WHONET is a free Windows-based desktop application developed by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance for the laboratory-based surveillance of infectious diseases and antimicrobial resistance.

The principal goals of the software are:

• to enhance capabilities for analyzing laboratory data; and
• to promote national and international collaboration through the exchange of data.

The software is used in over 80 countries around the world managing data from over 1000 clinical, public health, veterinary, and food laboratories. WHONET can be used by individual laboratories or as part of national and international surveillance networks.

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, available in 17 languages, can be downloaded 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.

Since BacLink cannot access the internal databases of your laboratory information system (LIS), the laboratory needs a data file exported from your system with the desired patient information and microbiological results. In many institutions, the most convenient type of file to create is a simple delimited text file, though BacLink can also accept a number of other formats. Information to be included in this export is suggested in Part 3, and the organization of the data in the file is discussed in Part 4.

Fortunately, most information systems do have the capability of creating such text files using existing data export, report, or interface options. In the case of the following systems, we have prepared detailed instructions and report templates that you should be able to apply directly:

– 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)

If you do not have any of the systems indicated above, then you should try to create a delimited text file with the information described below.

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.

Data fields

The following is a list of suggested data fields to be included in the export. The precise list should be discussed with laboratory staff, and should reflect the information available in your system and the data analysis needs of clinical staff. All of the fields are optional, though a few are highly recommended. Feel free to delete any fields which are unneeded and add additional fields that you desire.

Patient fields:
Identification number (e.g. Medical record number) – recommended
Patient first name and last name or Patient full name
Sex
Date of birth and/or age
Date of admission

Location fields
Patient location (ward or clinic) – recommended
Department or specialty
Institution or facility (in the case of a laboratory serving multiple institutions)
Type of location (for example, inpatient or outpatient)

Specimen fields
Specimen or accession number – recommended
Specimen collection date – recommended
Specimen type (blood, urine, cerebrospinal fluid, etc.) – recommended

Organism results
Organism – recommended
Antimicrobial susceptibility test results – recommended

Most of the above fields are self-explanatory. For antimicrobial susceptibility test results, a few additional comments are needed.

The three most common methods for performing antimicrobial susceptibility tests are:

1. Disk diffusion, also known as Kirby-Bauer. Results are measured in millimeters.

2. MIC determination. MIC = minimal inhibitory concentration. In routine laboratories, MICs are usually determined with automated susceptibility test instruments, such as MicroScan, Sensititre, and Vitek. Quantitative results are given in the form of a concentration, for example micrograms/milliliter (µg/ml).

3. Etest. This is a specialized version of a MIC test. It is a more expensive test than routine MIC tests. Results are also measured as concentrations, for example (µg/ml).

Laboratories may perform one, two, or all three of these methods. Some laboratories enter the quantitative test measurements directly into the computer system (millimeters or µg/ml) or the test interpretation (resistant, intermediate, or susceptible) or both. Examples of how you could export the antibiotic results are provided in Part 4.

There are some additional specialized antibiotic tests that you should also to try to export if feasible: beta-lactamase, ESBL, Dtest, etc. In many computer systems, these tests are treated in the same way as other antimicrobial tests, so no special handling is required to capture the results. In other systems, results are saved internally in a separate field that you should try to capture.

Data codes and date formats

BacLink has a flexible interface for mapping data codes and date formats. So you should export whatever codes and values are most convenient for you and your laboratory staff. If you have the choice between exporting a data code (e.g. UR) or the corresponding full text (URINE), the full text will probably be more convenient for the users who will do the code mapping.

What specimens should be included in the export file?

When you export results from your LIS, you can export results from all specimens or from a subset of specimens. The three most common options would be:

1. All specimens

2. All “positive” specimens (do not include specimens with “No growth”)

3. All “positive” specimens with antimicrobial susceptibility test results

Any of these approaches are reasonable options. The first approach will have the most information available for analysis, but these files can also be very large because of the large number of “negative” results. Option 2 is a reasonable compromise for many laboratories between the value of the information, the size of the data file, and the speed of data analysis.

File format

Most institutions find the use of delimited text files to be the most convenient means of exporting data to WHONET. The choice of field delimiter (comma, tab, semi-colon, etc.) is configurable by the user. Other options include fixed-column text, Microsoft Access, or dBASE. The use of a file header (the first row of the file indicates the names of the data fields) is often convenient for the data manager, but is not a requirement.

