Ann Clin Microbiol 2025;28(4):22. Whole-genome sequencing applications for evolution of clinical microbiology
| Item | Traditional approaches | Whole-genome sequencing |
|---|---|---|
| Principle | Phenotypic traits, such as culturing, serotyping, biochemical testing, or PCR-based detection | Sequencing the entire genome to identify pathogens and analyze genetic features |
| Applications | Detection, identification, and enumeration of pathogens | Outbreak tracing, source attribution, evolution study, and functional gene analysis |
| Testing speed | Time-consuming (days to weeks) | Faster results once sequencing infrastructure is established (hours to days) |
| Test sensitivity/specificity | Variable and dependent on culture conditions and the detection method applied | High sensitivity/specificity owing to genome analysis |
| Result output | Qualitative or semi-quantitative results (presence/absence or counts) | Quantitative and comprehensive genetic data (SNPs, resistome, or virulome) |
| Testing costs (initial and operational costs) | Lower initial and operational costs | High initial cost for WGS equipment; operational costs depend on scale and throughput; these elevated costs may limit some developing countries, or countries with fewer resources, from accessing this technology |
| Advantages | Cost-effective, well-established, and simple to implement in clinical laboratories | Provision of comprehensive genetic information on antimicrobial resistance and virulence factors |
| Disadvantages | Limited accuracy in strain differentiation and inability to detect nonculturable organisms. The methods may not detect viable but non-culturable cells or unculturable pathogens | High initial cost requiring advanced infrastructure, expertise, and bioinformatics capabilities, needing high-quality DNA, and generating large datasets that need robust bioinformatics pipelines for analysis |
Abbreviations: PCR, polymerase chain reaction; SNP, single-nucleotide polymorphism; WGS, whole-genome sequencing.