Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus

Abstract

Aspergillus fumigatus is both an environmental saprobe and an opportunistic human fungal pathogen. Knowledge of genomic variation across A. fumigatus isolates is essential for understanding the evolution of pathogenicity, virulence, and resistance to antifungal drugs. Here, we investigated 206 A. fumigatus isolates (133 clinical and 73 environmental isolates) aiming to identify genes with variable presence across isolates and test whether this variation was related to the clinical or environmental origin of isolates. The PanCore genome of A. fumigatus constitutes 13,085 ortholog groups, of which 7,773 (59.4%) are shared by all isolates (CORE) and 5,312 (40.6%) vary in their gene presence across isolates (ACCESSORY). Despite differences in the distribution of orthologs across all isolates, no significant differences were observed among clinical vs. environmental isolates when accounting for phylogeny. Orthologs that differ in their distribution across isolates tend to occur in low frequency and/or be restricted to specific isolates; thus, the degree of genomic conservation between orthologs of A. fumigatus is high. These results suggest that differences in the distribution of orthologs within A. fumigatus cannot be associated with the clinical or environmental origin of isolates.

IMA Genome – F19

“…This increases the number of genomes from environmental Sporothrix species to 15. These genomic resources have proven invaluable in the study of other fungal pathogens, with comparisons between environmental and clinical strains providing great insight into the acquisition or loss of pathogenicity, and the evolutionary mechanisms underlying these physiological differences (Pryszcz et al 2013;Desjardins et al 2017;Horta et al 2022) (Authors: Taygen Fuchs*, Deanné du Plessis, Chanel Thomas, Ariska van der Nest, Alishia van Heerden, Brenda D. Wingfield, and Michael J. Wingfield *Contact: taygen. fuchs@ fabi.…”

Host, pathogenic fungi and the microbiome: A genetic triangle in infection

“…Similarly, Ballard et al ( 51 ) reported that long-term Aspergillus infection in patients with chronic granulomatous disease is driven by host microevolution ( 51 ). Moreover, recent analyses of fungal pangenomes has shown that A. fumigatus environmental isolates do not differ in their gene content ( 52 ). However, it has been shown an increased number of accessory genes in clinical isolates compared to environmental that might help to better understand human disease ( 53 ).…”