whole-genome sequencing in the Management of fungal pathogenesis among immunocompromised hosts

Ananya Bose; V. Sharma; N. Reddy

doi:10.5281/zenodo.22812920

Authors

Ananya Bose Department of Medical Microbiology, Uruguay Center for Medical Microbiology Author https://orcid.org/5148-3753-2720-8835
V. Sharma Department of Clinical Medical Microbiology, Brahmaputra Research Center for Clinical Bacteriology Author https://orcid.org/2619-4284-2438-4610
N. Reddy Department of Medical Microbiology, Brahmaputra Research Center for Clinical Bacteriology Author https://orcid.org/5426-7659-8460-2180

DOI:

https://doi.org/10.5281/zenodo.22812920

Keywords:

whole-genome sequencing, fungal pathogenesis, immunocompromised hosts, antifungal resistance, genomic epidemiology

Abstract

Graphical abstract

Background: Invasive fungal disease is a major cause of morbidity in transplant recipients and other immunocompromised hosts, and multidrug-resistant Candida auris and azole-resistant Aspergillus fumigatus have spread across continents largely undetected by phenotypic diagnostics.

Objective: This review synthesizes how whole-genome sequencing has reshaped understanding of the genomic epidemiology and resistance evolution of the fungal pathogens most consequential for immunocompromised hosts.

Methods: We conducted a narrative synthesis of genomic epidemiology, outbreak, resistance mechanism, and guideline literature on whole-genome sequencing of Candida auris, Aspergillus fumigatus, and Cryptococcus in immunocompromised populations.

Findings: Sequencing has resolved independent emergence of resistant Candida auris clades, traced environmentally acquired azole resistance in Aspergillus fumigatus, and mapped virulence-associated Cryptococcus lineages.

Conclusions: Genomic surveillance now informs infection-control and empirical-therapy policy; converting it into a same-admission tool requires faster pipelines and tighter clinical-genomic integration.

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