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Example of linking genotype and phenotype

Examples of different gene-drug pairings for AMR detection preceding an exercise
Examples of different gene-drug pairings for AMR detection

table geno-pheno linking

For a set of strains, three different genes were sequenced and compared to phenotypic data for various drugs.

In scenario A) a clear presence/absence connection between gene 1 and resistance to drug 1 can be observed.

In scenario B) 4/5 strains with the S450L (Serine to Leucine at codon position 450 in the gene) mutation have resistance to drug 2, but one strain with this mutation is sensitive. This would be inconclusive in a strict presence/absence analysis but may be picked up by more statistics-based approaches.

In scenario C) there seems to be no association between the presence of gene 3 and resistance to drug 3. More data is likely needed to be completely sure of this, as there may be cryptic associations. If such an association is expected, in vitro methods may be needed to prove the connection.

Terminology for predictions

Linking genotype and phenotype is not an easy task, especially in complex cases where there is not an exact match. Most publications which try to undertake such linking report their outputs using the following terms:

  • True positive
    • The proposed genotypic resistance determinant definitely results in the isolate having the expected resistant phenotype
  • True negative
    • When the proposed resistance determinant is absent, the isolate has a susceptible phenotype
  • False positive (major error)
    • A resistance determinant is detected, but the isolate actually has a susceptible phenotype
  • False negatives (very major error)
    • No resistance determinant is detected, but the isolate has a resistant phenotype

It is important that we are open about our predictions and update our databases with the best information available.

© Wellcome Connecting Science
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Antimicrobial Databases and Genotype Prediction: Data Sharing and Analysis

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