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WHONET 5.6 & WHONET 2019

WHONET 1 - Getting Started - 1,081 kB
WHONET 2 - Laboratory configuration - 414 kB
WHONET 3 - Data entry - 652 kB
WHONET 4 - Data analysis I - 671 kB
WHONET 5 - Data analysis II - 523 kB
WHONET 6 - Expert systems - 579 kB
WHONET 7 - Macros and Excel reports - 815 kB
WHONET 8 - Cluster detection and SaTScan - 287 kB
How to run? - Antibiogram - 580 kB

WHONET 2019

WHONET for GLASS - English - 287 kB
WHONET for GLASS - Arabic - 287 kB
WHONET for GLASS - Chinese - 287 kB
WHONET for GLASS - French - 287 kB
WHONET for GLASS - Russian - 287 kB
WHONET for GLASS - Spanish - 287 kB

WHONET WEB

View our requirements - documentation

BacLink

BacLink 1 - Getting Started - 50 kB
BacLink 2 - Excel, text, other applications - 1,143 kB
BacLink 3 - Laboratory Information Systems - 68 kB
BacLink 4 - Cerner Classic - 291 kB
BacLink 5 - Meditech Magic - 142 kB
BacLink 6 - Microscan - 134 kB
BacLink 7 - Vitek - 122 kB

WHONET-AGISAR | Spanish language documents

1- Manuales Integrados Instalación y Carga de datos WHONET
Este documento contiene el paso a paso desde la instalación de WHONET hasta la configuración de un laboratorio WHONET argentina. Como te había adelantado en la página 11 de este manual, esta la configuración estandarizada de las salas. Este documento es el primer documento que tendrían que tener los participantes.
2- Instructivo para agregado de drogas nuevas CPT para Red WHONET
Este documento es un ejemplo para agregar drogas nuevas a las ya elegidas, también permite la modificación y/o agregado de puntos de corte
3- Protocolo WHONET consensuado 2017 final
Es nuestro protocolo de trabajo actual, básicamente que paneles de ATBs se usan para cada microorganismo.
4- Check list Protocolo WHONET 2016
Parecido al anterior, pero sire para asegurarse de tener la configuración actualizada en la planilla de ingreso.
5-Instructivo para la modificación y creación de nuevos campos 2017
Un poco lo que vimos en el taller, en este documento se muestra como crear los nuevos campos de mecanismos de resistencia. En nuestro caso no estábamos quedando sin campos disponibles, es por eso que optamos por crear campos que permitan un desplegable con nuevos mecanismos.
6- Listado de Campos WHONET 2015
Un check list de los desplegables WHONET Argentina, para los campos, diagnostico, enfermedad de base y factor de riesgo
7- Manual WHONET español comprimido
Esta es una traducción al “Argentino” del manual original de WHONET en ingles
8- VALORES DE PUNTOS DE CORTE PARA MODIFICAR EN WHONET
Es un repaso por todos los puntos de corte nuevos (CLSI 2017) realizado por Celeste Lucero. Para realizar los cambios, se puede utilizar el documento nro 2 como consulta.

I. Download WHONET here.
II. Click Run or Save as and open to run the installation wizard.

*The default settings will work for most configurations.

Configure your data:

How will you provide WHONET with data?

A.) By manually entering your data? Or,
B.) By converting your lab file to a WHONET file using BacLink?

Not using Data entry? Skip to our BacLink tutorials.

Data Entry

This tutorial includes the following sections.

Part 1. Creating a new data file
Part 2. Data entry
Part 3. Viewing the database
Part 4. Clinical reports
Part 5. Finishing up
Part 6. Other options for managing data files

In this tutorial, you will learn how to enter results into WHONET data files, how to edit isolate results, and how to print clinical reports.


Part 1. Creating a new data file

Begin WHONET, and select the laboratory “WHO Tutorial Hospital” that you created in the tutorial on laboratory configuration. If you did not do this tutorial, then select any of the laboratories available on your computer. Click on “Open laboratory”.

At the top of the screen, you will see the main “Data entry” menu. If you select this menu, you will see a number of options. To begin a new data file, select “New data file”. If you would like to continue working with a data file that already exists, click on “Open data file”. For this tutorial, select “New data file”.

Figure 1. Main WHONET menu with the Data entry options selected.

