Enteric pathogen testing changing to PCR

From Monday 2nd October 2023 Awanui Canterbury and Awanui Timaru will be replacing routine faecal culture and Giardia/Cryptosporidium EIA testing with a single multiplex faecal PCR test. PCR is more sensitive than culture and EIA testing, and this new method will improve detection of enteric pathogens with a similar or superior turnaround time. This is in keeping with best practice, and what most other laboratories in New Zealand are using.

The new faecal pathogen platform by AusDiagnostics includes the following targets:

Salmonella spp.Shiga toxin 1 and 2
Shigella spp.Giardia
Yersinia spp.E. histolytica
E. coli O157 

Any relevant pathogens detected by PCR that require typing or susceptibility testing will be cultured.

Vibrio and Aeromonas will still be tested by culture for those patients with fluid specimens, shellfish consumption, or relevant travel history.

Note: A single faecal specimen per episode of enteric illness is sufficient for routine enteric pathogen testing. Formed specimens will not be tested for faecal PCR. Clearance testing is rarely indicated and will only be performed on samples that meet Public Health guidelines (Te Whatu Ora Communicable Disease Control Manual, Appendix 2: Enteric Disease).

The majority of enteric parasite infections in New Zealand are caused by Giardia and Cryptosporidium. It is important to note that Blastocystis hominis and Dientamoeba fragilis are disputed pathogens in humans, and most cases do not require treatment. We will only test for these organisms when specifically requested with relevant supporting clinical information.

Detection of helminth eggs and other exotic parasites will only be performed when requested AND a relevant history is provided e.g. travel, eosinophilia, suspicion of uncommon worms (e.g. Tapeworm), or gastroenterologist request. Three specimens taken on consecutive days is recommended for detection of these parasites.

Please don’t hesitate to contact the lab if you have any questions.

Dr Aaron Keene Aaron.Keene@awanuilabs.co.nz