BacLink works with “flat” non-relational databases. Create one column for each of the fields that you intend to export: medical record number, patient location, collection date, organism, etc.

Antibiotic results – organization of records

Because each bacterial isolate is usually tested against multiple antibiotics and perhaps by one than one test method, there are a few possible acceptable ways of organizing your antibiotic test results in the export file. The two most common variations are described below. You should decide which of these two approaches would be easiest to implement and maintain in your system.

1. One isolate per row: Each row in the export file corresponds to the results from one organism. All results from this organism are saved in this one record. People entering data manually into Excel usually organize their data in this way – with all of the antibiotic results for one organism saved as part of the same record/data row. Some hospital systems also export data in this way.

   Example:
   First name, Last name, Sex, Location, Specimen type, Specimen date, Organism, PEN, ERY, VAN
   John, Smith, Male, Neurology, Blood, 1/1/2006, S. aureus, R, R, S
   Mary, Jones, Female, Nursery, CSF, 3/10/2006, S. pneumoniae, S, S, S
   Tom, Brown, Male, ICU, Wound, 5/8/2006, C. albicans
   The last record illustrates an isolate in which no antibiotics were tested.

2. One antibiotic result per row: Each row in the export file corresponds to one antibiotic test result. So if an organism is tested against 12 antibiotics, this organism would require 12 records in the export file. This approach is very commonly used when exporting data from relational databases, such as those common in LIS softwares or laboratory instruments.

   Example:
   First name, Last name, Sex, Location, Specimen type, Specimen date, Organism, Antibiotic, Result
   John, Smith, Male, Neurology, Blood, 1/1/2006, S. aureus, PEN, R
   John, Smith, Male, Neurology, Blood, 1/1/2006, S. aureus, ERY, R
   John, Smith, Male, Neurology, Blood, 1/1/2006, S. aureus, VAN, S
   Mary, Jones, Female, Nursery, CSF, 3/10/2006, S. pneumo, PEN, S
   Mary, Jones, Female, Nursery, CSF, 3/10/2006, S. pneumo, ERY, S
   Mary, Jones, Female, Nursery, CSF, 3/10/2006, S. pneumo, VAN, S
   Tom, Brown, Male, ICU, Wound, 5/8/2006, C. albicans

An advantage of the first approach is that files are much smaller in size; these files are also easy to manage in Excel and other data management softwares. An advantage of the second approach is that it is often easier to maintain in the long-term as additional antibiotics are added to the database. If the laboratory starts testing a new antibiotic, the first approach would require the programmer to add new columns to the data export, and if this is not done, the new antibiotic will not be captured. In the second approach, new antibiotics will generally show up automatically as additional rows in the export file, requiring no change in the structure of the data file.

Antibiotic results – test measurements and test interpretations

As mentioned above, it is possible to export test measurements (mm or µg/ml), test interpretations (resistant, intermediate, or susceptible), or both to the export files. If you have both, you should export both if possible. If you must decide between the two, the measurement is more valuable since the interpretation can be deduced from the measurement.

Example with disk diffusion data – exporting the measurement and the interpretation
First name, Last name, Specimen type, Specimen date, Organism, Antibiotic, Measurement, Interp.
John, Smith, Blood, 1/1/2006, S. aureus, PEN, 6, R
John, Smith, Blood, 1/1/2006, S. aureus, ERY, 10, R
John, Smith, Blood, 1/1/2006, S. aureus, VAN, 19, S

Example with MIC data – exporting the measurement and the interpretation
First name, Last name, Specimen type, Specimen date, Organism, Antibiotic, Measurement, Interp.
Mary, Jones, CSF, 3/10/2006, S. pneumo, PEN, 0.064, S
Mary, Jones, CSF, 3/10/2006, S. pneumo, ERY, <=0.25, S
Mary, Jones, CSF, 3/10/2006, S. pneumo, VAN, 1, S

Antibiotic results – test methods

If your laboratory only uses one test method, then there is no need for you to indicate the test method in the exported data file, as in the examples given above. On the other hand, if your laboratory does testing by more than one method, then you should also try to indicate the test method in the exported data file.

