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To describe the population genomics, serotype distribution, and predicted antimicrobial resistance profiles of invasive Streptococcus pneumoniae strains in England using routine whole-genome sequencing.

May 24, 2025The Lancet MicrobeOpen Access

Whole-genome sequencing, strain composition, and predicted antimicrobial resistance of Streptococcus pneumoniae causing invasive disease in England in 2017–20: a prospective national surveillance study

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To describe the population genomics, serotype distribution, and predicted antimicrobial resistance profiles of invasive Streptococcus pneumoniae strains in England using routine whole-genome sequencing.
Analyzed prospective national surveillance data comprising 15,400 invasive pneumococcal disease cases in England between July 1, 2017, and February 29, 2020.
Conducted whole-genome sequencing on 13,749 quality-controlled isolates to determine serotypes, assign global pneumococcal sequencing clusters (GPSCs), and predict antimicrobial resistance (AMR) profiles.
Linked genomic findings to patient clinical outcomes from general practitioner questionnaires and performed multivariable logistic regression to evaluate mortality predictors.
Serotype 8 was the most prevalent serotype at 22·4% (n=3,074/13,749), with 98·7% belonging to GPSC3, whereas 13-valent pneumococcal conjugate vaccine (PCV13) types accounted for 20·0% (n=2,751).
Most isolates (74·2%, n=10,198) lacked predicted AMR genes; resistance was highest for co-trimoxazole (17·0%, n=2,331), tetracycline (8·7%, n=1,199), and β-lactams (8·4%, n=1,149).
Patient mortality was significantly higher with AMR-associated genes (odds ratio [OR] 1·18, 95% CI 1·01–1·38) and the GPSC12 lineage (OR 1·88, 95% CI 1·48–2·38).

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Implication

Prospective national surveillance study reveals high serotype diversity and baseline antimicrobial resistance in invasive pneumococcal disease, highlighting genomic drivers of mortality.

Cite This Study

D'Aeth et al. (2025) studied this question.

synapsesocial.com/papers/6a7f77bcc18c3471006571bf https://doi.org/10.1016/j.lanmic.2025.101102

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Implication

Prospective national surveillance study reveals high serotype diversity and baseline antimicrobial resistance in invasive pneumococcal disease, highlighting genomic drivers of mortality.

Whole-genome sequencing, strain composition, and predicted antimicrobial resistance of Streptococcus pneumoniae causing invasive disease in England in 2017–20: a prospective national surveillance study

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Implication

Cite This Study

Whole-genome sequencing, strain composition, and predicted antimicrobial resistance of Streptococcus pneumoniae causing invasive disease in England in 2017–20: a prospective national surveillance study

Key Points

Discussion

Implication

Cite This Study

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