Botswana AMR Implementation Guide
0.1.0 - 0.1.0
Botswana AMR Implementation Guide - Local Development build (v0.1.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions
Contents:
This page provides a list of the FHIR artifacts defined as part of this implementation guide.
These are custom operations that can be supported by and/or invoked by systems conforming to this implementation guide.
| Export WHONET Flat File |
Exports AMR DiagnosticReport data as a WHONET-compatible flat file or GLASS submission file. The operation flattens the FHIR resource graph (DiagnosticReport -> OrganismObservation -> SusceptibilityObservation) into isolate-centric rows suitable for WHONET import or WHO GLASS batch upload. |
These define constraints on FHIR resources for systems conforming to this implementation guide.
| Botswana AMR DiagnosticReport |
Bundles AMR culture results into one comprehensive report. References top-level observations (gram stain and organism identifications). Susceptibility and special test results are accessed via OrganismObservation.hasMember. |
| Botswana AMR Encounter |
Captures the clinical encounter context for AMR surveillance: ward type (inpatient/outpatient/ICU), admission date, department, and facility. Required for WHONET export and GLASS hospital-acquired vs community-acquired classification. |
| Botswana AMR Gram Stain Observation |
Records gram stain results for specimens in Botswana AMR surveillance |
| Botswana AMR Organism Identification Observation |
Records organism identification results from culture in Botswana AMR surveillance. Acts as the parent observation for susceptibility and special test results via hasMember. |
| Botswana AMR Patient |
Patient profile for Botswana AMR surveillance capturing essential demographics |
| Botswana AMR Special Test Observation |
Records special AMR test results (ESBL, Carbapenemase, D-Zone, MRSA) in Botswana AMR surveillance. Should be referenced from the parent OrganismObservation via hasMember. |
| Botswana AMR Specimen |
Specimen profile for Botswana AMR surveillance with required collection details |
| Botswana AMR Susceptibility Observation |
Records S/I/R (and optional MIC) for a single antibiotic test on a specimen. Should be referenced from the parent OrganismObservation via hasMember. |
These define constraints on FHIR data types for systems conforming to this implementation guide.
| Specimen Collection Location |
Ward or facility location where specimen was collected |
These define sets of codes used by systems conforming to this implementation guide.
| Botswana AMR AST Method |
Antimicrobial susceptibility testing methods used in Botswana AMR surveillance |
| Botswana AMR Antibiotic Susceptibility LOINC |
Collection of LOINC codes for antibiotic-susceptibility tests (MIC panel and individual drugs) |
| Botswana AMR Gram Stain Results |
Gram stain results used in Botswana AMR surveillance |
| Botswana AMR Interpretation |
Only Susceptible, Intermediate, or Resistant |
| Botswana AMR Organism Identification Methods |
Methods used for organism identification in Botswana AMR surveillance |
| Botswana AMR Organism ValueSet |
Organisms identified in Botswana AMR surveillance. Includes all descendants of SNOMED CT 'Organism' (410607006) plus local codes for organism combinations that labs report together. |
| Botswana AMR Special Tests |
Special antimicrobial resistance tests performed in Botswana AMR surveillance |
| Botswana AMR Specimen Collection Sites |
Anatomical sites where specimens are collected for Botswana AMR surveillance |
| Botswana AMR Specimen Type VS |
Specimen types used in Botswana AMR data collection, reusing v3-SpecimenType codes |
| Botswana AMR Test Result Status |
Status values for test results in Botswana AMR surveillance |
| Botswana AMR Ward Type |
Ward/location types for AMR surveillance, aligned with WHONET location type and GLASS origin classification |
These define new code systems used by systems conforming to this implementation guide.
| Botswana AMR Local Identification Method Codes |
Local codes for identification methods used in Botswana AMR surveillance |
| Botswana AMR Local Organism Codes |
Local codes for organism combinations and complex designations used in Botswana AMR surveillance |
These define transformations to convert between codes by systems conforming with this implementation guide.
