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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.

Locations

John Radcliffe Hospital:

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

Churchill Hospital:

John Warin Ward
Chest Clinic
Haematology Ward
Transplant Ward
Geoffrey Harris Ward
RMDCU
OCRM,
Haematology Day Treatment Unit

Horton General Hospital:

Private patient locations:

Wytham
Foscote
Manor Hospital
Oxford Clinic

All community hospitals

All GP locations

Doctors

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

The laboratory turnaround time for these tests is up to six days.

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.