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Respiratory samples for culture

The isolation and correct identification of respiratory pathogens is an important aid in the diagnosis and management of infected patients.

Clinical conditions may be both acute and chronic, and the interpretation and relevance of microbiological findings may vary considerably.

Request TB / fungi / Nocardia spp. if relevant.

For information on culture of samples for tuberculosis, please see:

Laboratory investigation of Mycobacteria tuberculosis

Specimen requirements

All specimens should be fresh and preferably taken before antimicrobial treatment is started.

Specimens should be transported and processed as soon as possible. Swabs for bacterial and fungal culture should be in appropriate transport medium. Specimens should be collected in sterile leak-proof container and transported in a sealed plastic bag.

Samples should be transported to the laboratory as soon as possible. If specimen transport will be delayed, e.g. from primary care, specimens should be stored in a refrigerator until transported to the laboratory.

  • Antral / Sinus Washouts
  • Bronchoalveolar Lavage (BAL) or Bronchoalveolar Washings / Brushings / Aspirates; must be obtained by skilled personnel with appropriate protection / isolation facilities.
    See the BAL caresets on EPR
  • Cough Swabs
  • Endotracheal Tips
  • Pleural Aspirates / Chest Drain Fluids: state how the specimen was collected
  • Sputum, Endotracheal or Tracheal Aspirates, Nasopharygeal Aspirates / Secretions: ensure specimen comprises sputum (not saliva / food); samples of saliva only will not be processed
  • Induced Sputum: must be obtained by skilled personnel with appropriate protection / isolation facilities. (Pneumocystis detection is performed in the Cytology department.)
  • Transbronchial / Lung Biopsy Samples

PCR for a wide range of respiratory viruses is available for ventilated or immunocompromised individuals. For more information on the range of tests offered by the laboratory, please refer to the manual.

Microbiology Laboratory Users Manual (pdf, 684 KB)

Focused testing

Examination of sputum has a low predictive value for clinical decision-making unless aspirated (except for suspected TB). However, there may be circumstances where a result is beneficial i.e. Cystic Fibrosis, Bronchiectasis, COPD, Chest Unit patients, those under chest physicians and immunocompromised patients.

Therefore, sputum samples from the following locations / doctors only will be examined.


John Radcliffe Hospital:

  • ED
  • SEU
  • EAU
  • CTU
  • Kamran's Ward
  • ITU
  • NITU
  • PITU
  • John Warin Ward
  • 6B (medical assessment)

Churchill Hospital:

  • Chest Clinic
  • Haematology Ward
  • Transplant Ward
  • Geoffrey Harris Ward
  • OCRM,
  • Haematology Day Treatment Unit

Horton General Hospital:

  • ED
  • ICU
  • EAU

Private patient locations:

  • Wytham
  • Foscote
  • Manor Hospital
  • Oxford Clinic

All community hospitals

All GP locations


  • Dr Chapman
  • Dr Flight
  • Dr Ives
  • Dr Thompson
  • Dr Hull
  • Dr Greyez
  • Dr Scarborough
  • Dr Brent
  • Dr Lomascabeza

Clinical details

  • Cystic fibrosis
  • Brochiectasis
  • Immunocompromised
  • Private patient

Laboratory turnaround time

Please see Turnaround times

Laboratory method

Respiratory samples are processed using culture media in order to select the pathogen from the normal commensal flora.

Depending on the nature of the specimen and the patient's clinical details, the specimens are inoculated onto different selective media and the media are incubated for different lengths of time.

All the respiratory specimens are processed in a microbiological safety cabinet in Containment Level 3 room due to aerosol risk to the staff and the higher probability that the sample may contain an ACDP Category 3 pathogen.

Primary plates are then examined for growth following incubation and interpretation is performed taking into consideration the individual merits of each sample.

Where to find results of these tests

  • All results are returned electronically where possible (EPR, SunquestICE).
  • Some results may be phoned to clinicians and GPs.
  • Results are never given directly to patients by the laboratory staff.

Further information and contact details

For further information please email:

Confidential patient information should only be sent from accounts.

Microbiology Laboratory Users Manual (pdf, 684 KB)