The AST form in SEDRI-LIMS allows users to enter susceptibility test results from any combination of disk diffusion tests, MIC assays or gradient diffusion tests. It can be entered by selecting the AST icon, either on the appropriate culture row in the culture section of the specimen record-view, or from within the culture-view itself (on the top row). Both options are illustrated below:
<Image of culture row with AST icon in the specimen record-view>
OR
<Image of AST button along the top of the culture record-view>
If the identity of an isolate has already been recorded when entering the AST form, the system will search for appropriate test patterns by matching the isolate identity against the organism scope binding of each test pattern configured in the system. Once the form appears, all matched test patterns appear as options of the Matched Test Patterns drop-down field at the top-left of the form, under the section entitled Test Pattern Selection (see below). In the example shown, the recorded organism, Streptococcus pneumoniae, has matched two test patterns: “CLSI - Streptococcus pneumoniae” and “CLSI Alpha-haemolytic Streptococcus”. The former has been automatically selected, as it’s a more direct match to the organism (by virtue of its unseen direct binding to Streptococcus pneumoniae).
Given two or more matched test patterns, if no single pattern binding represents the closest match to the organism, then no test pattern is automatically selected and the user must make an explicit choice. For instance, if in the above case, there was a third test pattern called “CLSI - Streptococcus pneumoniae #2”, also bound directly to Streptococcus pneumoniae, this would represent an unresolvable conflict and no test pattern would be automatically selected.
A way to resolve such conflicts in advance is to set one of the (potentially) conflicting test patterns to be a default and the other not to be (see ??????).
To the right of the Matched Test Patterns field, also shown in the above screen-shot, is the All Test Patterns field. This drop-down field includes every test pattern configured in the system. If the system has failed to automatically select a test pattern or has failed to select the desired test pattern, an alternative test pattern can be selected, at any point, either from the Matched Test Patterns options or the All Test Patterns options. Note, however, that any susceptibility data previously entered will be lost (unless previously saved).
When a test pattern is selected, either manually or automatically, the antibiotic rows associated with the test pattern are rendered on the form, as shown below.
This accounts for the first three columns entitled: Antibiotic, Dosage (ug) and Guidelines, plus the Include in Report? column, all of which originate from the test pattern definition. The Zone Diameter (mm) / MIC (ug/mL) (measurement) and Susceptibility columns are added for the AST form only.
A test pattern may include a mixture of disk diffusion, MIC, and gradient diffusion tests. Disk tests appear in the Disk Tests section (immediately below the Test Pattern Selection), while both MIC and gradient tests are catered for by the MIC Tests section, below the Disk Tests section. Gradient tests do not currently have their own dedicated section and are entered in the same manner as MIC tests.
In the typical workflow, zone diameters, MIC values, or gradient measurements are entered into the corresponding fields of each test row. Once an entry is registered — by clicking away from the field or pressing Tab — the system will apply any matching breakpoints, determine the qualitative susceptibility, and populate the Susceptibility field automatically.
You may override the automatically assigned interpretation at any time. You may also manually select a susceptibility category even if no measurement is entered. Although, omitting measurements is not recommended — as it prevents the system from reapplying breakpoints in the future — the system does not restrict you from doing so.
Any of the fields populated from the test pattern (Antibiotic, Dosage (ug), Guidelines and Include in Report?) can be adjusted at any time. This is useful if, for example, a depleted antibiotic must be substituted with an alternative pending re-stock. Caution is advised, however, as the antibiotics and disk potencies defined in the test pattern are aligned with the breakpoint tables in the selected reference guideline.
Rows that are not required or cannot be performed may be removed by selecting the X icon at the far right of the row. This may be necessary when an antibiotic is unavailable and no suitable replacement exists. Additional rows (disc or MIC) may also be added if an appropriate antibiotic becomes available that is not included in the test pattern.
