Gaps #87143
Updated by Vasuki Muniratnam 5 months ago
To generate statistics on dominant organisms identified through microbiological testing, such as the most commonly identified pathogens by specimen type, etc. HUMS to provide details relevant to the required report Comment: To clarify/confirm with client on UI placement !clipboard-202508211736-f1oc2.png! Request to clarify with clients on these points below: How should we define "dominant" organisms? Suggestion for the above: By highest number of isolates, specimen type, resistance pattern, location/unit, infection severity or clinical impact. !clipboard-202508221213-mm5el.png! Example Report: Top 5 Dominant Organisms (Urine, August 2025) *MIS REPORT* *Report Name:* Dominant Organism Analysis Report *Search Criteria* | Filter | Control | Remarks | | Unit Facility | Dropdown | Default value: Hospital Universiti Malaysia Sabah (HUMS). Data shall be retrieved based on the selected unit. | | Ward / Unit | Dropdown | Populate ward list based on patient ward/location master. Include "All" option.Searchable. | | From Collection Date | Date Picker | Culture specimen collection start date. | | To Collection Date | Date Picker | Culture specimen collection end date. | | Specimen Type | Multi-select Dropdown | Populate from Microbiology Specimen Type Master. Include "All" option. Searchable | | Source Type | Multi-select Dropdown | Populate based on patient encounter category (ER, Inpatient, Outpatient, Day Care). Include "All" option. | | Bacteria | Optional Search | Optional searchable field to filter by identified organism/bacteria name. | | Show Report | Button | Generate report based on selected criteria. | Screen Layout: !clipboard-202606031538-zpjj1.png! *Output Grid* | Bacteria Rank | Organism Name | Specimen Type | Source Type | Unit No. of Isolates | Ward |No. % of Total Isolates | | 1 | Escherichia coli | Urine | Inpatient | 130 | 43% | | 2 | Klebsiella pneumoniae | Urine | Outpatient | 80 | 27% | | 3 | Enterococcus faecalis | Urine | Inpatient | 40 | 13% | | 4 | Proteus mirabilis | Urine | Walk-In | 25 | 8% | | 5 | Pseudomonas aeruginosa | Urine | Referral | 20 | 6% | | Sample output grid image: !clipboard-202606031609-qnelu.png! *Sorting* Default sorting: No. of Isolates: DECREASING ORDER Highest isolate count appears first. *Calculation Logic:* 1. Step 1 : Retrieve all finalized positive microbiology culture results within the selected: i) Collection Date range ii) Ward iii)Specimen Type iv) Source Type v) Bacteria 2. Step 2 Exclude: Negative cultures No growth cultures Contaminated cultures Pending cultures *Include only cultures with identified organisms.* 3. Step 3 *Isolate Counting Rule*: a.) Only finalized positive culture results shall be included in the report. b.) Each positive culture result shall be counted as one isolate. c.) If the same patient has multiple positive cultures for the same organism and specimen type on d.) the SAME collection date, it shall be counted as one isolate only. e.) If the same patient has positive cultures for the same organism and specimen type on f.) DIFFERENT collection dates, each occurrence shall be counted as a separate isolate. g.) Positive cultures from different specimen types shall be counted as separate isolates even when collected on the same collection date. *1.) Same patient + same organism + same specimen type + same collection date = Count once * *2.) 2.) Same patient + same organism + same specimen type + different collection date = Count separately * separately* Step 4 5 Calculation of Number of Isolates * Only finalized positive culture results shall be included. * A unique isolate shall be identified based on: Patient Organism Name Specimen Type Collection Date * Multiple positive culture results for the same patient, organism, specimen type, and collection date shall be counted as one (1) isolate. * Positive culture results collected on different collection dates shall be counted as separate isolates. * The report shall calculate the Number of Isolates by grouping identified isolates based on: Organism Name Specimen Type Source Type Ward * Results shall be displayed in descending order of Number of Isolates. First, Identify Unique Isolates *Group by:* Patient + Bacteria + Specimen Type + Collection Date After unique isolates are identified, generate the report by grouping: Organism Name + Specimen Type + Source Type + Ward Then, Count Isolates Sort by, No of isolates, in Decreasing Order. No. of Isolates Step 6 Calculate Percentage Formula: (Organism Isolates ÷ Total Isolates for same specimen type) × 100 Example: Organism Isolates E. coli 130 Klebsiella 80 Enterococcus 40 Proteus 25 Pseudomonas 20 Total 303 E. coli = 130 ÷ 303 × 100 = 43% Recommended Grid Columns Column Rank Organism Name Specimen Type Source Type Ward No. of Isolates % of Total Isolates Adding Ward is important because the client specifically requested ward-level analysis. Without the Ward column, users cannot identify where the organism prevalence originates.