A practical TB laboratory gap analysis with the GLI quality framework

A tuberculosis laboratory gap analysis is a structured comparison between current practice and the quality requirements needed for safe, reliable, timely TB testing. It helps a laboratory identify weaknesses before they affect diagnosis, drug-resistance detection, reporting or patient care.

The GLI Quality Tool makes this process manageable by combining a four-phase improvement roadmap with twelve Quality Systems Essentials. These essentials cover the complete laboratory system, including personnel, equipment, facilities, documents, information, assessment, safety and continual improvement.

For Australian laboratories, the exercise should reflect the operating environment rather than rely on a generic checklist. A metropolitan service in Melbourne or Brisbane may have automated molecular testing and established courier networks, while a remote service may face long transport distances, limited staffing and intermittent access to maintenance support.

The most useful gap analysis produces evidence, priorities, owners and deadlines. It is not simply a compliance exercise or an audit report. When performed with laboratory staff, clinicians, collection services and quality managers, it becomes a practical improvement plan for TB testing.

Define the scope and intended outcome

Start by deciding what the analysis will cover. It may include the entire TB testing pathway, from specimen collection and transport to microscopy, culture, molecular testing, antimicrobial susceptibility testing, reporting and referral. A smaller laboratory might focus initially on the molecular platform, sample reception or systems for detecting rifampicin resistance.

Set a clear purpose before reviewing documents. The aim could be preparation for accreditation, implementation of a new GeneXpert or Truenat service, improvement of turnaround times, or better continuity during staff absences. Define the sites, tests, staff groups and reporting interfaces involved, along with the period being assessed.

Use the GLI phase structure to match the assessment to the laboratory’s maturity. Early phases help establish essential infrastructure and controlled processes. Later phases support implementation, monitoring and continuous improvement. This prevents a laboratory from spending time on advanced indicators while basic safety procedures, stock control or document management remain unreliable.

Map the TB testing pathway

Draw the full workflow as it operates in practice, not as it appears in a policy. Include ordering, patient identification, sputum collection, packaging, courier pickup, accessioning, testing, result verification, referral testing, notification and record retention. Mark every handover between the laboratory, respiratory clinic, hospital ward, public health unit and external provider.

This mapping often reveals gaps outside the testing bench. A specimen may be correctly processed but delayed because a collection centre does not know the courier cutoff. A result may be technically valid but fail to reach the treating team because the laboratory information system does not clearly flag a resistant result.

For retreatment cases, a controlled tracking process is particularly valuable because previous results, treatment history and current specimens must be connected. The GLI guidance on a sample tracking system can help laboratories examine identifiers, status updates, referral points and escalation rules.

Assess the twelve quality essentials

Review each Quality Systems Essential using objective evidence. Relevant areas include organisation, personnel, equipment, purchasing and inventory, process management, information management, documents and records, customer focus, assessment, facilities and safety, occurrence management and continual improvement. Use the GLI checklists to guide interviews and observations, but verify each response.

For every requirement, record whether it is fully implemented, partly implemented, absent or not applicable. Avoid treating “we usually do this” as evidence. Look for an approved procedure, completed record, maintenance log, competency assessment, incident report, quality indicator or meeting minute that demonstrates the practice.

Ask staff to describe how work is actually done, then compare their answers with controlled documents. Differences may indicate outdated procedures, informal workarounds or training needs. In Australia, this evidence should also be considered alongside NATA expectations and the requirements of the laboratory’s applicable ISO 15189 accreditation arrangement.

Examine safety, facilities and equipment

TB work requires a deliberate review of biosafety and occupational health controls. Observe specimen opening, aerosol-generating procedures, cabinet use, decontamination, waste handling, respiratory protection and incident response. Check that staff know what to do after a spill, exposure or equipment failure, and that relevant records are completed.

Facilities may work differently across Australia. A large Sydney or Perth laboratory may have dedicated containment areas and engineering support, while a regional or remote service may depend on a shared room, scheduled maintenance visits and strict limits on procedures performed locally. The gap analysis should distinguish between risks that require immediate control and improvements that need capital funding.

Assess equipment beyond whether it switches on. Review installation qualification, calibration, preventive maintenance, service agreements, temperature monitoring, backup power, environmental conditions and downtime arrangements. Confirm that staff can identify invalid runs, contamination risks and instrument errors, and know when testing must be stopped or referred.

Review people, competency and workload

Compare the required competencies for each TB method with the skills currently available on every shift. Evidence should include induction, supervised practice, initial competency assessment, refresher training and review after a method or platform changes. Do not assume that general molecular laboratory experience automatically demonstrates competence in TB testing.

