Implementing responsible research data stewardship for the whole genome sequencing of bacteria - Festival of Genomics and Biodata Poster 2025

The sequencing of bacterial genomes has been crucial in our understanding of infectious disease pathogenesis and antimicrobial resistance (AMR). Bacterial whole genome sequencing (WGS) is an important analysis tool, which provides the framework for understanding the characteristics of a particular bacterial strain. The significance of obtaining complete bacterial genomes was demonstrated by the acquisition of the first WGS of the largest bacterial genome, which was acquired for the clinical Pseudomonas aeruginosa strain PAO1. Sequencing and analysing this genome in such detail, provided valuable insights into the genetic diversity and vast functional characteristics of this important human pathogen, and provided an insight on the association between genome size and genetic complexity. The success and precision of the PAO1 sequencing project resulted in the development of the opensource Pseudomonas Genome Database, which continues to provide a high quality, annotated genome library for the bacterial research community.

Appropriate stewardship is necessary throughout the whole research lifecycle to accurately conduct high-quality bacterial genomics investigations. The best approaches for implementing responsible research data stewardship for the WGS of bacteria are reviewed in this work. It discusses the application of the FAIR Principles to the selection and use of:

• DNA extraction techniques and sequencing technologies,
• assembly methods and annotation standards,
• appropriate reference genomes,
• bioinformatics tools,
• analysis platforms and data storage,
• metadata collection and,
• suitable sequencing data repositories.

This work aims to support the bacterial research community to maximise the potential value of WGS data for the investigation of infectious disease pathogenesis and AMR.