WHONET Training Course

Module 1 – Introduction to WHONET

Division of Infectious Diseases, Brigham

and Women’s Hospital, Boston, United
States

WHO Collaborating Centre for

Surveillance of Antimicrobial Resistance
1 WHONET Training Course Modules

1. Introduction to WHONET
2. Laboratory configuration
3. Data entry
4. Data analysis – Introduction
5. Data analysis – Data analysis types
6. Data analysis – Quick analysis
1
Module 1. Introduction to WHONET

A What is WHONET?

B Download and installation

C WHONET main menu

1

A What is WHONET?
1 What is WHONET?
WHONET is a widely-used free software developed for the
A management and analysis of microbiology laboratory data
to support local, national, regional, and global activities to
understand and fight infectious diseases with a special
focus on antimicrobial resistance.

WHONET is a desktop software

developed for Microsoft Windows.
Two new versions of WHONET are in

development

- Web-based data entry

- Version compatible with MacOS and Linux

1 Antimicrobial susceptibility testing
Historical perspective
Clinical perspective
A
William Kirby, Alfred Bauer, John Sherris, and Marvin Turck
developed the disk diffusion method as a practical method
to be used by routine microbiology laboratories to support
therapy decisions by healthcare providers.
Bauer, AW, WMM Kirby, JC Sherris, and M Turck. 1966. Antibiotic
susceptibility testing by a standardized single disk method. Am. J.
Clin. Pathol. 36:493-496

Epidemiological perspective

Thomas O’Brien understood that disk diffusion zone diameters

could be analyzed to recognize and track distinct and evolving
microbial subpopulations and changing threats in antimicrobial
resistance.
O'Brien TF, Kent RL, Medeiros AA. Computer-generated plots of results of antimicrobial-
susceptibility tests. JAMA. 1969 Oct 6. 210(1):84-92.

The name WHONET was given to the software in 1989, but the early programming
work started on mainframe computers in the 1960s.
1
WHONET – Vision
A Human health, animal health, food, and environmental microbiology
laboratories worldwide generate a detailed window into evolving
microbial populations in real-time. Yet this resource remains largely
untapped and underutilized to support policy development and
resistance containment interventions.
The use of a common software could and should support local,
national, regional, and global collaboration and analyses to support:
• Infection and resistance containment
• Recognition, tracking, and containment of emerging threats in real-time
• Treatment guidelines and antimicrobial stewardship programs
• Public health awareness, advocacy, policy, and interventions
• Basic science, clinical, and operational research
• Diagnostic stewardship and continuous quality improvement in laboratory practices
1 WHONET and Surveillance objectives
A Objectives Local National Regional Global
Policy and advocacy
Priority setting and funding X X X X
Awareness and education X X X X
Legislation and regulation X X
Epidemiology of resistant microbes
Pathogen and resistance trends X X X X
Recognition of emerging threats X X X X
Disease and economic burden X X X X
Benchmarking X X X
Resistance containment
Treatment guidelines X X
Response to emerging threats X X X X
Assessment of interventions X X X X
New diagnostics and therapeutics X X
Capacity-building
Laborotory capacity X X X X
Epidemiological capaciy X X X X
1
WHONET and Surveillance objectives
A A simplified view
• Improve the use of local data for local action
• Make proper treatment decisions and therapy
guidelines
• Detect, confirm, and respond to new threats, such as
new resistance and outbreaks
• Improve laboratory capacity
• Long-term sustainability of surveillance efforts
requires that data generators derive sufficient value
for their efforts

