Pertussis specimen collection

Collecting a pertussis specimen

We had a bit of confusion of pertussis collection this weekend, so I put together a brief overview on pertussis with focus on nasopharyngeal specimen collection for pertussis.

What is pertussis?

It is a respiratory tract infection caused by a bacterium Bordetella pertussis. Young children are the primary suffers from this vaccine preventable disease. It is also known as “Whooping cough”

Often mistaken for a “flu” or bronchitis it can last for up to 10 weeks during which the patient has a severe intractable cough that often ends in vomiting, sometimes nearly passing out. In children it can cause severe breathing difficulty, seizures and occasionally death.

First described in 1906 it is a very common disease of the 20th century and a major cause of childhood death and debility.

It can be highly contagious, especially spreading quickly in groups, households where there is poor vaccination coverage. This has unfortunately been the trend as many families have chosen not to vaccinate their children on misguided fears that their children are harmed by vaccines. See my posts on vaccines for more information. As a result many communities are seeing rising rates of Pertussis.

California saw the highest number of cases (4461) or 11.4 cases per 100,000 population in 2010, the highest number since 1955.


The introduction of vaccination saw a 98% drop in the number of cases but a gradual rise since the 1990s creating concern.

case graph


How is it spread?

  • From human to human- there are no animal or environmental reservoirs– If all humans are immune then there is no one reservoir from which to get the disease
  • Coughing and sneezing can transmit this bacteria
  • There is no seasonal pattern

Who should be screened for pertussis?

  • Anyone with a cough lasting greater than two weeks
  • Anyone with a prolonged cough regardless of immunization history
  • Cough that ends with vomiting

How is a specimen collected?

A nasopharyngeal swab is collected for PCR assay

  • It is a special swab, made of aluminum with a nylon tip. Traditional cotton tip swabs interfere with the test
  • A special transport media is needed- call the lab for it
  • Wear a surgical mask, protective eye wear and gloves while collecting the specimen
  • Place the patients head on the bed pillow or against a wall so that they do not move backwards
  • The swab will go straight backwards like placing an NG tube, it should go the distance between the nostril and the ear into the throat. This is different from a nasal swab for MRSA or influenza
  • The swab is rotated for a bout 5–10 seconds to get enough epithelial cells on it
  • Remove the swab and place it in the transport media and sent it to lab


Here is a video on specimen collection


ALL contacts of the case regardless of age or immunization status are given prophylaxis for 7 days with a macrolide such as azithromycin.



  • Children with DTaP
  • Adults under 65 who have close contact with infants under 12 months should receive Tdap
  • Healthcare workers under 65 who have direct contact patient contact should get a dose of Tdap

adult vaccine