Whole genome sequencing of bacterial genomes - tools and applications

The course covers Whole genome sequencing (WGS), which is increasingly important for medical professionals. WGS technology is high up on the international political agenda. The traditional methods have been replaced by WGS technology. Therefore, bioinformatic tools will be essential for people in the sector. They can analyze data to obtain interpretable results and use them for various purposes. This course provides a foundation for learners to be able to comprehend and familiarize themselves with WGS technologies in the surveillance of bacteria, including species identification and typing as well as characterizing antimicrobial resistance traits and virulence genes. Through demonstrations of how these tools can be used, and the completion of exercises that require the use of WGS analysis tools freely accessible online, learners will be able learn more about them.

1. Define the Principles of Typing Bacteria

2. Here are some examples of Whole Genome Sequencing for Surveillance and Antimicrobial Resistance

3. Use genomic tools to sub-typing or surveillance

4. Define Next-Generation Sequencing.

5. How to de novo assemble raw data to contigs

6. Identify the mechanisms behind species identification, MLST Typing and Resistance Gene Detection.

7. Use the tools to identify species, MLST type and detect resistance genes in actual cases of other bacterial or pathogenic genomes.

8. Describe the techniques used to identify plasmid replicons, plasmid typing and Salmonella typing

9. Use the tools to type Salmonella, E.coli and plasmid replicons in cases of real pathogen and bacterial genomes.

10. Explain this concept to be able use the integrated bacteria analysis pipeline for batch analysis, and type of genomic data

11. Demonstrate the ability to create a phylogenetic tree using SNPs

12. Use the phylogenetic instrument to create phylogenetic tree and determine the relationship between bacterial or pathogen strains

13. How to make your own sequence database

14. Use the MyDbFinder to find genetic markers of concern from whole-genome sequencing