Abstract
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 Candida albicans, two C. parapsilosis, and two Aspergillus fumigatus were analyzed. All Candida spp. isolates were susceptible to micafungin and azole drugs (fluconazole, voriconazole, posaconazole, itraconazole, isavuconazole). A. fumigatus isolates were susceptible to micafungin and all triazole drugs except fluconazole (intrinsic resistance). Multilocus sequence typing (MLST) of C. albicans 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. A. fumigatus 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.
Highlights
Species Distribution of Fungal Isolates Recovered from COVID-19 Patients
Twenty-one fungal isolates were cultured from specimens of COVID-19 patients and archived at The Department of Pathology (HUMC) in April and May 2020
We based our study on available microbiological material—21 fungal isolates that were recovered from cultures of sputum and blood of 19 severely ill COVID-19 patients at the Department of Pathology at Hackensack University Medical Center (HUMC) in Hackensack, New Jersey, USA
Summary
The emergence and subsequent pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health crisis with 154.6M+ confirmed cases and 3.2M+ deaths worldwide (as of 6 May 2021) [1]. The relatively high incidence of severe disease and mortality in COVID-19 patients is expected to be enhanced by secondary infections, alongside a lack of natural immunity and viral replication in the lower respiratory tract leading to severe lung injury and acute respiratory distress syndrome (ARDS). Bacterial and fungal infections are common complications of viral pneumonia which lead to an increased need for intensive care and higher mortality rates. Invasive pulmonary aspergillosis (IPA) has been described as a confounder in critically ill patients admitted to the intensive care unit (ICU) with influenza pneumonia [3].
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