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Changes in serotype prevalence of Streptococcus pneumoniae in Southampton, UK between 2006 and 2018

Changes in serotype prevalence of Streptococcus pneumoniae in Southampton, UK between 2006 and 2018
Changes in serotype prevalence of Streptococcus pneumoniae in Southampton, UK between 2006 and 2018

Streptococcus pneumoniae continues to cause significant disease burden. Whilst pneumococcal conjugate vaccines (PCV) have substantially reduced this burden, serotype replacement partially negates this success due to increased disease associated with non-vaccine serotypes (NVTs). Continued surveillance is therefore essential to provide crucial epidemiological data. Annual cross-sectional surveillance of paediatric pneumococcal carriage was started in Southampton, UK following PCV7 roll-out in 2006. Nasopharyngeal swabs were collected from children < 5 years old each winter (October to March) from 2006/07 and for each consecutive year until 2017/18. Pneumococcal serotype was inferred from whole genome sequencing data. A total of 1429 (32.5%) pneumococci were isolated from 4093 children. Carriage ranged from 27.8% (95%CI 23.7-32.7) in 2008/09 to 37.9% (95%CI 32.8-43.2) in 2014/15. Analyses showed that carriage increased in children aged 24-35 months (p < 0.001) and 47-60 months (p < 0.05). Carriage of PCV serotypes decreased markedly following PCV7 and/or PCV13 introduction, apart from serotype 3 where the relative frequency was slightly lower post-PCV13 (pre-PCV13 n = 7, 1.67%; post-PCV13 n = 13, 1.27%). Prevalence of NVTs implicated in increased disease was low with 24F (n = 19, 1.4%) being the most common followed by 9N (n = 11, 0.8%), 8 (n = 7, 0.5%) and 12F (n = 3, 0.2%).

Carrier State/epidemiology, Child, Child, Preschool, Cross-Sectional Studies, Humans, Infant, Nasopharynx, Pneumococcal Infections/prevention & control, Pneumococcal Vaccines, Prevalence, Serogroup, Streptococcus pneumoniae/genetics, United Kingdom/epidemiology, Vaccines, Conjugate
2045-2322
Cleary, David W.
f4079c6d-d54b-4108-b346-b0069035bec0
Jones, Jessica
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Gladstone, Rebecca A.
da3bc262-bd79-4af6-86d5-aaed2ebf37f3
Osman, Karen L.
9df79583-5da6-480e-ad25-189e8a4d63f2
Devine, Vanessa T.
242490ce-18b3-42ab-956b-5d2f2d202b41
Jefferies, Johanna M
d3c7f86b-c08e-4c8f-9ce1-c2ac5a511746
Bentley, Stephen D.
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Faust, Saul N
f97df780-9f9b-418e-b349-7adf63e150c1
Clarke, Stuart C.
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17
Cleary, David W.
f4079c6d-d54b-4108-b346-b0069035bec0
Jones, Jessica
69dbdb74-21d8-4d10-9ac4-3539f2b54142
Gladstone, Rebecca A.
da3bc262-bd79-4af6-86d5-aaed2ebf37f3
Osman, Karen L.
9df79583-5da6-480e-ad25-189e8a4d63f2
Devine, Vanessa T.
242490ce-18b3-42ab-956b-5d2f2d202b41
Jefferies, Johanna M
d3c7f86b-c08e-4c8f-9ce1-c2ac5a511746
Bentley, Stephen D.
438443a4-8033-4a5d-a5a5-538dbd4e8d60
Faust, Saul N
f97df780-9f9b-418e-b349-7adf63e150c1
Clarke, Stuart C.
f7d7f7a2-4b1f-4b36-883a-0f967e73fb17

Cleary, David W., Jones, Jessica, Gladstone, Rebecca A., Osman, Karen L., Devine, Vanessa T., Jefferies, Johanna M, Bentley, Stephen D., Faust, Saul N and Clarke, Stuart C. (2022) Changes in serotype prevalence of Streptococcus pneumoniae in Southampton, UK between 2006 and 2018. Scientific Reports, 12 (1), [13332]. (doi:10.1038/s41598-022-17600-6).

