Bacterial WGS

PathoSense can assist you with the isolation of DNA from your bacterial isolates and our goal is to obtain long reads for better genome assembly.

Long-read sequencing allows to reach complete circular genome assemblies for bacteria, including the identification of plasmids. This is a strong advantage over short-read sequencing. These high-quality genome assemblies can then be used for downstream analysis. We are open to receiving cultures or DNA isolates, and to deliver sequencing data or complete reports with data-analysis.

Sometimes novel species or strains are recovered from clinical samples. In this situation, MALDI-TOF may be insufficient and there whole genome sequencing can provide quick answers. We can identify the exact species of your strains using scientifically accepted methods.

We use phylogenetic analysis methods to analyse the genetic relatedness & evolutionary relationship between different strains. Phylogenetic trees can be enriched with strains sequenced at PathoSense and publicly available genomes from GenBank. Analyses can be conducted on whole genome sequences and can also target specific genes of interest. As the entire genome is at hand, multi-locus sequence (MLST) typing can also be used to classify strains according to available & internationally used MLST schedules for different types of bacteria.

Bacteria can harbour different types of virulence factors. Using the genetic information we can screen for the presence of virulence factors, which eventually can be used to assess the pathogenicity of some isolates. Antimicrobial resistance is a big challenge for animal and human health. Most analyses are conducted using phenotypic analysis methods but also the genetic code can be used to analyse potential antimicrobial resistance. This can be done by assessing the presence of genes or point mutations that are linked to antimicrobial resistance.

A complete genome annotation can be performed upon request.