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. 2025 Sep 5;17(1):20.
doi: 10.1186/s41479-025-00174-y.

Changes in carriage and serotype diversity of Streptococcus pneumoniae and other respiratory pathobionts in the UK between pre-PCV13 (2006-10), early-PCV13 (2010-12) and late-PCV13 (2012-23) periods

David W Cleary  1   2 , Rebecca Anderson  3 , Jessica Jones  3 , Rebecca A Gladstone  4   5 , Karen L Osman  3 , Vanessa T Devine  3 , Denise E Morris  3 , Alex J J Lister  3 , Stephen Gomer  3 , Rebecca E Hocknell  3 , Emily J Dineen  3 , Johanna M Jefferies  3 , James Campling  6 , Maria Lahuerta  7 , Kyla Hayford  7 , Jo Southern  7 , Bradford D Gessner  7 , Stephanie W Lo  5   8 , Stephen D Bentley  5 , Saul N Faust  3   9   10 , Stuart C Clarke  11   12   13   14
Affiliations

Changes in carriage and serotype diversity of Streptococcus pneumoniae and other respiratory pathobionts in the UK between pre-PCV13 (2006-10), early-PCV13 (2010-12) and late-PCV13 (2012-23) periods

David W Cleary et al. Pneumonia (Nathan). .

Abstract

Background: The ongoing burden of mortality and morbidity associated with Streptococcus pneumoniae infections requires that monitoring of carriage epidemiology continues. Here, we present data from the annual, cross-sectional surveillance study in Southampton UK on serotype epidemiology and diversity, as well as carriage of other frequent colonisers of the respiratory tract in over 7000 children over a period of seventeen years (2006–2023).

Methods: Children were recruited from two sites: Site 1 - Southampton General Hospital, administered by University Hospital Southampton (UHS) NHS Foundation Trust and Site 2– a collection of community health care facilities within the Solent NHS Trust region. Recruitment was limited to children < 5-years-old. Pneumococcal serotyping was done using whole genome sequence data.

Results: A total of 7,686 swabs were collected from which 2,386 (31%) pneumococci were recovered. Carriage of pneumococci has remained consistent (median carriage prevalence 31.4%) even with the almost complete removal of vaccine-type (VT) serotypes. Examining three PCV13 periods separately (pre, early and late), carriage was not significantly different at 27.7%, 35.3% and 39.3% respectively. A decrease in carriage of Haemophilus influenzae, Staphylococcus aureus and Moraxella catarrhalis was seen pre-PCV13 (following PCV7 implementation) but has since stabilised. Continued, low-level persistence of VTs 3, 19A and 19F was noted. PCV13 did not impact the pneumococcal serotype rank abundance despite clear reductions in targeted serotypes and fluctuations in other non-VT serotypes such as 15A, 23B and 23B1. Non-PCV13 PCV20 serotypes 10A and 11A, in addition to paired prevalence of 15B and 15C (15B/C) were in the five most isolated serotypes in the late-PCV13 period (2012 to present). Non-PCV13 PCV20 serotypes now account for approximately 40% of all carriage. By contrast, the serotypes only included in PCV15 (22F and 33F) represented just 7% in the same period.

Conclusion: With consistent carriage prevalence in this UK paediatric population since PCV13 introduction, serotype epidemiology is now dominated by non-PCV13 serotypes that are in higher valency vaccines.

Supplementary Information: The online version contains supplementary material available at 10.1186/s41479-025-00174-y.

Keywords: Carriage epidemiology; PCV; Streptococcus pneumoniae.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: The UK National Health Service (NHS) Research Ethics Service approved this study (06/Q1704/105 and 14/NS/1064). All methods and research practises outlined below were performed in accordance with relevant regulations and the Declaration of Helsinki. Written informed consent was provided by parents or legal guardians for each child. Consent for publication: Not applicable. Competing interests: 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. JC, ML, KH, JS and BG are employees of Pfizer Inc and, as such, may hold stocks. All other authors have no conflicts of interest.

Figures

Fig. 1
Fig. 1
Carriage prevalence of S. pneumoniae across all years (left) and by PCV13 period (right). Left - Error bars represent 95% CI. From 2017/18 (year 12) onwards data has been split into Site 1 (Hospital) and Site 2 (community clinics). Combined mean carriage was 31.2%, ranging from a low of 19.2% in 2020/21 (year 15) to 37.9% in 2014/15 (year 9). Year 15 denotes a period when the UK was under various forms of non-pharmaceutical intervention (NPI). PCV13 introduction is shown as vertical dashed line; Right– Box and whisker plot showing a comparison of overall pneumococcal carriage prevalence (%) by PCV13 period. Error bars represent 95% CI. Age groups are illustrated by colour with connecting lines across PCV13 periods. No statistically significant difference was found between the pre-PCV13 and either early or late PCV13 periods
Fig. 2
Fig. 2
Prevalence of serotypes grouped by inclusion in PCVs. The reduction in PCV7 serotypes post-PCV7 from >50% is shown in black and of PCV13 serotypes (purple) from a high of ~20% post-PCV13. NVTs, here split to illustrate those that may be targeted by PCV20, equates to 94.0% of carriage in 2022/23
Fig. 3
Fig. 3
Isolation of PCV-type serotypes following PCV13 introduction in 2010. In recent years, 19F and 3 have been the most frequently isolated PCV targeted serotypes
Fig. 4
Fig. 4
Bar plot showing serotype proportions by PCV era from the pre-PCV13 period (top) to early-PCV13 period (middle) and late-PCV13 period (bottom). Pre-PCV13: 01/01/2006-30/06/2010 inclusive; early PCV13: 01/07/2010-30/06/2012 inclusive; late PCV13: 01/07/2012 to the end of the study period. Serotypes are coloured according to vaccine type status: PCV7– black bars, PCV13– blue bars, PCV20– green, and NVT– pale green. Noticeable decreases in VT serotypes can be seen, with residual serotype 3 and 19A carriage. PCV20 serotypes 11A and 15B/C are the two most common serotypes now observed
Fig. 5
Fig. 5
Principal Components Analysis of serotype abundance between pre-PCV13, early- and late-PCV13 periods. PCV eras are shown as coloured points with serotypes that explain the variance as arrows with the amount of variance explained indicated by arrow length. Pre-PCV13 era composition is defined by the presence of VTs 6B, 6A, 19A, 19F, 23F and the non-VT 6C
Fig. 6
Fig. 6
Serotype Rank-abundance distributions models in pre-, early- and late-PCV13 periods. Five models were used to examine serotype abundance. Null is equivalent to the broken-stick model. In all three the Preemption model was the best fit with the lowest AIC and suggests no disruption to population structure has occurred due to PCV13 introduction
Fig. 7
Fig. 7
Box and whisker plots showing carriage prevalence of Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis and non-pneumococcal Alpha-haemolytic Streptococci contrasted between pre-PCV13, early- and late-PCV13 periods. Error bars show 95% CI. Significant increases in all four species are apparent between the pre-PCV13 and early-PCV13 period. No significant differences are seen between early and late-PCV13 periods
See this image and copyright information in PMC

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