Record type: Article

Abstract

Streptococcus pneumoniae continues to cause significant disease burden. Whilst pneumococcal conjugate vaccines (PCV) have substantially reduced this burden, serotype replacement partially negates this success due to increased disease associated with non-vaccine serotypes (NVTs). Continued surveillance is therefore essential to provide crucial epidemiological data. Annual cross-sectional surveillance of paediatric pneumococcal carriage was started in Southampton, UK following PCV7 roll-out in 2006. Nasopharyngeal swabs were collected from children < 5 years old each winter (October to March) from 2006/07 and for each consecutive year until 2017/18. Pneumococcal serotype was inferred from whole genome sequencing data. A total of 1429 (32.5%) pneumococci were isolated from 4093 children. Carriage ranged from 27.8% (95%CI 23.7-32.7) in 2008/09 to 37.9% (95%CI 32.8-43.2) in 2014/15. Analyses showed that carriage increased in children aged 24-35 months (p < 0.001) and 47-60 months (p < 0.05). Carriage of PCV serotypes decreased markedly following PCV7 and/or PCV13 introduction, apart from serotype 3 where the relative frequency was slightly lower post-PCV13 (pre-PCV13 n = 7, 1.67%; post-PCV13 n = 13, 1.27%). Prevalence of NVTs implicated in increased disease was low with 24F (n = 19, 1.4%) being the most common followed by 9N (n = 11, 0.8%), 8 (n = 7, 0.5%) and 12F (n = 3, 0.2%).

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Accepted/In Press date: 27 July 2022
Published date: 3 August 2022
Additional Information: Funding Information: This work was supported by Pfizer as an investigator-led research grant. Funding for whole genome sequencing was provided by the Wellcome Sanger Institute. Funding Information: DWC was a post-doctoral researcher on GSK funded projects in 2014/15, and currently receives grant support from Pfizer and the National Institute for Health via the NIHR Southampton Biomedical Research Centre. SNF receives support from the National Institute for Health Research funding via the NIHR Southampton Wellcome Trust Clinical Research Facility and the NIHR Southampton Biomedical Research Centre. SNF and SCC act as principal investigators for clinical trials and other studies conducted on behalf of University Hospital Southampton NHS Foundation Trust/University of Southampton that are sponsored by vaccine manufacturers. No personal payments are received from them. SNF, JMJ and SCC have participated in advisory boards for vaccine manufacturers but receive no personal payments for this work. SNF, SCC and JMJ have received financial assistance from vaccine manufacturers to attend conferences. All grants and honoraria are paid into accounts within the respective NHS Trusts or Universities, or to independent charities. RAG, VTD and JJ received PhD studentships via the University of Southampton from Pfizer. RAG received post-doctoral support in 2012 on a GSK funded research project via the University of Southampton. KLO received PhD studentship support from GSK, again via the University of Southampton. All other authors have no conflicts of interest. Funding Information: We would like to acknowledge the support of our technical colleagues, namely Rebecca Anderson, Denise E. Morris, Stephen Gomer and Emily J. Dineen in the collection and processing of samples for the study. We are grateful to staff in both the Pathogen Genomics team and those associated with the Global Pneumococcal Sequencing Project at the WSI for their support in genome sequencing of collected isolates. We are indebted to staff at the NIHR Southampton Wellcome Trust Clinical Research Facility for their assistance in the collection of samples and to staff at Public Health England for swab processing between 2006/07 and 2011/12. The authors also acknowledge the use of the IRIDIS High Performance Computing Facility, and associated support services at the University of Southampton, in the completion of this work. Finally, we acknowledge both the guardians and participants without whom this study would not have been possible. Publisher Copyright: © 2022, The Author(s).
Keywords: Carrier State/epidemiology, Child, Child, Preschool, Cross-Sectional Studies, Humans, Infant, Nasopharynx, Pneumococcal Infections/prevention & control, Pneumococcal Vaccines, Prevalence, Serogroup, Streptococcus pneumoniae/genetics, United Kingdom/epidemiology, Vaccines, Conjugate

Identifiers

Local EPrints ID: 470145
URI: http://eprints.soton.ac.uk/id/eprint/470145
ISSN: 2045-2322
PURE UUID: 5a5dde5f-2cf8-4c75-a924-52ffc0cc8403
ORCID for David W. Cleary: ORCID iD orcid.org/0000-0003-4533-0700
ORCID for Saul N Faust: ORCID iD orcid.org/0000-0003-3410-7642
ORCID for Stuart C. Clarke: ORCID iD orcid.org/0000-0002-7009-1548

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Date deposited: 04 Oct 2022 16:36
Last modified: 07 Jan 2023 02:48

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Contributors

Author: David W. Cleary ORCID iD
Author: Jessica Jones
Author: Rebecca A. Gladstone
Author: Karen L. Osman
Author: Vanessa T. Devine
Author: Johanna M Jefferies
Author: Stephen D. Bentley
Author: Saul N Faust ORCID iD

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