Evaluation of Level of Agreement in Bordetella Species Identification in Three U.S. Laboratories during a Period of Increased Pertussis

While PCR is the most commonmethod used for detecting Bordetella pertussis in the United States, most laboratories use inser-tion sequence 481 (IS481), which is not specific for B. pertussis; therefore, the relative contribution of other Bordetella species is not understood. The objectives of this study were to evaluate the proportion of other Bordetella species misidentified as B. per-tussis during a period of increased pertussis incidence, determine the level of agreement in Bordetella species detection between U.S. commercial laboratories and the CDC, and assess the relative diagnostic sensitivity of CDC’s PCR assay when using a differ-ent PCRmaster mix. Specimens collected betweenMay 2012 andMay 2013 were tested at two U.S. commercial laboratories for B. pertussis and B. parapertussis detection. Every fifth specimen positive for IS481 and/or IS1001with cycle threshold (CT) values of <35 was sent to CDC for PCR testing that identifies Bordetella species. Specimens with indeterminate or negative results in the CDC PCRwere tested using an alternate PCRmaster mix. Of 755 specimens, there was agreement in species identification for 83.4 % (n 630). Of the specimens with different identifications (n 125), 79.2 % (n 99) were identified as indeterminate B. pertussis at CDC. Overall, 0.66 % (n 5) of the specimens were identified as B. holmesii or B. bronchiseptica at CDC. Of 115 specimens with indeterminate or negative results, 46.1 % (n 53) were B. pertussis positive when tested by an alternate master mix, suggesting a possible increase in assay sensitivity. This study demonstrates good agreement between the two U.S. commer-cial laboratories and CDC and little misidentification of Bordetella species during the 2012 U.S. epidemic. Pertussis, commonly known as whooping cough, is the mostpoorly controlled vaccine-preventable bacterial disease in th