Bordetella - Respiratory - PCR

Consistent with O. Reg. 671/92 of the French Language Services Act, laboratory testing information on this page is only available in English because it is scientific or technical in nature and is for use only by qualified health care providers and not by members of the public.

This page provides information on real-time polymerase chain reaction (qPCR) testing for Bordetella at Public Health Ontario’s (PHO’s) laboratory. Bordetella pertussis is the causative agent of whooping cough, and other species in this genus (e.g. B. parapetussis and B. holmesii) cause similar but usually milder illness. This assay can detect nucleic acid from each of these three organisms.  


  • Alignment of reporting instruction for Bordetella pertussis -positive specimen to the Medical Officer of Health as per Ontario Health Protection and Promotion Act
  • Removal of LAB-SD-047, Bordetella Molecular Testing- Changes to Result Reporting from the TIS webpage

Testing Indications

Patients with signs and symptoms consistent with pertussis should be tested by PCR to confirm the diagnosis. The optimal time to collect a sample for PCR testing is in the first 3 weeks of illness, while bacterial DNA is still present in the nasopharynx. After the fourth week of illness, the amount of bacteria in the nasopharynx diminishes quickly, which increases the risk of a false-negative result.1

PCR testing is not recommended for asymptomatic patients because false-positive results are more likely in these individuals.2

Acceptance/Rejection Criteria

Specimen must be collected in PHO-provided Bordetella pertussis BP collection kit; Kit order# 390052.

Specimen collected in dry cotton tip swab or other transport medium (including Aimes) are rejected for testing.

Specimen Collection and Handling

Specimen Requirements

Test Requested Required Requisition(s) Specimen Type Minimum Volume Collection Kit

Bordetella pertussis

Nasopharyngeal (NP) swab or
NP aspirate, preferred

Sputum (Including induced), or Tracheal aspirates are acceptable


Bordetella pertussis BP collection kit; Kit order# 390052

Submission and Collection Notes


Follow the instructions found in the Bordetella pertussis BP Kit Instruction Sheet.


Complete all fields of the General Test Requisition Form.  Include, the patient’s full name, date of birth, Health Card Number (must match the specimen label), enter the name of the test requested, source of specimen, date of onset, date of collection, outbreak/investigation number, physician name and address, and clinical diagnosis.


Label the specimen container(s) with the patient’s first and last name, date of collection, and one other unique identifier such as the patient’s date of birth or Health Card Number. For additional information see: Criteria for Acceptance of Patient Specimens. Failure to provide this information may result in rejection or testing delay.


Bordetella pertussis BP collection kit is the only acceptable transport medium. Do not use Multi-organism transport medium or other molecular transport medium.

Timing of Specimen Collection

Specimens should be collected during the acute phase of illness.

Storage and Transport

Specimens should be stored at 2-8°C following collection and shipped to PHO’s laboratory on ice packs. Maximum storage/transit time at 2-8°C is within 5 days of collection.

All clinical specimens must be shipped in accordance to the Transportation of Dangerous Good Act

Special Instructions

For samples that are part of an outbreak ensure the Public Health Unit assigned outbreak number is indicated on the requisition. For any cluster investigation, please contact PHO’s laboratory Customer Service at 416-235-6556/1-877-604-4567 regarding assigning an investigation number prior to sample submission

Requisitions and Kit Ordering

Test Frequency and Turnaround Time (TAT)

Bordetella PCR testing is performed daily Monday to Friday at PHO’s Laboratory- Toronto and Kingston.

Turnaround time is up to 4 days from receipt by PHO’s laboratory.

Stat and Critical Specimens Testing

STAT testing is not available but if urgent testing is required (i.e. critical samples) notify PHO’s laboratory Customer Service to ensure the sample is on the next available run.

Test Methods

Bordetella - respiratory specimens are tested by a real-time Polymerase Chain Reaction (qPCR) test that detects Bordetella pertussis, Bordetella parapertussis and Bordetella holmesii. The qPCR is >99% specific, and more sensitive than routine culture.


The following table provides possible test results with associated interpretations:







Positive for (Genus species)

Positive for (Genus species)


Indeterminate for (Genus species)

Indeterminate for (Genus species)

A low level of DNA was detected in this sample.  The clinical significance of this is not known and should be interpreted in combination with available clinical and epidemiological information.  Consider collecting a second nasopharyngeal swab for repeat PCR testing if clinical illness is compatible with pertussis.



Result not available due to presence of inhibitory substance in specimen. Please resubmit.


Results are reported to the physician, authorized health care provider (General O. Reg 45/22, s.18) or submitter as indicated on the requisition.

Positive specimens for Bordetella pertussis are reported to the Medical Officer of Health as per the Ontario Health Protection and Promotion Act.


  1. U.S. Department of Health and Human Services, Centers for Disease Control and Prevention. Manual for the Surveillance of Vaccine-Preventable Diseases: Chapter 10 – Pertussis.
  2. U.S. Department of Health and Human Services, Centers for Disease Control and Prevention. Best practices for healthcare professionals on the use of polymerase chain reaction (PCR) for diagnosing pertussis.
Updated 11 March 2024