Molecular epidemiology and antifungal susceptibility patterns of Aspergillus and Candida species isolated from Argentinian patients with COVID-19-associated pulmonary aspergillosis and candidemia

COVID-19-associated pulmonary aspergillosis (CAPA) and candidemia (CAC) have emerged as serious complications with poor prognoses among critically ill patients with SARS-CoV-2 pneumonia and acute respiratory distress syndrome at intensive care units (ICU). This study aimed to provide an overview of the diversity of Aspergillus and Candida species in critically ill patients with CAPA and CAC, as well as to analyze their antifungal susceptibility profiles. Ninety-six Aspergillus isolates were recovered from respiratory specimens of 78 COVID-19 patients with probable CAPA, and 52 Candida isolates were recovered from blood stream specimens of 50 COVID-19 patients with proven CAC. All patients were admitted to ICUs in different medical centers across from Argentina, between August 2020 and August 2021. Aspergillus species were identified by morphology and DNA sequencing, while Candida species were identified using matrix assisted laser desorption/ionization time-of-flight mass spectrometry. Antifungal susceptibility testing was performed by microdilution. The Aspergillus isolates were identified as members of the sections Fumigati (n=51), Flavi (n=23), Nigri (n=17), Terrei (n=4), and Nidulantes (n=1). The Candida isolates belonged to the following clades or genera: Lodderomyces (n=41), Nakaseomyces (n=4), Meyerozyma (n=2), Metschnikowia (n=2), Yarrowia (n=1), and members of the family Wickerhamomycetaceae (n=2). All Aspergillus isolates were susceptible to the tested antifungal agents, whereas 26.9% of Candida isolates exhibited a non-wild-type or resistant phenotype to at least one antifungal drug. Our results provide insights into the diversity of Aspergillus and Candida species, as well as their antifungal susceptibility profiles, in critically ill COVID-19 patients.