CA TB LWP: TRF Requirements

Update TRF to include WGS and tNGS

LWP TRF/UI provides users ability to order WGS and tNGS as part of their TB test panel ordering

Test Requested

TB-REQ-01

ADD:

Sequencing-Based DST (performed by default)

Please see detailed testing algorithm on test information webpage

Required (Default)

Text “test information webpage” should be hyperlink to: http://www.aphl.org/tbdst

Test Requested

TB-REQ-02

ADD

Additional test options(s):

Phenotypic DST (pDST) is recommended to be performed in conjunction with sequencing-based DST, unless pDST has already been performed or will be conducted elsewhere. Please choose pDST test below (leave blank if not needed):

Add text to Test Requested Section

Test Requested

TB-REQ-03

UPDATE/CHANGE:

• CHANGE First-line DST to

  • First-line pDST (RIF, INH, PZA, EMB)

• CHANGE Second-line DST to

  • Second-line pDST (MOX, AMK, CAP, ETA, KAN, RFB)

• CHANGE PSQ and First-Line DST for 4-month RPT-Mox regimen to

  • First-line pDST for 4-month RPT-MOX regimen (RIF, INH, PZA, MOX)

Optional

Test Requested

TB-REQ-04

REMOVE:

• First-line and Second-line DST

• Pyrosequencing (PSQ) and First-line DST

• Pyrosequencing (PSQ) and First-line DST and Second-line DST

Remove test options from TRF

Test Requested

TB-REQ-05

ADD

WGS Genotyping (performed by default and data submitted to the CDC)

This testing is performed by default on culture submissions or isolates obtained from submitted sediments and will be submitted to the CDC for analysis/National Surveillance.

*Please confirm that you would like TB DST Reference Center to perform WGS Genotyping:

• Yes, please perform default testing
• No, submitter will be responsible for submitting necessary isolate and/or data elsewhere

Required

22 Nov 2023

"Yes" option is auto-populated

If NO is selected, then the genotyping is not added [currently genotyping is auto-added to all panels]

Test Requested

TB-REQ-06

Remove:

• Patient is from a region with high prevalence of drug resistant TB

• Patient is a contact of an individual with drug resistant TB

• Patient is known to have adverse reactions to INH or RIF

• Patient has wide exposure to others or potential exposure to vulnerable population

• Non-viable culture (Only PSQ will be performed)

• DST failed due to low growth

Replace list of current AOEs with list of AOEs in REQ-06

Test Requested

TB-REQ-07

UPDATE/CHANGE:

• Has PSQ been performed previously? * to

  • Has sequencing-based DST been performed previously?

• Yes
• No

Optional

Test Requested

TB-REQ-08

Remove:

• Remove Comment from Test Requested section

SUBMITTING LABORATORY’S RESULTS

TB-REQ-09

UPDATE/CHANGE:

For the AOE Question “*Has any Rifampin resistance (RIF-R) been detected previously in the submitted specimen by molecular or growth-basted testing?”, if “Detected” is selected, CHANGE pop up window/Informational text:

• "Sample should be sent to CDC for MDDR and not to MDL for PSQ". Change popup text to:

  • "Sample should be sent to CDC for MDDR and not to MDL for sequencing-based DST"

Required

SUBMITTING LABORATORY’S RESULTS

TB-REQ-10

UPDATE/CHANGE:

• Indicate reason(s) for PSQ submission below * to

  • Indicate reason(s) for sequencing-based DST below, if applicable:

UPDATE/CHANGE AOE List Options to:

• Drug resistant TB has been previously detected in this patient

• Patient is not responding to treatment or was previously treated for TB

• Mixed culture

• Non-viable culture

• Phenotypic DST failed due to low growth

• Other reason(s), please specify:

Optional

• Multi-Select Field

• If “Other reason(s), please specify” is selected, a MANDATORY free text field should appear for user comments

SUBMITTING LABORATORY’S RESULTS

TB-REQ-11

UPDATE/CHANGE:

• Change “Comments” to:

  • Comments on Submitting Laboratory’s Results

Optional

UPDATE/CHANGE:

• Change to Bold font: 'Sequencing- Based DST (performed by default)

• Add see detailed testing algorithm on test information webpage: link to http://www.aphl.org/tbdst

29 Nov 2023

UPDATE/CHANGE:

Elevate General Comments to own section as it is for “SHIPPING” See Image >>

22 Nov 2023

UPDATE/CHANGE:

Add question mark “ ?” after shipping question See image >>

22 Nov 2023

UPDATE/CHANGE:

All information from webpage test request form, should appear on PDF version

is “Comments on Submitting Laboratoryˆas Results” correct to : Laboratory’s

22 Nov 2023

UPDATE/Change

spell out "Whole Genome Sequencing" in the title "WGS Genotyping" so it shows as: "Whole Genome Sequencing (WGS) Genotyping". See Image >>

Update.Change

Updates to Material Type and add new specimen type under other

Move “Sediment-AFB Negative” from “Other” to “Sediment” a. if “Sediment-AFB Negative” selected: i. show selection “*Material approved by CDPH”: Yes/No AND ii. display message: Under “Other” add additional options: a. Processed tissue b. Mixed culture c. Non-viable culture d. Other (add comment field, if selected) Rename “Other” to “Other (e.g. tissue, mixed culture)”

If user selects processed tissue, mixed culture and/or non-viable culture under “Other” and order/map to tNGS panel

22 Nov 2023

• QUESTION: Should the list of reasons for “Indicate reason(s) for sequencing-based DST below, if applicable” always be visible? Or should this list be visible if one of the test request is selected? And if so, which test?

Answer: List of AOEs should always be visible

20 Sep 2023