Microbiology requesting during COVID-19 testing surge

The current community outbreak of the COVID-19 Delta variant has caused a huge surge in local demand for SARS-CoV-2 testing, averaging over 2000 tests per day over the past 5 days for Pathlab.

Other microbiology and molecular requests need to be urgently reduced in order to re-allocate staff for COVID testing. We would ask please that all “routine” testing is minimised as much as possible. Please note the following in particular:


(Please note that all non-COVID-19 molecular testing will potentially impact on our turnaround times for SARS-CoV-2 testing, as well as using up molecular reagents)

  • Asymptomatic Chlamydia and Gonorrhoea Testing: Testing should be postponed wherever possible.
  • HSV/VZV and viral eye swabs: Should only be requested in exceptional clinical cases (e.g. immunocompromise, pregnancy).
  • Faeces: Please request only if systemic symptoms, risk factors for Clostridium difficile, or as part of a public health outbreak investigation.

Please note the turnaround times for non-COVID molecular tests will be prolonged.


  • Urines: Please strictly reserve laboratory urine testing to cases of complicated UTI including pregnancy and empiric therapy failure.
  • Superficial skin or wound swabs: Please restrict to where systemic symptoms are present, or there is empiric therapy failure.
  • Mycology skin scrapings, toe and fingernail clippings: Testing should be postponed wherever possible.
  • Sputum samples: Sputum samples from the community setting should only be sent in exceptional circumstances.
  • Ear swabs: Please send ear swabs only where systemic infection is present or ENT specialists have been involved.
  • Throat swabs: Please restrict to where there are risk factors for rheumatic fever or where the patient is systemically unwell.

These changes in requesting should be implemented immediately. Thank you for your understanding and assistance at this time. We will send out a further update when COVID-19/SARS-CoV-2 testing volumes settle down to manageable levels.