Example with disk and MIC data
First name, Last name, Specimen type, Specimen date, Organism, Antibiotic, Method, Measurement, Interp.
John, Smith, Blood, 1/1/2006, S. aureus, Disk, PEN, 6, R
John, Smith, Blood, 1/1/2006, S. aureus, Disk, ERY, 10, R
John, Smith, Blood, 1/1/2006, S. aureus, Disk, VAN, 19, S
Mary, Jones, CSF, 3/10/2006, S. pneumo, MIC, PEN, 0.064, S
Mary, Jones, CSF, 3/10/2006, S. pneumo, MIC, ERY, <=0.25, S
Mary, Jones, CSF, 3/10/2006, S. pneumo, MIC, VAN, 1, S
Tom, Brown, Wound, 5/8/2006, C. albicans

For many laboratories, this last example presented could be a useful model to emulate when you develop your export routine. In addition to the fields shown in this example, you should also export the other relevant fields described earlier.

The frequency of data exports will depend on how often the laboratory staff would like to update their databases for analysis. If the focus is only on general trends in infection and resistance, then once a quarter or once a year may be adequate. However, if there is interest in tying data analysis to prompt outbreak detection and isolate alerts, then a monthly or weekly export would be more appropriate.

An automated daily download and analysis would be the ideal solution. This has been implemented in a few institutions, and we are currently working on interface tools to make this a more viable option for laboratories, but at the present time, most laboratories accomplish the data conversions and analyses interactively on a weekly, monthly, or quarterly basis.

For information on the use of BacLink in automated batch mode, please contact us directly for details at jstelling@rics.bwh.harvard.edu.

If you succeed in creating a text file with the information described above, the next step is to use BacLink to convert the text file to the WHONET data format. This can be accomplished by the IT Department, by the laboratory, or by both groups in collaboration. For information on how to get started with BacLink, continue with the tutorial on “BacLink – Getting started”.

If you have any questions about BacLink or WHONET, feel free to contact us at jstelling@rics.bwh.harvard.edu. If you would like to assist us in the development of additional interface options for BacLink, we would also be very glad to hear from you.

The WHONET and BacLink softwares are available free-of-charge from the World Health Organization website: www.who.int/drugresistance/whonetsoftware You will see a file called: whonet54setup.exe

Save this file onto your computer. Then double-click on the file to begin the installation process. This process will install both the WHONET and BacLink softwares, by default into the c:\whonet5 folder. When you complete the installation, you will see icons for WHONET and BacLink on your desktop. Manuals for both softwares can be found in c:\whonet5\docs.

The below steps described the extract of both archived data (from historic EH01 and MB01 records) and active data (PR05 and MB01 records). The steps are very similar.

1. In the folder c:\whonet5\machines, you will find a number of CCL query files. Copy the files Cerner_archived_data.ccl, Cerner_active_data.ccl, and Cerner_report.ccl into your ccl directory. If you are using the Reflections emulation software, you should use File, Transfer.

2. For archived data
   Edit the file Cerner_achived_data.ccl at the indicated approximate line numbers to adapt the CCL queries for use in your laboratory, indicating the desired values which your Cerner system is using:

   67: Following “MEASUREMENT = “: Indicate which procedure(s) contain the MIC Values in your system. In the example, the procedures 6200830 and 6200832 are used.

   73: Following “INTERPRETATION = “: Edit the line to indicate the same procedure(s) you indicated in line 67, e.g. 6200830 and 6200832. This will exclude the MIC values from the MIC interpretation field.

   95: After the text “Enter Procedure Number range for Microbiology”, enter the range of procedure numbers used for microbiology test results. In the example, this is: BETWEEN 6200000 AND 6400000

   99: Optional. If needed, edit the pattern for the specific accession numbers desired. In the example: S1.ACCESSION1 IN ("*BL*","*MB*")

   102: Optional. If you want a full year of data, you could edit out the line stating AND PERIOD = S1.PERIOD1. Otherwise, leave this line in.

   107: Indicate the procedure number used in your Cerner which indicates a FINAL REPORT. In the example, this code is 6200885.

   129: Optional: If you only wish to export certain patient types, edit this line. Options in the example include EH.PAT_TYPE IN ("L","I","F","E").

