Gastrointestinal Pathogens Stool PCR-Bacterial - Provincial
Discipline
Microbiology
Overview
Description
- Bacterial stool PCR is a multiplex, real-time PCR assay for direct detection of DNA or RNA of over 95% of bacteria causing infectious gastroenteritis. Species detected include Shigatoxin producing Escherichia coli (STEC), Shigella spp., Enteroinvasive E.coli (EIEC), Campylobacter spp. (jejuni and coli), Salmonella spp., Yersinia entercolitica, Plesiomonas shigelloides, Enterotoxigenic E.coli (ETEC) and Vibrio spp (cholera, vulnificus and parahemolyticus).
Ordering Recommendations
- Patients with acute diarrheal syndromes and signs of infection
- Patients hospitalized for 3 days or less
- This test is not recommended as a test of cure
- Clostridium difficile testing should be ordered separately
- Repeat PCR testing not indicated within 7 days of a negative or 14 days of a positive result
- Positive PCR samples are cultured and recovered culture isolates are sent to RRPL for surveillance and typing. Typing and surveillance is reported separately.
- Bacterial culture for test of cure is a separate test code, and can only be requested by Public Health/IPAC
Specimen Information
Specimen types accepted
- Stool in Cary-Blair transport media (Enteric Culture Transport Media)
- Stool in sterile containers is NOT accepted
- Rectal swabs are NOT accepted
Collection procedure
- Do not let urine or water mix with stool specimen
- Do not use toilet paper to collect stool
- You will need a separate, sterile disposable container to collect stool prior to placing inside Cary-Blair transport media. Using the plastic paddle attached to the lid of the Cary-Blair tube, collect small portions from each end and the middle of the stool, especially sampling areas of stool that contain mucus or blood
- Place solid stool about the size of a walnut into the Cary-Blair vial
- Fill liquid stool to the fill indicator line on the container label. DO NOT FILL PAST THIS MARK.
- Place cap on container securely.
- Ensure outside of container is not contaminated with stool.
- Wash hands with soap and water.
Required volume
- 1 stool specimen
- Recommended walnut sized solid stool or to Cary-Blair fill line for liquid stool
Transport and stability
- Store at 2-8 °C and transport without delay
- Specimen should be received by lab within 48h of collection
- Specimens older than 4 days will be rejected
Testing Information
Relevant clinical history
- Please indicate if food poisoning is suspected
- If patient is part of an outbreak, include the outbreak number
- Patient should not take any laxatives, enemas or antibiotics for 1 week prior to specimen collection
- If Vibrio spp. is requested, patient must have a history of travel to an endemic area or ingestion of shellfish
Performance
Methodology
- BD Max Enteric Bacterial and Extended Bacterial PCR Panels
Days/times performed
Availability
- Test performed 7 days per week
Maximum laboratory time
Result Reporting
- 24-48h turnaround time for PCR
- Final culture results up to 5 days
Specimen retention time
Specimen Retention
- Specimens are retained for 3 days after initial processing
Other information
- Bacterial culture identification is only routinely reported if Aeromonas spp. positive, Staphylococcus aureus/MRSA abundant, or susceptibility testing is performed.
- Antibiotic susceptibility testing is not done on Campylobacter spp., Yersinia, Aeromonas, Plesiomonas and Vibrio spp. since disease is self-limiting
- Shigatoxin positive E.coli is not treated with antimicrobials since treatment is associated with an increased risk of hemolytic uremic syndrome
- Antibiogram is done on Salmonella/Shigella spp., but released only in specific circumstances (on request, immunocompromised, neonates less than 3 months, presence of S.typhi/paratyphi)
Last Updated: April 18, 2024