Author:
ME Mead1*, PA de Castro2, JL Steenwyk1, M Hoenigl3, J Prattes3, R Rautemaa-Richardson4, CB Moore4, C Lass-Flörl5, JP Gangneux6, H Guegan6, N Van Rhinj4, A Rokas1, GH Goldman2, S Gago4
Author address:
1Biological Sciences, Vanderbilt University, Nashville, USA
2Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
3Division of Infectious Diseases, Medical University of Graz, Graz, Austria
4Manchester University NHS Foundation Trust, Wythenshawe Hospital, Manchester, UK
5European Excellence Center of Medical Mycology (ECMM), Medical University of Innsbruck, Innsbruck, Austria
6CHU Rennes, University of Rennes, Rennes, France
Full conference title:
10th Advances Against Aspergillosis and Mucormycosis
Date: 2 February 2022
Abstract:
Purpose:
Coronavirus disease 2019 (COVID-19) continues to be a global health issue and superinfections involving fungi have widely been reported in patients with severe cases of this novel disease. COVID-19-associated pulmonary aspergillosis (CAPA) is one of such superinfections and while many CAPA fungal isolates have been reported, there is a dearth of publicly available whole genome sequences for those isolates. We set out to increase the number of whole genome sequences of CAPA isolates available to the community and characterize those isolates using both phylogenomic and phenotypic analyses.
Methods:
11 newly isolated CAPA clinical isolates from Europe were sequenced. Standard pipelines were used to assemble these genomes and predict gene annotations.
To build a phylogenomic tree that included the 11 new CAPA isolates, four previously reported European CAPA clinical isolates, 43 non-CAPA clinical and environmental Aspergillus fumigatus isolates that span the known diversity of the species, and three outgroup Aspergillus strains from two different species, we used a previously constructed data set of 4,525 single-copy orthologous genes. Of the 4,525 orthologs, we found 4,515 to be present in single copy in all the newly sequenced CAPA genomes. These 4,515 single-copy orthologs from each of the 61 strains were then aligned, trimmed, concatenated, and then used to construct a phylogenetic tree using maximum likelihood methods.
In addition, we characterized the CAPA strains for their antifungal susceptibility and response to growth in many infection-relevant conditions: the presence of macrophages, sorbitol, hypoxia, Congo red, hydrogen peroxide, high temperature, and high- and low-iron levels.
Results:
The resulting phylogenetic tree showed that the 11 new CAPA strains are more genetically diverse than the previously sequenced CAPA strains and appear to span A. fumigatus genomic
diversity based on their placements on the phylogeny. There also appears to be low correlation between geographic location and genetic relatedness in these CAPA strains.
Our antifungal susceptibility experiments showed that there is low heterogeneity amongst a subset of the isolates, and they respond to antifungals in a manner similar to two reference strains, Af293 and A1163. When grown under infection-relevant stresses and compared to the two reference strains, the new CAPA strains were more similar to Af293 than A1163.
Conclusion:
Our results suggest that CAPA strains exhibit genomic heterogeneity amongst each other yet are similar to other A. fumigatus strains both in their genetic diversity and phenotypic response to disease-relevant stresses; a novel finding compared to our previous studies that utilized a smaller number of CAPA strains. This information will likely be of great interest to molecular biologists, as well as clinicians and epidemiologists as they continue to address the fungal disease implications of the COVID-19 pandemic.
Abstract Number: 43
Conference Year: 2022
Link to conference website: https://aaam2022.org/
URL Conference abstract: