What is the recommended method for testing for pertussis (whooping cough)?

How to Test for Pertussis

The CDC endorses only two diagnostic tests for pertussis: nasopharyngeal culture (100% specific) and PCR testing, but PCR should only be used when the patient meets the clinical case definition of cough lasting >2 weeks with paroxysms, inspiratory "whoop," or post-tussive vomiting. 1

Clinical Case Definition Required Before Testing

Before ordering any laboratory test, confirm the patient meets clinical criteria 1:

• Cough persisting >2 weeks without another apparent cause 1
• Plus at least one of the following:
  • Paroxysms of coughing 1
  • Post-tussive vomiting 1
  • Inspiratory whooping sound 1

Recommended Testing Algorithm

First-Line Testing: Nasopharyngeal Culture

• Collect nasopharyngeal aspirate or use a Dacron swab of the nasopharynx for culture as the initial confirmatory test 1
• Culture is 100% specific but has variable sensitivity (30-60% in practice) 1
• Critical timing consideration: Begin testing as early as possible in the illness course 1
• Sensitivity drops dramatically after 2+ weeks of cough (only 1-3% sensitive after 3 weeks) 1
• Sensitivity also decreases after antimicrobial treatment or previous pertussis vaccination 1
• Results require 1-2 weeks for definitive negative results 1
• Despite limitations, culture remains essential for antimicrobial susceptibility testing and molecular subtyping 1

PCR Testing: When and How to Use

• PCR is endorsed by the CDC only when the clinical case definition is also met 2, 1
• PCR has increased sensitivity (80-100%) and provides results within 24-48 hours 1
• PCR is 2-3 times more likely than culture to detect B. pertussis when classic symptoms are present 1
• Use nasopharyngeal specimens collected with a Dacron swab or nasopharyngeal aspirate 1
• PCR remains superior even after antibiotic initiation (after 2 days of antibiotics, culture sensitivity drops dramatically while PCR maintains sensitivity) 1

Critical Pitfall: PCR Specificity Issues

The lack of FDA-licensed PCR test kits and standardized protocols means analytical sensitivity, accuracy, and quality control vary widely among laboratories 2. Approximately 100 different PCR protocols exist with varying DNA purification techniques, primers, and detection methods 2. Use of PCR tests with low specificity can result in false-positives leading to unnecessary treatment and inappropriate chemoprophylaxis of contacts 2. This is why the CDC requires the clinical case definition be met before using PCR 2.

Tests NOT Endorsed by CDC

Serology

• CDC guidelines for laboratory confirmation do not include serologic testing 2
• Single-sample serology lacks standardization and cannot differentiate between recent disease, remote disease, or vaccination 2, 3
• Paired sera showing fourfold rise in titers can confirm infection retrospectively but results become available too late (weeks) to guide acute management 2, 1, 3
• No FDA-licensed serologic assays exist for routine pertussis diagnosis in the United States 2, 3

Direct Immunofluorescence (DFA)

• Not mentioned in CDC guidelines and has poor sensitivity and specificity in research studies 4, 5

Treatment Considerations

Do not delay treatment while awaiting test results 1. Early treatment within the first 2 weeks will rapidly clear B. pertussis from the nasopharynx and decrease coughing paroxysms 1. Patients should be isolated for 5 days after starting antibiotic therapy 1.

Confirmed Diagnosis Criteria

A confirmed diagnosis requires one of the following 1:

• Isolation of B. pertussis from nasopharyngeal culture
• Clinical case with PCR confirmation
• Clinical case with epidemiologic linkage to a confirmed case