Every file on a computer needs: 1) a name; and 2) a location. By default, the location of WHONET files is c:\whonet5\data on your computer’s hard drive, but you can put the file wherever is most convenient for you, for example on a central server accessible to many computers.

For the file name, WHONET suggests a name indicating the year of the data, the country code, and the laboratory code, for example w06who.wth. For the tutorial, change the option to “Month/Year”, and WHONET will suggest a name such as w0606who.wth for June 2006. If the data are from a different month, indicate the correct month. For this tutorial, change the file name to w0106who.wth to indicate that you will enter data from January 2006 from the country “WHO” from the “WTH” laboratory. Then click “OK”.


Figure 2. Indicate the name of the new WHONET data file.

Part 2. Data entry

WHONET will proceed to data entry. In this step, you will enter results from three clinical isolates and one quality control strain. For the first isolate, enter the following patient information.
First isolate
Identification number = 12345
Last name = Smith
First name = John
Sex = Male = m
Date of Birth = 1/1/80
Diagnosis = Pneumonia = pneumo
Location = neuro
Specimen number = 1111
Specimen date = 10/12/05
Specimen type = Blood = bl
Organism = S. aureus = sau

Antibiotic results
Beta-lactamase = Positive = +
Cefoxitin = 20
Erythromycin = 18
Penicillin G = 12
Trimethoprim/sulfamethoxazole = 19
Vancomycin = 17

When you finish, your screen should look like the following. As you put in the antibiotic measurements, WHONET will automatically determine and display the interpretation.

Figure 3. Data entry screen after the entry of the first isolate.

Note: For date formats, WHONET uses the defaults set up for your computer. For example, if you type 10/12/05 on a computer outside of the United States, WHONET will probably (depending on your computer) interpret this as 10-Dec-05. On the other hand, if you are in the United States, WHONET will probably interpret this as 12-Oct-05. When WHONET displays the date back to you as “10-Dec-05” or “12-Oct-05”, you will see whether WHONET correctly interprets your intention.

Note: In WHONET, you can enter either quantitative measurements (disk diffusion zone diameters or MIC values in ug/ml) or test interpretations (resistance, intermediate, susceptible). However, we strongly recommend that you enter the test measurements for several reaons: 1. It is the correct way to do the test, and the only way to be certain that measurements and interpretations were done correctly, rather than “eye-balling” the result.
2. Interpretative breakpoints can change over time. If there is a change in breakpoints, you will not be able to compare new statistics with your older statistics if you do not record the test measurements.
3. By reviewing the distribution histograms of test results, you can assess the quality of routine test practices and the reliability of results; and
4. By reviewing the test measurement measurements, you can learn a lot about the mechanisms of resistance and the epidemiology of distinct resistant clones – useful both for research studies and infection control investigations of possible outbreaks.

After you enter all of the results, click on “Save isolate”. From the choices given, select “Save the isolate and continue with the same specimen.”

Figure 4. Save the isolate and continue with the same specimen

Now enter a second bacterial isolate for the same blood specimen with the following results.

Second isolate
Organism = E. coli = eco
Ampicillin = 6
Ceftriaxone = 10

As soon as you put the ceftriaxone result, WHONET will display some alerts in the lower right-hand corner of the screen indicating that this organism may be an ESBL-producing organism. WHONET has many alerts that warn you of possible typing or laboratory testing errors or of important results that should be confirmed and reported to responsible authorities, such as the infection control team or a national reference center.

Continue entering antimicrobial results:
Ciprofloxacin = 22
Gentamicin = 13
Imipenem = 12

As soon as you put the results for imipenem, you will get the following “High priority” alert about carbapenem non-susceptible results.

Figure 5. High-priority alert for Enterobacteriaceae non-susceptible to carbapenems.

Now click on “Save isolate” to see the following screen. The top part of the screen is unchanged from before, but below appears a summary of the isolate alerts.

Figure 6. Saving the results with a summary of the microbiologicial alerts for this isolate.

Save the isolate, and continue with the next isolate. Enter the following results.

Third isolate
Identification number = 67890
Last name = Jones
First name = Mary
Sex = Female = f
Date of Birth = 3 January 2006
Diagnosis = Meningitis = mening
Location = nicu
Specimen number = 2222
Specimen date = 27 January 2006
Specimen type = Blood = bl
Organism = S. pneumoniae = spn
Serotype = Streptococcus pneumoniae serotype 23F
Erythromycin = 18
Trimethoprim/sulfamethoxazole = 7
Vancomycin = 17
Penicillin Etest = 8ug/ml = 8
Ceftiaxone Etest = 8

To enter the Etest results, click on “Etest”.

If you need to enter a result for an antibiotic test that does not appear on the panel for the organism you enter, change “Antibiotic panel” to “All antibiotics”. If the antibiotic test you want still doesn’t appear, you will need to go back to Laboratory configuration and add the additional tests to your antibiotic list.

Save the isolate as before by clicking on “Save isolate” and “OK”.

Fourth isolate
Identification number = atcc25922
Last name = atcc25922
First name = atcc25922
Location = lab
Specimen number = 3333
Specimen date = 15 January 2006
Specimen type = Quality control = qc
Organism = E. coli = eco
Ampicillin = 16
Ceftriaxone = 22
Ciprofloxacin = 18
Imipenem = 15

When you leave the imipenem result, you will see that the result gets an asterisk “!”. To see why there is an asterisk, return to the imipenem box. On the right side of the screen, you will see the comment “The result is out of the acceptable QC range.”


Save the isolate as before by clicking on “Save isolate” and “OK”.

Part 3. Viewing the database

You have now entered the results for four strains into WHONET. To see these results, click on “View the database” to get the following screen listing all of the results.

Figure 7. Viewing the database in table format


From this screen, you have a number of options:

Sorting the results: If you click on any column heading, WHONET will sort the database by that column. This can help you to find results from a certain patient or with a certain organism. It can also help find errors in data entry, for example in the specimen date column.

Edit the isolate: If there is a mistake in the database or if you have additional information to add, click on “Edit the isolate” to edit the isolate on the main data entry screen. When you finish, click on “Save isolate”.

Edit the table: You can also edit the table directly. Click on “Edit the table” and you can make changes directly to the table.

Delete: Use this button to delete a record.

Search: Use this button to search for records, for example certain patients, specimen numbers, or organisms.

Print: This feature is described further in the next step.

When finished reviewing these features, click on “Continue” to return to the main Data entry screen.

Part 4. Clinical reports

Some laboratories use WHONET to report laboratory results back to clinicians. WHONET still has some limitations in this regard, but it has worked reasonably for many institutions.

To print out clinical reports or logbook isolate listings, click on “Print” from either the main Data entry screen or from the “View database” screen.


Figure 8. Print clinical reports and isolate listings

You have the choice between printing isolate listings (for example fifty isolates per page) or individual patient reports (one to three reports per page). You also have the option of choosing to print only the current isolate selected or a number of isolates with criteria that you specific (date of data entry, specimen number, etc.).

For this tutorial, you will print clinical reports and an isolate listing for the four isolates entered above.

1. Click on “Clinical reports”. Choose “Select isolates”. The default is to print out all isolates entered today (“Date of data entry” = today’s date). Click on “Print”, and then “Print” on the following screen. WHONET will now print the individual clinical reports, two per page.


2. Click on “Isolate listing”. Leave the other selections unchanged, and click on “Print”, and then “Print” again. WHONET will now print out the isolate listing.


If you would like to change the format of the clinical report, you can choose the option “Modify clinical report” to make a number of changes. Among other options, you can indicate how many results to print per page, which fields should be included in the print, the fonts for the printout, and whether to include a standard page header or footer.

Figure 9. Editing the clinical report.

Part 5. Finishing up

After you finish exploring the Data entry program, click on “Exit” to return to the main WHONET menu.

In the above steps, you saw how to create a new data file in WHONET and entered results for four isolates. You will now see how to return to open a data file which already exists. Click on “Data entry”, and you will see the following choices.


Figure 10. The main WHONET screen with the most recently opened data file highlighted.

You will notice that the data file w0106who.wth appears at the bottom of the list. WHONET shows you the list of the most recently open files. Click on “w0106who.wth” to open the file. Alternatively, you could use “Open data file” to open any data file.

You are now back in the data entry program where you can enter results for additional isolates or edit or print results from existing isolates.

