Designing A Reliable Xpert CT Control Chart For TB Testing

A quality control chart for Xpert CT values helps a tuberculosis laboratory detect gradual assay drift, unusual run-to-run variation and problems linked to cartridges, instruments or handling. Used properly, it turns molecular test data into an early warning system rather than a retrospective explanation for an unreliable result.

The chart should support, not replace, the manufacturer’s instructions, internal quality control requirements and the laboratory’s broader quality management system. For Australian services, that means fitting the process to NATA expectations, local procedures and the realities of testing across metropolitan, regional and remote settings.

Define What The Chart Is Meant To Detect

First, specify the assay and instrument covered by the chart. Xpert MTB/RIF and Xpert MTB/RIF Ultra produce cycle threshold values, commonly called Ct values, for detected targets, while also reporting qualitative or semi-quantitative information. A lower Ct generally indicates more target nucleic acid in the reaction, but Ct is not a direct measure of viable bacillary load and should not be interpreted as a standalone measure of infectiousness.

A control chart is most useful for monitoring a consistent control material under stable conditions. It can reveal a shift after a new cartridge lot, a trend caused by instrument performance, or increased imprecision linked to storage and workflow. It should not be used to establish a clinical reference interval or to set an arbitrary patient-result cut-off.

Write a short purpose statement in the procedure. For example, the chart may monitor the Ct of a positive external control, confirm acceptable amplification behaviour, and trigger investigation when the result moves outside defined limits. Record whether the chart applies to one assay version, one instrument module, or several modules managed under a common protocol.

Select Suitable Control Material And Data

Use a stable, well-characterised positive control that contains the relevant Mycobacterium tuberculosis complex target, inactivated material or another approved control format. The control must be safe to handle, stable for the stated storage period and suitable for the Xpert platform. A control with a Ct close to the assay’s detection limit can be useful for sensitivity monitoring, but it may show greater natural variation than a stronger control.

Keep the control matrix and preparation method consistent. Record the control lot, aliquot date, expiry, storage temperature, cartridge lot, instrument serial number, module, operator and run date. These fields make the chart actionable when a result changes. Do not pool unrelated data from different control concentrations, assay versions or instrument modules unless validation demonstrates that they behave equivalently.

Collect enough results to establish a baseline under routine conditions. Laboratories commonly use at least 20 results gathered across several runs, days and operators, provided the data are accepted as in-control. Remove only results linked to a documented assignable cause, such as a known pipetting error or an instrument failure, and retain the reason in the quality record.

Build The Levey-Jennings Chart

Calculate the baseline mean Ct and standard deviation for the selected control. Plot each accepted result in chronological order on a Levey-Jennings chart, with the mean at the centre and lines at one, two and three standard deviations. Because Ct is an inverse indicator of target quantity, a rising Ct may suggest reduced amplification or less target in the control, while a falling Ct may indicate increased apparent target. The direction matters less than the consistency and size of the change.

Use a separate chart when the control lot, concentration, assay chemistry or instrument configuration changes materially. A new baseline may be needed after a documented change, but do not reset the chart simply to make an uncomfortable result disappear. Compare old and new control lots in parallel where feasible, then approve the new mean and limits through the laboratory’s quality process.

Avoid treating every point beyond two standard deviations as a failed test. Statistical limits describe expected variation; they do not automatically prove that a patient result is wrong. Your procedure should state the response to one result beyond two standard deviations, one result beyond three, or a sustained pattern such as several points on one side of the mean or a steady upward trend.

Investigate Trends, Shifts And Outliers

When a Ct value breaches a rule, pause and check the complete run record. Confirm that the correct control was used, the cartridge was within expiry, the control was stored correctly and the instrument passed its start-up and maintenance checks. Review error codes, environmental conditions, operator notes and any concurrent control results. If the control is outside acceptance criteria, follow the laboratory’s policy for withholding or assessing affected patient reports.

A single outlier may reflect preparation or loading error, whereas a shift across several runs can point to a new cartridge lot, reagent storage issue, module problem or control deterioration. A gradual trend deserves attention before the formal limit is reached. Check whether the pattern is confined to one GeneXpert module or appears across the platform, since that distinction narrows the investigation.

Do not delete an unusual value because it seems inconvenient. Mark it as excluded only after the cause is documented and authorised. If repeat testing is performed, retain both the original and repeat results, with an explanation. The investigation should lead to a corrective action, such as retraining, cartridge-lot review, instrument service or revised storage monitoring, followed by evidence that the action worked.

Connect The Chart With Laboratory Safety And QMS

Ct monitoring is one part of quality control, not a substitute for competency assessment, equipment management, document control or biosafety. Work with the laboratory’s risk assessment to ensure that control preparation, cartridge loading, waste disposal and spill response are clear. A practical laboratory safety checklist can help connect the molecular workflow with routine safety checks, particularly where staff perform several roles.

Document the chart method in a controlled procedure. Include the control source, frequency, acceptance rules, calculation method, responsibilities, escalation pathway and record-retention period. Train staff to distinguish a Ct value, an error code, an invalid result and a failed control. Competency assessment should include interpretation of a normal chart, an isolated outlier and a sustained shift.

In Australia, a metropolitan reference laboratory may have dedicated quality staff, while a small hospital laboratory in the Northern Territory, Western Australia or Far North Queensland may run GeneXpert testing with limited on-site technical support. Procedures should therefore state who can authorise a run, who can review a trend remotely and how urgent advice is obtained. The system also needs to work when courier delays, extreme distances or intermittent supply affect cartridge availability.

Link chart review to management review and continual improvement. The GLI continual improvement phase provides a useful framework for turning monitoring data into documented corrective action, follow-up and review. For services supporting Aboriginal and Torres Strait Islander communities, reliable local testing can reduce delays associated with sending specimens to major centres, while culturally safe communication and appropriate clinical interpretation remain essential.

Apply Practical Recommendations

Use the following controls when establishing or reviewing an Xpert CT monitoring process:

• Define one control material, assay version and instrument or module for each baseline chart.
• Establish the mean and standard deviation from stable results collected across routine operating conditions.
• Record cartridge lot, control lot, module, operator, storage conditions and any error code with every result.
• Set written rules for outliers, shifts and trends, with clear authority to stop, release or investigate testing.
• Review charts at a defined frequency, such as each run and formally at monthly quality meetings.
• Re-establish or verify the baseline after significant changes, including control lots, assay updates, module replacement or major maintenance.
• Keep the chart, investigation, corrective action and effectiveness check together in the quality record.

Make the chart easy to read at the bench. A spreadsheet may be adequate for a small service if version control, access permissions, formulas and backups are managed. Larger networks may prefer a laboratory information system or quality dashboard, but automation should not conceal the underlying data. Staff must be able to see the control result, identify a rule breach and locate the associated investigation.

Review performance across time rather than focusing only on the latest point. A chart with tightly grouped values can still be misleading if the control preparation is inconsistent or if only convenient results were included. Periodically compare internal trends with external quality assessment findings, maintenance records and relevant manufacturer notices.

A well-designed chart should lead to proportionate action. A minor statistical signal may require observation and documentation; a confirmed control failure may require withholding results, repeat testing and technical support. The goal is timely detection of loss of control while avoiding unnecessary wastage of cartridges and delays for patients.

Begin by selecting the control material and gathering the first dependable results from routine Xpert runs. Have the laboratory’s authorised quality lead approve the baseline, rules and response pathway, then review the chart at scheduled quality meetings. With disciplined records and clear escalation, Ct monitoring can become a practical part of TB laboratory quality assurance across Australia.