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:

Required

Nov 22, 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?

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

TB-REQ-12

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

Nov 29, 2023

TB-REQ-13

UPDATE/CHANGE:

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

Nov 22, 2023

TB-REQ-14

UPDATE/CHANGE:

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

Nov 22, 2023

TB-REQ-15

UPDATE/CHANGE:

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

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

Nov 22, 2023

TB-REQ-15

UPDATE/CHANGE:

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

TB-REQ-17

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

Nov 22, 2023

TB-REQ-18

UPDATE/CHANGE:

Add field: Culture Type to TRF

add another section (b/w) Material Submitted and Material Type Modifier

If user selects Culture, create new section “Culture Type” [Mandatory field] and have option to select

Pure Isolate, Mixed Culture ,Non-Viable Culture

Map all to “Comment 1” in SL

Functionality: Selection should be default to Pure Isolate in Culture Type; user can only select 1 option in culture type

TB-REQ-19

UPDATE/CHANGE:

Remove Mixed and Non-viable culture options from “Submitting Laboratory’s Results” section now that we added those to Specimen Info

TB-REQ-20

UPDATE/CHANGE:

Add Sediment-AFB Negative in Material Type Modifier >Sediment Section

In Material Type Modifier Section, if user selects Sediment, Add Sediment-AFB Negative as option

If Sediment-AFB Negative is selected, the following instructional text should appear: "Please contact MDL-Mycobacteriology for approval of material submitted by e-mailing cdphtbdst@cdph.ca.gov or calling (510)412-3929. Please provide us with the sample type and the reason for submitting a sample other than a culture or AFB smear positive sediment."

TB-REQ-21

UPDATE/CHANGE:

Sediment option order

Options for Sediment should appear in the following order on the TRF:

• Sediment-AFB 1+

• Sediment-AFB 2+

• Sediment-AFB 3+

• Sediment-AFB 4+

• Sediment-Few AFB

• Sediment-Many AFB

• Sediment-Rare AFB

• Sediment-AFB Negative

TB-REQ-22

UPDATE/CHANGE:

Other>Material Type Modifier Updates needed

If Material Submitted, is user selects "Other" the following options should appear in *Material Type Modifier: Processed Tissue Sterile Body Fluid Other (specify) _________________

Functionality: No selection should be defaulted for the above options

TB-REQ-23

UPDATE/CHANGE:

If Material Submitted, is user selects "Other" the following options should appear in *Material Type Modifier: Processed Tissue Sterile Body Fluid Other (specify) _________________ Functionality: No selection should be defaulted for the above options

TB-REQ-24

UPDATE/CHANGE:

Add field

missing the field under Specimen information -> Other:

*Material approved by CDPH : Yes, NO

--Functionality: DO NOT default to any option It should appear after “*Material Submitted” options and before “Material type modifier”:

TB-REQ-25

UPDATE/CHANGE:

Change instructional text:

Change instructional text to remove AFB smear positive text--change to: "Please contact MDL-Mycobacteriology for approval of material submitted by e-mailing cdphtbdst@cdph.ca.gov or calling (510)412-3929. Please provide us with the sample type and the reason for submitting a sample other than a culture or sediment." 11/29: Please contact MDL-Mycobacteriology for approval of material submitted by e-mailing cdphtbdst@cdph.ca.gov or calling (510)412-3929.

TB-REQ-26

UPDATE/CHANGE:

Remove duplicate PreApproval Message

remove the first one when it shows up at the top. See attached screenshot with suggestion on which one to keep. See mage >>

TB-REQ-27

UPDATE/CHANGE:

Preapproval Note on TRF

Note "Please contact MDL-Mycobacteriology for approval of material submitted by e-mailing cdphtbdst@cdph.ca.gov or calling (510)412-3929." appears on the printed TRF for the Material Submitted that does NOT require preapproval (e.g. Culture - Pure Isolate or Sediment-AFB1+).

This note should be removed from printed TRF when material that does NOT require preapproval is selected. The note should only be present for material that DOES require preapproval: Culture-Mixed Culture, Culture-Non-Viable Culture, Sediment- Sediment-AFB Negative, Other. P.S.: on the website version of TRF the corresponding note is absent for the material selection that doesn't require preapproval, which is an expected behavior. See Image >>

TB-REQ-28

UPDATE/CHANGE:

Make pre-approval question mandatory for mixed/non-viable cultures

When select Material Submitted "Culture" - Culture type "Mixed" or "non-viable", the question "Material approved by CDPH" should be mandatory (with no default selection). Currently it is not mandatory for that material type. It displayed correctly as mandatory for other material types, when applicable. See attached screenshot See Image>>

TB-REQ-29

UPDATE/CHANGE:

TRF - removal of approval for submission mixed and non-viable culture

TRF Section: Specimen Information Field selection: Material Submitter/Culture Type

Issue: When the following selections are made Material Submitted = Culture Culture Type = "Mixed Culture" or "Non - Viable Culture" we want the following text and the material approved selection to be removed - " Please contact MDL-Mycobacteriology for approval of material submitted by e-mailing cdphtbdst@cdph.ca.gov or calling (510)412-3929. Material approved by CDPH * Yes No Referred to attached picture if needed. See Image>>

TB-REQ-30

UPDATE/CHANGE:

TRF Section: Specimen Information Field selection: Material Submitter/Culture Type Issue: When the following selections are made Material Submitted = Culture Culture Type = "Mixed Culture" or "Non - Viable Culture" we want the following text and the material approved selection to be removed - " Please contact MDL-Mycobacteriology for approval of material submitted by e-mailing cdphtbdst@cdph.ca.gov or calling (510)412-3929. Material approved by CDPH * Yes No Referred to attached picture if needed. See Image>>

TB-REQ-31

UPDATE/CHANGE:

Remove warning note

Section: Submitting Laboratory's Results Question: Has any Rifampin resistance (RIF-R) been detected previously in the submitted specimen by molecular or growth-based testing? Selection: Detected

Remove the pop-up note "Sample should be sent to CDC for MDDR and not to MDL for sequencing-based DST"

• 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

Sep 20, 2023