When you finish reviewing data entry, select “Exit” from the data entry screen to return to the main WHONET menu

Part 6. Other options for managing data files

The following additional features are not essential, but are useful to many users. For purposes of this tutorial, look at the screens that are described, but there is no need to run any of the features. When you finish, select “File”, “Exit” to leave WHONET completely.

Combining data files: In the above example, you created a data file for January 2006. If you continue in this way, you will have twelve monthly files at the end of the year. Many users find it convenient at the end of the year to combine the twelve files into a single larger monthly file.

To use this feature, click on “Data entry” from the main WHONET screen. Choose “Combine or export data files”. Indicate the data files that you want to combine and the name of the new file that you want to create. Then click on “Combine”. When WHONET finishes, the original data files will be unchanged, but you will now have a new large data file which includes all of the results from the original files.


Figure 11. Combining WHONET data files.

Encryption: If you want to share your data files with other institutions, you may wish to protect the confidentiality of patients with this feature. When you use this option, WHONET will create a copy of your data file but with patient and specimen information either removed or encrypted. WHONET uses a uni-directional encryption, so subsequent “decryption” of the results is not possible.

To use this feature, click on “Data entry” from the main WHONET screen. Choose “Encrypt data files”. Indicate the data file that you want to encrypt and the name of the new file that you want to create. Then click on “Encrypt”. When WHONET finishes, the original data file will be unchanged, but you will now how a new data file in which the patient and sample information has either been removed or encrypted.


Figure 12. Encrypting patient information.

Data file locations: When you install WHONET, by default, all data files will be saved into the c:\whonet5\data folder. For people using WHONET on a single computer not connected to a network, this is a practical location. However, for computers connected into a network, it if often more convenient to put the data files onto a central common computer where multiple users can have access to the same data files. In this way, data entry and data analysis can be done with the same data files by several individuals using different computers.

If you save your data files on a network computer, it would be convenient for users if you change the default location for WHONET data files. To do this, go to the main WHONET menu, and select “File”, “File locations”. To change the location of the data files, you can type in the desired location or use the Browse option to find the appropriate folder.

Figure 13. Changing the default file locations.

After checking this option, click on “OK” to return to the main WHONET menu. Click on “File”, “Exit” to completely leave the WHONET program.

Backing up files: As is true for any important document that you have on your computer, you should have a strategy for backing up your WHONET data files. This is important in the case of computer damage, theft, viruses, or accidental modifications. You can back files up by copying your WHONET files onto another computer, CD-ROM, USB-memory stick, or diskettes.

To make copies of your WHONET data files, go to c:\whonet5\data (or other location that you have selected), and find the files that you want to backup. Select these files and choose “Edit” from the main Windows screen and “Copy”. (Alternatively, you can use Ctrl-C or right-click on the file and select “Copy”.)

Then go to the location where you want to back up the files and select “Edit”, “Paste”. (Or Ctrl-V or right-click on the location and select “Paste.”)


Figure 14. Contents of the folder c:\whonet5\data. The WHONET data file w0106who.wth created in this tutorial is highlighted.

In addition to backing up your WHONET data files, you should also backup your WHONET laboratory configuration file. In this tutorial, the name of this file is labwho.wth. The file is in your c:\whonet5 folder. Go to this file, and copy and paste the file to the backup location.

Figure 15. Contents of the folder c:\whonet5. The WHONET laboratory configuration file labwho.wth created in this tutorial is highlighted.

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Take me back to the Data entry tutorials.

BacLink file conversions

This tutorial covers the following areas:

Part 1. What is BacLink?
Part 2. What systems are compatible with BacLink?
Part 3. How does BacLink work?
Part 4. What’s the next step?

Part 1. What is BacLink?

Many laboratories around the world already have well-established computer databases that meet the day-to-day needs of clinical reporting, specimen processing, and long-term data storage. Unfortunately most of these systems have limited capacity for sophisticated data analysis. It is in these areas that WHONET is a valuable supplement to existing systems.

This purpose of the BacLink software is the conversion and standardization of microbiology data from existing systems into WHONET. You can convert data on a weekly, monthly, or ad hoc basis, or in a number of institutions, it has also been possible to automate and schedule the entire process. Both WHONET and BacLink are available free-of-charge from the World Health Organization website: www.who.int/drugresistance/whonetsoftware.