• Promote national, regional, and global networks

collaborations and action… but long-term sustainability
at these levels relies on the ongoing efforts at the local
1 WHONET Data Sources
A • WHONET can be used for test results from human and
animal health laboratories and food and environmental
laboratories.
• WHONET can be used for data from routine daily work,
as well as from special surveys and research projects.
• Most laboratories use WHONET to manage data on
bacterial and fungal results.
• WHONET can also used be for the management of
results for parasites, viruses, and “negative” results,
such as “No growth” and “Normal flora”.
• WHONET can also accept clinical data, such as
diagnoses, risk factors, treatments, and outcomes. Such
data are usually not available to laboratories routinely,
but they often can be collected in special studies.
1 WHONET users
A A variety of professionals find value in WHONET data
analysis
• Microbiology laboratory staff
• Infectious disease and infection control teams
• Human and animal health clinicians
• Epidemiologists and information technology experts
• Pharmacy
• Food producers and environmental scientists
• Policymakers, researchers, and others
1 WHONET Modules
• Laboratory configuration
A
• Data entry
⚬ Option 1: Manual data entry
⚬ Option 2: Import existing data with BacLink
• Data analysis
• Interactive data analysis
• Quick analysis
• Public health reporting
1
Laboratory configuration
A
1 Data entry – Manual

A Sector
Patient, animal, food,
environmental details
Specimen location
Specimen details

Organism

Antibiotic results

Other
1 Data entry – Import with BacLink
Most laboratories in the world already have a computer system
A for managing their microbiology data.
⚬ Simple desktop systems: Excel, Access
⚬ Laboratory instruments: Vitek, Microscan, BD Phoenix, Sensititre
⚬ Laboratory information systems: Commercial systems or local systems
This is an obstacle because they are not directly compatible.
But it is also an opportunity! The electronic data have been
stored.
The goal of BacLink is converting data from existing incompatible
systems into common WHONET files.

WHONET
BacLink
Incompatible local Standard WHONET files
systems
BacLink will be covered in a separate course.
1 Data analysis - Interactive
A
1 Data analysis, alert, and report
features
%RIS and histograms Scatterplot
A Resistance profiles

Hospital F

Hospital C

Nursing homes
Hospital B

Microbiology alerts Outbreak detection

1 Quick Analysis - Output options
A Scree Excel Word
n

PDF (AMASS) DHIS2

www.amass.website www.dhis2.o
1 Data exports and interoperability
As mentioned in the discussion of “data imports” with BacLink, the
A principle of interoperability is very important to ensure efficiency,
sustainability, and impact of collaborative efforts.

This is also true in data exports. WHONET has the ability to export
to a number of public health reporting systems such GLASS modules
(GLASS-AMR, GLASS-FUNGI, GLASS-EGASP), DHIS2, AMASS, EARS-
Net, CAESAR, ASIARS-Net, MicroReact, and others.

WHO GLASS EARS-Net DHIS2 AMASS MicroReact

Figure 4: Screenshot of Microreact File for S. aureus 2015

A representative screenshot of a Microreact File showing

the geographical distribution of resistance phenotypes S.
aureus in the Philippines in the year 2015.
1 Adaptations for One Health surveillance

A • Introduced in 2001 with gradual improvements over time with

support from WHO, FAO, USDA, FDA, and many others
• Expanded data field lists, code lists, and analyses
⚬ Animal species, production types, food types, etc.
⚬ Specimen types, pathogens, antimicrobials, etc.
⚬ Data entry and report templates for FAO surveillance protocols, InFARM, and
the WHO ESBL-producing Escherichia coli TriCycle project
• Interpretation guidelines
⚬ CLSI Human and animal clinical breakpoints
⚬ EUCAST Human and animal clinical breakpoints
⚬ EUCAST Epidemiological Cutoff Values for MIC results
• Training data set with One Health results
⚬ 100 isolates each of human, animal, food, and environmental origin
1 Summary

A WHONET is free software widely used around the world for

the surveillance of evolving microbial populations
• One important focus is the annual surveillance of priority
resistance trends – to support awareness, treatment
guidelines, and advocacy
• But there are many other applications of greater value in
real-time
⚬to support the recognition and containment of emerging threats
including novel resistant strains and possible outbreaks
⚬to improve laboratory capacity and data quality
1

Download and installation

B
1 WHONET Home page – www.whonet.org
B
1 Two versions of the installation package
B

Recommendation – if you have a 32-bit version of

Microsoft Office, we recommend installing the 32-bit
version of WHONET. If you have a 64-bit version of
Microsoft Office, then we recommend installation the
64-bit version of WHONET.
1 Do you have a 32-bit or a 64-bit version of
B Microsoft Office?
1. Open Microsoft Excel or Microsoft Word.

