This section gives an introduction about senaite.ast. It assumes you
have SENAITE LIMS and
senaite.ast already installed. Please read the
Installation for further details.
Adding a pre-defined AST Panel¶
To add pre-defined AST Panels, click the “gear” icon from top right, go to “AST Panels” view.
From this view, you can either create a new AST Panel or edit an existing one:
From this view, you can choose both the Microorganisms and the Antibiotics. Please read the documentation of senaite.microorganism and the documentation of senaite.abx for further details.
If a “Clinical breakpoints table” is selected, the system will automatically use this breakpoints table to calculate the susceptibility testing category (S/I/R) when the diameter of the inhibition zone is submitted by the user. Still, user can change the breakpoints table to use for any given antibiotic and microorganism later, on susceptibility testing results introduction.
If the option “Include disk content in ug” is selected, an additional row for the introduction of the disk content (potency) in μg is displayed in the results entry view, above resistance call options.
If the option “Include zone diameter in mm” is checked, besides the qualitative analysis for antibiotic susceptibility, the system will also add analyses for the capture of the zone of inhibition in mms automatically when this panel is selected.
If the option “Selective reporting” is checked, the system will also add an analysis to allow the user to indicate the resistance results to be displayed in results report. If unchecked, all resistance results will be rendered. Besides, this option also allows the user to choose the extrapolated antibotics to be reported.
Adding a pre-defined Clinical Breakpoints Table¶
To add pre-defined Clinical Breakpoint Tables, click the “gear” icon from top right, go to “AST Breakpoints Tables” view.
From this view, you can either create a new AST Breakpoints Table or edit an existing one:
From this view, you can introduce the inferred sensitivity categories for each antibiotic and microorganism (or group of microorganisms) based on the diameter size of the inhibition zone in mm. The disk content (potency) for each row can also be set in this edit view.
Microorganism identification analysis¶
Besides AST Panels, this add-on creates a new analysis service with name “Microorganism identification” and the category “Antibiotic Sensitivity Testing (AST)” as well.
When this “Microorganism identification” service is assigned to a Sample (either from Sample Add form or later, through “Manage analyses”), a new analysis with pre-defined result options is added.
The selection list of this type of analysis is populated with the microorganisms registered in the system that are in “active” status.
This analysis behaves as a multi-selection list, so the user can choose as many microorganisms as required.
Assignment of an AST Panel to a Sample¶
For the assignment of an AST Panel to a sample, go to sample view. Below the analyses listing, a section for Sensitivity Testing is displayed:
Select one of the available AST Panels and press the button “Add”. Analyses are added automatically based on the settings of the AST Panel of choice.
If no AST Panels are displayed, please check that at least one of the microorganisms identified (see Microorganism identification analysis) is assigned to a pre-defined AST Panel.
You can add as many AST Panels as you wish, but only identified microorganisms will be added by default. Microorganisms are displayed in rows and Antibotics (abbreviations) in columns.
Custom AST Panel for a Sample¶
Sometimes user might want to add additional microorganisms, even if they were not initially identified or add new Antibiotics, even if they weren’t defined in the pre-defined AST Panel of choice.
From same view, press the “Custom” button and a matrix with microorganisms as rows and antibiotics as columns is displayed for easy selection. By default, only microorganisms identified are displayed. However, user can press “All microorganisms” button to extend the list with the rest of microorganisms registered in the system:
System allows unbalanced entries, so user can choose different antibiotics for different microorganisms at will.
Once the button “Save” is pressed, the user is redirected to the Sample view and the list of AST analyses is updated accordingly:
User can easily set the resistance results to be included in the results report by means of the “Report” analysis. However, there is also the option to define the selective reporting all-at-once. Press the “Selective reporting” button and a matrix with microorganisms as rows and antibiotics as columns is displayed for easy selection.
From this view, user can choose the tuples Microorganism-Antibiotic to be reported in results. Once the button “Save” is pressed, the value for analyses with name “Report” for all microorganisms are updated accordingly.