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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-whonet operation 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​

ProfilePurpose
DiagnosticReportBundles a complete culture result: gram stain, organism identifications, and susceptibility panels
EncounterWard type, admission date, and facility — required for GLASS origin classification
OrganismObservationIdentified organism per isolate, links to susceptibility and special test results via hasMember
SusceptibilityObservationS/I/R interpretation with optional MIC or zone diameter per antibiotic
SpecialTestObservationESBL, carbapenemase, MRSA, D-zone, and beta-lactamase detection
GramStainObservationGram stain morphology result
SpecimenSpecimen type, collection date, body site
PatientDemographics 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-whonet FHIR operation

Source Code​