Workflow Guide

This section explains how the Microbiology feature is used in practice before diving into implementation details.

Important: Document Db should be enabled for this feature to work.

Prerequisite Master Data Setup

Before Microbiology configuration is used, the lab needs prerequisite master data for organisms and antibiotics.

Where the user goes

1. Open the application sidebar.
2. Expand Drug Master / Panel Master.
3. Open Antibiotic Master or Organism Master depending on the master data being configured.

What the controls do

Antibiotic Master

Antibiotic Master defines the antimicrobial drugs used in susceptibility testing.

The list view shows:

• antibiotic name,
• sample type,
• antibiotic category,
• antibiotic code,
• status/action controls.

Antibiotics are mapped to organisms for standard antibiogram purposes. When disabling an antibiotic, the system checks for any linked organisms and displays them in a warning modal to prevent accidental disruption of antibiogram mappings.

Organism Master

Organism Master defines the microorganisms that may be detected in a clinical sample.

The list view shows:

• organism name,
• sample type,
• organism category,
• organism code,
• status/action controls.

When creating or updating an organism, the user can map antibiotics to the organism. The Antibiotic Mapping tab inside the organism creation/edit modal contains two sub-tabs:

1. Molecular Mapping — used by the Molecular feature's Antibiotic Resistance component. Antibiotics are added and prioritized with drag-and-drop sequence ordering.
2. Microbiology Ranges — used by the Microbiology feature's report-entry antibiogram grid. Antibiotics are added here and each mapping has an editable RIS range grid.

Microbiology Ranges Tab

After adding an antibiotic to the Microbiology Ranges sub-tab, the grid shows three rows per antibiotic — R (Resistant), I (Intermediate), and S (Sensitive) — each with four configurable fields:

The system validates that lower values are less than upper values. These configured ranges are used at report entry to auto-interpret the entered result as Sensitive, Intermediate, or Resistant.

How RIS interpretation works at report entry:

• When Detection Window is selected as the method type, the entered result_1 value is compared against the diameter breakpoints.
  • If the value falls within sensitive_diameter_lower ≤ result_1 ≤ sensitive_diameter_upper, the interpretation is Sensitive.
  • If the value falls within intermediate_diameter_lower ≤ result_1 ≤ intermediate_diameter_upper, the interpretation is Intermediate.
  • If the value falls within resistance_diameter_lower ≤ result_1 ≤ resistance_diameter_upper, the interpretation is Resistant.
• When MIC is selected, the same logic applies using the corresponding _mic_lower and _mic_upper fields.
• When Interpretation Only is selected, there is no automatic calculation; the user manually enters the interpretation text.

Note: The result_r, result_i, and result_s columns in the report entry grid are read-only and show the configured breakpoint ranges as reference strings in the format lower - upper.

When disabling an organism, the system checks for linked antibiotics and displays them in a warning modal.

Microbiology Report / Test Setup

After master data is configured, create a microbiology report from the Test List.

Where the user goes

1. Open Profile & Report Management.
2. Open Test List.
3. Click Add New Test.
4. On Test Information, set Test Type to Microbiology.
5. Save the test/report after report parameters are configured.

Selecting Microbiology as the test type (internally isRadiology: 4, test_type: "Microbiology") enables the microbiology-specific report component in the Report Parameters tab.

Microbiology Report Component

The Add New Parameter menu exposes the Microbiology category with one sub-component: Microbiology Parameter (component_type: "microbiology", type: 20).

Microbiology Form Fields

The Microbiology Parameter form includes the following configuration fields:

Note: If Max Number Of Micro Organisms is set to 1, the Render Pivot Table on PDF checkbox is automatically disabled.

Max Number Of Micro Organisms Enforcement

At report entry, when the user selects an organism from the Add Organism dropdown, the system counts the current number of distinct organisms already added. If the count equals or exceeds the configured max_allowed_microorganism, an alert is shown:

"Maximum {n} organism allowed"

and the organism is not added.

Type Of Method Behavior

When the Method Type is changed, updateMicroEditables(...) is called to hide or unhide the result/RIS columns accordingly. For Interpretation Only on a new report, the configuration is reduced to only name and result_2.

Primary User Workflow

1. User opens Drug Master / Panel Master.
2. User ensures required antibiotics are present in Antibiotic Master.
3. User creates organisms in Organism Master.
4. Inside each organism's Antibiotic Mapping tab, user opens the Microbiology Ranges sub-tab, searches and adds antibiotics, and configures the R/I/S diameter and MIC breakpoints.
5. User opens Profile & Report Management > Test List.
6. User creates a new test and selects Microbiology as the test type.
7. User adds the Microbiology Parameter component from the Add New Parameter menu.
8. User sets Referring List to Organisms, sets Max Number Of Micro Organisms, and selects Type Of Method.
9. User configures display columns in the Configuration tab.
10. Backend validates and persists the master data and report configuration.
11. At report entry, the user selects organisms from the Add Organism dropdown (limited by max_allowed_microorganism), and for each organism adds antibiotics from the organism's configured mapping.
12. When the user enters a result value in result_1, the system automatically fills in the result_2 interpretation based on the configured RIS ranges and method type.

Validation And Edge Cases