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

Author(s):Show less -

Steenwyk, Jacob L. ^[1] ; Mead, Matthew E. ^[1] ; de Castro, Patricia Alves ^[2] ; Valero, Clara ^[2] ; Damasio, Andre ^{[3, 4]} ; dos Santos, Renato A. C. ^[2] ; Labella, Abigail L. ^[1] ; Li, Yuanning ^[1] ; Knowles, Sonja L. ^[5] ; Raja, Huzefa A. ^[5] ; Oberlies, Nicholas H. ^[5] ; Zhou, Xiaofan ^[6] ; Cornely, Oliver A. ^{[7, 8, 9, 10, 11, 12]} ; Fuchs, Frieder ^[13] ; Koehler, Philipp ^{[7, 8, 9]} ; Goldman, Gustavo H. ^[2] ; Rokas, Antonis ^[1]

Affiliation:Show less -

^[1] Vanderbilt Univ, Dept Biol Sci, Nashville, TN 37235 - USA

^[2] Univ Sao Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Ribeirao Preto - Brazil

^[3] Univ Estadual Campinas, Inst Biol, UNICAMP, Campinas, SP - Brazil

^[4] Univ Estadual Campinas, UNICAMP, Expt Med Res Cluster EMRC, Campinas, SP - Brazil

^[5] Univ N Carolina, Dept Chem & Biochem, Greensboro, NC 27402 - USA

^[6] South China Agr Univ, Integrat Microbiol Res Ctr, Guangdong Lab Lingnan Modern Agr, Guangdong Prov Key Lab Microbial Signals & Dis Co, Guangzhou - Peoples R China

^[7] Univ Cologne, Cologne Excellence Cluster Cellular Stress Respon, Cologne - Germany

^[8] Univ Cologne, Med Fac, Cologne - Germany

^[9] Univ Hosp Cologne, Excellence Ctr Med Mycol ECMM, Dept Internal Med 1, Cologne - Germany

^[10] Clin Trials Ctr Cologne, ZKS Koln, Cologne - Germany

^[11] Univ Cologne, German Ctr Infect Res DZIF, Med Fac, Partner Site Bonn Cologne, Cologne - Germany

^[12] Univ Cologne, Univ Hosp Cologne, Partner Site Bonn Cologne, Cologne - Germany

^[13] Univ Cologne, Fac Med, Inst Med Microbiol Immunol & Hyg, Cologne - Germany

• Document type: Journal article
• Source: MICROBIOLOGY SPECTRUM; v. 9, n. 1 SEP 2021.
• Web of Science Citations: 3

Abstract

The ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for coronavirus disease 2019 (COVID-19), first described in Wuhan, China. A subset of COVID-19 patients has been reported to have acquired secondary infections by microbial pathogens, such as opportunistic fungal pathogens from the genus Aspergillus. To gain insight into COVID-19-associated pulmonary aspergillosis (CAPA), we analyzed the genomes and characterized the phenotypic profiles of four CAPA isolates of Aspergillus fumigatus obtained from patients treated in the area of North Rhine-Westphalia, Germany. By examining the mutational spectrum of single nucleotide polymorphisms, insertiondeletion polymorphisms, and copy number variants among 206 genes known to modulate A. fumigatus virulence, we found that CAPA isolate genomes do not exhibit significant differences from the genome of the Af293 reference strain. By examining a number of factors, including virulence in an invertebrate moth model, growth in the presence of osmotic, cell wall, and oxidative stressors, secondary metabolite biosynthesis, and the MIC of antifungal drugs, we found that CAPA isolates were generally, but not always, similar to A. fumigatus reference strains Af293 and CEA17. Notably, CAPA isolate D had more putative loss-of-function mutations in genes known to increase virulence when deleted. Moreover, CAPA isolate D was significantly more virulent than the other three CAPA isolates and the A. fumigatus reference strains Af293 and CEA17, but similarly virulent to two other clinical strains of A. fumigatus. These findings expand our understanding of the genomic and phenotypic characteristics of isolates that cause CAPA. IMPORTANCE The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID19), 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). CAPA is caused by Aspergillus fungal pathogens, but there is little information about the genomic and phenotypic characteristics of CAPA isolates. We conducted genome sequencing and extensive phenotyping of four CAPA isolates of Aspergillus fumigatus from Germany. We found that CAPA isolates were often, but not always, similar to other reference strains of A. fumigatus across 206 genetic determinants of infection-relevant phenotypes, including virulence. For example, CAPA isolate D was more virulent than other CAPA isolates and reference strains in an invertebrate model of fungal disease, but similarly virulent to two other clinical strains. These results expand our understanding of COVID-19-associated pulmonary aspergillosis. (AU)

• FAPESP's process: 19/07526-4 - Genetic variation of secondary metabolite gene clusters in clinical isolates of cryptic species in the Aspergillus fumigatus complex (section Fumigati )
• Grantee: Renato Augusto Corrêa dos Santos
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 17/21983-3 - Genomic analysis of Aspergillus cryptic species
• Grantee: Renato Augusto Corrêa dos Santos
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 18/00715-3 - Molecular characterization of Aspergillus fumigatus transcription factors involved in calcium metabolism.
• Grantee: Clara Isabel Valero Fernández
• Support Opportunities: Scholarships in Brazil - Post-Doctoral