Importance of whole genome sequencing

In the previous weeks we have learned about various phenotypic and molecular methods of detecting antimicrobial resistance. Although these methods are accurate, the information generated is limited to specific genes. Therefore multiple tests need to be performed to generate a resistance profile, making the process labour-intensive. In addition, these methods do not tell us anything about mechanisms of resistance or how the resistance was acquired in the first place.

By contrast, genome sequencing enables us to detect all the resistance determinants of a strain in a single experiment. The genetic information can also be used to determine genetic relatedness between the strains and infer transmission. Hence, genome sequencing offers a huge potential for use in clinical settings.

In the previous week, we learned about Min-Ion sequencing, which is one of the methods used for sequencing. In this section, we go through the process of sequence data analysis for identifying antimicrobial resistance in bacterial pathogens.

We will start by downloading the raw sequence data of an isolate from a publicly available database. Next we will perform assembly of the downloaded sequence data generating contigs. These contigs will then be used to detect antimicrobial resistance using a freely available online tool. The results of the genetic analysis will then be compared with the phenotypic susceptibility results. We will end the section by discussing troubleshooting in case of discordance between the genotype and phenotype results.