Fungal Whole Genome Sequencing

• G-2E for Candida auris specimens
• G-MYCO for all other mycological specimens

• Not required but notifying local/regional epidemiologists is helpful.
• Refer to the DSHS reporting contacts webpage for a list of public health region epis

• Human
• Food and environmental swabs (from registered food sanitarians only)

• Pure isolates and clinical specimens
  • Submission of duplicate specimens, which are specimens obtained from the same source on the same patient within a six-month period is discouraged.
  • Note: Clinical specimens or isolates obtained from different sources on the same patient (i.e., wound vs. stool) are acceptable since they are not considered duplicate specimens.

• Isolates: At least one viable colony.
• Clinical Specimens: At least one swab.

Please refer to guidance in the test description for the fungal specimen of interest (such as Candida spp.).

• WGS is commonly an internal reflex assay carried out on clinical specimens and isolates submitted for surveillance purposes.
• Please refer to the LTSM test directory found here for storage and shipping requirements for the organisms of interest (e.g. Candida spp., other yeast or fungi, etc.)

• For yeast and mold isolates, any media that supports growth (e.g., Sabouraud Dextrose agar or Chromagar for Candida).
• For liquid culture specimens, 2.0 mL liquid culture is acceptable.

• At least two patient identifiers required on specimen (e.g., patient full name, date of birth, medical record number).
• Three patient identifiers are preferred.
• Date of collection is required for all specimens.
• Patient identifiers on specimen label must exactly match identifiers on submission form. (e.g., abbreviated name on label and full name on form is not acceptable.).
• Specimen labels and submission forms must be legible.
• General DSHS Specimen Collection Submission Guidelines are available here.

• Category B specimens, ship according to Dangerous Goods Regulations, IATA, and/or CFR 49.
• Category B Biological Substance, UN3373 shipping requirements apply.
• Handle as infectious agent using universal precautions.
• Triple-contained in accordance with federal shipping regulations.
• Submitters are responsible for packaging and shipping specimens according to regulatory requirements.
• Specimen collection kits must be properly closed and secured to minimize leaks during shipping. Leaked specimens will not be tested.
• Laboratory does not provide collection kits or shipping materials for WGS specimens.
• Additional DSHS Laboratory specimen shipping guidelines are available here.

14 days from date of specimen receipt.

• Incorrect specimen collection or submission methods (e.g., not having minimum number of patient identifiers)
• Insufficient specimen growth
• Non-viable isolates
• Mixed specimen/contamination
• Incorrect storage conditions
• Expired reagents/media/collection container
• Collection containers broken in transit
• Discrepancies between G-2E submission form and specimen label
• Missing/incomplete/illegible submission form
• Cultures infested with mites

• Clinical specimens may be submitted with isolates from same patient.
• Fungal WGS Specimen Collection and Submission Instructions are available from the Sequencing Team. Please request directions via email at wgs.dshs@dshs.texas.gov.