International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.

ABSTRACT:

Background

Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background.

Methods

Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds

SUBMITTER: Gladstone RA 

PROVIDER: S-EPMC6557916 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature