How Yeast Antifungal Resistance Gene Analysis Is Essential to Validate Antifungal Susceptibility Testing Systems

Abstract

Objectives: The antifungal susceptibility testing (AFST) of yeast pathogen alerts clinicians about the potential emergence of resistance. In this study, we compared two commercial microdilution AFST methods: Sensititre YeastOne read visually (YO) and MICRONAUT-AM read visually (MN) or spectrophotometrically (MNV), interpreted with Clinical and Laboratory Standards Institute and European Committee on Antimicrobial Susceptibility Testing criteria, respectively.

Methods: Overall, 97 strains from 19 yeast species were measured for nine antifungal drugs including a total of 873 observations. First, the minimal inhibitory concentration (MIC) was compared between YO and MNV, and between MNV and MN, either directly or by assigning them to five susceptibility categories. Those categories were based on the number of MIC dilutions around the breakpoint or epidemiological cut-off reference values (ECOFFs or ECVs). Second, YO and MNV methods were evaluated for their ability to detect the elevation of MICs due to mutation in antifungal resistance genes, thanks to pairs or triplets of isogenic strains isolated from a single patient along a treatment previously analyzed for antifungal resistance gene mutations. Reproducibility measurement was evaluated, thanks to three quality control (QC) strains.

Results: YO and MNV direct MIC comparisons obtained a global agreement of 67%. Performing susceptibility category comparisons, only 22% and 49% of the MICs could be assigned to categories using breakpoints and ECOFFs/ECVs, respectively, and 40% could not be assigned due to the lack of criteria in both consortia. The YO and MN susceptibility categories gave accuracies as low as 50%, revealing the difficulty to implement this method of comparison. In contrast, using the antifungal resistance gene sequences as a gold standard, we demonstrated that both methods (YO and MN) were equally able to detect the acquisition of resistance in the Candida strains, even if MN showed a global lower MIC elevation than YO. Finally, no major differences in reproducibility were observed between the three AFST methods.

Conclusion: This study demonstrates the valuable use of both commercial microdilution AFST methods to detect antifungal resistance due to point mutations in antifungal resistance genes. We highlighted the difficulty to conduct conclusive analyses without antifungal gene sequence data as a gold standard. Indeed, MIC comparisons taking into account the consortia criteria of interpretation remain difficult even after the effort of harmonization.

Keywords: CLSI; EUCAST; MICRONAUT-AM; Sensititre TM YeastOne TM; antifungal susceptibility; diagnostic test; resistance genes.

Figure 1

Definition of the MIC categories and agreement levels. Five MIC categories were defined from highly sensitive (HS) to highly resistant (HR), based on dilution differences from a reference MIC value [breakpoint (s) or ECV/ECOFF].

Figure 2

Confusion matrix of MIC categories for all the data. (A) Comparison of YO versus MNV using breakpoints. (B) Comparison of YO versus MNV using ECV/ECOFF. (C) Comparison of MNV versus MN using breakpoints. (D) Comparison of MNV versus MN using ECV/ECOFF. VME, very major error (in red); ME, major error (in orange); mE, minor error (in yellow), NA, no analysis (in gray); no errors (in green). For each category of discrepancies, the number of event is indicated (n = xx) with the percent of possible comparisons it represents. Accuracy between the two methods and kappa score are indicated on the right side of the matrix.

Figure 3

Azole MIC increases of C. albicans and C. glabrata resistant strains as compared to matched susceptible ones for YO and MNV. (A) C. albicans matched strains. (B) C. glabrata matched strains. For all susceptible isolates, the MIC values are indicated in micrograms per millilliter of drugs, whereas for the matched resistant isolates, the respective number of azole dilutions to reach the MIC is indicated. When possible, the interpretation of the MIC, relative to existing breakpoints, is indicated in the YOI (for YO) and MNVI (for Micronaut-AM) columns.

Figure 4

Candin MIC increases of C. albicans and C. glabrata resistant strains as compared to matched susceptible ones for YO and MNV. (A) C. albicans matched strains. (B) C. glabrata matched strains. For all susceptible isolates, the MIC values are indicated in micrograms per millilliter of drugs, whereas for the matched resistant isolates, the respective number of azole dilutions to reach the MIC is indicated. When possible, the interpretation of the MIC, relative to existing breakpoints, is indicated in the YOI (for YO) and MNVI (for Micronaut-AM) columns.

Figure 5

MIC increases of C. lusitaniae resistant strains as compared to the matched susceptible one for YO and MNV. The MIC values are indicated for the susceptible isolate in micrograms per millilliter of drugs, whereas for the matched resistant isolates, the respective number of azole dilutions to reach the MIC is indicated. As none of the drug has breakpoint interpretation in both consortia for C. lusitaniae, we do not indicate any interpretation in this table.