The first stage is to extract genomic DNA from isolated bacterial samples and construct the library for sequencing. The second stage is to carry out the sequencing procedure and process the raw read sequences, including read trimming and quality control. Clean reads will then be used for the assembly of the whole-genome sequence. In some cases, the genome assembly might be replaced by k-mer-based genome analyses, but with a compromised discrimination power . The last stage involves in-depth analysis, such as in silicon detection of virulence genes and antimicrobial-resistance genes 16, 17, phylogeny analysis , source attribution 19, 20, and so on.
Whole-genome sequencing (WGS)-based subtyping demonstrates several advantages over traditional subtyping approaches, including enhanced discrimination resolution, prediction of antimicrobial profiles by detecting antibiotic-resistance genes, attribution of transmission sources, and showing great potential for microbial food-safety surveillance 6, 7, 8, 9, 10.
WGS-based subtyping provides more accurate and prompt detection of pathogens, and the source of outbreaks is clearly identified . In several outbreak cases, WGS-based subtyping demonstrates supreme discrimination accuracy over traditional subtyping, which correctly attributes different clinical Listeria isolates to different food-contamination outbreaks . From then on, the integration of WGS subtyping into surveillance programs has been widely adopted.