WHONET Training Course – Module 1: Getting Started (Notes) Installation Steps:

• Download the installation file and open it from your Downloads folder.
• Follow the usual installation steps: Accept → Next → Finish → Close.
What is WHONET? • Default installation folder: C:\WHONET
WHONET is a computer program created by the World Health • For shared use, install on a network drive.
Organization (WHO). It helps laboratories and hospitals collect, analyze, • Contact IT support or email help@[Link] for installation problems.
and share information about bacteria and how they respond to
antibiotics. This helps detect patterns of antimicrobial resistance (AMR)
After successful installation, two desktop icons will appear:
locally, nationally, and globally.
• WHONET – used for data entry, analysis, and reporting.
• BacLink – converts data from other systems into WHONET format.
In short, WHONET helps track which germs are becoming resistant to
which medicines.
BacLink supports systems like Excel, Access, Vitek, Microscan, Phoenix,
Sensititre, and LIS software (SEDRI-LIMS, SENAITE, Disa*Lab, OpenLDR,
1. WHONET Website SILAB).
Website: [Link] .When you open the WHONET homepage, you
will find different sections and links.
3. WHONET Main Menu
Main Menu at the Top:
3.1 Language Selection
1. Software
• Click 'Language and dates' after opening WHONET.
• Choose your language and click OK.
 Download WHONET (version updated annually).
• To switch back, repeat the process and choose English.
 BacLink is included in the installation package.
• Some translations may have small errors; corrections can be emailed to
 WHONET Automation Tool: Automates analyses, reports,
help@[Link].
and alerts.
 AMR Interpretation Engine: Used to interpret test results.
 WHONET Beta Version: Testing only (not recommended). 3.2 Opening WHONET
 WHONET 5.6: Old version, no longer updated since 2018. • Click 'Open laboratory' to go to the main menu.
• Menu options: File, Data Entry, Data Analysis, Help.
• In Help menu:
2. Training Center
- About: Shows WHONET team info and version.
- Documentation: Opens tutorial files in the Documents folder.
 Contains videos, slides, exercises, and tutorials for the
training course.
3.3 Exiting WHONET
 You will: watch videos, do exercises (not graded), and take
To close WHONET, click File → Exit, or click the 'X' button in the upper-
module exams (graded).
right corner.
 Additional materials: BacLink importing, Automation Tool
use, and exporting data to WHO GLASS, EARS-Net, and
CAESAR.

3. Webinars

 About two webinars per quarter.

 Watch videos and download slides for each topic.

4. Discussion Forum

 Public forum for users to discuss and collaborate.

 Create public or private chat groups.
 Joining is optional.

5. About

 Contains background information and an introduction video

about WHONET.

6. Contact

 Sign up for the WHONET mailing list.

 Email for technical support: help@[Link]

2. Downloading and Installing WHONET

1. Return to the WHONET homepage and choose the correct version for
your computer:
- 64-bit version: for most modern computers.
- 32-bit version: for older Microsoft Office installations.
2. If you choose the wrong version, simply uninstall and reinstall the
correct one.
3. WHONET is designed for Microsoft Windows. Mac users can find setup
instructions at [Link]/[Link].
Summary (Quick Review)
Topic Key Points

Purpose of WHONET Tracks and analyzes antimicrobial

resistance data.

Main Tools WHONET, BacLink, Automation Tool,

AMR Interpretation Engine.

Installation Download correct version (32-bit or

64-bit), install normally.

BacLink Use Converts lab data (Excel, LIS) to

WHONET format.

Training Center Videos, exercises, and exams for

each module.

Webinars Extra learning sessions held

quarterly.

Contact Email help@[Link]

Main Menu Tabs File, Data Entry, Data Analysis, Help.

Language Option Change display language anytime.