By converting data to WHONET, laboratories have the benefits of: 1. flexible data analysis capabilities; and 2. the ability to share data with other laboratories, for example in a national surveillance network.

Part 2. What systems are BacLink compatible with BacLink?

BacLink is compatible both with “User-defined” data formats as well as “Proprietary” or “Fixed” data formats. More specifically, BacLink can convert data from the following systems:

Standard desktop softwares and text files: BacLink can directly import data files with the following formats: Microsoft Access, dBASE, and EpiInfo. In addition, BacLink has a flexible, configurable interface for the import of simple text files. So most systems capable of creating text files (such as Excel and most laboratory information systems) should be able to create files that can be converted with BacLink.

Laboratory organism identification and susceptibility test instruments: BacLink is compatible with the following commercial systems.
– MIC systems: ATB, MiniAPI, Microscan, Pasco, Sceptor, Sensititre, Vitek, Wider
– Disk diffusion readers: Aura, Biomic, Osiris, SirScan, Videobac, Wider

In most cases, BacLink cannot access data from the internal, proprietary databases of these instruments since these are protected by the vendor. Fortunately, most systems have an “export”, “report”, or “interface” capability which can be used for the transfer of data to text files which BacLink can use to create WHONET files.

Laboratory information systems: We have developed specific guidelines for the export and conversion of data from the following commercial information systems.
– Meditech Magic
– Cerner Classic

It is also possible to convert data from the following systems, but we have not developed formal documentation describing the process. For further details, please contact us directly.
– ADBakt (Sweden, Denmark)
– MADS (Denmark)
– Oman Health Information System (Oman)
– WinPath (Malaysia)

Other standard formats: BacLink can understand the following standard data formats.
– EARSS (European Antimicrobial Resistance Surveillance System)
– JIAQA (Japan-International Association for Quality Assurance)
– NORM (Norwegian Resistance Monitoring)

If your system does not appear on these lists, you can still use BacLink if your system can create simple text files. Guidance on how to do this is provided in the document “BacLink and Laboratory information systems”

Part 3. How does BacLink work?

BacLink allows you to take data from a number of different sources and create new data files with the standard WHONET file structure. Detailed instructions for specific systems are provided in other tutorials or in the BacLink manual, but for each the overall process is the same:

Step 1. Create a file compatible with BacLink
If your data file is already compatible with BacLink, for example with simple text files, Access, and a few other formats, there is nothing that you need to do in this step – the data file that you have is already compatible with BacLink.

For most laboratory instruments and information systems, you will first need to export data from your system into a format compatible with BacLink, most frequently a delimited text file. The accompany tutorials and BacLink manual provide instructions on how you can accomplish this.

Step 2. Configure the conversion
You will need to tell BacLink what kind of file you want to import and details about the file: what is the file format (text, Access, Vitek, Cerner, etc.), what susceptibility test methods are included, how the data fields are organized, date formats, etc.

For propriety data structures, configuration is very easy since BacLink is already programmed with all of the necessary details about the file structure. For generic structures, there are a few additional screens where you provide details about the data file contents and organization. If you have multiple files with the same data format, configuration only needs to be done once.

Step 3. Running the conversion
After configuring the conversion, you are ready to convert your files. BacLink will show you the first three isolates on the screen so that you can check the accuracy of the conversion, and BacLink will also notify you of any problems or unrecognized codes that it encounters. The file created by the BacLink conversion is a valid WHONET data file that you can subsequently analyze with WHONET.

At the present time, most laboratories run BacLink interactively, for example once a week, month or quarter. For a number of systems, it is also possible to schedule BacLink, for example to convert data automatically on a daily basis.

Part 4. What’s the next step?

The next steps depend on the type of system that you have.

Standard desktop softwares: If you have data in Microsoft Access, Excel, EpiInfo or dBASE, or other system that can create simple text files, proceed with the tutorial “BacLink and Excel, text files, and other desktop applications”.

Laboratory instruments: If you want to transfer data from your laboratory instrument, consult the instructions provided in the main BacLink manual or specific guideline developed for that instrument.

Laboratory information systems: If you have a Meditech Magic or Cerner Classic system, continue with the detailed instructions provided with the accompanying documentation. For ADBakt, MADS, the Oman Hospital Information System, and WinPath, contact us for further details. For any other system, then you should proceed with the tutorial “BacLink and Laboratory information systems”.

