David
Kim
Microbiology and Immunology Genomic and Phylogenetic Delimitation of Non-neoformans/gattii Cryptococcus Species Fungal infections caused by neoformans and gattii species of Cryptococcus are well recognized as the predominant causes of cryptococcosis in humans. While infections involving other Cryptococcus species are increasingly observed, their clinical significance remains poorly understood. Species such as Cryptococcus albidus and Cryptococcus liquefaciens are often misidentified by traditional diagnostics, sometimes dismissed as colonizers, and may exhibit reduced sensitivity to cryptococcal antigen tests. Resistant to common antifungal treatments, these non-neoformans/gattii pose a challenge for selecting effective therapy and highlight the need for precise identification.
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Authors:
David Kim
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About Paper:
In this study, we sequenced the genomes of clinical and environmental isolates from Brazil and used the CBS "type" isolates of C. albidus and C. liquefaciens as a reference. To investigate and clarify the relationship between the isolates with the known CBS isolates, we initially generated variant call (VCF) and consensus sequence (FASTA) files. Using a phylogenetic inference (FastTree), we reconstructed trees to examine the evolutionary relationships of these isolates and other public data and to determine whether clinical strains cluster with established species or reveal potential diversity. We also calculated pairwise variant differences to directly quantify genomic divergence within and between groups, providing an additional metric for assessing species boundaries. By integrating antifungal susceptibility profiles and other phenotypic data, we aim to generate insights that 44 could clarify species treatment and clinical presentation. This approach would help establish a stronger framework for distinguishing pathogenic infections, and could ultimately inform decisions about when targeted antifungal therapy is most appropriate. Our work demonstrates how combining whole-genome sequencing, phylogenetic reconstruction, and direct measures of variance can improve the resolution of fungal identification, particularly for the increasing amount of non-neoformans/gattii Cryptococcus infections. Through an advancement of these genomic frameworks, we hope to contribute to future efforts that refine diagnostics, guide therapy, and enable earlier recognition of emerging or resistant lineages. Dayoung Yu:
Source:
Brown / The Department of Molecular Microbiology and Immunology
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Co-authors:
David Kim