Comparing the genotype and phenotype

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.