Tēnā koutou,

There have recently been some interim changes to the way microbiology laboratory services are provided at Invercargill hospital SCL laboratory. These changes were introduced in part to better streamline the workflow and improve turnaround times for critical results. They were also in response to on-going challenges with recruitment of suitably qualified Senior Microbiology Scientist staff. These new processes have been in place for the past 8 weeks and we are now looking to make these changes permanent in order to retain quality services to Invercargill clinicians and patients going forward.

The changes are outlined below:

• Community and hospital microbiology plate reading is now performed at Dunedin SCL,at the laboratory on site at Dunedin Hospital. Samples received into Invercargill laboratory are processed then transferred to Dunedin for plate reading, interpretation, reporting and validation.
  • Blood cultures continue to be incubated in the blood culture analyser at Invercargill hospital laboratory, with Gram staining performed on site in Invercargill.
  • Cell counts for samples other than urine (such as CSF, joint and fluid aspirates) are also performed on site in Invercargill.
• There are a number of additional molecular tests (PCR) now available on site at Invercargill hospital laboratory:
  • BioFire CSF multiplex panel for various pathogens that cause meningoencephalitis – is available 24/7, for CSFs where WBC count >5 x 10⁶/L cells. Samples with a normal WBC count require prior discussion with a clinical microbiologist
  • BioFire and GeneXpert positive blood culture panels:
    • The BioFire PCR panel includes the most commonly encountered blood culture pathogens and resistance mechanisms. The GeneXpert detects S. aureus and methicillin resistant S. aureus (MRSA). The GeneXpert is performed on blood cultures with gram positive cocci in clumps (resembling staphylococci).
    • The BioFire is performed on positive blood cultures with other organisms seen on Gram staining or out of hours (prior to midnight). These PCR panels provide rapid identification of blood culture isolates and major resistance mechanisms within 120 minutes of the blood culture flagging positive, a process which previously took at least 16 hours and often longer.
  • Blood cultures all still undergo the usual culture and susceptibility testing alongside the BioFire or GeneXpert PCR.
    • Note that blood cultures which flag positive but are negative on the BioFire PCR may still contain a pathogen since the PCR does not include all bacterial species.
  • TB PCR on sputum – if there is high clinical suspicion for TB infection. Available during normal working hours, however this also requires Clinical Microbiologist approval. TB PCR will be performed alongside referral of the sample for the usual microscopy and culture for suspected TB cases. Norovirus PCR on faeces – generally limited to use for hospital cases and outbreak investigation, requires Clinical Microbiologist approval. Not typically available for community patients unless on direction from Public Health.
• Diagnostic stewardship
  • Appropriate clinical details continue to be required for all microbiology tests (this has not changed, but this memo serves as a reminder to please always include information on the request form)
  • Urine sieving – urines are processed for culture/susceptibilities only if the urine WBC count is >10×10⁶/L Note that some patient groups are excluded from this requirement (e.g. neutropenic, pre-urological surgery, pregnant, paediatric)

The expanded availability of PCR on site at Invercargill laboratory will provide greater access to timely results for critical tests.

There is no evidence that transportation of samples to the Dunedin laboratory for plate reading and reporting impacts on the quality and accuracy of sample results. This process is well established in other parts of our business. Additional couriers have been put in place to ensure timely transportation.

For any questions or feedback on these changes, please contact

Dr Juliet Elvy, Clinical Microbiologist (Juliet.elvy@sclabs.co.nz – 0278393726)
Dr James Ussher, Clinical Microbiologist (james.ussher@sclabs.co.nz – 0277079576)
Craig Rodgers, Laboratory Manager (craig.rodgers@sclabs.co.nz – 0211332270)

Download a copy of this update here.