2. On the left menu, click on “Account”.

C
• If you do not see “Account”, then you probably
have a 32-bit version of Microsoft Office.

3. Click on “About Excel” or “About Word”.

4. The next screen will indicate “32-bit” or “64-bit”

1 Download WHONET
B 1. Click on the link for the 32-bit or the 64-bit
version of WHONET, and the installation
package will begin to download.
2. When the download has completed, click on
“Open” or “Run” to begin the installation.
• If you do not see installation package, you
can find it in your “Downloads” folder.
1 Step 1 - Select Install
B

C
11 Step 2. Allow this app to make
B changes? Select “Yes”

Note – Some computers will not ask this question.

1 Step 3 - WHONET Setup Wizard
B Select “Next”

C
1 Step 4 - Installation folder
By default, WHONET will be installed to the C:\
B
WHONET folder. Click “Next”.

Or you can use “Browse” to

C choose a different location on

the local hard drive or on a
network drive.
1 Step 5 - Final step Click “Install”
B

C
1 Step 6 - Installation completed
B Click “Finish”

C
1 Step 7 - Close the installation
B software Click “Close”.
1 After WHONET Installation
After the installation is complete, you should see icons
B
for WHONET and BacLink on your desktop.
Double-click on the WHONET icon to begin the software.

If you see the above screen, congratulations! You have

successfully installed WHONET.
1 If you have installation problems...
B • Try the process over again.

• Contact your IT team for assistance. In

many organizations, only IT staff have the
C ability to install new softwares.
• Try a different computer.

• Contact the WHONET team in Boston

⚬ [email protected]
1
If you have a MacOS computer
B • The current version of WHONET was made for Microsoft Windows.
Fortunately, there are a few approaches for installing Windows
programs onto a Mac computer.
⚬ Create a Windows partition on the Mac hard drive or install a
Windows Virtual Machine or a Windows emulation software.
⚬ You can find further details with a web search: “How do I install a
C Windows program on a Mac?”

• The WHONET team has made significant progress towards a version of

WHONET that can run on MacOS and Linux, but there is no estimate when
this will be available for testing.
1

C WHONET Main Menu

1 The WHONET Main Menu
List of laboratory configurations
C

C
1 1Language selection
C
1 1Language selected
C

• You can now click on “Idioma y fechas”, and select “English” to continue
the course with WHONET in English.
1 Languages in WHONET – 53
C languages
Here is the current list of languages available in WHONET.
• Afrikaans, Albanian, Arabic, Armenian, Bulgarian, Catalan, Chinese
(Traditional and Simplified), Croatian, Czech, Danish, Dutch, English,
Estonian, Farsi, Finnish, French, Georgian, German, Greek, Hebrew,
Hungarian, Icelandic, Indonesian, Irish, Italian, Japanese, Kazakh, Korean,
Lao, Latvian, Lithuanian, Macedonian, Malay, Mongolian, Norwegian
(Bokmål and Nynorsk), Polish, Portuguese, Romanian, Russian, Serbian,
Slovak, Slovene, Spanish, Swahili, Swedish, Thai, Turkish, Ukrainian,
Urdu, Vietnamese
Most of the translations were created with Amazon Web Services, and
there can be mistakes and suboptimal translations. If you would like to
help correct and improve the translations, please contact the WHONET
team at [email protected].
1 Open a laboratory
C
1 WHONET Main menu
C
11 Help -> Documentation
C
11 Help -> About
C
1 Thank you for watching Module 1:
Up next. Module 2: Laboratory
configuration