| WHONET Antibiotic Codes to LOINC Susceptibility Codes |
Maps WHONET antibiotic codes to LOINC susceptibility test codes. Derived from the AMR R package (https://github.com/msberends/AMR). Contains 271 WHONET antibiotic codes with LOINC mappings. Note: equivalence is 'relatedto' because one WHONET antibiotic code maps to multiple LOINC codes representing different test methods (MIC, disk diffusion, etc.). |
| WHONET Antibiotic Codes to SNOMED CT Substance Codes |
Maps WHONET antibiotic codes to SNOMED CT substance concept IDs. Derived from the official LOINC-SNOMED CT Ontology (September 2025) by tracing LOINC susceptibility codes through their SNOMED observable entity representations to the Component (704320005) relationship, which identifies the substance being tested. Contains 213 authoritative antimicrobial mappings. |
| WHONET Antibiotic Codes to WHO ATC Classification |
Maps WHONET antibiotic codes to WHO ATC (Anatomical Therapeutic Chemical) codes. Derived from the AMR R package (https://github.com/msberends/AMR). Contains 374 WHONET antibiotic codes with ATC mappings. |
| WHONET Organism Codes to SNOMED CT |
Maps WHONET organism codes to SNOMED CT concepts. Derived from the AMR R package (https://github.com/msberends/AMR) which integrates WHONET organism codes with SNOMED CT mappings. Contains 4995 WHONET organism codes. |
These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like.
| E. coli Special Test - ESBL (Negative) |
ESBL testing for E. coli isolate - Negative |
| E. coli Susceptibility - Amoxicillin/Clavulanate (S) |
E. coli amoxicillin/clavulanate susceptibility - Susceptible by disk diffusion |
| E. coli Susceptibility - Ampicillin (R) |
E. coli ampicillin susceptibility - Resistant by disk diffusion |
| E. coli Susceptibility - Ceftriaxone (S) |
E. coli ceftriaxone susceptibility - Susceptible by disk diffusion |
| E. coli Susceptibility - Ciprofloxacin (R) |
E. coli ciprofloxacin susceptibility - Resistant by disk diffusion |
| E. coli Susceptibility - Gentamicin (S) |
E. coli gentamicin susceptibility - Susceptible by disk diffusion |
| E. coli Susceptibility - Nitrofurantoin (S) |
E. coli nitrofurantoin susceptibility - Susceptible by disk diffusion |
| E. coli Susceptibility - Trimethoprim/Sulfamethoxazole (R) |
E. coli TMP/SMX susceptibility - Resistant by disk diffusion |
| Example AMR Diagnostic Report - Urine Culture |
Complete AMR diagnostic report for urine culture with E. coli and K. pneumoniae |
| Example Encounter - Inpatient at Princess Marina Hospital |
Inpatient encounter, admitted 2 days before specimen collection |
| Example Gram Stain - Gram-negative |
Gram stain showing Gram-negative organisms in urine specimen |
| Example Organism - Escherichia coli (Isolate 1) |
E. coli identified from urine culture, isolate 1 |
| Example Organism - Klebsiella pneumoniae (Isolate 2) |
Klebsiella pneumoniae identified from urine culture, isolate 2 |
| Example Patient - Keabetswe Motswana |
A 45-year-old female patient admitted to Princess Marina Hospital |
| Example Specimen - Mid-stream Urine |
Mid-stream clean catch urine specimen collected from inpatient |
| Klebsiella Special Test - ESBL (Negative) |
ESBL testing for Klebsiella pneumoniae isolate - Negative |
| Klebsiella Susceptibility - Amoxicillin/Clavulanate (I) |
Klebsiella pneumoniae amoxicillin/clavulanate susceptibility - Intermediate by disk diffusion |
| Klebsiella Susceptibility - Ampicillin (R) |
Klebsiella pneumoniae ampicillin susceptibility - Resistant by disk diffusion |
| Klebsiella Susceptibility - Ceftriaxone (S) |
Klebsiella pneumoniae ceftriaxone susceptibility - Susceptible by disk diffusion |
| Klebsiella Susceptibility - Ciprofloxacin (S) |
Klebsiella pneumoniae ciprofloxacin susceptibility - Susceptible by disk diffusion |
| Klebsiella Susceptibility - Gentamicin (S) |
Klebsiella pneumoniae gentamicin susceptibility - Susceptible by disk diffusion |
| Klebsiella Susceptibility - Meropenem (S) |
Klebsiella pneumoniae meropenem susceptibility - Susceptible by disk diffusion |