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EPIC CODE: LAB2303 Bordetella pertussis and Bordetella parapertussis, Molecular Detection, PCR, Varies

Additional Codes

Sunquest: PCRBPM
Mayo:        BPRP

Reporting Name

Bordetella PCR

Useful For

Preferred diagnostic test for the detection of Bordetella pertussis or Bordetella parapertussis

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Specimen Type


Specimen Required

Necessary Information

Specimen source is required.

Specimen Required

The high sensitivity of amplification by PCR requires the specimen to be processed in an environment in which contamination of the specimen by Bordetella pertussis or Bordetella parapertussis DNA is unlikely.


Submit only 1 of the following specimens:




Nasopharyngeal Swab (Rayon Mini-Tip Swab) (T515)

Specimen Type: Nasopharyngeal swab

Container/Tube: Rayon swab with an aluminum shaft placed in transport medium such as a green-top nasopharyngeal swab (rayon mini-tip) with Stuart's media (no charcoal) (T515), or Stuart's with charcoal, or Amies with or without charcoal (Transwab Nasopharyngeal with Charcoal System).

Additional Information:

1. Swab transport containers without charcoal must contain a pledget saturated with either Stuart's or Amies liquid media. Clear semi-solid/solid media is gel and will be rejected.

2. Other swab or media types may be inhibitory to PCR testing and will be rejected.



Specimen Type: Nasopharyngeal (not throat) aspirate/wash or nasal aspirate/wash

Container/Tube: Sterile container with a screw top cap (no transport media)

Specimen Volume: Entire collection

Specimen Minimum Volume

0.5 mL

Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Refrigerated (preferred) 7 days
  Ambient  7 days
  Frozen  7 days

Reference Values

Not applicable

Day(s) Performed

Monday through Friday, Sunday

Test Classification

This test was developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the US Food and Drug Administration.

CPT Code Information

87798 x 2

LOINC Code Information

Test ID Test Order Name Order LOINC Value
BPRP Bordetella PCR 78921-4


Result ID Test Result Name Result LOINC Value
SRC54 Specimen source 31208-2
34994 Bordetella pertussis PCR 43913-3
34995 Bordetella parapertussis PCR 42588-4

Clinical Information

Bordetella pertussis is the highly contagious etiological agent of pertussis or whooping cough. Bordetella parapertussis causes a similar, but generally less severe illness. Despite vaccination efforts, B pertussis remains common in the United States, underscoring the need for effective diagnostic tests. In the United States, pertussis is most common in the late summer months. Pertussis vaccination does not prevent B parapertussis infection, which generally occurs in a younger age group than disease caused by B pertussis. Diagnosis of pertussis is based on having a high clinical index of suspicion for the infection, along with confirmation by laboratory testing. Laboratory testing methods include nucleic acid amplification tests (eg, PCR), serology, culture and direct fluorescent antibody testing. Culture and direct fluorescent antibody testing are limited by low sensitivity, rendering nucleic acid amplification tests and serology the tests of choice.


The Centers for Disease Control and Prevention recommends PCR testing for patients suspected of having acute pertussis. B pertussis PCR detects roughly twice as many cases as culture. B pertussis DNA can be detected up to 4 weeks, or longer (up to 8 weeks in our experience),(1) after symptom onset. However, over time, the amount of B pertussis and B parapertussis DNA will diminish, rendering the assay less sensitive. A serologic response to B pertussis is typically mounted by 2 weeks following infection and, therefore, detection of IgG-class antibodies to pertussis toxin (PT), which is only produced by B pertussis, can be a useful adjunct for diagnosis at later stages of illness at a time when the amount of B pertussis may be below the limit of detection of the PCR assay.


A positive result indicates the presence of DNA from Bordetella pertussis or B parapertussis. In some cases, a patient may test positive for both B pertussis and B parapertussis. Cross-reactivity with B holmesii and B bronchiseptica may occur with the B pertussis assay (see Cautions).


A negative result indicates the absence of detectable B pertussis and B parapertussis DNA in the specimen but does not negate the presence of organism or active or recent disease (known inhibition rate of <1%) and may occur due to inhibition of PCR, sequence variability underlying primers and/or probes, or the presence of B pertussis or B parapertussis in quantities less than the limit of detection of the assay. Additionally, patients presenting late after symptom onset may test negative; in such cases, testing for B pertussis antibody, IgG, in serum may be considered.