Module 2 – Laboratory Configuration Exercises erythromycin 15µg, gentamicin 10µg,

imipenem 10µg, nitrofurantoin (300µg for CLSI or 100µg for EUCAST),
Brigham and Women’s Hospital WHO Collaborating Centre for penicillin G (10 units CLSI or 1 unit EUCAST),
Surveillance of Antimicrobial Resistance Boston, Massachusetts, United trimethoprim/sulfamethoxazole 1.25/23.75µg, vancomycin 30µg (CLSI)
States May 2024 or 5µg (EUCAST).
• Change test method to “Etest” and add: ceftiaxone, penicillin G, and
vancomycin.

Purpose

The purpose of laboratory configuration is to describe the WHONET 3. Configuring your antibiotics
details about your institution and your laboratory test practices. This
tutorial describes how to create a “new laboratory” from the very 3.1 Antibiotic Breakpoints: WHONET automatically applies official
beginning. CLSI/EUCAST breakpoints.
3.2 Antibiotic Panels: Assign antibiotics to organism groups for data entry
Note: If you are using BacLink, there is a short-cut to accomplish most of efficiency.
the following steps. See the BacLink tutorials for more information. The Example panels:
short-cut feature is called “Create a laboratory from a data file” and can be • Staphylococcus sp.: cefoxitin, erythromycin, penicillin,
found under the WHONET “File” menu option. trimethoprim/sulfamethoxazole
• Streptococcus pneumoniae: erythromycin,
trimethoprim/sulfamethoxazole, vancomycin, penicillin-Etest, ceftiaxone-
Etest
1. Describing your laboratory • Gram-negative: ampicillin, ceftriaxone, ciprofloxacin, gentamicin,
imipenem, nitrofurantoin, trimethoprim/sulfamethoxazole
1.1 Open WHONET and select “New Laboratory”. 3.3 Antibiotic Profiles: Used for multidrug resistance analysis.
1.2 Define the following laboratory characteristics:
• Country: Select “World Health Organization” or your correct country.
• Laboratory name: “WHONET Training Course Hospital” or your actual
hospital name. 4. Sample locations
• Laboratory code: “WTCH” or your actual code.
• For training purposes, select “Human” or “Human, animal, food, 4.1 Enter common human locations:
environment”. Neurology (neuro), Cardiac Surgery (csurg), Neonatal ICU (nicu), Diabetes
clinic (diab),
Health Center #5 (hc5), Kinshasa (kinsh), Shanghai (shang).
4.2 Non-human examples:
2. Selecting your antibiotics Farmer Brown (brown), Newtown Veterinary Clinic (nvc), McDonalds #5
(mcd5), Blue River Site #10 (blue10).
2.1 Choose antibiotics to include in your local list:
• Guidelines: CLSI or EUCAST
• Test method: Disk
• Add: Ampicillin 10µg (AMP_ND10 or AMP_ED10)
• Repeat for: cefoxitin 30µg, ceftriaxone 30µg, ciprofloxacin 5µg,
5. Data fields resistance, QC issues).
• Adjust or deactivate rules as needed.
5.1 WHONET provides standard fields like patient details, specimen info, • Add custom alerts for your institution.
and organism data.
5.2 You can modify lists, add new fields like “Diagnosis”, or create user-
defined ones.
5.3 Add code lists for new fields (e.g., Diagnosis: Pneumonia=pneumo, 7. Finishing laboratory configuration
UTI=uti, Meningitis=mening).
7.1 Save your configuration file (e.g., [Link]).
7.2 To modify configurations later, use File → Modify Laboratory.
7.3 End of exercise:
6. Microbiology alerts

6.1 WHONET provides predefined alerts (e.g., for important species,

WHONET Training Course • You can change the file name or save location before saving.
Module 3 – Data Entry Exercises • Click “Save” to create the file and advance to the data entry screen.
Brigham and Women’s Hospital
WHO Collaborating Centre for Surveillance of Antimicrobial Resistance 2. Data entry
Boston, Massachusetts, United States You will now enter results for several sample isolates including human,
May 2024 animal, food, environmental, and quality control samples.

