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

• A. fumigatus infections were frequent in patients with probable CAPA in Argentina. • Non-albicans Candida species were often isolated in CAC cases from Argentina. • Candida species non-WT/resistant phenotype to at least one antifungal were found. 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. La aspergilosis pulmonar (CAPA) y la candidemia asociadas a COVID-19 (CAC) son complicaciones graves con mal pronóstico en pacientes críticos con SARS-CoV-2 y síndrome de distrés respiratorio agudo en unidades de cuidados intensivos (UCI). Este estudio tuvo como objetivo analizar la diversidad de especies de Aspergillus y Candida en pacientes críticos con CAPA y CAC, y sus perfiles de sensibilidad a antifúngicos. Se aislaron 96 cepas de Aspergillus de muestras respiratorias de 78 pacientes con CAPA y 52 cepas de Candida de hemocultivos de 50 pacientes con CAC. Todos los pacientes fueron internados en UCI de distintos centros médicos de Argentina, entre agosto de 2020 y agosto de 2021. Las especies de Aspergillus fueron identificadas por morfología y secuenciación de ADN, mientras que las de Candida por espectrometría de masas por desorción/ionización láser asistida por matriz con análisis de tiempo de vuelo. Los aislamientos de Aspergillus pertenecieron a las secciones Fumigati (n = 51), Flavi (n = 23), Nigri (n = 17), Terrei (n = 4) y Nidulantes (n = 1). Los aislamientos de Candida pertenecieron a los siguientes clados o géneros: Lodderomyces (n = 41), Nakaseomyces (n = 4), Meyerozyma (n = 2), Metschnikowia (n = 2) y Yarrowia (n = 1); también se encontraron miembros de la familia Wickerhamomycetaceae (n = 2). Todos los aislamientos de Aspergillus fueron sensibles o presentaron un fenotipo salvaje a los antifúngicos evaluados, mientras que el 26,9% de los aislamientos de Candida mostraron un fenotipo no silvestre o resistente a al menos uno. Nuestros resultados aportan información sobre la diversidad de especies de Aspergillus y Candida , y sus perfiles de sensibilidad en pacientes críticos con COVID-19.