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Fecal Mycobiota Combined With Host Immune Factors Distinguish Clostridioides difficile Infection From Asymptomatic Carriage

  • Author Footnotes
    ∗ Authors share co-first authorship.
    Yangchun Cao
    Footnotes
    ∗ Authors share co-first authorship.
    Affiliations
    College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China

    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Author Footnotes
    ∗ Authors share co-first authorship.
    Lamei Wang
    Footnotes
    ∗ Authors share co-first authorship.
    Affiliations
    College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China

    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
    Search for articles by this author
  • Author Footnotes
    ∗ Authors share co-first authorship.
    Shanlin Ke
    Footnotes
    ∗ Authors share co-first authorship.
    Affiliations
    Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
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  • Javier A. Villafuerte Gálvez
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Nira R. Pollock
    Affiliations
    Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts

    Department of Laboratory Medicine, Boston Children’s Hospital, Boston, Massachusetts
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  • Caitlin Barrett
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Rebecca Sprague
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Kaitlyn Daugherty
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Hua Xu
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Qianyun Lin
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Junhu Yao
    Affiliations
    College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
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  • Yulin Chen
    Affiliations
    College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi Province, China
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  • Ciarán P. Kelly
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Yang-Yu Liu
    Correspondence
    Correspondence Address correspondence to: Yang-Yu Liu, PhD, Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Ave, Boston, Massachusetts 02115.
    Affiliations
    Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
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  • Xinhua Chen
    Correspondence
    Xinhua Chen, PhD, Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, Massachusetts 02215.
    Affiliations
    Division of Gastroenterology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
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  • Author Footnotes
    ∗ Authors share co-first authorship.

      Background & aims

      Although the role of gut microbiota in Clostridioides difficile infection (CDI) has been well established, little is known about the role of mycobiota in CDI. Here, we performed mycobiome data analysis in a well-characterized human cohort to evaluate the potential of using gut mycobiota features for CDI diagnosis.

      Methods

      Stool samples were collected from 118 hospital patients, divided into 3 groups: CDI (n = 58), asymptomatic carriers (Carrier, n = 28), and Control (n = 32). The nuclear ribosomal DNA internal transcribed spacer 2 was sequenced using the Illumina HiSeq platform to assess the fungal composition. Downstream statistical analyses (including Alpha diversity analysis, ordination analysis, differential abundance analysis, fungal correlation network analysis, and classification analysis) were then performed.

      Results

      Significant differences were observed in alpha and beta diversity between patients with CDI and Carrier (P < .05). Differential abundance analysis identified 2 genera (Cladosporium and Aspergillus) enriched in Carrier. The ratio of Ascomycota to Basidiomycota was dramatically higher in patients with CDI than in Carrier and Control (P < .05). Correlations between host immune factors and mycobiota features were weaker in patients with CDI than in Carrier. Using 4 fungal operational taxonomic units combined with 6 host immune markers in the random forest classifier can achieve very high performance (area under the curve ∼92.38%) in distinguishing patients with CDI from Carrier.

      Conclusions

      Our study provides specific markers of stool fungi combined with host immune factors to distinguish patients with CDI from Carrier. It highlights the importance of gut mycobiome in CDI, which may have been underestimated. Further studies on the diagnostic applications and therapeutic potentials of these findings are warranted.

      Graphical abstract

      Keywords

      Abbreviations used in this paper:

      ANCOM (analysis of composition of microbiomes), AUC (area under the curve), Carrier (asymptomatic carriers), CDI (Clostridioides difficile infection), GCSF (granulocyte colony-stimulating factor), Ig (immunoglobulin), IL (interleukin), ITS2 (internal transcribed spacer 2), MCP1 (monocyte chemoattractant protein 1), NAAT (nucleic acid amplification testing), OTU (operational taxonomic unit), PERMANOVA (permutational multivariate analysis of variance), TNF (tumor necrosis factor)
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