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Antifungal susceptibility testing is important in guiding patient therapy due to an increasing number of resistant <i>Candida</i> isolates. In the clinical strain collection of the Austrian resistance report (AURES), a high number of micafungin-resistant <i>C. albicans</i> isolates (18.2% 49/269) was detected in seven different centres in Austria from 2011–2016. Most of these isolates showed a micafungin MIC value that was just above the clinical breakpoint (CB) established by EUCAST (0.016 mg/L). The aim of this study was to analyse whether <i>C. albicans</i> strains showing a micafungin MIC value of 1–2 dilutions above the CB (0.032 mg/L and 0.064 mg/L) are associated with mutations in <i>FKS1</i> hotspot (HS) regions. 115 <i>C. albicans</i> candidemia strains showing a micafungin MIC one or two dilutions above the EUCAST CB (0.032 mg/L and 0.064 mg/L) were categorized as borderline resistant and screened for mutations in <i>FKS1</i> HS1, HS2, and HS3 regions, which are known locations for the development of echinocandin resistance. For this purpose, we implemented targeted resequencing utilizing a next generation sequencing technology. No missense mutations could be detected in <i>FKS1</i> HS1, HS2, and HS3 in any of the 115 isolates, which indicated that resistance conferred by alteration of <i>FKS1</i> seems unlikely.