Aspergillus fumigatus is the primary causative agent of aspergillosis. Cryptic species may exhibit variable pathogenic potential and antifungal resistance and, particularly those within the section Fumigati, have significant clinical and environmental relevance. However, the genomic and proteomic bases underlying these differences remain poorly understood. This study presents a comparative analysis of 42 genomes (including five newly sequenced genomes), together with their corresponding predicted proteomes, from A. fumigatus, and from four cryptic species: A. lentulus, A. udagawae, A. felis and A. hiratsukae. Notably, these represent the only genomes currently available for these cryptic species, allowing us to integrate antifungal resistance mechanisms, and virulence factors across the full existing genomic landscape. We showed that A. fumigatus retains a highly conserved core proteome, whereas A. felis and A. lentulus exhibit greater genomic plasticity. Our preliminary findings suggest that azole resistance is primarily driven by species-specific point mutations, which are not shared across the section Fumigati. Secondary metabolism pathways are the main difference observed among section Fumigati, with variations in biosynthetic gene clusters and mycotoxin production. Our findings emphasize the evolutionary balance between genomic conservation and evolutionary divergence in A. fumigatus sensu lato, determining azole resistance and pathogenicity-associated fitness.

Fungal disease is on the rise, coupled with fungal pathogens increasing in geographic range. Studies have shown that viable fungal pathogens may be present in beach sand and water, and consequently, efforts are ongoing in Europe to develop guidelines for fungi levels at beaches. In the USA, fungal diseases are a growing concern, and yet, they are not subject to public health reporting, and beach environments are currently not routinely monitored for fungal pathogens. This study measured fungal and enterococci levels at two beaches within a subtropical environment in Miami, FL. Samples were analyzed by culture-based methods, with fungi species confirmation by targeted PCR and sequencing. A unique aspect of this study is the analysis with higher incubation temperatures (37 °C and 40 °C) to isolate mesophilic fungi that can cause invasive infections. Results show that levels of fungi were strongly influenced by sample matrix (sand or water). The most common fungal species observed belonged to the Aspergillus and Candida genera, with the isolation of 25 taxa with reports of causing infections, of which 20 were previously reported to exhibit resistance to some or all classes of antifungals available. Results emphasize the need for fungal specific analyses to better understand beach-related disease risks. Given the current increase in cases of fungal diseases and the presence of viable fungi in the environment, integrating fungal measurements in routine microbiological monitoring programs is critical for assessing the beach transmission of pathogenic fungal disease and the control of emerging fungal pathogens.