Analysis of Microbiota and Mycobiota in Fungal Ball Rhinosinusitis: Specific Interaction between Aspergillus fumigatus and Haemophilus influenza?

Abstract

Fungal ball (FB) rhinosinusitis (RS) is the main type of non-invasive fungal RS. Despite positive direct examination (DE) of biopsies, culture remains negative in more than 60% of cases. The aim of the study was to evaluate the performance/efficacy of targeted metagenomics (TM) to analyze microbiota and mycobiota in FB and find microbial associations. Forty-five sinus biopsies from patients who underwent surgery for chronic RS were included. After DE and culture, DNA was extracted, then fungal ITS1–ITS2 and bacterial V3–V4 16S rDNA loci were sequenced (MiSeqTM Illumina). Operational taxonomic units (OTUs) were defined via QIIME and assigned to SILVA (16S) and UNITE (ITS) databases. Statistical analyses were performed using SHAMAN. Thirty-eight patients had FB and seven had non-fungal rhinosinusitis (NFRS). DE and culture of FB were positive for fungi in 97.3 and 31.6% of patients, respectively. TM analysis of the 38 FB yielded more than one fungal genus in 100% of cases, with Aspergillus in 89.5% (34/38). Haemophilus was over-represented in FB with >1000 reads/sample in 47.3% (18/38) compared to NFRS (p < 0.001). TM allowed fungal identification in biopsies with negative culture. Haemophilus was associated with FB. Pathogenesis could result from fungi–bacteria interactions in a mixed biofilm-like structure.

Analysing sinonasal microbiota of fungal rhinosinusitis by next‐generation sequencing

“…Delliere et al identified Aspergillus spp. in 89.5% of fungal balls with targeted metagenomics 3 . However, in our study, 60.71% of the reads from each fungal sample could not be assigned to an OTU and were, thus, annotated as unclassified.…”

“…in 89.5% of fungal balls with targeted metagenomics. 3 However, in our study, 60.71% of the reads from each fungal sample could not be assigned to an OTU and were, thus, annotated as unclassified. The ability to assign a significant number of reads at both the phylum and genus levels reveals the presence of several formerly unknown fungal taxonomic groups in fungal sinusitis and recapitulates the limitations of the existing fungal sequence databases.…”

“…Previous studies on fungal ball and non-fungal rhinosinusitis-associated bacterial microbiota have revealed that Haemophilus was highly dominant but also relatively abundant in fungal ball patients. 3 growth both in vivo and in vitro. 16 Zhang et al also reported that the presence of Pseudomonas aeruginosa was significantly associated with altered and broken mycelia within the fungal ball, and that co-infection with Pseudomonas may repress fungal filamentation and interfere with Aspergillus growth.…”

“…Next-generation sequencing (NGS) has recently been developed and used in many fields. Although some studies have investigated the microbiome of rhinosinusitis using NGS, 3,4 there is still limited data regarding its use in fungal rhinosinusitis.…”

Age-Associated Changes of Nasal Bacterial Microbiome in Patients With Chronic Rhinosinusitis

“…(2017) revealed that levels of specific gatekeeping genera, such as Corynebacterium , Peptoniphilus , and Propionobacterium , have been reduced in the microbiota of CRS patients, which might predispose the host to pathogen-driven inflammation. So far, much effort has been done to define the relationship between the type and amount of the microorganism and the severity of CRS using similar methods in microbiota analysis ( Cho et al., 2021 ; Delliere et al., 2021 ; Stryjewska-Makuch et al., 2021 ). Collectively, these studies suggest that bacterial microbiota might play a pathogenic role in CRS, with significant implications for disease management and treatment.…”