The Include in Report toggle is particularly useful for cascade reporting. For example, a broad-spectrum antibiotic may have this toggle disabled in the test pattern definition so that a susceptible result is not routinely reported. However, once testing is complete, if all narrow-spectrum antibiotics are interpreted as resistant, the setting for the broad-spectrum agent may be overridden so that its result is included in the report.
Some susceptibilities are specific to conditions that are unknown to the system. These are referred to as Special Considerations and fall into three main categories:
- Disease indications, e.g. meningitis, pneumonia or encephalitis
- Method of drug administration, e.g. oral or parenteral
- Surrogate test, e.g. screen-only
Where a breakpoint is bound to one or more of these special conditions, extra child rows are added to the AST form under the row they relate to, one per unique combination, as illustrated below.
In the example above, with an MIC value of 16 µg/mL, no unconditional qualitative susceptibility is assigned. Susceptibility outcomes are only valid under the specific conditions noted in each child row. If a row is determined to be irrelevant based on external information, it can be removed by clicking the X icon at the end of that row. Note that deleting the parent row will also remove all associated child rows. While this is a real example from CLSI M100, it is rare to see more than one or two or these conditional rows for a given antibiotic.
Below the MIC Tests section is the Resistance Enzymes section, which provides key result fields for resistance enzymes commonly screened during AST.
The current set includes Betalactamase, ESBL, and Carbapenemase. These correspond to a subset of the standard default culture tests that can be assigned, removed, and completed outside of the AST page.
- If already provisioned: When one or more of these tests have been added to the culture and completed in the usual way, their results will automatically populate the corresponding fields in this section of the AST form
- If not provisioned: If a test was not previously added to the culture, entering its primary result directly in the AST form will automatically create and mark it as a completed culture test once the AST form is saved
Think of their presence on the AST screen as a convenience feature: since these results are often available during AST testing, the system ensures they can be recorded seamlessly without requiring duplicate steps.
Below the Resistance Enzymes section is the Comments section, as illustrated below.
All comment fields in the AST form are optional.
- Comment 1 and Comment 2: These provide two separate opportunities to select from a set of pre‑defined AST comments curated by the administrator. Think of these as standard, reusable comments that help ensure consistency
- Additional Notes: This is a free‑text field that can be used to capture any details or context not covered by the pre‑defined comment set
Together, these fields allow users to combine standardized remarks with specific observations, ensuring both consistency and flexibility in documentation.
The final control on this form is the Remove Incomplete Rows toggle. The operation is as follows:
- Yes (default):
- Any rows without a measurement (Zone Diameter (mm) or MIC (µg/mL)) and without a Susceptibility result are automatically removed when the form is saved.
- These rows will not reappear when the form is reopened for editing.
- No:
- Unfilled rows are preserved and re‑rendered when the form is edited, provided they contain values for Antibiotic, Dosage (disk tests only), and Guidelines.
Practical Use
- When many results are unavailable and will never be provided:
Keeping the toggle set to Yes avoids the need to manually delete each unfilled row using the X icon. - When results are received incrementally (e.g., disk tests first, MIC tests later):
Setting the toggle to No ensures that partially completed rows remain available until all results can be entered.
Once all available results have been entered, selecting Save (bottom-right of the page) will store everything against the culture and the form will disappear. If the AST form was entered from the culture record-view, this view will be re-displayed, this time with resistance enzyme culture test results and the AST susceptibilities displayed in tables as illustrated below.
As always, when you hover over any culture test row, the system displays a summary of the results.
If the AST form was entered from the specimen record-view, or upon subsequent return to the specimen view, hovering over the corresponding culture in the Cultures table will result in a culture overlay that includes both the resistance enzyme results and the susceptibilities, as shown below.
Once an initial set of AST results has been saved, they can be edited, updated, or augmented at any time, typically up until specimen submission. To make changes, simply re‑enter the AST form in the same way as before (see instructions at the top of this article).