Prevalence and diversity of filamentous fungi in the airways of cystic fibrosis patients – A Dutch, multicentre study

Abstract

Background: Progressive lung injury in Cystic Fibrosis (CF) patients can lead to chronic colonization with bacteria and fungi. Fungal colonization is obtained from the environment which necessitates locally performed epidemiology studies. We prospectively analyzed respiratory samples of CF patients during a 3-year period, using a uniform fungal culture protocol, focusing on filamentous fungi and azole resistance in Aspergillus fumigatus. Methods: Over a 3-year period, all respiratory specimens collected from CF patients in 5 Dutch CF centers, were analyzed. Samples were inoculated onto the fungal culture media Sabouraud dextrose agar (SDA) and Medium B+. All fungal isolates were collected and identified in one centre, using Amplified Fragment Length Polymorphism (AFLP) fingerprinting, rDNA PCR and ITS, calmodulin and β-tubulin sequencing. Azole resistance was assessed for all A. fumigatus using a qPCR assay followed by phenotypic confirmation. Results: Filamentous fungi were recovered from 699 patients from at least one respiratory sample, corresponding with 3787 cultured fungal species. A. fumigatus was cultured most often with a mean prevalence of 31.7%, followed by Penicillium species (12.6%), non-fumigatus Aspergillus species (5.6%), Scedosporium species (4.5%) and Exophiala dermatitidis and Cladosporium species (1.1% each). In total 107 different fungal species were identified, with 39 Penicillium species and 15 Aspergillus species. Azole resistance frequency in A. fumigatus was 7.1%, with TR 34 /L98H being the dominant resistance mechanism. Conclusion: A vast diversity of filamentous fungi was demonstrated, dominated by Aspergillus and Penicillium species. We observed a mean azole resistance prevalence of 7.1% of A. fumigatus culture positive patients.

Neutrophil Adaptations upon Recruitment to the Lung: New Concepts and Implications for Homeostasis and Disease

“…Dendritic cells were also found to lack expression of surface costimulatory molecules, but this defect was rescued by coincubation with neutrophils following Aspergillus exposure [103]. Considering that neutrophils are essential for guarding the lungs against fungal pathogens it is surprising that CF patients, who experience widespread neutrophilic inflammation in the airways, are highly susceptible to respiratory fungal infections [104]. The cause may be neutrophils themselves.…”

The Human Lung Mycobiome in Chronic Respiratory Disease: Limitations of Methods and Our Current Understanding

“…However, as the disease progresses, the lung microbiome of patients with CF is dominated by the bacterium Pseudomonas aeruginosa [33]. Some recent studies have reported that co-colonisation of the airways by C. albicans or A. fumigatus with P. aeruginosa lead to more exacerbations and decreased lung function [34,35]. Other fungal species frequently detected in the airways from patients with CF include Penicillium species, nonfumigatus Aspergillus species, Scedosporium, Exophiala Fig.…”

“…Correct speciation can often only be accomplished by including tubulin and calmodulin sequences in the phylogenetic analysis. For distinguishing between members of the same species few markers are published; however, microsatellite markers and certain genes such as CYP51 are known to vary between isolates and could be used in isolate characterisation dermatitidis and Cladosporium species [34,36]. A positive correlation between community richness and patient health has been demonstrated using NGS [37].…”

Cystic fibrosis year in review 2018, part 1

“…A two medium approach utilizing yeast potato dextrose agar (YPDA) or Sabouraud medium and B (+) medium was recommended for evaluation of CF sputa, with additional media recommended based on patient clinical status. The use of Sabouraud and B (+) media was prospectively evaluated in a multicenter study from five Dutch CF Centers . In 699 patients, at least one respiratory sample was positive, with a total of 3787 cultures showing fungal species.…”

“…The use of Sabouraud and B (+) media was prospectively evaluated in a multicenter study from five Dutch CF Centers. 51 In 699 patients, at least one respiratory sample was positive, with a total of 3787 cultures showing fungal species. The most frequent was A. fumigatus (31.7%), followed by Penicillium (12.6%), nonfumigatus Aspergillus (5.6%), Scedosporium species (4.5%), and Exophiala dermatitidis and Cladosporium (1.1% each) species.…”