Genotyping Strategies for Medically Important Fungi: MLST, Microsatellites, and NGS
This review compares multilocus sequence typing and microsatellite-based methods for genotyping clinically relevant fungi including Candida, Aspergillus, Cryptococcus, and Pneumocystis, used to investigate outbreaks, nosocomial transmission, and resistance mechanisms. NGS emerges as the preferred method when established typing systems are unavailable. The authors stress that the choice of method depends on the clinical question, and that collection of epidemiological metadata remains essential regardless of the molecular tool used.
The original study
Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?
- Authors
- Alanio A, Desnos-Ollivier M, Garcia-Hermoso D, Bretagne S
- Journal
- Clinical microbiology reviews
- Type
- Journal Article, Review
- PMID
- 28490578
Original abstract
Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.