6.2 Genome sequencing techniques
Whole genome sequencing (WGS) can also be used to look at the bacterial genome and its associated plasmids. 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 primarily been used as a research tool, but Nanopore technology and other technologies which have the potential to offer relatively low cost, rapid sequencing are becomingly more common in district hospitals.
WGS can be used for instance to study a newly identified mechanism of resistance or to study the different genes found in a particular setting. It could be used to understand how the resistant organisms had spread in an institution by constructing a phylogenetic tree of the bacteria in a particular species and seeing how this related to the different plasmids and resistance genes. It is also possible to sequence just the resistance genes, which is a little faster and less complex.
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 still yet to be clearly defined.
More information about WGS can be found in the Whole genome sequencing in AMR surveillance course.
6.1 PCR tests
