Pertussis PCR Testing
(August 2002)
(Download 
Pertussis PCR Testing.pdf)
HAPS Microbiology has developed and validated a fast, sensitive, specific 'real-time' polymerase chain reaction (PCR) assay for Bordetella pertussis. The assay will be performed Monday to Friday and will offer next day results for specimens that are received before 11am Monday to Thursday.
Bordetella pertussis is a fastidious, slow growing organism that causes whooping cough. Cultures have poor sensitivity and may take up to 12 days for a positive result. PCR has been shown to improve sensitivity of detection markedly, enabling diagnosis of cases up to 3 weeks into the illness. As well, positive results can be obtained from patients who have been treated with antibiotics.
The new PCR assay targets a gene sequence called the IS481. Those samples that may be inhibitory to the PCR process may give a false negative result. In order to detect this sort of inhibition, the pertussis PCR assay incorporates an internal amplification control. Samples that are positive on initial PCR for IS481 will be confirmed by a secondary PCR assay against another pertussis gene target, the porin gene.
Pertussis PCR Testing
Nasopharyngeal swab (dry) or a nasopharyngeal aspirate are the preferred specimen types for this assay. If a patient refuses to have one of these samples taken, then a dry throat swab is a less preferable alternative. Ensure rapid transport (at 4° C) of the sample to the laboratory. If delay longer than 6 hours is anticipated, then the sample should be held at -20° C.
In patients with symptoms lasting longer than 3 weeks, consider the use of pertussis serology (IgA) for diagnosis (see below).
What sort of swab should be used for pertussis PCR samples?
A long wire dacron dry swab should be used for collections from the nasopharynx or throat. Charcoal or other bacterial transport swabs are not suitable and will result in specimen rejection. It is no longer necessary to utilise pertussis transport medium for specimens where PCR is requested.
How do I request Pertussis PCR?
Specify 'Pertussis PCR' on the HAPS request form. Please note that even if not requested, samples from within the Hunter region will be co-cultured for pertussis.
Does this assay detect Bordetella parapertussis?
No. This assay will reliably detect only Bordetella pertussis and a related new species Bordetella holmesii. B. holmesii is an emerging respiratory pathogen that has been associated with lower respiratory infection, including a pertussis-like syndrome and/or bacteraemia.
How useful is the pertussis IgA serology test?
This test has marginal sensitivity in children and infants. It may take 3-4 weeks to become positive in patients with symptomatic pertussis. Positive results obtained in the first 3 weeks of a cough illness should be regarded with caution- the result may be a false positive. In patients who present within 3 weeks of the onset of a pertussis-like illness, samples for PCR testing are to be greatly preferred.
Further Information
For further information regarding supplies of the necessary dacron swab type contact the Unit Supervisor for Microbiology, Ms Elizabeth Cyganski on 49214452.
About the Author
Dr John Ferguson, Director of Microbiology & Infectious Diseases, wrote this HAPS Communique. If you have any questions regarding this topic Dr Ferguson can be contacted on: Telephone: (02) 49214422, Facsimile: (02) 49214440, E-mail: John.Ferguson@hnehealth.nsw.gov.au
Microbiology & Infectious Diseases Contacts
Dr John Ferguson (Microbiologist & Infectious Diseases Physician) - Director - 49214422
Microbiology Laboratories - 49214000