# Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

## TL;DR

This paper reviews how combining whole genome sequencing and metagenomics can improve microbiological diagnostics and patient care.

## Contribution

The paper introduces a framework for integrating WGS and metagenomics data to enhance diagnostic accuracy and clinical outcomes.

## Key findings

- Combining WGS and metagenomics can provide synergistic insights for microbiological diagnostics.
- Customized bioinformatics pipelines and databases are essential for integrating these technologies.
- Such integration can improve infection control and pathogen surveillance.

## Abstract

Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.