Echinocandin heteroresistance causes prophylaxis failure and facilitates breakthrough Candida parapsilosis infection

Breakthrough infections of patients on antimicrobial prophylaxis represent a significant and often unexplained cause of morbidity. Here, we reveal that in high-risk patients on micafungin prophylaxis heteroresistance – the presence of a phenotypically unstable, low frequency subpopulation of resistant cells (∼1 in 10,000) – underlies breakthrough bloodstream infections by Candida parapsilosis misclassified as susceptible by standard antimicrobial susceptibility testing. By analyzing 219 clinical C. parapsilosis isolates from North America, Europe, and Asia, we demonstrate widespread micafungin heteroresistance. To facilitate detection of micafungin heteroresistance, we constructed a predictive machine learning framework that classifies isolates as heteroresistant or susceptible by a maximum of ten genomic features. Our results connect heteroresistance to unexplained prophylaxis failure and demonstrate a proof-of-principle diagnostic approach with the potential to inform clinical decisions. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by National Key Research and Development Program of China 2021YFA0911300, National Institutes of Health (NIH) grant nos. R01 AI093808, R21 AI105617, R21 AI156157, U19 AI158080, R01 AI141883, R01 AI148661, U01 AI124275, R01 AI137269, P30 CA008748, an Investigator in the Pathogenesis of Infectious Diseases Award from the Burroughs Wellcome Fund, the Ludwig Center for Cancer Immunotherapy, the Susan and Peter Solomon Divisional Genomics Program, Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) grant no. RO-5328/1-2, Science Foundation Ireland grant nos. 19/FFP/6668, 18/CRT/6214 ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Institutional Review Board of Memorial Sloan Kettering Cancer Center gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The data that support the findings of this study are available from the corresponding authors upon request. All sequencing data generated in this study will be deposited in the Sequence Read Archive upon acceptance.