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PCR testing
PCR and Pertussis
Journal of Clinical Microbiology, August 2002, p. 2801-2805, Vol. 40, No. 8
Issues Associated with and Recommendations for Using PCR To Detect Outbreaks of Pertussis -- Lievano et al. 40 (8): 2801 -- J..

The results of epidemiological and laboratory studies of these two outbreaks of cough illness illustrate the potential problems and consequences of relying exclusively on a PCR test to confirm pertussis. We confirmed by culture that pertussis was circulating in the community during these outbreaks. However, a significant epidemiological feature of one of these outbreaks was that unvaccinated children exposed to PCR-confirmed cases in day care centers did not become ill, whereas fully vaccinated children did. Thus, B. pertussis may not have been the primary or only cause of these outbreaks. Moreover, a positive PCR test due to transient colonization with the agent (15, 18, 20, 21, 22, 27, 28) or a falsely positive test could lead to misdiagnosis of pertussis in persons with cough illness due to other etiologies. Indeed, our results suggested that diagnostic reliance on a PCR assay for B. pertussis DNA together with probable false-positive test results likely overestimated the role of pertussis in these outbreaks.

The PCR for B. pertussis DNA was used by a private laboratory to confirm the majority of cases in these two outbreaks (93% in outbreak 1 and 83% in outbreak 2). When compared with testing at the state reference laboratory, the majority of the B. pertussis PCR results from the private laboratory were not substantiated (Table 2). Moreover, during proficiency testing of 10 blinded specimens, the private laboratory reported false-positive results for one-third of the non-B. pertussis specimens. After changing primers towards the end of the second outbreak, the private laboratory retested the 10 samples and correctly identified all 10 specimens. This suggested that DNA contamination may have caused an uncertain number of false-positive results during the two outbreaks. PCR false-positive results can be due to DNA contamination, which may have been exacerbated by the larger-than-normal volume of samples processed during the outbreaks.

The overdiagnosis of pertussis during these outbreaks had important public health consequences. These included the unnecessary treatment of asymptomatic individuals with a positive PCR result for B. pertussis DNA who may not have harbored B. pertussis, as well as inappropriate chemoprophylaxis for their close contacts. In outbreak 2, more than 1,100 persons in close contact with an individual with a positive PCR result for B. pertussis DNA were advised to take a 2-week course of chemoprophylaxis with a macrolide antibiotic. Staff at doctor offices, hospitals, and county health departments were overwhelmed with testing demands and follow-up of individuals who tested PCR positive for B. pertussis DNA. During outbreak 2, 10 percent of the 500-member staff of a community hospital, many of whom were asymptomatic, were furloughed for 5 days as a result of positive PCR tests.

Read rest of article here:
Issues Associated with and Recommendations for Using PCR To Detect Outbreaks of Pertussis -- Lievano et al. 40 (8): 2801 -- J..

Note the wide difference in PCR test results between private and state labs.
TABLE 2. Additional laboratory studies, pertussis outbreaks, New York, September 15, 1998 to November 14, 1999

Laboratory study nc Results of PCR for B. pertussis DNA

Private laboratory NYSDOH/WC

PCRa 33 20 PCR positive 8 PCR positive
13 PCR negative 25 PCR negative
QA testb 10 4 PCR positive for B. pertussis DNA 4 PCR positive for B. pertussis DNA
2 nonpertussis specimens PCR positive 6 nonpertussis specimens PCR negative
4 nonpertussis PCR negative

a PCR for B. pertussis DNA was performed by the private laboratory and NYSDOH/WC pertussis laboratory on dual samples from the same patients.

b Specimens were prepared by NYSHD/WC Proficiency Testing Laboratory (four with B. pertussis) and blind PCR tested by the private laboratory and NYSDH/WC pertussis laboratory.

c n, no. of samples studied.