AMR Sample Testing
Executive summary
As antimicrobial resistance (AMR) develops, treating a patient becomes more complex and difficult because standard antibiotics and antimicrobial treatments become less effective. This situation can lead to prolonged illness, higher medical costs, and an increased risk of spread of the resistant infection to others. Therefore, testing patients for resistant microorganisms becomes a key step in identifying and managing these hard-to-treat infections, ensuring that healthcare providers can make informed decisions about safer and more effective treatment options. We have helped HISP India develop improved tools to track the sample test lifecycle, follow up with patients depending on test results, and aggregating data for additional decision making as part of a larger AMR Combat effort.
Proposed solution
To be able to effectively follow up on patients getting tested and treated for AMR, three different DHIS2 tracker programs were developed and tested. Relevant working lists that track patients or samples in their appropriate states were also made available for each program. When a patient is due for AMR sample testing, they will be registered as a Tracked Entity into DHIS2. This tracked entity will then be enrolled into an initial program that handles all registration and sample-data. If the results of the sample show antimicrobial resistance, the tracked entity will be moved to either program 2 (Gram positive) or program 3 (Gram negative). A detailed breakdown of these programs and working lists are described in the section below.
Registering a patient
A patient becomes a Tracked Entity in the DHIS2 system upon registration for AMR testing. Basic patient data is collected through this monitored entity, including mandatory fields like "Medical record number," "Patient Full Name," and "Age." These attributes make it easier for hospitals and clinics to manage their patient information, match samples to the right clients, and avoid duplication. View the complete list of attributes in the table below, whereby red cells are designated as system requirements, yellow cells as necessary, and green cells as desired fields that record additional data that the facility might need. Health professionals use the core Tracker capture app to complete this registration.
| Form Name/Input | Value type |
|---|---|
| Medical record number * | Unique ID |
| Patient Full Name* | Text |
| Date | Date |
| Age* | Age |
| Region | Org unit |
| Zone/sub City | Org unit |
| Tele. NO. | Number |
Sample testing program
The previously created tracked entity is registered in a sample testing program when the clinic or hospital collects the sample and registers it in DHIS2. The status and sample details are saved in this program as events. Details regarding the sample, the time and date of the collection, and the collector's name would be provided in the sample details by the clinician. The clinician must choose both the organism group and the specific species, which will then trigger the opening of an antibiotic panel tailored to that selection. The table below shows every data element that is collected in the program stage. The color scheme used in the previous table is also used in this one.
| Form Name | Value type | Dropdown |
|---|---|---|
| Sample type | Text | * Organism Detected* Sterile |
| Growth | Text | |
| Specimen Collection Date | Date | |
| Time | Time | |
| Lab Id | Text | |
| Date when received in the lab | Date | |
| Time when received in the lab | Time | |
| Received by | Text | |
| Test Requested* | Text | * Routine Culture* Fungus Culture* Routine culture (Back up service)* Others (text field) |
| Organism | Text |
After the lab sample is successfully analyzed, the results are stored in a separate event in this program.
Gram Positive & Gram Negative
If the lab sample results from the previous program is positive, the patient is then enrolled into a Gram Positive or Gram Negative program, depending on the type of resistant cells. Each program contains a separate treatment plan that the patient needs to go through. For those identified with Gram-positive infections, the treatment plan generally entails a different class of antibiotics that are effective against the thick cell wall structure of these bacteria. In contrast, treatment for Gram-negative infections typically involves a different strategy due to their additional outer membrane, which requires a distinct class of antibiotics that can penetrate this protective layer.
Patient lists / Working lists
Patient lists are a set of working lists that show information about tracked entities based on specific programs, location, enrollment details, or other factors. These lists can be set up to show only the records that need attention or action. Common examples include records that need follow-up, records with a value exceeding a set limit, or active cases within a certain location. The working lists we provided in AMR Combat have been arranged to show which patients and lab samples need to be addressed next, effectively serving as a queue or checklist for patient care.
Patient lists for clinicians
Clinicians will be able to view a list of patients at the hospital whose samples the lab has collected and examined. The list will summarize the current testing status for the patient's sample and, if available, will inform the healthcare provider on the results. The list will only allow healthcare providers to read the data and will not allow them to add any information to the patient's record. Lab results for the patient will be displayed in the list or queue as soon as a sample has been obtained. The patient will be removed from this list as soon as the patient's outcome is updated.
Patient lists for lab technicians
The lab technicians will be given access to two kinds of queues/ patient lists based on the sample testing or antibiotic susceptibility testing (AST)
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Patient lists for sample testing
The lab technician will be able to view this list of patients whose samples have been obtained and whose tests results are still pending. The list will include every patient for whom a sample has been collected. The patient will be deleted from the list as soon as the sample result is updated.
Patient lists for AST
This list will show patients for whom sample has been tested positive for any pathogen and AST results are pending. Once AST results are reported, the patient will be removed from the list.
Impact
Testing patients for antimicrobial resistance (AMR) is crucial to identify and manage hard-to-treat infections. To improve tracking and decision making, new tools have been developed to track sample test lifecycles, follow up with patients, and aggregate data. Three DHIS2 tracker programs have been created for registering patients, testing samples, and tracking patient outcomes. These programs collect various data elements, including patient information, sample details, and test results. Working lists help healthcare providers identify which patients and lab samples need attention or action. Effective follow-up and treatment planning are essential for patients identified with Gram-positive or Gram-negative infections based on their resistant cells.️