An evaluation of the level of agreement in XXXX species identification in three United States laboratories during a period of increased pertussis.

@entity7320 @entity12024 @entity34168
UNASSIGNED: While PCR is the most common method used for detecting @entity7320 in the US, most laboratories use insertion sequence 481 (IS481), which is not specific for @entity7320 ; therefore, the relative contribution of other @entity34168 species is not understood. The objectives of this study were to evaluate the proportion of other @entity34168 spp. misidentified as @entity7320 during a period of increased pertussis incidence, determine the level of agreement in @entity34168 species detection between US commercial laboratories and CDC, and assess the relative diagnostic sensitivity of CDC's PCR assay when using a different PCR master mix. Specimens collected between May 2012-2013 were tested at two US commercial laboratories for @entity7320 and @entity34168 detection. Every fifth specimen positive for IS481 and/or IS1001 with Ct values  <=35 was sent to CDC for PCR testing that identifies @entity34168 species. Specimens with CDC PCR indeterminate or negative results were tested using an alternate PCR master mix. Of 755 specimens, there was agreement in species identification for 83.4% (n=630). Of those with different identifications (n=125), 79.2% (n=99) were identified as indeterminate @entity7320 at CDC. Overall, 0.66% (n=5) of the specimens were identified as B. holmesii or @entity12024 at CDC. Of 115 specimens with indeterminate or negative results, 46.1% (n=53) were @entity7320 positive when tested by an alternate master mix, suggesting possible increase in assay sensitivity. This study demonstrates good agreement between the two US commercial laboratories and CDC and little misidentification of @entity34168 species during the 2012 US epidemic.
