Abstract

Background The UK transition from a 2 + 1 to a 1 + 1 infant immunisation schedule with the 13-valent pneumococcal conjugate vaccine (PCV13) on Jan 1, 2020, coincided with the start of the COVID-19 pandemic. We describe the epidemiology of invasive pneumococcal disease (IPD) in England over 6 financial years (April 1 to March 31) between 2017–18 and 2022–23. Methods We used prospective national surveillance data, including serotyping and whole-genome sequencing of invasive isolates, to analyse IPD trends in England by age and financial year. We compared breakthrough infections and vaccine failure rates in 2022–23 among children eligible for the 1 + 1 schedule with rates in cohorts of children eligible for the 2 + 1 schedule between 2017–18 and 2019–20. We assessed genomic changes over time by comparing Global Pneumococcal Sequencing Clusters and multilocus sequence types among PCV13 serotypes causing IPD. Findings There were 4598 laboratory-confirmed IPD cases in 2022–23, 3025 in 2021–22, 1240 in 2020–21, and 5316 in 2019–20. IPD incidence in 2022–23 was 14% lower than in 2019–20 (incidence rate ratio [IRR] 0·86, 95% CI 0·81–0·91; p<0·001). IPD incidence in 2022–23 compared with 2019–20 was 34% higher in children (aged <15 years) (378 cases vs 292 cases; IRR 1·34, 95% CI 1·08–1·68; p=0·009) and 17% lower in adults (aged 15 years and older; 4220 vs 5024; 0·83, 0·78–0·88; p<0·001). The proportion of PCV13-type IPD increased from 19·4% (95% CI 18·2–20·4; 957 of 4947) in 2019–20 to 29·7% (28·3–31·0; 1283 of 4326) in 2022–23, mainly due to serotype 3, but also serotypes 19F, 19A, and 4, alongside a decrease in non-PCV13 serotypes 8, 12F, and 9N. The increase in IPD incidence due to serotypes 3, 19A, and 19F was driven by clonal expansion of previously circulating strains, whereas serotype 4 expansion was driven by newer strains (ie, sequence types 801 and 15603). Breakthrough infections and vaccine failure rates were similar in children eligible for the 1 + 1 (1·08 per 100 000 person-years) and 2 + 1 (0·76 per 100 000 person-years; IRR 1·42, 95% CI 0·78–2·49; p=0·20) PCV13 schedules. Interpretation Overall, IPD incidence in England was lower in 2022–23, 2 years after removal of pandemic restrictions, than in 2019–20. Breakthrough and vaccine failure rates were not significantly different between children who received the 1 + 1 compared with the 2 + 1 PCV13 immunisation schedule. The post-pandemic increase in childhood IPD incidence and especially PCV13-type IPD will require close monitoring. Funding None.