Analyzing Candida genomes with candida.app & Solu

Candida auris genomics: useful yet difficult

Genomics has been a great help in categorizing and tracking recent Candida auris outbreaks, as with any emerging pathogen. Whole genome sequencing is especially useful for Candida auris for the following reasons:

• species identification is hard, especially with old firmware
• multidrug-resistance
• tracking healthcare-associated infections
• identifying new clades when they emerge

For these reasons and more, the CDC has set up it’s own Candida auris surveillance program. However, genomic characterization of Candida auris is still difficult, especially for non-bioinformaticians.

Current methods include looking up specific mutations with BLAST and candidagenome.org, or using existing fungal genome pipelines (MycoSNP & TheiaEuk), but both methods require bioinformatics knowledge, computing resources, and result interpretation.

CGPS’s user-friendly pathogen.watch platform can analyze Candida auris, but is limited to a subset of known resistance mutations (the most well-known database for antifungal resistance, ARFBase, contains over 30 references for Candida auris).

Candida.app - analyze Candida auris genomes online

We created a free online tool for fast genomic characterization of Candida auris isolates.

The tool accepts genomes (contigs or scaffolds) and performs basic quality standardization and error correction. Species id and clade assignment is performed using mash distances. A custom AMR database was created using AFRBase and annotated with AMRFinderPlus. Assembly quality reports are generated with QUAST.

Candida.app features:

• Drag-and-drop upload
• Species ID and clade detection
• Antifungal resistance
• Assembly quality report with Quast
• Link sharing and Excel export
• Works on mobile and desktop

Candida.app is intended for research use only.

Case study: analyzing Candida genomes with candida.app

Let’s look at a real example. This genome was isolated from a patients’ groin and sequenced by Orange County Public Health lab.

The second isolate is collected from same location, from a urine sample 3 months later.

From the candida.app reports, we see that the second isolate belongs to a different clade. Both isolates have a mutation in the ERG11 gene conferring antifungal resistance. Both assemblies look good.

Detailed analysis with Solu

Uploading both genomes to Solu Platform, we get access to phylogenetic features (batch upload, collections, SNP distances and tree).

The SNP distance between these samples is 24,000, which confirms that these isolates are not related.

Future Developments

While our custom antifungal resistance implementation only supports Candida auris, it could be extended to cover the entire Candida genus, and later to other fungal species. There are also emerging reports of a sixth C.auris clade. We are working on a validation publication of Candida.app.

We welcome collaboration and feedback from the microbiology community! The more usage and our free tools get, the more likely it is we’ll continue developing them.