1.2 Isolates Browser

Background

Historically, identifying tobramycin resistance in Acinetobacter baumannii has been difficult using automated methods. Here we will look for A. baumannii isolates that have conflicting phenotypes (i.e., tobramycin resistance with one method and susceptibility with another method).

Exercises

Login to NCBI account if you have not already done so. This is necessary to be able to do some of the exercises below.

• Go to Isolates Browser: https://www.ncbi.nlm.nih.gov/pathogens/isolates/
• Use command:

AST_phenotypes:tobramycin=R AND (AST_phenotypes:tobramycin=I OR AST_phenotypes:tobramycin=S)

• Link: https://www.ncbi.nlm.nih.gov/pathogens/isolates/#AST_phenotypes:tobramycin=R%20AND%20(AST_phenotypes:tobramycin=I%20OR%20AST_phenotypes:tobramycin=S)
• Go to Filters
• Go to Organism group; note there are two species–also note counts of isolates in each species
• Select "Acinetobacter baumannii" box Now all A. baumannii isolates with conflicting phenotypes will be displayed. This display can be downloaded as a .tsv file.

Click Cross-Browser Selection button, and then select MicroBIGG-E, so we can look at the resistance elements.

• In Filters, go to Subclass and select "TOBRAMYCIN"
• Then in Filters, open Element Symbol. This will provide a list of resistance elements associated with tobramycin resistance in these isolates with counts for each element.

Click Cross-Browser Selection button (image), and then select AST Browser to compare phenotypes.

• In Filters, select Antibiotic "tobramycin"

• Note the additional information such as testing method and so on.

• These data can be downloaded as a .tsv file.

• For the curious, Vitek is S/I, Phoenix is I/R, and Microscan is R.