High-level overview of the Microbiology feature: purpose, scope, and core concepts.

Overview

Microbiology in the medical laboratory involves the identification of microorganisms such as bacteria, fungi, and other pathogens in clinical samples through culture and susceptibility testing. The Microbiology feature supports labs in configuring antibiotic susceptibility reports by linking organisms to antibiotics, defining RIS (Resistant / Intermediate / Sensitive) ranges, and generating structured antimicrobial susceptibility grids at report entry.

Microbiology

Microbiology provides the product foundation for managing organism-antibiotic susceptibility configuration and report entry behavior. Before a microbiology workflow can be used in billing or report entry, labs must define the underlying organism catalog and map antibiotics to each organism with their associated RIS breakpoint ranges (Detection Window or MIC). This setup ensures that microbiology tests use consistent susceptibility patterns and interpretations across the workflow.

After prerequisite master data is ready, a microbiology report/test is created from Profile & Report Management > Test List. When the test type is selected as Microbiology, the report parameter builder exposes a Microbiology Parameter component.

Prerequisites

Requirement	Why it matters	Where it is enforced
Organism master data must exist	The Microbiology component lets report-entry users add organisms from the organism catalog	Organism Master module in `livehealth-frontend`; backend persistence in `livehealthapp` and `crelio-app`
Antibiotic master data must exist	An antibiotic record represents a drug used to determine susceptibility patterns	Antibiotic Master UI and related backend APIs
Organism must be mapped to antibiotics with RIS ranges	RIS breakpoints (Diameter / MIC) on each organism-antibiotic mapping drive the automatic interpretation shown in the report entry grid	Organism Master → `Antibiotic Mapping` tab → `Microbiology Ranges` sub-tab
User must have access to Drug Master / Panel Master screens	The master setup for organisms and antibiotics is managed from the Drug Master / Panel Master area in the application sidebar	Frontend route/sidebar permissions and backend authorization
Microbiology test/report must be created with test type `Microbiology`	The Microbiology report component is available only after selecting the Microbiology test type	Test List / Add New Test flow in `livehealth-frontend`

What Is It For

Frontend perspective

Provide Organism Master and Antibiotic Master screens under Drug Master / Panel Master.
Let users create, update, disable, download, and bulk-manage organism and antibiotic records.
Let users define organism-to-antibiotic mappings with RIS breakpoint ranges under the Microbiology Ranges sub-tab inside the organism creation flow.
Show system default, custom, disabled, and all-record views where applicable.
Create a microbiology report/test by selecting test type Microbiology.
Add the Microbiology Parameter report component from the report parameter menu.
Configure max number of organisms, type of method (Detection Window / MIC / Interpretation Only), referring list (Organisms), and display field columns.
At report entry, enforce the maximum organism count and auto-calculate interpretation from entered results against the configured RIS ranges.

Backend perspective

Persist organism and antibiotic master data across livehealthapp and crelio-app.
Validate required fields such as organism name/category/code and antibiotic name/category/code/unit.
Maintain relationships between organisms and antibiotics through the OrganismAntibiotics table (standard antibiogram) with RIS diameter and MIC breakpoints.
Maintain molecular-specific organism-to-antibiotic ordering and active state through the MolecularOrganismAntibiotics table.
Persist microbiology report parameter configuration and component metadata for report entry and billing workflows.

Types / Modes

Type	Example	Runtime behavior	Notes
Organism	E. coli, S. aureus, K. pneumoniae	Defines microorganisms with name, category, code, cut off, sample type, and description; linked to antibiotics through `OrganismAntibiotics`	Base entity for microbiology report entry
Antibiotic	Ciprofloxacin, Cefotaxime, Amikacin	Defines antimicrobial drugs with name, category, code, method, unit, sample type, device name, and dosage	Shared between Organism master and Molecular master contexts
Microbiology Parameter component	Microbiology	The single report component for microbiology test type	Configured with Method Type, Max Number Of Micro Organisms, Referring List, and column fields
Detection Window method	Disk diffusion susceptibility	Interpretation computed using diameter breakpoints (lower–upper range per RIS category)	`result_r`, `result_i`, `result_s` columns show configured breakpoint ranges
MIC method	Minimum Inhibitory Concentration	Interpretation computed using MIC breakpoints (lower–upper range per RIS category)	Uses MIC lower/upper per RIS category
Interpretation Only method	Text-only interpretation	Hides result columns; shows only organism name and manual interpretation	No automatic RIS calculation

