5.4.5 Whole genome sequencing (WGS)
Whole genome sequencing (WGS) is a method for rapid sequencing of the chromosomal DNA and mitochondrial DNA (and chloroplasts DNA in plants). WGS is carried out using next-generation sequencing (NGS) technologies, which allows the rapid generation of large quantities of genomic data.
WGS has the potential to become an important tool in pathogen surveillance. However, the challenge in AMR is the timely processing of the large volumes of data, particularly during emergency pathogen outbreaks (Bogaerts, 2021 and Jauneikaite, 2023). As a result, the Surveillance and Epidemiology of Drug-resistant Infections Consortium (SEDRIC, n.d.) working group are working on a series of recommendations on the use of genomic surveillance via WGS for AMR. The working group has identified various advantages and barriers to the use of WGS in AMR.
Advantages
Healthcare-associated infections in hospitalised patients pose a significant challenge globally. Genomic AMR surveillance of pathogens using WGS from healthcare-associated infections can provide much better identification of the causative agent, such as genomic subtypes. It can also help to identify facility-level trends.
One particular advantage of WGS is its use to investigate outbreaks and to improve support for infection prevention and control in AMR surveillance in healthcare facilities. It can help to identify complex epidemiological patterns, such as the emergence of new strains and expansion of new multidrug-resistant strains.
Barriers
Despite many advantages, there are still many barriers to WGS in AMR surveillance. The initial set-up and running costs can be prohibitive, or the equipment difficult to obtain due to poor distribution networks and supply chains.
There are also significant challenges in the analysis and interpretation of the genomic data, which typically requires bioinformaticians. Quality assurance processes for both laboratory sequencing and bioinformatic analysis have yet to be clearly defined.
The course Whole genome sequencing in AMR surveillance discusses WGS in more detail.
5.4.4 PCR-based bacterial identification
