Wastewater-based genomic surveillance (WWGS) has proven effective for monitoring SARS-CoV-2 and other viruses within communities. It enables rapid detectio

Recent advances in high-throughput sequencing technologies have enabled the collection and sharing of a massive amount of omics data, along with its associated metadata—descriptive information that contextualizes the data, including phenotypic traits and experimental design. Enhancing metadata availability is critical to ensure data reusability and reproducibility and to facilitate novel biomedical discoveries through effective data reuse. Yet, incomplete metadata accompanying public omics data may hinder reproducibility and reusability and limit secondary analyses. Our study assesses the completeness of metadata in over 253 scientific studies, covering more than 164,000 samples from both human and non-human mammalian studies. We find that over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available in publications or public repositories. Notably, public repositories alone contain 62% of the phenotypes, surpassing the textual content of publications by 3.5%. Only 11.5% of studies completely shared all phenotypes, while 37.9% shared less than 40% of the phenotypes. Additionally, studies with non-human samples are more likely to include complete metadata compared to human studies. Similar trends are observed in an extended dataset comprising 61,000 studies and 2.1 million samples from the Gene Expression Omnibus (GEO) data repository. These findings highlight significant gaps in metadata sharing, underscoring the need for standardized practices to improve metadata availability. Enhanced metadata reporting would foster data reusability, support better-informed decision-making, and promote reproducible research across the biomedical field.

Sequencing-based wastewater surveillance offers a scalable and cost-effective approach for monitoring pathogens circulating within communities. We explore innovations and necessary actions, calling for standardized procedures for sample collection, processing, and sequencing, improved pathogen enrichment and targeted sequencing methods, and dedicated bioinformatics tools and databases to strengthen wastewater-based pathogen surveillance.

Objectives: The high incidence of sepsis necessitates the development of practical decision-making tools for intensivists, especially during the early, critical phases of management. This study evaluates a multi-agent system intended to assist clinicians with antibiotic therapy and adherence to current sepsis management guidelines before diagnostic results become available.Methods: A multi-agent system incorporating three specialized agents was developed: a sepsis management agent, an antibiotic recommendation agent, and a sepsis guidelines compliance agent. A sepsis case from the MIMIC IV database, organized as a clinical vignette, was used to integrate and test these agents for generating management recommendations. The system leverages retrieval-augmented generation to improve decision-making through the integration of current literature and guidelines.Results: The application produced management recommendations for a sepsis case associated with pneumonia, including early initiation of broad-spectrum antibiotics and close monitoring for clinical deterioration. Two expert intensivists evaluated these recommendations as “acceptable” and reported moderate interrater agreement (Cohen’s kappa = 0.622, p = 0.003) across various aspects of recommendation usefulness.Conclusions: The multi-agent system shows promise in enhancing decision-making for sepsis management by optimizing antibiotic therapy and ensuring guideline compliance. However, reliance on a single case study limits the generalizability of the findings, highlighting the need for broader validation in diverse clinical settings to improve patient outcomes.