How was the Pneumococcal Genome Library (PGL) created?
We screened 1,091 PubMed articles and identified 211 peer-reviewed publications with at least one naturally-occurring pneumococcal genome. Genomic data were unavailable for 42/211 (20%) articles. We identified discrepancies in a further 54 (26%) articles, e.g. the inclusion of invalid accession numbers or an incorrect total of accession numbers. We began by adding data from publications for which all data could be recovered.
What data are currently in the Pneumococcal Genome Library?
The PGL contains 33,480 genomes from 130 publications. Articles were published between 2001 and 2020, and individual genomes were included in up to 52 publications. Isolates were collected in 82 countries between 1916 and 2018 and correspond to >90 serotypes.
Will more genomes be added to the Pneumococcal Genome Library?
The first version of the PGL was created in 2019 with a major update in 2021. Of the remaining publications, 69/81 require author follow-up. If you are an author of a pending publication and would like to discuss having your article added to the PGL, please contact Melissa Jansen van Rensburg and Angela Brueggemann.
Using and contributing to the Pneumococcal Genome Library
We hope that this will become a useful resource for the community and we welcome feedback. If you have studies that you would like added to the library, please contact melissa.jansenvanrensburgndph.ox.ac.uk (Melissa Jansen van Rensburg) and angela.brueggemannndph.ox.ac.uk (Angela Brueggemann).