This article is part of the network’s archive of useful research information. This article is closed to new comments due to inactivity. We welcome new content which can be done by submitting an article for review or take part in discussions in an open topic or submit a blog post to take your discussions online.
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: Ourdatasetof 13,454genomes, combinedwithfourpublishedgenomicdatasets, representedAfrica (40%),
Asia(25%),Europe(19%),NorthAmerica(12%),andSouthAmerica(5%).These20,027pneumococcalgenomeswere
clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our
dataset,weadditionallyderivedserotypeandsequencetype,andpredictedantibiotic sensitivity.Wethenmeasured
invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage.