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A multitarget real-time PCR assay with three targets, including insertion sequence481 (IS481 ), IS1001 , and an IS1001 -like element, as well as pertussis toxin subunit S1 (ptxS1 ), for the detection ofBordetella species was evaluated during a pertussis outbreak. The sensitivity and specificity were 77 and 88% (PCR) and 66 and 100% (culture), respectively. All patients with an IS481 CT of &lt;30 also tested positive byptxS1 assay and were clinical pertussis cases. No patients with IS481 CT values of ≥40 tested positive by culture. Therefore, we recommend that culture be performed only for specimens with IS481 CT values of 30 ≤CT &lt;40.

Evaluation of a Multitarget Real-Time PCR Assay for Detection of Bordetella Species during a Pertussis Outbreak in New Hampshire in 2011