A Portable and Scalable Genomic Analysis Pipeline for Streptococcus pneumoniae Surveillance: GPS Pipeline

Abstract

Ever increasing global sequencing capacity provides an unprecedented opportunity in utilising genomic information captured from whole-genome sequencing to enhance pathogen surveillance. However, there is a growing need for developing user-friendly tools to effectively analyse the increasing volume of data. To meet this need, we have developed a genomic analysis pipeline, GPS Pipeline, which is portable and scalable to analyse genomes of Streptococcus pneumoniae, a major bacterial pathogen that is estimated to cause 317,000 child deaths worldwide every year. The GPS Pipeline is based on Nextflow and containerisation technology, and designed to enable researchers generating public health relevant output, including in silico serotypes, pneumococcal lineages (i.e. GPSCs), multilocus sequence types, and antimicrobial susceptibilities against 20 commonly used antibiotics,with minimal software setup requirements and bioinformatic expertise, in order to analyse genomic data at scale with ease. The GPS Pipeline provides a streamlined workflow that improves responsiveness in genomic surveillance on pneumococci. Data SummaryThe GPS Pipeline is available on GitHub at github.com/GlobalPneumoSeq/gps-pipeline. Published data from the GPS Database is available on Monocle Data Viewer at data.monocle.sanger.ac.uk and associated sequence read files are searchable and downloadable in the European Nucleotide Archive at ebi.ac.uk/ena via their ERR accession numbers. Impact StatementThe GPS Pipeline advances global genomic surveillance of Streptococcus pneumoniae by providing a scalable, portable, and user-friendly tool for analysing whole-genome sequencing data. Leveraging Nextflow and containerisation technology, it minimises bioinformatics expertise requirements and infrastructure needs, making it particularly valuable in low- and middle-income countries where pneumococcal disease burden is high. This pipeline ensures reproducibility and stability across platforms, facilitating rapid and accurate pneumococci genomic analysis. By streamlining data processing, the GPS Pipeline enhances pathogen surveillance, generates evidence to support vaccine strategy development, and empowers researchers worldwide, ultimately contributing to improved public health outcomes.