Structure Of Microbiology

Layer	What it stores or owns	Table / state / file	Why it exists
Antibiotic master layer	Antimicrobial drug definitions	`Antibiotic`	Provides the base antibiotic catalog shared by organism susceptibility workflows
Organism master layer	Microorganism definitions with antibiogram mappings	`Organism` with `OrganismAntibiotics` and `MolecularOrganismAntibiotics`	Represents detected organisms and their RIS susceptibility patterns
RIS range layer	Per-organism, per-antibiotic breakpoints	`OrganismAntibiotics` (resistance/intermediate/sensitive diameter and MIC fields)	Drives automatic interpretation at report entry based on entered result
Microbiology report layer	Microbiology report/test configuration and component	`Profile & Report Management > Test List > Add New Test > Test Type: Microbiology > Report Parameters`	Defines report-entry behavior for organism identification and antibiotic susceptibility grids
Frontend UI layer	Lists, modals, filters, bulk actions, add/update flows	`Drug Master / Panel Master` screens and `Test List > Report Parameters` builder	Lets users manage prerequisite master data and configure microbiology report components
Backend service layer	APIs, validation, persistence, permissions	`Organism`, `Antibiotic`, `OrganismAntibiotics`, `MolecularOrganismAntibiotics` plus microbiology handling inside generic report-submit flows	Owns source-of-truth behavior for master data, billing defaults, and report submission

Master Data Model Notes

Organisms maintain two relationships to antibiotics:

OrganismAntibiotics: standard antibiogram mappings that carry RIS breakpoint values (diameter and MIC lower/upper per R/I/S category). This is what the Microbiology Ranges tab inside Organism Master populates.
MolecularOrganismAntibiotics: molecular-specific ordered and activatable mappings with sequence and is_active fields. This is managed under the Molecular Mapping sub-tab and is used by the Molecular feature's Antibiotic Resistance component.

Key OrganismAntibiotics breakpoint fields populated by Microbiology Ranges:

Field	Description
`resistance_diameter_lower` / `resistance_diameter_upper`	Disk diffusion diameter range for Resistant
`intermediate_diameter_lower` / `intermediate_diameter_upper`	Disk diffusion diameter range for Intermediate
`sensitive_diameter_lower` / `sensitive_diameter_upper`	Disk diffusion diameter range for Sensitive
`resistance_mic_lower` / `resistance_mic_upper`	MIC range for Resistant
`intermediate_mic_lower` / `intermediate_mic_upper`	MIC range for Intermediate
`sensitive_mic_lower` / `sensitive_mic_upper`	MIC range for Sensitive

Key Features

Organism Master list with organism name, sample type, organism category, organism code, and status.
Antibiotic Master list with antibiotic name, sample type, antibiotic category, antibiotic code, and status.
Organism Antibiotic Mapping tab with two sub-tabs: Molecular Mapping (for molecular workflows) and Microbiology Ranges (for microbiology susceptibility breakpoints).
Microbiology Ranges sub-tab shows an editable grid per antibiotic with R, I, S rows, each configurable with Diameter Upper, Diameter Lower, MIC Upper, and MIC Lower fields.
Microbiology report parameter component configured with Referring List, Max Number Of Micro Organisms, Type Of Method, and column Configuration.
At report entry: the Add Organism dropdown is capped by the configured max_allowed_microorganism; adding beyond the limit shows an alert and blocks addition.
Once an organism is added at report entry, the user can add antibiotics (drawn from the organism's OrganismAntibiotics mappings) to each organism section.
Entering a result value in result_1 triggers automatic interpretation (result_2) based on the configured method type and RIS breakpoints.
result_r, result_i, result_s columns are read-only and display the configured breakpoint ranges for reference.
Interpretation Only method type hides result and RIS columns; only organism name and manual interpretation are shown.

Overview

On this page