2.1 Isolate #1 – Human health: Patient Smith, John. Diagnosis: Pneumonia.

Organism: Staphylococcus aureus. Antibiotic results include Cefoxitin,
WHONET – Getting Started - Exercises Erythromycin, Penicillin G, and Trimethoprim/Sulfamethoxazole.
In these exercises, you will learn how to create new WHONET data files,
enter and edit results, and print clinical reports.
2.2 Isolate #2 – Human health: Organism Escherichia coli. Antibiotics:
Ampicillin, Ceftriaxone, Ciprofloxacin, Gentamicin, Imipenem. WHONET
1. Creating a new data file will show alerts for ESBL and carbapenem resistance.
1.1 Selecting the laboratory
2.3 Isolate #3 – Human health: Organism Streptococcus pneumoniae.
• Double-click on the WHONET icon on your desktop to begin WHONET. Includes both disk diffusion and Etest results (Ceftriaxone, Penicillin,
• You will see a list of laboratory configurations currently defined on your Vancomycin).
computer. Select the laboratory configuration for the “WHONET Training
Course Laboratory” (WTCL) that you created in the Exercises for Module 2.4 Isolate #4 – Quality control: E. coli (ATCC 25922). WHONET will note
2 – Laboratory Configuration. when results are out of QC range.

1.2 Selecting the laboratory 2.5 Isolate #5 – Animal health: Salmonella Enteritidis from cattle.
Demonstrates how human and veterinary breakpoints differ.
• From the “Data entry” menu, select “New data file”.
• WHONET will automatically suggest a name like WHO-WTCL-
[Link].
2.6 Isolate #6 – Food safety: Campylobacter jejuni from a chicken meat 3. Pick an analysis type (e.g., Isolate listing, Frequency of organisms, etc.).
sample. 4. Select filters (date range, specimen type, organism, ward, etc.).
5. Choose the type of results (e.g., disk diffusion, MIC, interpretation:
2.7 Isolate #7 – Environmental sample: Escherichia coli from river water. R/I/S).
6. Click 'Begin analysis' to view or export results.
3. Viewing the database
After entering data, click “View database” to review, edit, or print results. 4. Data Filtering and Options
Options include sorting, editing, deleting, searching, and printing records. • You can filter data by:
– Date range
4. Clinical reports – Specimen type (blood, urine, etc.)
4.1 You can print reports from the Data Entry screen or the database
view. Choose to print to a printer or as a PDF. – Ward or location (ICU, ER, OPD)
4.2 Modify report format under “Modify clinical report” to adjust layout, – Organism (E. coli, S. aureus, etc.)
font, and included fields. – Infection type or patient information.

5. Finishing data entry • These filters help narrow down specific results for reports or
surveillance.
5.1 Click on “Exit” to return to the main WHONET menu.
5.2 To reopen files later, use the Data entry menu or select “Open data
file”. 5. Output Formats
5.3 When finished, select “File”, “Exit” to close WHONET. After analysis, WHONET can display data in different formats:
• Tables – for detailed data.
• Graphs – for visual trends.
• Reports – summary tables for presentations.
WHONET Module 4 – Data Analysis (Notes for Exam)
These notes summarize the WHONET Training Course Module 4: Data You can export results to Excel or Word for easier sharing and editing.
Analysis. It explains how to use WHONET to view, filter, and analyze
microbiology data. 6. Example Analyses
• Isolate listing – See each patient’s isolate, specimen, and antibiotic
1. Opening WHONET result.
• Open WHONET by double-clicking the WHONET icon on your desktop. • Frequency of organisms – Count isolates per species.
• From the main menu, click 'Open laboratory' to access your lab • Resistance summary – See which antibiotics have the highest resistance.
database. • Trend analysis – Watch how resistance changes over months or years.
• You’ll see options like File, Data Entry, Data Analysis, and Help. Click on
'Data Analysis' to begin. 7. Exporting Results
When your analysis is complete:
2. Data Analysis Overview • Click 'Export' to save results as Excel or Word files.
WHONET lets you explore lab data, detect trends, and prepare reports. • You can also print reports directly from WHONET.
You can view data by organism, specimen type, location, and antibiotic • These exported files can be used for presentations or reports to
results. infection control committees.
Some key analysis types include:
• Listing: View all data in table form. 8. Importance of Data Analysis
• Isolate listing: See patient/sample-level details. WHONET analysis helps laboratories and health authorities:
• Frequency of organisms: Count how many times each organism appears. • Detect outbreaks early.
• Antibiotic resistance profiles: See which antibiotics each organism • Track antibiotic resistance trends.
resists. • Improve infection control and antibiotic use.
• Trend analysis: Check changes over time (month, quarter, year). • Contribute data to WHO GLASS and national AMR surveillance
programs.
3. Basic Steps for Data Analysis
1. Click 'Data Analysis' from the main menu.
2. Choose your laboratory database.

