2 The diagnostic workflow in the clinical microbiology laboratory

Clinicians make diagnoses based on the patient’s history and risk factors, physical findings on examination and the results of diagnostic testing (such as imaging, laboratory tests, etc.).

Laboratory diagnostic testing can be broken down into three stages:

  1. Pre-analytical: Test-related decision-making and specimen collection.
  2. Analytical: The test itself and any associated laboratory practices, including test methods, microscopy, culture and identification, antimicrobial susceptibility testing (AST), and protocol validation.
  3. Post-analytical: Reporting and use of laboratory data, such as selective reporting of antimicrobial susceptibility data to encourage the use of narrower spectrum agents.

From the clinical perspective, diagnostic stewardship focuses on stages 1 (pre-analytical) and 3 (post-analytical); most clinicians are not involved in the actual test performed in laboratory (stage 2). The overall value of the test itself relies on good quality at all stages, not just at the analytical stage.

Figure 2 shows the workflow from initial presentation of the patient through to the collection and use of the data to inform further action and strategy. Not all patients will require all the steps: for example, not everyone will require imaging or biopsies, and not all infections will need public health interventions.

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Figure 2 The workflow in diagnostic stewardship.
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The pre-analytical stage includes looking at signs and symptoms; the infection site is identified by clinical examination; imaging, biopsies or an X-ray are performed; and the infection is documented. In the analytical stage, laboratory tests are required; the organism is identified (rapid, conventional or molecular methods); AST is performed; and the dose and duration of antibiotics is identified. The post-analytical stage includes the route of administration; other factors; and surveillance, outbreak investigation and public health.

Figure 2 The workflow in diagnostic stewardship.

Key processes of laboratory diagnostic testing in the pre-analytical, analytical and post-analytical steps are shown in Table 1.

Table 1 A systematic approach to testing infectious agents.
StageProcess
Pre-analytical
  • Advice to clinicians regarding infection management (diagnosis, treatment and prevention).
  • Advice is empiric, usually based on syndrome or differential diagnosis.
  • Recommendations for appropriate microbiological sampling.
Analytical
  • Selection of the rapid diagnostic tests that are the most relevant in clinical practice (may improve infection management and antibiotic prescribing behaviour).
  • Timely and accurate microbiology results.
  • Advanced tests to establish molecular mechanisms underlying AMR and genotyping of pathogens.
Post-analytical
  • Improved reporting of results to clinicians, to influence their infection management and antibiotic prescribing behaviour (e.g. selective reporting).
  • Definitive advice on organism-directed treatment by de-escalation, stopping or continuation of AMU.
  • Definitive diagnosis based on test results and clinical findings.
  • Surveillance (epidemiological data) and generation of essential data that inform institutional treatment guidelines based on local resistance epidemiology.

Sections 3–5 will consider the three stages in more detail. The personnel involved in each stage will depend on the institution, but will usually include physicians, laboratory staff, infection prevention and control teams, and pharmacists. Where available, clinical microbiologists (medical doctors who have specialised in microbiology) should oversee and coordinate the pathway.

1.3 Finding the ‘sweet spot’

3 The pre-analytical stage