PneumoWiki: a pan-genome-based database for the pathogen Streptococcus pneumoniae

Clinical Snapshot

Key Findings

• Effect Size: 43 strains with comprehensive functional annotation

• Primary Outcome: Successfully created PneumoWiki database integrating genomic data from 43 S. pneumoniae strains

• Nnt Or Sensitivity: Database covers >100 capsular serotypes with pan-genome functionality

Clinical Application

Highly feasible - web-based, free access, user-friendly interface Relevant for Australian pneumococcal surveillance, vaccine research, and TGA regulatory submissions for pneumococcal therapeutics Researchers studying pneumococcal infections, vaccine development, and antimicrobial resistance

Abstract

UNLABELLED: The Gram-positive bacterium Streptococcus pneumoniae is a major human pathogen that exhibits more than 100 different capsular serotypes and considerable genomic variability. S. pneumoniae is also an important model organism for basic and biomedical research, with a number of strains with different characteristics being used. To address this, we have created the manually curated pan-genome database PneumoWiki (https://pneumowiki.med.uni-greifswald.de) that integrates genomic data of 43 S. pneumoniae strains with various aspects of functional annotation. All data relating to a specific gene and gene product are compiled on a Gene page. In addition to the gene and protein sequences and annotation from NCBI RefSeq, this includes, for example, data on gene expression, protein function, and localization. The information is supplemented with links to the data sources as well as to other databases and relevant literature. The basic concept of PneumoWiki is the interlinked presentation of pan-genome-based and strain-specific information. Therefore, register tabs with strain names at the top of the Gene pages allow switching between orthologous genes and the corresponding pan-genome page. The pan-genome gene pages contain a summary with functional information and the occurrence of the gene, an ortholog table for the 43 S. pneumoniae strains, a multiple-strain genome viewer as well as a protein sequence alignment. PneumoWiki was developed as a user-friendly tool and is available free of charge. The data collected in PneumoWiki are accessible via various download options. Overall, PneumoWiki is a resource for the research community that supports the analysis and interpretation of experimental data and, in particular, enables the integration of the knowledge available for different S. pneumoniae strains. IMPORTANCE: Databases that integrate and curate the large amounts of genomic data and functional information available for well-studied organisms play an increasingly important role in many areas of life sciences, including infection research. Streptococcus pneumoniae is a major human pathogen associated with high morbidity and mortality rates. The species exhibits high variability in its genome sequence, and a number of strains with different characteristics are used in pneumococcal research. We created the wiki-type database PneumoWiki to provide researchers with curated, up-to-date information on a range of pneumococcal genomes, focusing on the individual genes and encoded proteins and their functional annotation. The key feature of PneumoWiki is the pan-genome approach, which allows combining information of individual strains, thereby supporting the analysis of experimental data and comparisons between studies using different strains. In this way, the database becomes a valuable research tool that can contribute to a better understanding of pneumococcal physiology.

References

1. 1.Mehlan, H., Hirschmann, S., Busch, L. M., Hennig, A., Nieselt, K., Völker, U., Hammerschmidt, S., & Mäder, U. (2026). PneumoWiki: a pan-genome-based database for the pathogen Streptococcus pneumoniae. Microbiology Spectrum. https://doi.org/10.1093/bioinformatics/btae677