Specific associations between fungi and bacteria in broncho-alveolar aspirates from mechanically ventilated intensive care unit patients

ABSTRACT

The detection of fungi in the human respiratory tract may represent contamination, colonization or a respiratory infection. To develop effective management strategies, a more accurate and comprehensive understanding of the lung fungal microbiome is required. Therefore, the objective of the present study was to define the “mycobiome” of mechanically ventilated patients admitted to an intensive care unit (ICU) using broncho-alveolar aspirate (“sputum”) samples and correlate this with clinical parameters and the bacterial microbiota. To this end, the mycobiome of 33 sputum samples was analyzed by Internal Transcribed Spacer2 (ITS2) amplicon sequencing of the ribosomal operons. The results show that in the investigated sputa of mechanically ventilated patients Candida spp. were most frequently detected, independent of pneumonia or antimicrobial therapy. The presence of Candida excluded in most cases the presence of Malassezia, which was the second most-frequently encountered fungus. Moreover, a hierarchical clustering of the sequence data indicated a patient-specific mycobiome. Fungi detected by culturing (Candida and Aspergillus) were also detected through ITS2 sequencing, but other yeasts and fungi were only detectable by sequencing. While Candida showed no correlations with identified bacterial groups, the presence of Malassezia and Rhodotorula correlated with oral bacteria associated with periodontal disease. Likewise, Cladosporium correlated with other oral bacteria, whereas Saccharomyces correlated more specifically with dental plaque bacteria and Alternaria with the nasal-throat-resident bacteria Neisseria, Haemophilus and Moraxella. In conclusion, ITS2 sequencing of sputum samples uncovered patient-specific lung mycobiomes, which were only partially detectable by culturing, and which could be correlated to specific nasal-oral-pharyngeal niches.

KEYWORDS:

• Respiratory
• mycobiome
• 18S rRNA
• culture-independent
• mechanical ventilation
• sputum

Acknowledgments

We thank Paola Lisotto and staff of the bacterial diagnostics laboratory at UMCG for technical support, and the research nurses of the ICU department of UMCG for sample and data collection.

Authors contribution

JS, WD and JMvD contributed to the design and sample collection. AS, JS and LL performed the experimental work, data analysis and visualization. AS, HJMH and JMvD wrote the manuscript. JS, WD, HJMH and JMvD reviewed and edited the manuscript. All authors consented to the final manuscript..

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The sequencing data that support the findings of this study are openly available at NCBI at https://www.ncbi.nlm.nih.gov/bioproject/; BioProject ID: PRJNA878464 and SAMN30726734.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/21505594.2022.2146568

Additional information

Funding

AS, JMvD and HJMH were funded by CEC MSCA-ITN grant 713660 (Pronkjewail). JS and SH were funded by the Deutsche Forschungsgemeinschaft grant GRK 1870. LL was funded by the China Scholarship Council grant (CSC201908320432). AS, LL and JS were supported by the Graduate School of Medical Sciences of the University of Groningen. This research received no other specific grant from funding agencies in public, commercial, or not-for-profit sectors.