Pseudo-Outbreak of Pertussis Attributable to False Positive PCR Results From Clinic Contamination of Specimens

Background: Verifying pertussis outbreaks is difficult because clinical diagnosis is challenging and laboratory testing is suboptimal. Exclusive use of polymerase chain reaction (PCR) increases the likelihood that false positives will prompt unnecessary or ineffective interventions and response. We investigated a prolonged pertussis outbreak, characterized by atypical cases confirmed only by PCR, which persisted despite high vaccine coverage and routine control measures.

Objectives: The investigation objectives were to: a) characterize the outbreak, (b) determine the etiological agents and (c) advise on control measures.

Methods: We conducted case ascertainment using modified CSTE case definitions, and performed confirmatory pertussis testing (PCR, culture, serology) and alternate pathogen testing.  We observed clinic practices, sampled clinics for environmental pertussis DNA, and reviewed laboratory PCR quality indicators to evaluate the potential for false positives.

Results: Between November 2008 and September 2009, 125 cases were reported, of which 92 (74%) were PCR positive. In cases occurring after April (n=79; 63%), we observed a shift to fewer classic pertussis symptoms (98% to 63%; p<0.01), smaller amounts of detected pertussis DNA (mean PCR cycle threshold value: 33.7 to 40.8, p<0.01), and an increase in the proportion of PCR positive results among all tests (6% to 36%; p<0.01). Cultures and serology for Bordetella pertussis were negative, but evidence of other common respiratory pathogens was detected.  We identified factors which likely resulted in specimen contamination at the point of collection and subsequent false positives: clinic contamination with pertussis DNA from vaccine and/or true cases; lapses in appropriate specimen handling; use of liquid transport media; and lack of clinically relevant PCR interpretation criteria.

Conclusions: Our results suggest a multi-factorial “pseudo” pertussis outbreak. Based on these findings, recommended changes in clinic specimen collection, cleaning protocols and reporting of PCR results were implemented. Cautious interpretation of epidemiologic, clinical and laboratory data should inform outbreak responses.