Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.
Srinithi PurushothamanMarco MeolaAdrian EgliPublished in: International journal of molecular sciences (2022)
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.
Keyphrases
- antimicrobial resistance
- single cell
- single molecule
- electronic health record
- antibiotic resistance genes
- big data
- public health
- healthcare
- mental health
- escherichia coli
- staphylococcus aureus
- magnetic resonance
- human health
- case report
- risk assessment
- circulating tumor
- genome wide
- cell free
- machine learning
- drug delivery
- magnetic resonance imaging
- health information
- dna methylation
- genetic diversity
- social media
- cystic fibrosis
- biofilm formation
- wastewater treatment
- mass spectrometry