[multiple Wfs] C. Auris Clade 6 Support

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:pushpin: Introduction

The recent discovery of C. auris clade VI has sparked interest in the scientific community, and it is essential to ensure that our workflows are compatible with this newly described clade. Candida auris is a highly virulent fungus that has been causing significant concern globally, and its classification is crucial for effective management and treatment. In this article, we will discuss the importance of supporting C. auris clade VI in our workflows and the necessary steps to achieve this goal.

:pushpin: Explain the Request

This is a low-priority internal request, but it is essential to plan for its completion later this year. The various fungal workflows, including TheiaEuk, Cauris_CladeTyper, GAMBIT, and the GAMBIT fungal database, need to be updated to support C. auris clade VI typing. This will enable our workflows to accurately classify samples as belonging to this clade.

C. auris clade VI is a recently described clade from samples collected in Bangladesh. While it is essential to understand the intricacies of this clade, it is also crucial to ensure that our workflows are compatible with it. The CDC has reported that clade VI is most closely related to clade IV, which suggests that the current C. auris clade typer implemented via TheiaEuk may call these samples as clade IV or not assign a clade at all. However, this is purely speculative, and further investigation is necessary to confirm this hypothesis.

:pushpin: Current Status

The page under construction has a spreadsheet listing some samples that are considered clade VI as part of the study. This spreadsheet can be accessed at https://github.com/CDCgov/mycosnp-nf/wiki/Validation-study:-Pre‐MycoSNP-taxonomic-classification-and-subtyping. However, it is essential to note that there may not be a specific high-quality reference genome available for Clade VI. Therefore, it is crucial to consult with the CDC MDB folks and the staph-b working group for MycoSNP to align with their methods and reference genomes.

:pushpin: Importance of C. auris Clade VI Support

Supporting C. auris clade VI in our workflows is essential for several reasons:

  • Accurate classification: Our workflows need to accurately classify samples as belonging to C. auris clade VI to ensure effective management and treatment.
  • Compatibility with CDC guidelines: The CDC has reported that clade VI is most closely related to clade IV, which suggests that our workflows need to be compatible with this classification.
  • Alignment with scientific community: Supporting C. auris clade VI in our workflows will align with the scientific community's efforts to understand and manage this highly virulent fungus.

:pushpin: Next Steps

To achieve C. auris clade VI support in our workflows, the following steps need to be taken:

  • Consult with CDC MDB folks and staph-b working group: It is essential to consult with the CDC MDB folks and the staph-b working group for MycoSNP to align with their methods and reference genomes.
  • Update workflows: The various fungal workflows, including TheiaEuk Cauris_CladeTyper, GAMBIT, and the GAMBIT fungal database, need to be updated to support C. auris clade VI typing.
  • Test and validate: It is crucial to test and validate our workflows to ensure that they accurately classify samples as belonging to C. auris clade VI.

:pushpin: Conclusion

Supporting C. auris clade VI in our workflows is essential for accurate classification, compatibility with CDC guidelines, and alignment with the scientific community. By consulting with the CDC MDB folks and the staph-b working group, updating our workflows, and testing and validating our results, we can ensure that our workflows are compatible with this newly described clade of C. auris.

:pushpin: Future Directions

As we continue to learn more about C. auris clade VI, it is essential to stay up-to-date with the latest research and developments. Some potential future directions include:

  • Publication of high-quality reference genome: A high-quality reference genome for Clade VI would be essential for accurate classification and management of this clade.
  • Development of new workflows: New workflows may be developed to support C. auris clade VI typing, which would require consultation with the CDC MDB folks and the staph-b working group.
  • Continued testing and validation: Ongoing testing and validation of our workflows will be essential to ensure that they accurately classify samples as belonging to C. auris clade VI.

:pushpin: References

  • CDCgov/mycosnp-nf/wiki/Validation-study:-Pre%E2%80%90MycoSNP-taxonomic-classification-and-subtyping
  • [Insert other relevant references here]

:pushpin: Acknowledgments

:pushpin: Q&A

Q: What is C. auris clade VI?

A: C. auris clade VI is a recently described clade of the fungus Candida auris. It was discovered in samples collected in Bangladesh and is most closely related to clade IV.

Q: Why is it essential to support C. auris clade VI in our workflows?

A: Supporting C. auris clade VI in our workflows is essential for accurate classification, compatibility with CDC guidelines, and alignment with the scientific community. This will enable us to effectively manage and treat this highly virulent fungus.

Q: What are the current workflows that need to be updated to support C. auris clade VI typing?

A: The current workflows that need to be updated to support C. auris clade VI typing include TheiaEuk, Cauris_CladeTyper, GAMBIT, and the GAMBIT fungal database.

Q: What is the current status of the page under construction that lists some samples considered clade VI?

A: The page under construction has a spreadsheet listing some samples that are considered clade VI as part of the study. This spreadsheet can be accessed at https://github.com/CDCgov/mycosnp-nf/wiki/Validation-study:-Pre‐MycoSNP-taxonomic-classification-and-subtyping.

Q: Is there a specific high-quality reference genome available for Clade VI?

A: There may not be a specific high-quality reference genome available for Clade VI. Therefore, it is crucial to consult with the CDC MDB folks and the staph-b working group for MycoSNP to align with their methods and reference genomes.

Q: What are the next steps to achieve C. auris clade VI support in our workflows?

A: The next steps to achieve C. auris clade VI support in our workflows include:

  • Consulting with the CDC MDB folks and the staph-b working group for MycoSNP to align with their methods and reference genomes.
  • Updating the various fungal workflows, including TheiaEuk, Cauris_CladeTyper, GAMBIT, and the GAMBIT fungal database, to support C. auris clade VI typing.
  • Testing and validating our workflows to ensure that they accurately classify samples as belonging to C. auris clade VI.

Q: What are the potential future directions for C. auris clade VI support in our workflows?

A: Some potential future directions for C. auris clade VI support in our workflows include:

  • Publication of a high-quality reference genome for Clade VI.
  • Development of new workflows to support C. auris clade VI typing.
  • Ongoing testing and validation of our workflows to ensure that they accurately classify samples as belonging to C. auris clade VI.

Q: Who should I contact for more information about C. auris clade VI support in our workflows?

A: You can contact the CDC MDB folks and the staph-b working group for MycoSNP for information about C. auris clade VI support in our workflows.

:pushpin: Conclusion

Supporting C. auris clade VI in our workflows is essential for accurate classification, compatibility with CDC guidelines, and alignment with the scientific community. By consulting with the CDC MDB folks and the staph-b working group, updating our workflows, and testing and validating our results, we can ensure that our workflows are compatible with this newly described clade of C. auris.