Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Apr;8(4):000746.
doi: 10.1099/mgen.0.000746.

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

Kedibone M Ndlangisa  1 , Mignon du Plessis  1   2 , Stephanie Lo  3 , Linda de Gouveia  1 , Chrispin Chaguza  3 , Martin Antonio  4 , Brenda Kwambana-Adams  5   6 , Jennifer Cornick  7 , Dean B Everett  7   8 , Ron Dagan  9 , Paulina A Hawkins  10   11 , Bernard Beall  11 , Alejandra Corso  12 , Samanta Cristine Grassi Almeida  13 , Theresa J Ochoa  14 , Stephen Obaro  15 , Sadia Shakoor  16 , Eric S Donkor  17 , Rebecca A Gladstone  3 , Pak Leung Ho  18 , Metka Paragi  19 , Sanjay Doiphode  20 , Somporn Srifuengfung  21 , Rebecca Ford  22 , Jennifer Moïsi  23 , Samir K Saha  24 , Godfrey Bigogo  25 , Betuel Sigauque  26 , Özgen Köseoglu Eser  27 , Naima Elmdaghri  28 , Leonid Titov  29 , Paul Turner  30 , K L Ravi Kumar  31 , Rama Kandasamy  32 , Ekaterina Egorova  33 , Margaret Ip  34 , Robert F Breiman  35 , Keith P Klugman  2   36 , Lesley McGee  11 , Stephen D Bentley  3 , Anne von Gottberg  1   2 , The Global Pneumococcal Sequencing Consortium  37
Affiliations

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

Kedibone M Ndlangisa et al. Microb Genom. 2022 Apr.

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.

Keywords: South Africa; Streptococcus pneumoniae; global pneumococcal sequence cluster; serotype 35B.

PubMed Disclaimer

Conflict of interest statement

Professor Anne von Gottberg and Dr Mignon du Plessis received funding from Pfizer Vaccines Research and Sanofi Pasteur. Dr Gladstone reports PhD studentship from Pfizer outside the submitted work (2009–2012). The other authors declare that they have no conflicts of interest directly relating to this manuscript.

Figures

Fig. 1.
Fig. 1.
Invasive pneumococcal disease cases and isolates obtained from 2005 through 2014 among South African (a) children <5 years and (b) individuals ≥5 years old.
Fig. 2.
Fig. 2.
Distribution of penicillin non-susceptible and susceptible serotype 35B pneumococcal isolates causing invasive disease in South Africa among (a) children <5 years old (N=104) during the pre-PCV (2005–2008) (n=17), PCV7 (2009–2010) (n=16) and PCV13 (2011–2014) period (n=71) and (b) patients ≥5 years old (N=158) during the pre-PCV (2005–2008) (n=48), PCV7 (2009–2010) (n=20) and PCV13 (2011–2014) period (n=90).
Fig. 3.
Fig. 3.
Distribution of global pneumococcal sequence clusters (GPSCs), clonal complexes (CC) and sequence types (STs) among 63 serotype 35B isolates causing invasive disease in South Africa during the pre-PCV (2005–2008) (n=24), PCV7 (2009–2010) (n=2) and PCV13 (2011–2014) period (n=37).
Fig. 4.
Fig. 4.
Phylogeny of GPSC5 (CC172) isolates causing invasive disease in South Africa (N=115) during the pre-PCV (2005–2008) (n=46), PCV7 (2009–2010) (n=25), and PCV13 (2011–2014) (n=44) period. Leaf nodes on the tree are colour coded according to serotype. Microreact: https://microreact.org/project/M-plmPZP5.
Fig. 5.
Fig. 5.
Phylogeny of GPSC5 isolates (N=262) causing pneumococcal disease globally, 2005–2014. Leaf nodes on the tree are colour coded according to serotype, only nodes for isolates from South Africa are shown.
See this image and copyright information in PMC

References

    1. Gladstone RA, Lo SW, Lees JA, Croucher NJ, van Tonder AJ, et al. International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact. EBioMedicine. 2019;43:338–346. doi: 10.1016/j.ebiom.2019.04.021. - DOI - PMC - PubMed
    1. Ndlangisa KM, du Plessis M, Lo S, de Gouveia L, Chaguza C, et al. 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. Figshare. 2022. DOI: 10.6084/m9.figshare.16621984 - PMC - PubMed
    1. Miller E, Andrews NJ, Waight PA, Slack MP, George RC. Herd immunity and serotype replacement 4 years after seven-valent pneumococcal conjugate vaccination in England and Wales: an observational cohort study. Lancet Infect Dis. 2011;11:760–768. doi: 10.1016/S1473-3099(11)70090-1. - DOI - PubMed
    1. Tyrrell GJ, Lovgren M, Chui N, Minion J, Garg S, et al. Serotypes and antimicrobial susceptibilities of invasive Streptococcus pneumoniae pre- and post-seven valent pneumococcal conjugate vaccine introduction in Alberta, Canada, 2000-2006. Vaccine. 2009;27:3553–3560. doi: 10.1016/j.vaccine.2009.03.063. - DOI - PubMed
    1. Pilishvili T, Lexau C, Farley MM, Hadler J, Harrison LH, et al. Sustained reductions in invasive pneumococcal disease in the era of conjugate vaccine. J Infect Dis. 2010;201:32–41. doi: 10.1086/648593. - DOI - PubMed

Publication types

MeSH terms