WHONET Training Course Analysis Type Purpose

Brigham and Women’s Hospital
WHO Collaborating Centre for Surveillance of Antimicrobial Resistance Frequency of Isolates Counts number of isolates per
Boston, Massachusetts, United States organism.
May 2024
% Resistant, Intermediate, Displays percentage of isolates
Module 5 – Data Analysis and Macros Susceptible (RIS) that are resistant, intermediate, or
susceptible.
Overview
In this module, you learned how to use WHONET’s Data Analysis features Zone Diameter and MIC Analysis Analyzes raw test measurement
to explore laboratory data. You also learned to create and use macros — values.
saved sets of analysis parameters — that can help automate repetitive
tasks.
Antibiogram by Location or Summarizes resistance by hospital
Specimen unit or sample type.
1. Data Analysis Overview
WHONET’s Data Analysis allows laboratories to review antimicrobial
Trend Analysis Tracks changes over time to
resistance (AMR) data using several approaches. Analysts can select
monitor outbreaks or emerging
analysis types, organisms, antibiotics, filters, and visualization formats.
resistance.
2. Creating an Analysis
1. Open WHONET → Data Analysis → Analysis Type.
2. Choose analysis (e.g., %RIS Analysis).
3. Select Organism, Antibiotic, and Data Files.
4. Set Isolate Filters (optional).
5. Click Begin Analysis to view results.

3. Using Macros
Macros automate your routine analyses. They remember all your
selections — analysis type, filters, and outputs — so you can rerun them
anytime with one click.

4. Example Exercises
• %RIS Analysis of Staphylococcus aureus – Shows resistance percentages
for each antibiotic.
• Antibiogram Reports – Compare Gram-positive and Gram-negative
organisms.
• Filter by Location – Compare resistance patterns between ICU and
Outpatient.
• Filter by Specimen Type – See which organisms are common in urine,
blood, or sputum samples.

5. Exporting Results
You can export results to Excel, Word, or graphs for use in presentations
and reports.

6. Summary
Module 5 teaches you how to analyze AMR data, create and use macros,
apply filters, and export analyses for sharing.

Module 6 – Quick Analysis and Standard Reports

Overview
This module introduces Quick Analysis, a faster way to produce
predefined or custom reports. It includes WHONET Standard Reports
created by the Boston team and User-defined Reports made using macros.

1. WHONET Standard Reports for Screen and Excel

These reports include organism statistics, stratifications, and
antibiograms. You can export tables and graphs to Excel for detailed
review.

2. WHONET Standard Reports for Microsoft Word – Epidemiology Report

This report provides an overview of data volume, sample details,
organism statistics, antimicrobial resistance summaries, and cluster
detection results.

3. WHONET Standard Reports for Microsoft Word – Data Quality Report

This report summarizes data completeness, QC testing, identification
accuracy, test practices, and microbiology alerts for quality assurance.

4. User-defined Reports
You can create your own Quick Analysis reports using macros. Combine
analyses for custom stakeholder needs and export them to Excel.

Summary
Module 6 teaches how to run quick analyses, generate standard WHONET
reports, create customized reports, and share results.
Congratulations! You have completed the WHONET Training Course.
For feedback or assistance, contact: help@who