Solu: a cloud platform for real-time genomic pathogen surveillance
Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega-Sanz, Jacob L. Steenwyk, Samuel Sihvonen
Abstract
BACKGROUND: Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in terms of infrastructure, expertise, and security when it comes to continuous surveillance. The existing pipelines often require the user to set up and manage their own infrastructure and are not designed for continuous surveillance that demands integration of new and regularly generated sequencing data with previous analyses. Additionally, academic projects often do not meet the privacy requirements of healthcare providers. RESULTS: We present Solu, a cloud-based platform that integrates genomic data into a real-time, privacy-focused surveillance system. EVALUATION: Solu's accuracy for taxonomy assignment, antimicrobial resistance genes, and phylogenetics was comparable to established pathogen surveillance pipelines. In some cases, Solu identified antimicrobial resistance genes that were previously undetected. Together, these findings demonstrate the efficacy of our platform. CONCLUSIONS: By enabling reliable, user-friendly, and privacy-focused genomic surveillance, Solu has the potential to bridge the gap between cutting-edge research and practical, widespread application in healthcare settings. The platform is available for free academic use at https://platform.solugenomics.com .