Antifungal Drug Susceptibility and Genetic Characterization of Fungi Recovered from COVID-19 Patients

• Main Authors: Milena Kordalewska, Kevin D. Guerrero, Rocio Garcia-Rubio, Cristina Jiménez-Ortigosa, José R. Mediavilla, Marcus H. Cunningham, Frank Hollis, Tao Hong, Kar Fai Chow, Barry N. Kreiswirth, David S. Perlin
• Format: Article
• Language: English
• Published: MDPI AG 2021-07-01
• Series: Journal of Fungi
• Subjects: <i>Candida albicans</i>; <i>Candida parapsilosis</i>; <i>Aspergillus fumigatus</i>; antifungal susceptibility; secondary infections; <i>Candida</i> pneumonia
• Online Access: https://www.mdpi.com/2309-608X/7/7/552

Fungal infections are common complications of respiratory viral infections and are associated with the increased need for intensive care and elevated mortality. Data regarding microbiological and molecular characteristics of such infections in COVID-19 patients are scarce. Here, we performed a comprehensive analysis, including species identification, antifungal susceptibility testing, molecular resistance determinants analysis, typing, and retrospective clinical data review, of fungal isolates recovered from 19 COVID-19 patients, who were hospitalized at the Hackensack University Medical Center (HUMC) in Hackensack, New Jersey, USA, in the initial phase of the pandemic from April–May 2020. In total, 17 <i>Candida albicans</i>, two <i>C. parapsilosis</i>, and two <i>Aspergillus fumigatus</i> were analyzed. All <i>Candida</i> spp. isolates were susceptible to micafungin and azole drugs (fluconazole, voriconazole, posaconazole, itraconazole, isavuconazole). <i>A. fumigatus</i> isolates were susceptible to micafungin and all triazole drugs except fluconazole (intrinsic resistance). Multilocus sequence typing (MLST) of <i>C. albicans</i> isolates revealed 15 different sequence types (STs), which clustered below the clade-defining limit of p-distance < 0.04. Pulsed-field gel electrophoresis (PFGE) karyotyping revealed no chromosomal rearrangements in these isolates. <i>A. fumigatus</i> isolates were of different, non-related genotypes. We speculate that virus- and drug-induced immunosuppression (94.7% of the patients received corticosteroids), together with prolonged hospital stay (median duration of 29 days) and mechanical ventilation (median duration of 24 days) likely increased the susceptibility to secondary respiratory and bloodstream infections in the studied patient population. The presence of fungi in blood or respiratory tract fluid was a prognosticator for poor clinical outcome, which presented as an 89.5% 30-day mortality in our patient cohort.