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. 2019 Mar 21;19(1):276.
doi: 10.1186/s12879-019-3869-7.

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

Fahima Moosa  1 , Mignon du Plessis  2   3 , Nicole Wolter  2   3 , Maimuna Carrim  2 , Cheryl Cohen  2   3 , Claire von Mollendorf  2   3 , Sibongile Walaza  2   3 , Stefano Tempia  2   4 , Halima Dawood  5 , Ebrahim Variava  3   6 , Anne von Gottberg  2   3
Affiliations

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

Fahima Moosa et al. BMC Infect Dis. .

Abstract

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 IS481, pIS1001, hIS1001 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 (Ct) value cut-offs, IS481 positive cases were classified as confirmed (Ct < 35) or possible (Ct 35-39) pertussis disease.

Results: Among 12,922 samples, 146 (1.1%) were IS481 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 IS481 positive specimens could be considered as B. pertussis infection, and potentially pertussis disease with supportive clinical information.

Keywords: Attributable fraction; Bordetella pertussis; Confirmed-pertussis; Influenza-like illness (ILI); Possible-pertussis; Real-time PCR; Severe respiratory illness; South Africa; Surveillance.

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Conflict of interest statement

Ethics approval and consent to participate

Ethics for SRI (M081042) and ILI (M120133) surveillance and B. pertussis testing were approved by the University of the Witwatersrand (M130260) and the University of KwaZulu Natal (BF081/12), South Africa. Written informed consent was obtained from all individuals enrolled into the study by trained surveillance officers upon interview. Surveillance officers approached adult patients directly to obtain consent. Parents, legal guardians or primary care giver were approached for cases who were minors; in addition, where a minor was old enough to understand, assent was obtained.

Consent for publication

Not applicable.

Competing interests

Halima Dawood has received honoraria/travel grants from Pfizer-South Africa, MSD329 South Africa and Mylan-South Africa. Anne von Gottberg has previously received grants from the US Centers for Disease Control and Prevention and Pfizer-South Africa. All other authors declare that they have no commercial or other association that may pose a conflict of interest.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Flow diagram depicting breakdown of individuals enrolled, specimens collected and tested, and B. pertussis prevalence for severe respiratory (SRI) and influenza-like illness (ILI) surveillance, and controls, South Africa, June 2012 – May 2016. NP: nasopharyngeal aspirates from children < 5 years of age and combined nasopharyngeal and oropharyngeal swabs from individuals aged ≥5 years. *Confirmed = positive for B. pertussis with IS481 Ct < 35; Possible = positive for B. pertussis with IS481 35 ≥ Ct ≤ 39
Fig. 2
Fig. 2
Distribution of real-time PCR IS481 Ct values for confirmed (n = 90) and possible (n = 56) pertussis cases, by surveillance population, South Africa, June 2012 – May 2016. SRI = severe respiratory illness; ILI = influenza-like illness
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