Genomic characterization of Bordetella pertussis in South Africa, 2015–2019

Fahima Moosa; Mignon du Plessis; Michael R. Weigand; Yanhui Peng; Dineo Mogale; Linda de Gouveia; Marta C. Nunes; Shabir A. Madhi; Heather J. Zar; Gary Reubenson; Arshad Ismail; M. Lucia Tondella; Cheryl Cohen; Sibongile Walaza; Anne von Gottberg; Nicole Wolter

doi:10.1099/mgen.0.001162

Volume 9, Issue 12

Research Article

Open Access

Genomic characterization of Bordetella pertussis in South Africa, 2015–2019

Fahima Moosa^1,2, Mignon du Plessis^1,2, Michael R. Weigand³, Yanhui Peng³, Dineo Mogale¹, Linda de Gouveia¹, Marta C. Nunes⁴, Shabir A. Madhi^5,6, Heather J. Zar⁷, Gary Reubenson⁸, Arshad Ismail^9,10,11, M. Lucia Tondella³, Cheryl Cohen^1,12, Sibongile Walaza^1,12, Anne von Gottberg^1,2 and Nicole Wolter^1,2
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Affiliations: ¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa ² School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa ³ Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA ⁴ Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa ⁵ South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa ⁶ Wits Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa ⁷ Department of Pediatrics and Child Health, Red Cross Children’s Hospital, Cape Town, South Africa; MRC Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa ⁸ Rahima Moosa Mother & Child Hospital, Department of Pediatrics & Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa ⁹ Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa ¹⁰ Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa ¹¹ Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa ¹² School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
*Correspondence: Fahima Moosa, [email protected]
Published: 20 December 2023 https://doi.org/10.1099/mgen.0.001162

Abstract

Pertussis remains a public health concern in South Africa, with an increase in reported cases and outbreaks in recent years. Whole genome sequencing was performed on 32 Bordetella pertussis isolates sourced from three different surveillance programmes in South Africa between 2015 and 2019. Genome sequences were characterized using multilocus sequence typing, vaccine antigen genes (ptxP, ptxA, ptxB, prn and fimH) and overall genome structure. All isolates were sequence type 2 and harboured the pertussis toxin promoter allele ptxP3. The dominant genotype was ptxP3-ptxA1-ptxB2-prn2-fimH2 (31/32, 96.9 %), with no pertactin-deficient or other mutations in vaccine antigen genes identified. Amongst 21 isolates yielding closed genome assemblies, eight distinct genome structures were detected, with 61.9 % (13/21) of the isolates exhibiting three predominant structures. Increases in case numbers are probably not due to evolutionary changes in the genome but possibly due to other factors such as the cyclical nature of B. pertussis disease, waning immunity due to the use of acellular vaccines and/or population immunity gaps.

Received: 29/09/2023
Accepted: 04/12/2023
Published Online: 20/12/2023

Keyword(s): B. pertussis , genome structural characterization , Illumina sequencing , PacBio sequencing , vaccine antigen genes and whole genome sequencing

Funding

This study was supported by the:

National Institutes of Health (Award D43TW011255)
- Principle Award Recipient: Annevon Gottberg
Sanofi Pasteur (Award PER00059)
- Principle Award Recipient: FahimaMoosa
Centers for Disease Control and Prevention (Award 5U51IP000155)
- Principle Award Recipient: CherylCohen

This is an open-access article distributed under the terms of the Creative Commons Attribution License.

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Genomic characterization of Bordetella pertussis in South Africa, 2015–2019

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Volume 9, Issue 12

Research Article

Open Access

Genomic characterization of Bordetella pertussis in South Africa, 2015–2019

Abstract

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