RSYD-BASIC: a bioinformatic pipeline for routine sequence analysis and data processing of bacterial isolates for...

Area of Science:

• Clinical microbiology
• Bioinformatics
• Genomic analysis

Background:

• Whole-genome sequencing of bacterial isolates is standard in clinical microbiology.
• Current analysis often requires bioinformatician expertise, limiting workflow robustness and bioinformatician availability.
• A need exists for a user-friendly pipeline for bacterial genome assembly and routine analysis.

Purpose of the Study:

• To create a robust, customizable bioinformatic pipeline for bacterial genome analysis.
• To enable non-bioinformaticians to initiate comprehensive sequence analysis.
• To improve workflow efficiency and free up bioinformatician time.

Main Methods:

• Introduction of the RSYD-BASIC pipeline for bacterial isolate sequence analysis.
• Demonstration using two datasets of publicly available bacterial genome sequences.
• Evaluation of pipeline performance against existing methods and clinical data.

Main Results:

• The RSYD-BASIC pipeline provides comparable results to original methods for most analyses.
• The pipeline generated additional, clinically relevant information, including in vitro correlations.
• Routine use demonstrated its utility in typing bacterial pathogens and disproving a potential outbreak.

Conclusions:

• The RSYD-BASIC pipeline is a configurable, non-expert-operated tool for bacterial genome analysis.
• It simplifies outbreak investigation for expert users and enhances clinical microbiology workflows.
• Standardized methods are crucial, and this pipeline offers comparable performance while promoting standardization.