Mechanism Behind Deadly Fungal Infection with Influenza or Covid-19 Deciphered

Every year, hundreds of thousands of people worldwide end up in intensive care with influenza or Covid-19. About 15% of them develop an additional lung infection with the common fungus Aspergillus (aspergillosis).

For critically ill patients with an underlying influenza or Covid-19 infection, however, aspergillosis can be deadly: the fungus can start to grow in the tissue of their respiratory tract and lungs and cause irreversible damage. The mortality rate of these patients becomes 40% to 50%, about twice as high as that of ICU patients who only have severe influenza or Covid-19.

A large team of international clinical scientists led by those at the University Hospitals Leuven (Leuven, Belgium) retrospectively recruited 169 patients who had been admitted to the intensive care unit (ICU), requiring non-invasive or invasive ventilation because of severe influenza or COVID-19, with or without aspergillosis, between Jan 1, 2011, and March 31, 2021, and whose bronchoalveolar lavage samples were available at the hospital biobank.

The scientists used nCounter (NanoString, Seattle, WA, USA) gene expression analysis of 755 genes linked to myeloid innate immunity and protein analysis using ELISA or multiplex bead-based assays of 47 cytokines, chemokines, and growth factors on the bronchoalveolar lavage samples. Gene expression data were used to infer cell fractions by use of CIBERSORTx, to perform hypergeometric enrichment pathway analysis by use of the ClueGO plug-in (with Gene Ontology biological process as the pathway database) in Cytoscape and gene set enrichment analysis.

The investigators performed RNAScope (Advanced Cell Diagnostics, Inc., Newark, NJ, USA) ultrasensitive single molecule RNA in-situ hybridization targeting influenza virus or SARS-CoV-2 RNA on formalin-fixed, paraffin-embedded sections of in vivo tracheobronchial biopsy samples from patients with influenza-associated pulmonary aspergillosis (IAPA) or COVID-19-associated pulmonary aspergillosis (CAPA) and invasive Aspergillus tracheobronchitis.

The team reported that a downregulation of genes associated with antifungal effector functions in patients with IAPA and, to a lesser extent, in patients with CAPA. They found a downregulated expression of several genes encoding proteins with functions in the opsonization, recognition, and killing of conidia in patients with IAPA versus influenza only and in patients with CAPA versus COVID-19 only. Several genes related to LC3-associated phagocytosis, autophagy, or both were differentially expressed. Patients with CAPA had significantly lower neutrophil cell fractions than did patients with COVID-19 only.

Patients with IAPA or CAPA had downregulated IFNγ signaling compared with patients with influenza only or COVID-19 only, respectively. The concentrations of several fibrosis-related growth factors were significantly elevated in the bronchoalveolar lavage fluid from patients with IAPA versus influenza only and from patients with CAPA versus COVID-19 only. In one patient with CAPA, they visualized an active or very recent SARS-CoV-2 infection disrupting the epithelial barrier, facilitating tissue-invasive aspergillosis.

Joost Wauters, MD PhD, an Intensivist Professor and principal investigator of the study, said, “We discovered that, in patients with serious influenza or Covid-19 who develop this type of fungal infection, the innate immune system had been affected in various areas. Their immune cells, which in healthy people are responsible for eliminating fungal spores in the lungs, were compromised. Furthermore, the white blood cells that would normally clean up fungal hyphae did not seem to function properly in those influenza or Covid-19 patients. It was surprising to see that partly similar deviating immune processes come into play in both Covid-19 and influenza.” The study was published on August 24, 2022 in the journal The Lancet Respiratory Medicine.

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