Botswana AMR Implementation Guide#
The Botswana AMR Implementation Guide defines FHIR R4 profiles and terminology for antimicrobial resistance surveillance as part of the Botswana AMR Data Analytics Platform — a collaboration between the University of Botswana and Children's Hospital of Philadelphia.
The Problem#
Antimicrobial Resistance (AMR) now causes more deaths than HIV/AIDS and malaria worldwide and is estimated to be the number-5 leading cause of death in Botswana. Approximately 1 in 10 patients admitted to a hospital in Botswana will experience a health-associated infection.
What This IG Does#
The IG standardizes AMR culture and susceptibility data using FHIR, enabling:
- Electronic surveillance — structured data capture replaces paper-based reporting
-
WHONET compatibility — a
$export-whonetoperation generates flat files for WHONET import - GLASS reporting — ward type, admission date, and facility data support WHO Global AMR Surveillance System submissions
- Interoperability — standard FHIR profiles allow integration with national health information systems and the National Data Warehouse
Profiles#
| Profile | Purpose |
|---|---|
| DiagnosticReport | Bundles a complete culture result: gram stain, organism identifications, and susceptibility panels |
| Encounter | Ward type, admission date, and facility — required for GLASS origin classification |
| OrganismObservation |
Identified organism per isolate, links to susceptibility and special test results via
hasMember
|
| SusceptibilityObservation | S/I/R interpretation with optional MIC or zone diameter per antibiotic |
| SpecialTestObservation | ESBL, carbapenemase, MRSA, D-zone, and beta-lactamase detection |
| GramStainObservation | Gram stain morphology result |
| Specimen | Specimen type, collection date, body site |
| Patient | Demographics with Omang (national ID) support |
Technology Stack#
- IG authoring: FSH (FHIR Shorthand) compiled with SUSHI
- Data capture: Flutter/Dart mobile application using fhir_r4
- Server: Any FHIR R4 server (designed to work with FHIR ANT for mobile-first deployments)
- WHONET export: Server-side
$export-whonetFHIR operation
Source Code#
- IG repository: github.com/Dokotela/bw-amr-ig