A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV-Reference-Cited by-同舟云学术

A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine use of PCV

Published:2022-04-06 Issue:4 Volume:8 Page:
ISSN:2057-5858
Container-title:Microbial Genomics
language:en
Short-container-title:

Author:

Ndlangisa Kedibone M.¹^ORCID,du Plessis Mignon²¹,Lo Stephanie³^ORCID,de Gouveia Linda¹,Chaguza Chrispin³^ORCID,Antonio Martin⁴,Kwambana-Adams Brenda⁵⁶^ORCID,Cornick Jennifer⁷,Everett Dean B.⁸⁷,Dagan Ron⁹,Hawkins Paulina A.¹⁰¹¹,Beall Bernard¹⁰^ORCID,Corso Alejandra¹²^ORCID,Grassi Almeida Samanta Cristine¹³^ORCID,Ochoa Theresa J.¹⁴,Obaro Stephen¹⁵^ORCID,Shakoor Sadia¹⁶^ORCID,Donkor Eric S.¹⁷,Gladstone Rebecca A.³^ORCID,Ho Pak Leung¹⁸^ORCID,Paragi Metka¹⁹,Doiphode Sanjay²⁰,Srifuengfung Somporn²¹^ORCID,Ford Rebecca²²^ORCID,Moïsi Jennifer²³^ORCID,Saha Samir K.²⁴,Bigogo Godfrey²⁵,Sigauque Betuel²⁶,Eser Özgen Köseoglu²⁷^ORCID,Elmdaghri Naima²⁸,Titov Leonid²⁹,Turner Paul³⁰^ORCID,Kumar K. L. Ravi³¹,Kandasamy Rama³²,Egorova Ekaterina³³^ORCID,IP Margaret³⁴^ORCID,Breiman Robert F.³⁵,Klugman Keith P.³⁶²,McGee Lesley¹⁰,Bentley Stephen D.³,von Gottberg Anne²¹^ORCID,

Affiliation:

1. National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service, Johannesburg, South Africa

2. School of Pathology, University of the Witwatersrand, Johannesburg, South Africa

3. Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK

4. WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia

5. West Africa Partnerships and Strategies, Medical Research Council Unit The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, Gambia

6. NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK

7. Malawi-Liverpool-Wellcome-Trust, Blantyre, Malawi

8. Centre for Inflammation Research, Queens Research Institute, University of Edinburgh, Edinburgh, UK

9. The Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel

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

11. Rollins School Public Health, Emory University, Atlanta, USA

12. Administración Nacional de Laboratorios e Institutos de Salud, Buenos Aires, Argentina

13. Center of Bacteriology, Adolfo Lutz Institute, São Paulo, Brazil

14. Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru

15. University of Nebraska Medical Center, Omaha, USA

16. The Aga Khan University, Karachi, Pakistan

17. Department of Medical Microbiology, University of Ghana Medical School, Accra, Ghana

18. Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China

19. National Laboratory of Health, Environment and Food, Ljubljana, Slovenia

20. Hamad Medical Corporation, Doha, Qatar

21. Faculty of Pharmacy, Siam University, Bangkok, Thailand

22. Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea

23. Agence de Médecine Préventive, Paris, France

24. Child Health Research Foundation, Dhaka, Bangladesh

25. Kenya Medical Research Institute, Kisumu, Kenya

26. Centro de Investigação em Saúde da Manhiça, Maputo, Moçambique

27. Hacettepe University Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey

28. Faculty of Medicine and Pharmacy & Ibn Rochd University Hospital Center, Casablanca, Morocco

29. The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus

30. Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK

31. Kempegowda Institute of Medical Sciences Hospital & Research Center, Bangalore, India

32. University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK

33. G. N. Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, Russia

34. Department of Microbiology, Chinese University of Hong Kong, Hong Kong, PR China

35. The Emory Global Health Institute, Atlanta, USA

36. Hubert Department of Global Health, Rollins School of Public Health, and Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, USA

Abstract

Pneumococcal serotype 35B is an important non-conjugate vaccine (non-PCV) serotype. Its continued emergence, post-PCV7 in the USA, was associated with expansion of a pre-existing 35B clone (clonal complex [CC] 558) along with post-PCV13 emergence of a non-35B clone previously associated with PCV serotypes (CC156). This study describes lineages circulating among 35B isolates in South Africa before and after PCV introduction. We also compared 35B isolates belonging to a predominant 35B lineage in South Africa (GPSC5), with isolates belonging to the same lineage in other parts of the world. Serotype 35B isolates that caused invasive pneumococcal disease in South Africa in 2005–2014 were characterized by whole-genome sequencing (WGS). Multi-locus sequence types and global pneumococcal sequence clusters (GPSCs) were derived from WGS data of 63 35B isolates obtained in 2005–2014. A total of 262 isolates that belong to GPSC5 (115 isolates from South Africa and 147 from other countries) that were sequenced as part of the global pneumococcal sequencing (GPS) project were included for comparison. Serotype 35B isolates from South Africa were differentiated into seven GPSCs and GPSC5 was most common (49 %, 31/63). While 35B was the most common serotype among GPSC5/CC172 isolates in South Africa during the PCV13 period (66 %, 29/44), 23F was the most common serotype during both the pre-PCV (80 %, 37/46) and PCV7 period (32 %, 8/25). Serotype 35B represented 15 % (40/262) of GPSC5 isolates within the global GPS database and 75 % (31/40) were from South Africa. The predominance of the GPSC5 lineage within non-vaccine serotype 35B, is possibly unique to South Africa and warrants further molecular surveillance of pneumococci.

Funder

United States Agency for International Development’s Antimicrobial Resistance Initiative

Bill and Melinda Gates Foundation Grant

Publisher

Microbiology Society

Subject

General Medicine

Reference34 articles.

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