Results Interpretation and Database Management Module 7: Xpert MTB/RIF Results Interpretation and Database Management Global Laboratory Initiative – Xpert MTB/RIF Training Package

Contents of this module Visualizing test results Reasons to repeat a test Generating reports

Learning objectives At the end of this module, you will be able to: Analyse the different possible results displayed by the software Describe the reasons for repeating the test Generate reports

Visualizing the test results Click on “VIEW RESULTS” To visualize one particular result, click on «VIEW TEST»

Visualizing the test results (contd.) «VIEW TEST»: Double click on the test you want to see

Visualizing the test results (contd. – 2) Information about test Interpretation of results Real-Time PCR curves

Edit test-related information of the test result If necessary you can edit the test related information and notes after the end of test of while it’s running 1. All the white fields in this section are editable 2. After editing click on “Save Changes”

Edit test-related information of the test result (contd.) 3. Click “Yes” to confirm the changes 4. The history of the changed information is saved under the tab “History”

MTB not detected: Negative Result

MTB detected / RIF resistance not detected

MTB detected / RIF resistance detected

MTB detected / RIF resistance indeterminate The concentration of MTB in the sample was very low and resistance could not be determined due to insufficient data collected to interpret resistance-related signals

Reasons to repeat the test: Invalid Result Presence or absence of MTB could not be determined due to: Sample Processing Control (SPC) did not meet acceptance criteria Sample was not properly processed PCR was inhibited

Reasons to repeat the test: Error Probe Check Control failed and the assay was aborted due to: The reaction tube being filled improperly A reagent probe integrity problem was detected The maximum pressure limits were exceeded A GeneXpert module failure Specific errors, reasons and remedies are discussed in Module 9

Reasons to repeat the assay: No Result Insufficient data were collected due to: Power failure Test stopped by the operator Etc.

Reasons to repeat the assay: RIF resistance indeterminate Concentration of MTB in the sample was too low to provide sufficient data for interpreting resistance-related signals Collect and test another sample

Understanding the Growth Curves This slide may be considered optional for trainings of basic users During PCR amplification, DNA sequences are copied at each cycle The amount of DNA in the reaction doubles at each cycle, resulting in an exponential amplification of the initial target DNA The reaction is measured at the log- linear phase of amplification Plateau Log-linear Baseline 17

Real-time Growth Curve: Cycle threshold (Ct) This slide may be considered optional for trainings of basic users Plateau Detected Log-linear Not detected Baseline

Xpert MTB/RIF Semi-Quantitative Results This slide may be considered optional for trainings of basic users Depending on the Ct value of the MTB target, the MTB result is displayed as: High (less than 16 cycles) Medium (from 16 to 22 cycles) Low (from 23 to 28 cycles) Very Low (more than 28 cycles)

Xpert MTB/RIF Semi-Quantitative Results This slide may be considered optional for trainings of basic users Ct < 16: MTB detected High Ct > 28: MTB detected Very Low Ct 16 – 22: MTB detected Medium Ct 22 – 28: MTB detected Low The graph is from http://depts.washington.edu/genomelb/RTPCR20graphSml.gif

Sample Processing Control: passed This slide may be considered optional for trainings of basic users Target Negative SPC Positive Target Positive SPC Negative

Sample Processing Control: invalid This slide may be considered optional for trainings of basic users Result invalid SPC negative Target negative

Generate a result report 1. Click on “VIEW RESULTS” 2. Click on «REPORT»

Generate a result report in pdf 3b. Click on “Preview pdf” for immediate vizualisation 3. Select the result to visualize in the pdf 4. Click on “Generate Report File”

Generate a Specimen report in pdf 1. Click Reports -> Specimen Report 3a.“Generate Report File” will save the report in GeneXpert Folder -> Report 2. Fill in the Sample ID 3.“Preview PDF” will open the pdf file

Generate a Patient report in pdf 1. Click Reports -> Patient Report 3a.“Generate Report File” will save the report in GeneXpert Folder -> Report 2. Fill in the Patient ID 3.“Preview PDF” will open the pdf file

How to print automatically a test report - Connect and install your printer - NOTE: You can print any report once test is finished 1.Click on ‘’Setup’’, then “System configuration” 2.Select the appropriate option ‘’Print Test Report At End of Test’’ 3.Click ‘’OK’’

How to copy/paste data to excel 1. Click “Data Management” 2. Click “Archive test” 3. Put the mouse cursor on first test click and hold the left mouse Button Drag the mouse down until the last line * 4. While the lines marked press Cltr+C at the same time on your keyboard *

How to copy/paste data to excel (contd.) 1. Open MS Excel by clicking Start -> All Programs -> Microsoft Office -> Microsoft Excel 2010 2. Click the right mouse button and in the menu and choose “Match destination Formatting”  click on it – see below 3. The chosen results will be pasted in excel sheet *

Summary GeneXpert software allows visualization of test results as well as the editing of the test result information and the generation of a printable result reports (by specimen or patient) Errors, invalid results, no results, and RIF resistance indeterminate results are possible outcomes of tests, which warrant a repeat test to be performed

Assessment List the different results obtainable from an Xpert MTB/RIF test List the different reasons to repeat an Xpert MTB/RIF test

Acknowledgements The Xpert MTB/RIF Training Package has been developed by a consortium of GLI partners, including FIND, KNCV, US CDC, USAID, TB CARE I and WHO, with funding from USAID. The modules are based on materials originally developed by FIND, KNCV and Cepheid.