Molecular methods to diagnose pertussis: a case of confusion with Bordetella bronchiseptica

ABSTRACT Background Prompt identification of clinically relevant Bordetella (e.g., B. pertussis and B. parapertussis ) is critical for both treatment and isolation decisions to mitigate transmission among close contacts. Due to the organisms’ fastidious growth requirements, nucleic acid amplification tests (NAATs) have become a mainstay for identification and differentiation of B. pertussis and B. parapertussis . For NAATs detecting these closely related species, the nucleic acid target dictates assay sensitivity and specificity and varies between commercially available platforms. Case Summary This case report describes a child’s course of cough and post-tussive emesis following bone marrow transplant for an underlying immunodeficiency. While an initial BioFire Respiratory Panel 2.1 (BioFire Diagnostics, LLC, Salt Lake City, UT, USA) detected B. pertussis DNA, a subsequent maxillary sinus culture grew B. bronchiseptica , identified by MALDI-TOF MS and whole-genome sequencing. Furthermore, on two subsequent occasions, nasopharyngeal specimens were positive for B. pertussis on the BioFire RP2.1; however, they were negative for B. pertussis on the DiaSorin Molecular Simplexa Bordetella Direct (DiaSorin Molecular LLC, Cypress, CA, USA). These seemingly disparate results can be explained by molecular target differences on the respective platforms and a rare instance of cross-reactivity with the genetic target for B. pertussis ( ptxP ) in an isolate of B. bronchiseptica . Conclusion This case, where the presence of ptxP was confirmed by whole genome sequencing in an isolate of B. bronchiseptica , highlights a caveat to the molecular diagnosis of pertussis and emphasizes the importance of understanding gene targets to interpret results when false positive detections are suspected.