General Advice:
 
For investigation of lower respiratory tract infections (LRTI) expectorated sputum samples should be sent.  Salivary samples do not reflect organisms in the lower respiratory tract and should not be sent.  24 hour sputum collections are not recommended because there is a greater likelihood of contamination. Advice on how to obtain a suitable specimen is given below:
 
Expectorated Sputum

• If possible have the patient rinse mouth and gargle with water immediately before obtaining the specimen
• Patient should be instructed not to expectorate saliva or postnasal discharge into the container.
• Early morning sputum should be obtained
• Collect specimen resulting from deep cough in sterile, screw-cap universal or other suitable sterile collection jars
• When sputum production is scant, induction with nebulized saline may be effective.
   
  In instances where the patient is seriously ill and/or intubated, bronchial aspirates or bronchial washings can be sent for analysis. These samples should be sent in sterile universals or other suitable sterile collection jars. These samples are generally taken from hospital inpatients.
   
   
  Suspected Pneumonia:
   
  If the patient is suspected to have pneumonia, blood cultures should also be sent for routine culture (advice on collection of these is given in the Blood Cultures section)
   
  Mycobacterium investigations:
   
  If Mycobacterial infection is suspected, please collect 3 non-salivary sputum samples, on separate days. Early Morning Gastric aspirates/suctions are used primarily for the detection of M. tuberculosis in patients (usually children) unable to produce quality sputum.
   
  Viral Infections: 
   
  If viral infection is suspected please send a non-salivary sputum sample in viral transport medium (VTM). Should a VTM be unavailable, the sample can be sent in a sterile universal.
   
  For Influenza A/B only, a nasal or throat swab in VTM should be sent. The test used for this includes RSV and SARS-CoV-2 (COVID-19) targets, and therefore results for all four pathogens will be issued. 
   
  Common respiratory viruses cause an enormous burden to health systems and economic costs to society in direct medical expenses and indirect productivity losses. Furthermore, emerging respiratory viruses, such as severe acute respiratory syndrome (SARS), H5N1 avian influenza, and pandemic (H1N1) 2009 represent threats to global health security. Coronavirus disease (COVID-19) is an infectious disease caused by a newly discovered coronavirus SARS-CoV-2 responsible for the recent pandemic. Other respiratory virus includes Respiratory syncytial virus (RSV) which is an enveloped RNA virus and is in the same family as the human parainfluenza viruses and mumps and measles viruses. RSV is one of the common viruses that cause coughs and colds in winter. RSV usually causes mild respiratory infection in adults and children, but it can be severe in infants who are at increased risk of acute lower respiratory tract infection. RSV is the most common cause of bronchiolitis in children aged under 2 years
   
  Legionella pneumophila  and Streptococcus pneumoniae infections:
   
  Rapid detection of Legionella pneumophila and Streptococcus pneumoniae (pneumococcal) antigen is available in certain circumstances using mid-stream urine samples. Please discuss suspected cases of Legionellosis with the Clinical Microbiologist to ensure that all appropriate tests are set up promptly. 
   
  Blood Tests:
   
  Acute and convalescent serology for Mycoplasma sp., Chlamydia sp., and viral respiratory pathogens may provide a retrospective diagnosis. For this testing please provide 5-10mls clotted blood for acute and convalescent samples.
  Please note that serology testing for legionella infection is now deemed to be no longer clinically effective and is no longer available. For testing to aid diagnosis, antigen detection or culture is recommended.