LIMS Microbiology Overview - hmislk/hmis GitHub Wiki

Microbiology Overview

The LIMS supports a dedicated microbiology reporting workflow that is separate from general biochemistry and haematology. Microbiology reports handle culture and sensitivity results, where the lab identifies the organism(s) isolated from a patient's sample and then tests those organisms against a panel of antibiotics. This article explains what makes microbiology different and when to use the microbiology report type.

How Microbiology Differs from General Reporting

Feature General / Biochemistry report Microbiology report
Result type Numeric values (e.g., 5.2 mmol/L) Text identification + sensitivity categories
Antibiotic testing Not applicable SENSITIVE / RESISTANT / INTERMEDIATE per antibiotic
Multiple organisms Not applicable Multiple organisms can be reported independently from the same sample
Result grouping All parameters in one list Results grouped by organism — each organism has its own antibiotic panel
Report layout Tabular with reference ranges Organism identification + sensitivity table

The Microbiology Report Type

When an investigation is configured with the Microbiology report type by the lab administrator, the result entry screen automatically displays the microbiology-specific layout instead of the standard tabular form. You do not need to switch between modes — the correct layout is determined by the investigation's configuration.

Investigations using the microbiology layout include (but are not limited to):

  • Urine Culture & Sensitivity (C&S)
  • Blood Culture
  • Sputum Culture
  • Wound Swab C&S
  • High Vaginal Swab (HVS) C&S
  • Stool Culture

The Microbiology Workflow

Sample accepted at the lab
        ↓
Open the report for data entry (Menu > Lab > Report Management)
        ↓
Enter preliminary culture findings (growth / no growth, incubation observations)
        ↓
Identify organism(s) isolated
        ↓
Add antibiotic sensitivity results for each organism
        ↓
If multiple organisms isolated → add a new group for each organism
        ↓
Approve the report
        ↓
Print and/or send to patient

Key Concepts in Microbiology Reporting

Organism Identification

The organism identification section is a free-text (memo) field where the microbiologist enters the identity of the isolated organism — for example, Escherichia coli or Staphylococcus aureus. Other preliminary findings such as colony morphology, Gram stain result, and preliminary identification can also be recorded here.

Antibiotic Sensitivity

For each isolated organism, a panel of antibiotics is tested and the result recorded as:

  • SENSITIVE — the organism is susceptible to this antibiotic at therapeutic concentrations.
  • RESISTANT — the organism is not inhibited by this antibiotic.
  • Intermediate — the organism shows intermediate susceptibility; may respond to higher doses or site-specific concentrations.

Organism Groups

When more than one organism is isolated from the same sample, each organism gets its own group in the report. Within each group:

  • The organism is identified in the memo field.
  • A complete antibiotic panel is listed and results entered independently.

This means the clinician can see exactly which antibiotics are effective against each specific organism in a polymicrobial infection.

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