Skip main navigation

Comparing the genotype and phenotype

Comparing the genotype-based predictions with phenotypic susceptibility results
© Wellcome Genome Campus Advanced Courses and Scientific Conferences

When comparing the phenotypic drug susceptibility results to the genomic determinants identified, there could be some cases with discrepancies. These can occur because of the following reasons:

1. Phenotype sensitive but the genotype is resistant

This refers to the cases where the resistance genes are identified but the strain is phenotypically sensitive. In such cases first, re-phenotype the strain. If unresolved, check for insertion or deletion in the resistance gene identified that results in premature termination making the gene non-functional. This can be performed by looking at the sequence in Artemis.

2. Phenotype resistant but the genotype is sensitive

This refers to the cases where the strain is resistant phenotypically but the resistant gene could not be identified. The first step would be to repeat the phenotypic test and if unresolved perform resequencing of the isolate. If the case remains unresolved the strain might have some novel resistance mechanism that is not in the databases.

Can you think of any other reasons why the phenotype and genotype might contradict? Suggest some examples in the discussion.

© Wellcome Genome Campus Advanced Courses and Scientific Conferences
This article is from the free online

Bacterial Genomes: Antimicrobial Resistance in Bacterial Pathogens

Created by
FutureLearn - Learning For Life

Our purpose is to transform access to education.

We offer a diverse selection of courses from leading universities and cultural institutions from around the world. These are delivered one step at a time, and are accessible on mobile, tablet and desktop, so you can fit learning around your life.

We believe learning should be an enjoyable, social experience, so our courses offer the opportunity to discuss what you’re learning with others as you go, helping you make fresh discoveries and form new ideas.
You can unlock new opportunities with unlimited access to hundreds of online short courses for a year by subscribing to our Unlimited package. Build your knowledge with top universities and organisations.

Learn more about how FutureLearn is transforming access to education