Rationale Disruption of respiratory bacterial communities predicts poor clinical outcomes in critical illness; however, the role of respiratory fungal communities (mycobiome) is poorly understood.

Objectives We investigated whether mycobiota variation in the respiratory tract is associated with host-response and clinical outcomes in critically ill patients.

Methods To characterize the upper and lower respiratory tract mycobiota, we performed rRNA gene sequencing (internal transcribed spacer) of oral swabs and endotracheal aspirates (ETA) from 316 mechanically-ventilated patients. We examined associations of mycobiome profiles (diversity and composition) with clinical variables, host-response biomarkers, and outcomes.

Measurements and Main Results ETA samples with >50% relative abundance for C. albicans (51%) were associated with elevated plasma IL-8 and pentraxin-3 (p=0.05), longer time-to-liberation from mechanical ventilation (p=0.04) and worse 30-day survival (adjusted hazards ratio (adjHR): 1.96 [1.04-3.81], p=0.05). Using unsupervised clustering, we derived two clusters in ETA samples, with Cluster 2 (39%) showing lower alpha diversity (p<0.001) and higher abundance of C. albicans (p<0.001). Cluster 2 was significantly associated with the prognostically adverse hyperinflammatory subphenotype (odds ratio 2.07 [1.03-4.18], p=0.04) and predicted worse survival (adjHR: 1.81 [1.03-3.19], p=0.03). C. albicans abundance in oral swabs was also associated with the hyper-inflammatory subphenotype and mortality.

Conclusions Variation in respiratory mycobiota was significantly associated with systemic inflammation and clinical outcomes. C. albicans abundance emerged as a negative predictor in both the upper and lower respiratory tract. The lung mycobiome may play an important role in the biological and clinical heterogeneity among critically ill patients and represent a potential therapeutic target for lung injury in critical illness.

Competing Interests: Dr. Kitsios has received research funding from Karius, Inc. Drs. Kitsios and Morris have received research funding from Pfizer, Inc. Dr. McVerry has received research funding from Bayer Pharmaceuticals, Inc. and consulting fees from Boehringer Ingelheim. Y. Zhang is an employee of Associates of Cape Cod, Inc. the manufacturer of the test used to determine (1→3)-β-glucan concentrations. All research funding from industry was unrelated to this work. All other authors disclosed no conflict of interest.

Funding information: Dr. Kitsios: KARAT Award, Department of Medicine, University of Pittsburgh; National Institutes of Health (P01 HL114453 [BJM], K23 HL139987 [GDK], R03 HL162655 [GDK], R01HL159805 [PVB], R01AA028436 [PVB]); Veterans Affairs (IK2BX004886 [WB]).

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We enrolled subjects following admission to the hospital and obtained informed consent from the patients or their legally authorized representatives under the study protocol STUDY19050099 approved by the University of Pittsburgh Institutional Review Board (IRB).

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Data Availability Statement: Sequencing data collected for this study are publicly available through the Sequencing Resource Archive, Accession number PRJNA726955