3. For active data
   Edit the file Cerner_active_data.ccl at the indicated approximate line numbers to adapt the CCL queries for use in your laboratory, indicating the desired values which your Cerner system is using:

   77: Following “MEASUREMENT = “: Indicate which procedure(s) contain the MIC Values in your system. In the example, the procedure 6200832 is used.

   83: Following “INTERPRETATION = “: Edit the line to indicate the same procedure(s) you indicated in line 77, e.g. 6200832. This will exclude the MIC values from the MIC interpretation field.

   102: After the text “Enter Procedure Number range”, enter the range of procedure numbers used for microbiology test results. In the example, this is: BETWEEN 6200000 AND 6400000

   105: Optional. If needed, edit the pattern for the specific accession numbers desired. In the example: S1.ACCESSION1 IN ("*BL*","*MB*")

   110, 114, and 142: Indicate the procedure number used in your Cerner which indicates a FINAL REPORT. In the example, this code is 6200885.

   119: Optional: Enter any site-specific edits if you wish to exclude any specific comments, observations, etc.

   129: Optional: If you only wish to export certain patient types, edit this line. Options in the example include PR.PAT_TYPE IN ("L","I","F","E").

4. Include the CCL query files in your system, for example with the following syntax:
   (%I CCLPROG:CERNER_ACHIVED_DATA.CCL)
   (%I CCLPROG:CERNER_ACTIVE_DATA.CCL)
   (%I CCLPROG:CERNER_REPORT.CCL)

5. Go to the ccl prompt.
   For archived data, type: 1WN GO
   For active data, type: 1WHONET GO

   For archived data, you will see the following interface:

   
   

   For active data, the following screen will appear

   

6. When you run a report, the report files will be written to the T directory.

7. Optional – Feel free to add any additional prompts to your interface, for example asking the user to indicate a specific Institution or Client for the export. You may also add the queries to CCM or create a TIM Record, and run from the Select prompt.

   Note: You should NOT change the record length.

   SAMPLE TIM RECORD

   

Now that you have created a data file with the desired data from the Cerner system, BacLink can be used to convert this export file to the WHONET file format. The below instructions are meant as a quick guide. Detailed instructions can be found in the BacLink manual, baclink2manual.doc, by default in the folder: c:\whonet5\docs.

Start the BacLink program by double-clicking on the BacLink shortcut icon installed on your desktop. The BacLink program screen appears.

1. Configuring BacLink for Cerner data
   The first time that you use BacLink, you will the tell the software what kind of data file you would like to import, as well as the name and a code for your laboratory.

   Click on the New Format button. The File Format screen opens.
   From the drop down box, select the Country: for example, United States.
   Enter the Laboratory Name – the name of your laboratory, for example Boston General Hospital. If you will potentially import data from a number of different sources (Cerner, Excel, etc.), you may wish to indicate this in the laboratory name, for example Boston General Hospital (Cerner).
   Enter up to three characters for the Laboratory Code, for example BGH. The laboratory code that you indicate will be used by BacLink and WHONET as the default file extension for your WHONET data files.

Click on the File Structure button, and the below screen will appear. Set the selections as follows:

File Structure – Cerner

File Location – Indicate the folder where you plan to save your downloaded Cerner files. c:\whonet5\data is the default location suggested by BacLink, but any convenient location can be used. In many institutions, data files are placed in a folder on a central server.

File Name – If your downloaded data files will generally end in “.txt”, then leave the default response as “*.txt”. Otherwise, indicate an appropriate filter which will facilitate finding your data files, for example: “*.*”, “*.csv”, “micro*.*”, etc. If the name of the downloaded data file will not change over time, you may indicate the fixed name, for example: “download.txt”

File Origin – DOS (ASCII)

Click on the OK button.



Though not required, you may wish to click on the New data file button. On this screen, you can indicate the default data File location for your new WHONET files. By default, BacLink will put the WHONET files in the same location as your original Cerner files. You can also indicate the name of the WHONET file that you will create, though it is generally more convenient to give a file name later, just before a file conversion, and not here on this screen. The default WHONET file name will have the three-letter laboratory code as the file extension. Click on the OK button. Click on Save. Give a name to the BacLink configuration file, which will save the above-indicated user selections, for example “bwh.cfg” or “cerner download.cfg”. You may give any valid Windows file name. BacLink will add “.cfg” as a file extension to indicate to BacLink that this is a configuration file.

