Molecular Typing of Candida Species in Clinical Epidemiology

Molecular typing of Candida species underpins the investigation of fungal transmission, outbreak dynamics and the emergence of antifungal resistance. Techniques such as multilocus sequence typing (MLST), whole-genome sequencing (WGS), short tandem repeat (STR) profiling and microsatellite analysis provide complementary resolution to distinguish closely related strains. These methods have illuminated the population structure of major pathogens such as Candida albicans and Candida glabrata, revealing clade distributions, microevolutionary events and the persistence of resistant lineages within healthcare settings. High-throughput approaches now capture mixed-strain populations within individual samples, challenging traditional single-colony paradigms and informing treatment strategies by uncovering unrecognised antifungal resistance. Global surveys of clonal complexes have demonstrated geographic clustering, while longitudinal studies trace mother-to-infant transmission and community reservoirs. The integration of molecular epidemiology into routine surveillance programmes enhances infection control by identifying transmission chains, guiding antifungal stewardship and underpinning the development of new diagnostic assays. Future directions focus on standardising typing schemes, expanding global reference databases and leveraging real-time sequencing to track outbreaks with unprecedented speed and granularity.

Research from Nature Portfolio

Recent studies have applied deep sequencing to elucidate genotypic and phenotypic diversity in Candida glabrata bloodstream infections. By sequencing multiple colonies from individual blood cultures, researchers uncovered mixed populations of clonally related but genetically distinct strains within single patients. These variants exhibited differential susceptibility to fluconazole and divergent virulence traits, including small-colony morphologies linked to resistance. Crucially, fluconazole-resistant subpopulations, initially undetected by standard clinical microbiology, emerged during persistent or relapsing infections. This work supports a population-based model of Candida glabrata diversity in invasive disease and underscores the importance of high-resolution typing to guide antifungal therapy and improve patient outcomes.

Molecular Typing of Candida Species in Clinical Epidemiology publication trend

The graph below shows the total number of articles in molecular typing of candida species in clinical epidemiology across all publications each year (not limited to Nature Index journals).

Technical terms

Multilocus sequence typing (MLST): A method that sequences multiple housekeeping gene fragments to assign isolates to defined sequence types for epidemiological studies.

Short tandem repeat (STR) genotyping: A technique comparing the number of repeated DNA motifs at specific loci to discriminate between closely related strains.

Whole-genome sequencing (WGS): The determination of an organism’s complete DNA sequence, enabling single-nucleotide polymorphism analysis and high-resolution strain comparison.

Microsatellite genotyping: The assessment of short, repetitive DNA elements (microsatellites) to track genetic relatedness and transmission pathways.

Antifungal susceptibility: The measurement of a fungal isolate’s growth response to antifungal agents, typically reported as minimum inhibitory concentrations.

Diploid sequence type (DST): A strain identifier in diploid organisms like Candida, combining allelic profiles across multiple loci for precise typing.

References

1. Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures. Nature Communications (2023).
2. Vertical Transmission and Antifungal Susceptibility Profile of Yeast Isolates from the Oral Cavity, Gut, and Breastmilk of Mother–Child Pairs in Early Life. International Journal of Molecular Sciences (2023).
3. Multi-Locus Next-Generation Sequence Typing of DNA Extracted From Pooled Colonies Detects Multiple Unrelated Candida albicans Strains in a Significant Proportion of Patient Samples. Frontiers in Microbiology (2018).
4. Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential. Mycopathologia (2024).