Challenges and clinical relevance of molecular detection of Bordetella pertussis in South Africa

Background We assessed the utility of a multi-target, real-time PCR assay for Bordetella pertussis detection and diagnosis in patients with severe respiratory illness (SRI), influenza-like illness (ILI), and asymptomatic controls. Methods Real-time PCR detection of IS 481 , pIS 1001 , hIS 1001 and ptxS1 was performed on nasopharyngeal specimens (SRI, ILI and controls) and induced sputum (SRI) collected from June 2012 to May 2016 through respiratory illness surveillance. Using PCR cycle threshold (C t ) value cut-offs, IS 481 positive cases were classified as confirmed (C t < 35) or possible (C t 35–39) pertussis disease. Results Among 12,922 samples, 146 (1.1%) were IS 481 positive of which 62% (90/146) were classified as confirmed. The attributable fraction (AF) was 92.2% (95% CI, 65.6 to 98.2%) and 90.5% (95% CI, 57.5 to 97.9%) amongst SRI and ILI PCR-confirmed pertussis cases, respectively. Amongst possible pertussis cases, AF was 36.9% (95% CI, − 142.3 to 83.6%) and 67.5% (95% CI, − 30.6 to 91.9%) in the SRI and ILI groups, respectively. Conclusion All IS 481 positive specimens could be considered as B. pertussis infection, and potentially pertussis disease with supportive clinical information.