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

Moosa F1, du Plessis M2,3, Wolter N2,3, Carrim M2, Cohen C2,3, von Mollendorf C2,3, Walaza S2,3, Tempia S2,4, Dawood H5, Variava E3,6, von Gottberg A2,3.

Author information

1

Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa. fahimam@nicd.ac.za.

2

Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Private Bag X4, Sandringham, Gauteng, 2131, South Africa.

3

University of the Witwatersrand, Johannesburg, South Africa.

4

Centers for Disease Control and Prevention, Atlanta, GA, USA.

5

Pietermaritzburg Metropolitan Hospitals, KwaZulu-Natal, and Caprisa, University of KwaZulu-Natal, Durban, South Africa.

6

Klerksdorp-Tshepong Hospital, North West Province, Klerksdorp, South Africa.

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

PMID:

 

30898099

 

PMCID:

 

PMC6429695

 

DOI:

 

10.1186/s12879-019-3869-7

[Indexed for MEDLINE] 

Free PMC Article

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