Whole-Genome Sequencing (WGS)
Whole-genome sequencing (WGS) is a molecular method that determines the complete DNA sequence of an organism’s genome. In AMR surveillance, WGS is increasingly used to characterise resistant bacteria and track transmission.
Role in AMR Surveillance
WGS complements traditional culture-based antimicrobial susceptibility testing by providing:
- Resistance gene identification - Detection of known and novel resistance mechanisms
- Outbreak tracking - High-resolution phylogenetic analysis to trace transmission pathways
- Strain characterisation - Typing of high-priority pathogens (e.g., MRSA, CPE, VRE)
- Surveillance of emerging threats - Early detection of new resistance patterns
WGS in Nordic Countries
Molecular methods, particularly WGS, are being integrated into Nordic surveillance systems:
- Denmark has the most advanced WGS integration, with routine sequencing for many pathogens through SSI and DANMAP
- All Nordic countries perform WGS for selected multidrug-resistant or extensively resistant pathogens
- PCR-based methods complement WGS for targeted resistance gene detection
Not yet routine for all pathogens
While WGS is increasingly used, it is still often targeted rather than routine. Integration with clinical surveillance data is still developing.
Metagenomic Approaches
Beyond isolate-based WGS, metagenomics enables culture-independent analysis of AMR genes in complex samples such as:
- Wastewater (see Environmental AMR Surveillance)
- Soil and water samples
- Gut microbiome studies
The Nordic countries have a high density of publicly available genomic datasets - 2.96 sequence datasets per 1,000 humans compared to 0.38 globally in the European Nucleotide Archive.