5] * To date, these are the only mutations associated with clinical failures due to azole and echinocandin drugs.…”

Application and Perspectives of MALDI–TOF Mass Spectrometry in Clinical Microbiology Laboratories

“…Another MALDI–TOF MS combined approach currently used by few clinical microbiology laboratories is the Fourier Transform Infrared Spectroscopy (FTIRS), uses molecular vibration fingerprints, primarily the C–O stretching of biomacromolecules, to determine the molecular composition of a wide range of sample types [ 92 ]. By strain-specific absorbance patterns in the infrared spectrum [ 93 ], FTIRS characterizes a microbial sample by reflecting its biomolecular content to correlate with its genetic information [ 94 ]. FTIRS has been successfully applied in many studies to discriminate among bacteria at different taxonomic levels, (e.g., serogroup or serotype) and even at the strain level, to provide simple, quick, high-throughput, cost-effective bacterial typing [ 95 , 96 , 97 ].…”

“…FTIRS has been successfully applied in many studies to discriminate among bacteria at different taxonomic levels, (e.g., serogroup or serotype) and even at the strain level, to provide simple, quick, high-throughput, cost-effective bacterial typing [ 95 , 96 , 97 ]. The IR Biotyper (Bruker Daltonics, Bremen, Germany) is being used in the field of microbial strain typing, such as for the study of nosocomial outbreaks and their dynamics to prevent the spread of pathogens inside the hospitals [ 93 ].…”