Whole-Genome Sequencing Reveals a Novel Subclade of Pansusceptible <i>Candida auris</i> in Ontario, Canada
Bibliographic record
Abstract
Background: Candida auris is an emerging pathogen that has recently disseminated globally and caused challenging outbreaks in healthcare facilities (HCFs), in part because it is commonly multidrug-resistant. Candida auris remains rare in Canada, with ~20 known cases to date. We describe the emergence of a novel subclade of C. auris in Ontario, Canada, using whole-genome sequencing (WGS). Methods: In Ontario, many HCFs submit yeast isolates from sterile sites requiring species-level characterization and antifungal susceptibility testing (AFST) to the provincial reference laboratory. Yeasts were identified using a combination of standard methods (morphology, API 20C, MALDI-ToF MS) including ITS2 sequencing. Sensititre YO9 panels were used for AFST. Genomic analysis of C. auris was performed using an Illumina HiSeq platform with at least 50× coverage; variants were called against the reference genome by using the previously published North Arizona SNP pipeline (NASP). Phylogenetic trees were produced by maximum parsimony method (MEGA7.0). Results: Between 2014 and 2018, yeast isolates from 5 different patients from 4 HCFs in the same region of Ontario were confirmed to be C. auris by ITS2 PCR and sequence analysis (Table 1). Based on interim CDC criteria for antifungal drug break points, all isolates were pansusceptible to common antifungals. WGS analysis demonstrated that the C. auris isolates were part of the South American clade (IV) and formed an isolated subclade that is well supported by bootstrap analysis, indicating clonal relationships among these isolates (Fig. 1). Conclusions: Although C. auris isolates are usually drug resistant, all 5 initial Ontario isolates were pansusceptible. WGS determined that these isolates clustered within clade IV and were clonal. This cluster of C. auris appears to represent a new subclade of the South American clade that has been transmitted among patients within a region of Ontario. C. auris may have been present in Ontario for some time, escaping earlier detection due to lack of screening programs in HCFs, historical challenges with microbiologic detection of C. auris , and the antifungal susceptibility of the circulating isolates. Investigations are underway to determine clinical features and epidemiologic relatedness among patients in this cluster. Funding: None Disclosures: Susy Hota, Contracted Research - Finch Therapeutics
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".