Cross-reactivity with Bordetella holmesii may occur with the B pertussis PCR assay. The prevalence of B holmesii is relatively low, with positivity in <1% of nasopharyngeal swabs.(2) Please note that B holmesii has been associated with pertussis-like symptoms.(2)


Cross-reactivity of the B pertussis assay has been demonstrated with a limited number of Bordetella bronchiseptica isolates. The prevalence of the insertion sequence target, IS481, has been reported to be between 1% and 5% in B bronchiseptica isolates. 


This assay is not recommended for screening asymptomatic individuals who may carry B pertussis or parapertussis.


This assay is not recommended for follow up of patients previously diagnosed with pertussis (ie, as a test of cure).


Some B pertussis acellular vaccines (ie, Pentacel, Daptacel, Adacel) contain PCR detectable DNA. Contamination of specimens with vaccine can cause false-positive B pertussis PCR results. Specimens should not be collected or processed in areas that are exposed to B pertussis vaccine material.

Supportive Data

The assay targets the multicopy insertion gene sequences, IS481 and IS1001, of Bordetella pertussis and Bordetella parapertussis, respectively. This assay was previously performed using analyte specific reagents from Roche Diagnostics(3); these reagents are no longer available. The assay was revalidated using probes and primers with the same sequence, but provided by an alternate vendor. Performance of the new assay was then compared to the previous assay, which used the Roche analyte specific reagents, using 374 nasopharyngeal swabs and washings submitted for Bordetella testing. Fifty-four specimens were positive (48 Bordetella pertussis and 6 Bordetella parapertussis) and 314 specimens were negative by both assays. Five nasopharyngeal specimens were positive for Bordetella pertussis or Bordetella parapertussis by the new assay and negative by the old assay. One nasopharyngeal specimen was positive for Bordetella pertussis by the old assay but negative by the new assay. Overall, there was 98% (368/374) agreement between the 2 assays. Bordetella holmesii cannot be distinguished from Bordetella pertussis by the assay. The analytical sensitivity of the assay is 1 target/mcL for nasopharyngeal swabs and 10 targets/mcL for nasopharyngeal wash/aspirates.

Clinical Reference

1. Theofiles AG, Cunningham SA, Chia N, et al: Pertussis outbreak, southeastern Minnesota, 2012. Mayo Clin Proc 2014 Oct;89(10):1378-1388

2. Guthrie JL, Robertson AV, Tang P, et al: Novel duplex real-time PCR assay detects Bordetella holmesii in specimens from patients with pertussis-like symptoms in Ontario, Canada. J Clin Microbiol 2010;48:1435-1437

3. Sloan LM, Hopkins MK, Mitchell PS, et al: Multiplex LightCycler PCR assay for detection and differentiation of Bordetella pertussis and Bordetella parapertussis in nasopharyngeal specimens. J Clin Microbiol 2002;40:96-100

Method Description

The LightCycler instrument platform amplifies and monitors the development of target nucleic acid sequences by fluorescence after each cycle of PCR. The automated detection of amplified products is based on the fluorescence resonance energy transfer (FRET) principle. The assay uses the repetitive (50-100 copies) insertion sequence (IS481) found in Bordetella pertussis and the repetitive (35-50 copies) insertion sequence (IS1001) found in B parapertussis as targets. Detection and differentiation of Bordetella targets is performed through melting curve analysis. The probes were designed to obtain a 10 degree C temperature shift between B pertussis and B parapertussis that is seen in the melting curve analysis. Analysis of the PCR amplification and probe melting curves is accomplished through the use of the LightCycler software.(Sloan LM, Hopkins MK, Mitchell PS, et al: Multiplex LightCycler PCR assay for detection and differentiation of Bordetella pertussis and Bordetella parapertussis in nasopharyngeal specimens. J Clin Microbiol 2002;40:96-100)

Report Available

1 to 3 days

Specimen Retention Time

3 days

Reject Due To

Other Nose, nasal, or throat swab; calcium alginate or cotton-tipped swab; swab sent in gel transport medium, viral/universal transport medium, or Regan Lowe media; ESwab; swabs with solid plastic shaft; dry swab

NY State Approved


Method Name

Polymerase Chain Reaction (PCR)/DNA Probe Hybridization

Includes DNA preparation from specimen, PCR amplification, and hybridization


If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.