One-Step Soft Agar Enrichment and Isolation of Human Lung Bacteria Inhibiting the Germination of Aspergillus fumigatus Conidia

Fungi of the genus <i>Aspergillus</i> are widespread in the environment, where they produce large quantities of airborne conidia. Inhalation of <i>Aspergillus</i> spp. conidia in immunocompromised individuals can cause a wide spectrum of diseases, ranging from hypersensitivity responses to lethal invasive infections. Upon deposition in the lung epithelial surface, conidia encounter and interact with complex microbial communities that constitute the lung microbiota. The lung microbiota has been suggested to influence the establishment and growth of <i>Aspergillus</i> spp. in the human airways. However, the mechanisms underlying this interaction have not yet been sufficiently investigated. In this study, we aimed to enrich and isolate bacterial strains capable of inhibiting the germination and growth of <i>A. fumigatus</i> conidia from bronchoalveolar lavage fluid (BALF) samples of lung transplant recipients using a novel enrichment method. This method is based on a soft agar overlay plate assay in which bacteria are directly in contact with conidia, allowing inhibition to be readily observed during enrichment. We isolated a total of five clonal bacterial strains with identical genotypic fingerprints, as shown by random amplified polymorphic DNA PCR (RAPD-PCR). All strains were identified as <i>Pseudomonas aeruginosa</i> (strains b1-b5). The strains were able to inhibit the germination and growth of <i>Aspergillus fumigatus</i> in a soft agar confrontation assay, as well as in a germination multiplate assay. Moreover, when compared with ten <i>P. aeruginosa</i> strains isolated from expectoration through standard methods, no significant differences in inhibitory potential were observed. Additionally, we showed inhibition of <i>A. fumigatus</i> growth on Calu-3 cell culture monolayers. However, the isolated <i>P. aeruginosa</i> strains were shown to cause significant damage to the cell monolayers. Overall, although <i>P. aeruginosa</i> is a known opportunistic lung pathogen and antagonist of <i>A. fumigatus</i>, we validated this novel one-step enrichment approach for the isolation of bacterial strains antagonistic to <i>A. fumigatus</i> from BALF samples as a proof-of-concept. This opens up a new venue for the targeted enrichment of antagonistic bacterial strains against specific fungal pathogens.