Whole Genome Sequencing (WGS) provides the most comprehensive overview of a bacterial strain. The genome composition can be analyzed by using WGS variants identification techniques such as Single Nucleotide Polymorphisms (SNPs/wgSNP) or whole genome Multilocus Sequence Typing (wgMLST) to identifying the virulome, resistome, and antibioresistome.
wgMLST uses WGS data (assembled or not) to complete MLST analysis on a genome extense scale. For each sample, locus presence is analyzed and, when present, allele variants are determined. For each locus, new sequences are assigned new consecutive allele numbers. wgMLST is progressively being advised for subtyping purposes at any taxonomic level. MultiLocus Sequence Typing data provides close-to-ultimate discriminatory power to differentiate isolated bacterial strains.
The wgSNP bioinformatic pipelines detect SNP variants by mapping the WGS reads to a reference sequence. This approach has been also demonstrated to be suitable for bacterial strain genotyping/strain typing.
Moreover, WGS would give the opportunity from genomic data achievable to predict a set of genes that contribute to the virulence of a bacterium as well as for mapping its resistome and antibioresistome.
Bacterial WGS holds serious promise for enhancing pathogen diagnostics, as well as industrial, agricultural and environmental strain exploration. A variety of applications including comparative genomics (i.e. differentiation between strains, strain typing) can be evaluated through WGS.
WGS has greatly transformed the field of epidemiology and is particularly useful for investigating outbreaks of foodborne diseases. WGS allows differentiation between outbreak and non-outbreak strains of foodborne pathogens by comparing their microbial genomes. It has been confirmed that strain typing foodborne pathogens by WGS gives superior resolution to existing subtyping methods such as pulsed-field gel electrophoresis (PFGE). WGS is now used as a method by the FDA and the CDC in the United States to characterize Salmonella and Listeria monocytogenes food and clinical isolates.
Agri-food chains are increasingly interested in these techniques to identify perfectly the contamination source and assess the risks associated with contaminating bacteria.
From isolated strain to final report
- DNA extraction from isolated strains
- Library construction
- Sequencing on Illumina® MiSeq® system
- Bioinformatics analysis of the sequencing data (bioinformatics pipeline with the use of Applied Maths/Bionumerics applications, a bioMérieux Company)
- A detailed scientific report including tables and graphs that summarize information on the different samples and complete method summary