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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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1 University of Southampton, University Hospital Southampton Foundation NHS Trust, Faculty of Medicine & Institute for Life Sciences, Southampton, UK (GRID:grid.5491.9) (ISNI:0000 0004 1936 9297); University Hospital Southampton Foundation NHS Trust, NIHR Southampton Biomedical Research Centre, Southampton, UK (GRID:grid.123047.3) (ISNI:0000000103590315)
2 University of Southampton, University Hospital Southampton Foundation NHS Trust, Faculty of Medicine & Institute for Life Sciences, Southampton, UK (GRID:grid.5491.9) (ISNI:0000 0004 1936 9297)
3 Wellcome Sanger Institute, Parasites and Microbes, Hinxton, UK (GRID:grid.10306.34) (ISNI:0000 0004 0606 5382); University of Oslo, Department of Biostatistics, Institute of Basic Medical Sciences, Oslo, Norway (GRID:grid.5510.1) (ISNI:0000 0004 1936 8921)
4 Wellcome Sanger Institute, Parasites and Microbes, Hinxton, UK (GRID:grid.10306.34) (ISNI:0000 0004 0606 5382)
5 University of Southampton, University Hospital Southampton Foundation NHS Trust, Faculty of Medicine & Institute for Life Sciences, Southampton, UK (GRID:grid.5491.9) (ISNI:0000 0004 1936 9297); University Hospital Southampton Foundation NHS Trust, NIHR Southampton Biomedical Research Centre, Southampton, UK (GRID:grid.123047.3) (ISNI:0000000103590315); University Hospital Southampton Foundation NHS Trust, NIHR Southampton Clinical Research Facility, Southampton, UK (GRID:grid.123047.3) (ISNI:0000000103590315)
6 University of Southampton, University Hospital Southampton Foundation NHS Trust, Faculty of Medicine & Institute for Life Sciences, Southampton, UK (GRID:grid.5491.9) (ISNI:0000 0004 1936 9297); University Hospital Southampton Foundation NHS Trust, NIHR Southampton Biomedical Research Centre, Southampton, UK (GRID:grid.123047.3) (ISNI:0000000103590315); University of Southampton, Global Health Research Institute, Southampton, UK (GRID:grid.5491.9) (ISNI:0000 0004 1936 9297)