Our group is currently working on the development of interface options for Meditech Client/Server, Cerner Millenium, and Mysis. If you would like to assist in the development or testing of interfaces for these systems or any other system, please contact John Stelling at jstelling@rics.bwh.harvard.edu or click the link to email him directly.

Data Analysis

This tutorial covers the following topics.

Part 1. Getting started
Part 2. Setting up an analysis: %RIS and test measurements
Part 3. Running the analysis and interpreting the results
Part 4. Transferring WHONET results to Excel and other softwares
Part 5. %Susceptible summary
Part 6. Isolate listing and summary

This tutorial will illustrate some of the most important features of the WHONET data analysis program. Applications of these analyses include:

- continuous quality improvement: assessing laboratory test practices and utilization of laboratory services by clinical departments
- describing trends in the epidemiology of microbial populations and antimicrobial resistance
- characterizing the molecular epidemiology of antimicrobial resistance trains
- guiding antimicrobial therapy recommendations and policy
- supporting infection control interventions, in particular the early identification of hospital and community outbreaks

This tutorial focuses on two of the most commonly used analysis options: 1. %RIS and test measurements; and 2. Isolate listing and summary.

Part 1. Getting started

Double-click on the WHONET icon on your desktop to begin the software. You will see a screen similar to the following. For purposes of this tutorial, select the laboratory called “WHO Test Hospital”, and click on “Open laboratory”.


Figure 1. Laboratory selection.

From the main WHONET screen, click on “Data analysis” and “Data analysis” again. You will now see the main WHONET analysis screen. From this screen, you will be able to tell WHONET the type of analysis you want to perform.


Figure 2. The WHONET data analysis screen.

Part 2. Setting up an analysis: %RIS and test measurements

In the main analysis screen, there are three sections on the left that you must answer: Analysis type, Organisms, and Data files. On the right, there are some additional options that may be useful to you.

Analysis type: First, you must indicate the kind of analysis that you want WHONET to perform. To do this, click on “Analysis type”. You will see several analysis options. For this first analysis, select the option “%RIS and test measurements”. Click “OK” to return to the main analysis screen.


Figure 3. Analysis type: Select the kind of analysis you want to run, as well as the format of the output – graphs, tables, listings, summaries, etc.

Organisms: Click on Organisms. On this screen, as in many of the WHONET screens, you will see the options available to you on the left side of the screen. On the right side of the screen, you will put your selections.

On the left-hand side, you will first of all see a list of relatively common bacteria and fungi. Choose two organisms for this first analysis: E. coli (eco) and S. aureus (sau). You can select an organism in several possible ways: double-click on the organism or single-click on the organism and hit the right-arrow button “–>” or type the three-letter code and hit . Your screen should look like the following.


Figure 4. Organism: Select the organisms or organism groups that you want to analyze.

There are some other useful options on this screen as well.

Extended list: Initially, WHONET shows you the list of relatively common organisms. To see the complete list, click on “Extended list”. You can use the “Search” box to quickly find an organism.

Organism groups: If you click on “Organism groups”, you will see that WHONET permits you to analyze groups of microorganisms such as “All organisms”, “All Enterobacteriaceae”, and “All Salmonella”.

Analyze as one organism: WHONET generally will analyze each organism selected separately. If you would like WHONET to average results together from multiple organisms (for example “Klebsiella pneumoniae”, “Klebsiella oxytoca” and “Klebsiella sp.”), then click on the option “Analyze as one organism”.

When you finish looking at the available options, click “OK” to return to the main analysis screen.

Data files: Click on “Data files” to select the data files to include in the analysis. For this tutorial, select the file w0195who.tst”. You can do this by double-clicking on the file or by single-clicking and using the right-arrow button “–>”. After selecting the file, click on “OK” to return to the main analysis screen.

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Quick Analysis

• *Use Quick analysis to run our predefined reports.
• Open WHONET and select your lab.
• Click on Data analysis.
• Select Quick analysis.
• Select one of our predefined reports.
• Select the WHONET files you wish to analyze.
• Select the Output option, Excel, Access, Screen.
• *If you select anything other than screen, you will need to name your file and remember where you want to save it. By default, WHONET saves analysis files to C:\WHONET\Output\
• Select Begin analysis.