Training should cover interpretation as well as operation. Staff need to understand specimen suitability, internal controls, invalid results, resistance markers, contamination, repeat testing and urgent communication. The GLI resource on molecular testing training provides a useful basis for checking whether instruction is practical, documented and linked to competency.

Consider workload and resilience. A single experienced scientist may be carrying undocumented knowledge, or a service may rely on one person who can troubleshoot the platform. Include leave coverage, after-hours escalation, recruitment, supervision and succession planning. Remote and rural Australian laboratories may also need arrangements for travel, telehealth support and delayed access to specialist advice.

Check documents, data and supplies

Collect the documents that control TB work: procedures, forms, result templates, referral instructions, safety documents, equipment manuals, quality plans and corrective action records. Check version control, approval, review dates, access at the point of work and withdrawal of obsolete copies. A procedure that exists only on a shared drive but cannot be found during a busy shift is a practical gap.

Examine information flow from accessioning to final report. Patient identifiers, specimen type, collection date, test method, resistance result, authorisation and notification status should be traceable. Australian laboratories must handle this information consistently with organisational policy and applicable privacy obligations, including the Privacy Act 1988 where relevant, as well as state and territory health-record requirements.

Review stock management for cartridges, reagents, controls, culture media, personal protective equipment and critical spare parts. Record expiry monitoring, minimum stock levels, lot acceptance, cold-chain conditions and supplier contingencies. Australian procurement can be affected by import delays, limited rural distribution and platform-specific contracts, so the analysis should test how the service would operate during a supply interruption.

Rank risks and plan corrective action

Convert each gap into a concise finding that states the requirement, observed evidence, risk and likely cause. “No current training records for molecular testing” is more useful than “training needs improvement.” Link the finding to a Quality Systems Essential and identify whether it affects safety, result validity, turnaround time, traceability or regulatory compliance.

Rank findings using a simple risk method. Immediate risks include unsafe specimen handling, uncontrolled result reporting, missing resistance alerts and equipment operating outside validated conditions. Medium-priority findings may involve incomplete stock records or irregular internal audits. Lower-priority items can include formatting changes that improve consistency without changing risk.

Assign one owner and one due date to every action. Actions should be specific, such as validating a new transport route, introducing a daily temperature log, completing competency assessments or configuring an urgent-result alert. Define the evidence that will close the action, and review progress at quality meetings rather than leaving the plan in a static spreadsheet.

Monitor progress and repeat the review

Select a small group of indicators that show whether changes are working. Useful measures include specimen rejection, invalid molecular runs, turnaround time, amended reports, stock-outs, equipment downtime, overdue competency assessments and completion of corrective actions. Trends are more informative than a single result, especially when testing volumes vary.

Include feedback from clinicians, collection sites, public health teams and patients where appropriate. In Australia, communication arrangements may need to account for state TB programs, Aboriginal Community Controlled Health Services, interstate referrals and remote transport networks. A service should know whether results are reaching the people responsible for treatment decisions in time.

Repeat the gap analysis after major changes, such as a new instrument, relocation, staffing restructure, revised referral pathway or accreditation assessment. A periodic review can be shorter than the initial exercise if the evidence base is maintained. The goal is to move through the GLI phases while keeping quality management embedded in daily work.

Area	Evidence to review	Common gap	Practical action
Specimen pathway	Collection, transport and reception records	Delayed or untraceable specimens	Define identifiers, courier cutoffs and escalation steps
Personnel	Training and competency files	Staff can operate a platform but cannot interpret errors	Use supervised assessment and refresher training
Equipment	Maintenance, calibration and downtime logs	Unplanned outages disrupt testing	Establish service support, backup plans and referral criteria
Information management	Worksheets, LIS records and reports	Resistance results are not clearly escalated	Standardise verification and urgent notification
Safety	Observation, incident and waste records	Procedures differ between shifts	Reinforce controlled procedures and incident drills
Improvement	Indicators and corrective action reviews	Findings remain open without evidence	Assign owners, deadlines and closure criteria

Use the completed assessment as a working management tool. Share a prioritised version with laboratory leadership, quality staff and relevant clinical partners, while protecting confidential patient and personnel information. Revisit the highest-risk items first and document decisions when a recommendation cannot be implemented immediately.

A well-run TB laboratory gap analysis gives Australian services a defensible view of their current capability and a realistic route forward. Apply the GLI Quality Systems Essentials to the whole testing pathway, support findings with evidence, and turn each priority into a measurable action that improves safety, reliability and access to timely TB diagnosis.