Neonatal sepsis remains a major cause of morbidity and mortality worldwide, particularly in low- and middle-income countries. Advances in whole-genome sequencing (WGS) and other high-throughput genomic technologies have transformed our ability to study the epidemiology, transmission dynamics, and antimicrobial resistance patterns of pathogens causing neonatal sepsis. However, the full value of genomic data can only be realized when it is accompanied by high-quality, standardized metadata.
This repository contains the Neonatal Sepsis Metadata Standard, a structured and harmonized framework designed to support genomic epidemiology studies of neonatal sepsis. The standard aims to enable consistent data collection, interoperability across studies and platforms, and meaningful comparison and reuse of genomic datasets.
Neonatal sepsis is a systemic infection occurring in newborns, typically classified as early-onset or late-onset based on the timing of symptom onset. It is caused by a diverse range of bacterial and fungal pathogens and is influenced by host, environmental, and healthcare-associated factors. Despite improvements in diagnostics and clinical care, neonatal sepsis continues to pose significant challenges due to nonspecific clinical presentation, evolving pathogen landscapes, and increasing antimicrobial resistance.
Genomic epidemiology has emerged as a powerful approach to:
- Identify and track causative pathogens
- Understand transmission routes within neonatal units
- Characterize virulence and antimicrobial resistance determinants
- Inform infection prevention and control strategies
Robust metadata describing the host, clinical context, sample, and laboratory processes are essential to interpret genomic findings accurately and to place them in an epidemiological context.
Metadata standards define a common structure, vocabulary, and set of expectations for describing data. In genomic epidemiology, standardized metadata:
- Improves data quality and completeness
- Enables interoperability across databases, tools, and studies
- Facilitates data sharing and reuse in line with FAIR principles (Findable, Accessible, Interoperable, Reusable)
- Supports reproducibility and transparent interpretation of results
Without standardized metadata, genomic datasets are difficult to integrate, compare, or interpret beyond their original study context. Developing a domain-specific metadata standard for neonatal sepsis ensures that critical clinical and epidemiological variables are captured in a consistent and meaningful way.
This metadata standard is intended to support genomic epidemiology of neonatal sepsis by defining a harmonized set of metadata elements relevant to pathogen genomics, clinical context, and epidemiological analysis. The standard is designed for use in research, public health surveillance, and data sharing initiatives.
This standard:
- Focuses on metadata accompanying pathogen genomic data related to neonatal sepsis
- Is applicable across diverse geographic, laboratory, and healthcare settings
- Supports retrospective and prospective genomic studies
This standard is not intended to:
- Replace clinical diagnostic criteria or treatment guidelines
- Serve as a comprehensive electronic health record schema
- Function as a regulatory or clinical decision-support tool
This repository serves as the authoritative home for the Neonatal Sepsis Metadata Standard and its supporting materials. It is intended for use by researchers, clinicians, public health professionals, and data stewards working in genomic epidemiology and neonatal health.
Specifically, this repository aims to:
- Provide a clear and well-documented metadata specification for neonatal sepsis genomic studies
- Support consistent implementation of the standard across projects and institutions
- Enable testing, validation, and iterative improvement of the standard
- Promote transparency and community engagement in standard development
This repository includes the following components:
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Metadata Dictionaries The core definition of the neonatal sepsis metadata standard, including fields, descriptions, data types, and controlled vocabularies where applicable.
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Metadata Template Metadata template in Excel format to support implementation and adoption by users.
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Documentation Supporting documentation explaining design decisions, scope, assumptions, and intended use cases.
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Versioning and Change History Records of updates, revisions, and known issues to support traceability and long-term maintenance.
This repository is intended for:
- Genomic epidemiology researchers studying neonatal sepsis
- Clinical and public health teams generating or using pathogen genomic data
- Bioinformaticians and data managers implementing metadata standards
- Standards developers and stakeholders interested in neonatal health data harmonization
Contributions, feedback, and issue reports are welcome. Community input is essential to ensure the metadata standard remains relevant, practical, and scientifically robust. Please see the contribution guidelines for details on how to get involved.
If you use, adapt, or reference this metadata standard in your work, please credit:
Public Health Alliance for Genomic Epidemiology (PHA4GE)
A formal citation and citation file (CITATION.cff) may be added in future releases.
License information is provided in this repository.