Genomic adaptations of fungal pathogens for human colonization and drug resistance

Supervisors

Isabel Gordo
GIMM,2nd supervisor

Objectives

Fungal pathogens, particularly yeast species of the Candida clade, pose an increasing health risk due to the growing immunocompromised population and rising drug resistance. Recent findings suggest that these pathogens are opportunistic colonizers primarily adapted to non-human environments. We will investigate the genomic adaptations that enable Candida to colonize Human hosts and rapidly respond to drugs and immune defences. Specific objectives:

• Identify genomic traits in Candida species that facilitate human colonization, focusing on traits likely selected in natural environments.

• Explore mechanisms of rapid adaptation to drug treatments and immune responses during infection or colonization through genomic and transcriptomic analyses

Methodology

Whole genome sequencing, population genomics, metagenomics, transcriptomics, in-vitro evolution, phylogenomics.

Required Skills

Experience in microbiology, metagenomics, and bioinformatics
Familiarity with biology of diverse microbial pathogens.
Programming: Python or R.
Knowledge and experience in population genomics and transcriptomics tools
Knowledge and experience compartive genomics.
Use of HPC cluster.
Fluency in spoken and written English.

Expected results

The project will uncover key genomic adaptations in fungal pathogens that support human colonization and drug resistance. Insights from this research may inform strategies to manage fungal infections and combat multidrug resistance in opportunistic pathogens.

Planned Secondments

GIMM (Gordo) in year 2 (2 months) to receive training on antibiotic resistance research and models.
Microomics in year 3 (1 month) to learn about high-throughput microbiome quantification methods.
CRG (Dias) in year 3 (2 weeks) to receive basic training on machine learning approaches.

Enrolment in doctoral programs

The PhD student will be enrolled at the Universitat of Barcelona

References

Gabaldón T. Threats from the Candida parapsilosis complex: the surge of multidrug resistance and a hotbed for new emerging pathogens. Microbiol Mol Biol Rev. 2024 Dec 18;88(4):e0002923. doi: 10.1128/mmbr.00029-23. Epub 2024 Nov 7. PMID: 39508581; PMCID: PMC11653726.

Schikora-Tamarit MÀ, Gabaldón T. Recent gene selection and drug resistance underscore clinical adaptation across Candida species. Nat Microbiol. 2024 Jan;9(1):284-307. doi: 10.1038/s41564-023-01547-z. Epub 2024 Jan 4. PMID: 38177305; PMCID: PMC10769879.