Synopsis
Choose and handle respiratory samples intelligently, understand what bronchoscopy can answer, and translate laboratory results into safe clinical decisions without mistaking detection for disease.
- Begin with a clinical question: routine bacterial culture, tuberculosis or non-tuberculous mycobacteria, fungal disease, viral infection, cytology, diffuse lung disease or an endobronchial lesion require different samples and laboratory handling.
- Collect sputum before antimicrobials when this is safe, but never delay treatment of severe infection merely to obtain a perfect sample.
- A good lower-respiratory specimen is freshly expectorated after mouth rinsing into the correct sterile container; saliva and delayed transport reduce interpretability.
- Microscopy, culture and susceptibility must be interpreted beside sample quality, prior antibiotics, airway disease, immune status and the distinction between colonisation and invasive infection.
- Bronchoscopy permits airway inspection, bronchial washing, bronchoalveolar lavage, brushing and biopsy; each has a different diagnostic yield and risk profile.
- CT should usually define the target and the least invasive useful sampling route before bronchoscopy for suspected malignancy or focal disease.
- Negative sputum or bronchoscopy results do not exclude malignancy, tuberculosis or infection when pre-test probability remains high; review whether the correct site and tests were sampled.
- Request mycobacterial or fungal studies explicitly and alert the laboratory to unusual exposures, immunosuppression and high-consequence pathogens because routine culture does not answer every question.
- Consent covers the intended procedures, sedation plan, alternatives and material risks; use the procedural checklist and verify antithrombotic, allergy and fasting instructions locally.
- Do not prescribe an antibiotic simply because an organism is reported: decide whether it explains the syndrome, then use local susceptibility and antimicrobial guidance.
Key red flags
Severe pneumonia, treatment failure, immunosuppression, unusual exposure, cavitation or recurrent infection makes microbiological definition more valuable. Ask what organism class matters and collect the least invasive high-quality sample that can answer it.
Chronic cough, weight loss, fever, night sweats, haemoptysis, compatible imaging or epidemiological risk should trigger the local TB pathway, appropriate respiratory precautions and specifically labelled mycobacterial specimens rather than ordinary bacterial culture alone.
Diffuse infiltrates in an immunocompromised patient may justify early specialist bronchoalveolar lavage for bacterial, viral, fungal or pneumocystis testing, balanced against oxygenation, bleeding risk and whether a safer sample is available.
New hypoxaemia, wheeze, haemoptysis, pleuritic pain, fever, hypotension or reduced consciousness can represent bronchospasm, bleeding, pneumothorax, sedation toxicity or infection. Assess immediately rather than dismissing symptoms as expected recovery.
Investigation priorities
Identify plausible bacterial pathogens and guide narrower treatment.
Management branches
A lower respiratory infection question where microbiology could change management.
- Define the syndrome and request: routine bacterial culture, mycobacteria, fungi, viral testing or cytology need distinct instructions and sometimes different containers.
- Before antimicrobials when clinically safe, ask the patient to rinse the mouth, take deep breaths and expectorate lower-airway sputum directly into a labelled sterile pot.
- Record site, time, current antimicrobials, immune status and key exposures; transport promptly according to the receiving laboratory handbook.
- When the report returns, review sample quality and whether the organism fits the illness before narrowing, stopping or changing therapy with local guidance.