Genomic and Phenotypic Analysis of COVID-19-Associated Pulmonary Aspergillosis Isolates of Aspergillus fumigatus

Abstract

The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has already killed millions of people. COVID-19 patient outcome can be further complicated by secondary infections, such as COVID-19-associated pulmonary aspergillosis (CAPA).

Multiple Secondary Healthcare-Associated Infections Due to Carbapenem-Resistant Organisms in a Critically Ill COVID-19 Patient on Extensively Prolonged Venovenous Extracorporeal Membrane Oxygenation Support—A Case Report

“…Determining the cause of fever in patients with severe COVID-19 receiving ECMO is challenging because fever can be caused by many infectious conditions, including VAP, CRBSI, catheter-associated urinary tract infection, ECMO device-related infection, Clostridioides difficile infection, other bacterial infections (e.g., meningitis, sinusitis, biliary tract infections, and deep abscesses), non-bacterial infections (e.g., aspergillosis, CMV infection); non-infectious conditions (e.g., cerebral infarction/hemorrhage, venous thromboembolism, adrenal insufficiency, crystal arthritis, and drug fever), and COVID-19 recurrence [2,[7][8][9][10]. The accurate diagnosis of HAIs is often hampered by difficulties distinguishing HAIs from other infections and non-infectious conditions.…”

Regulation of gliotoxin biosynthesis and protection in Aspergillus species

“…The resulting nucleotide alignments were trimmed using ClipKIT, v1.1.3 (Steenwyk et al, 2020), with the 'smart-gap' option. All 1,133 genes were concatenated into a single matrix with 2,446,740 sites using the 'create_concat' function in PhyKIT (Steenwyk et al, 2021). The resulting alignment was used to reconstruct the evolutionary history of the 55 species using IQ-TREE, v2.0.6 (Minh et al, 2020).…”

“…SMs can cause damage to the host immune system, protect the fungus from host immune cells, or can mediate the acquisition of essential nutrients (Shwab et al 2007;Losada et al 2009;Yin et al 2013;Wiemann et al 2014;Bignell et al 2016;Knox et al 2016;Raffa and Keller 2019;Blachowicz et al 2020). Gliotoxin (GT) is the best studied A. fumigatus SM and has been detected in vivo in murine models of invasive aspergillosis (IA), in human cancer patients (Lewis et al, 2005), and is produced among isolates derived from patients with COVID-19 (Steenwyk et al, 2021).…”

“…fumigatus SM and has been detected in vivo in murine models of invasive aspergillosis (IA), in human cancer patients (Lewis et al, 2005), and in isolates derived from patients with COVID-19 and aspergillosis secondary co-infections (Steenwyk et al, 2021).…”

Phylogenetic Distribution of csp1 Types in Aspergillus fumigatus and Their Correlates to Azole Antifungal Drug Resistance

“… Aspergillus fumigatus is a ubiquitously distributed saprophytic mold and a leading cause of invasive aspergillosis in human hosts. Invasive aspergillosis is mainly associated with immunocompromising conditions such as neutropenia, solid organ transplantation, hematopoietic stem cell transplantation, chemotherapy, or as a secondary infection to tuberculosis, influenza ( 1 ), or lately COVID-19 ( 2 , 3 ). Invasive aspergillosis is per se a difficult-to-treat condition in already weakened patients.…”