1. Pan-omics-based characterization and prediction of highly multidrug-adapted strains from an outbreak fungal species complex
- Author
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Xin Fan, Lei Chen, Min Chen, Na Zhang, Hong Chang, Mingjie He, Zhenghao Shen, Lanyue Zhang, Hao Ding, Yuyan Xie, Yemei Huang, Weixin Ke, Meng Xiao, Xuelei Zang, Heping Xu, Wenxia Fang, Shaojie Li, Cunwei Cao, Yingchun Xu, Shiguang Shan, Wenjuan Wu, Changbin Chen, Xinying Xue, and Linqi Wang
- Subjects
Science (General) ,Q1-390 - Abstract
Summary: Strains from the Cryptococcus gattii species complex (CGSC) have caused the Pacific Northwest cryptococcosis outbreak, the largest cluster of life-threatening fungal infections in otherwise healthy human hosts known to date. In this study, we utilized a pan-phenome-based method to assess the fitness outcomes of CGSC strains under 31 stress conditions, providing a comprehensive overview of 2,821 phenotype-strain associations within this pathogenic clade. Phenotypic clustering analysis revealed a strong correlation between distinct types of stress phenotypes in a subset of CGSC strains, suggesting that shared determinants coordinate their adaptations to various stresses. Notably, a specific group of strains, including the outbreak isolates, exhibited a remarkable ability to adapt to all three of the most commonly used antifungal drugs for treating cryptococcosis (amphotericin B, 5-fluorocytosine, and fluconazole). By integrating pan-genomic and pan-transcriptomic analyses, we identified previously unrecognized genes that play crucial roles in conferring multidrug resistance in an outbreak strain with high multidrug adaptation. From these genes, we identified biomarkers that enable the accurate prediction of highly multidrug-adapted CGSC strains, achieving maximum accuracy and area under the curve (AUC) of 0.79 and 0.86, respectively, using machine learning algorithms. Overall, we developed a pan-omic approach to identify cryptococcal multidrug resistance determinants and predict highly multidrug-adapted CGSC strains that may pose significant clinical concern.
- Published
- 2024
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