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

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). 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. 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. 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.