2. Converting data with BacLink

Original data file
From the main BacLink screen, click on the File Format configured in the previous step. On the BacLink 2 screen under “Original data file”, “File name”, select the download file to be converted. Example c:\whonet5\data\jan2003.txt.

New data file
Enter a name for the new WHONET data file that you wish to create with your converted data. Example: c:\whonet5\data\jan2003.xxx, where ‘xxx’ refers to your three-letter laboratory code. Your screen should then look similar to the following:



Click on Begin Conversion. BacLink begins converting the downloaded delimited file to a WHONET 5 file. BacLink will show you the first three isolates to permit a visual inspection of the accuracy of the conversion. The information from your data file, as read by BacLink, appears to the left of the screen. The information which will be saved in the WHONET file appears to the right of the screen. Where appropriate, WHONET will change your codes and formats to those used by WHONET.



If you notice any discrepancies or errors in the field mappings, you may correct these from the main BacLink screen using “Edit format”. Click “Next” to advance through the first three isolates. BacLink will then continue until the file is completely converted.

If BacLink does not understand some of the data codes in your file, the program asks whether you would like to define the unrecognized codes. If you answer Yes, you will be shown a list of the various organism, antibiotic, specimen type, location, gender, and test result codes that could not be understand. Click on a variable of interest, such as “Organism”, and click Define codes.

You will subsequently be shown a list of each of the unrecognized code. Select a code and click Define code. For most variables (except Location), you will be asked to select the matching or closest term from a list of WHONET codes. For Location, you will have the option of defining the patient department and type (inpatient, outpatient, ICU, etc.). Continue defining codes until you have defined all, or at least the most important and frequent, data elements. When finished, click “OK”, “OK” to return to the main BacLink screen.

If you have defined some additional codes, you should then convert the same file a second time in order to include the new code matchings in the converted data file. When finished with BacLink, click Exit.

Now that you have created a valid WHONET file using BacLink and your Cerner data, you can proceed to WHONET. For details on the use of WHONET, consult the manual WHONET 5.0 whonet5manual.doc, as well as available update pages describing the enhancements of further versions of the software.

1. Creating a laboratory configuration
   To begin using WHONET, you must first create a “Laboratory configuration” with descriptive information about your laboratory -- antibiotics, breakpoints, patient locations, etc. For laboratories not using BacLink, this is typically done with a feature called New laboratory. However, for users of BacLink, there is a shortcut available called Create a laboratory from a data file.

   Double-click on the WHONET icon. You will be shown a list of WHONET laboratories defined on your computer (with the default installation, you will see a single laboratory – “USA Test Hospital”). To access the aforementioned shortcut, click on Cancel. Then click File from the main WHONET menu, and then the option Create a laboratory from a data file.

   You will be requested to indicate your country, laboratory name, and laboratory code. Enter the responses using the same country and laboratory code which you selected in BacLink.

   You will then be requested to select a valid WHONET data file. Search and select for the file which you created above using BacLink. Then click OK. At this point, WHONET will scan the contents of this file – antibiotics, location codes, etc. – and create a valid WHONET laboratory configuration. When requested, you can click Yes if you want to review the details of the configuration. Otherwise, click No, and you can continue with Data analysis.

   Note: After creating the configuration utilizing the here-described shortcut, further edits, such as any modifications to the antibiotic breakpoints, can be done with Modify laboratory.

2. Using WHONET
   Once you have defined a laboratory configuration, it will appear in the list of laboratories when you enter WHONET. Click on your laboratory name. For data entry or data analysis options, click on Open laboratory. If you wish to modify the laboratory information in the configuration, click on Modify laboratory. For use of the WHONET analysis features, explore the screen display and/or consult the manual.

The WHONET and BacLink softwares are available free-of-charge from the World Health Organization website: www.who.int/drugresistance/whonetsoftware You will see a file called: whonet54setup.exe

Save this file onto your computer. Then double-click on the file to begin the installation process. This process will install both the WHONET and BacLink softwares, by default into the c:\whonet5 folder. When you complete the installation, you will see icons for WHONET and BacLink on your desktop. Manuals for both softwares can be found in c:\whonet5\docs.

1. Installing the BacLink NPR reports
   After installing WHONET, you will find copies of two BacLink NPR files “meditec1” and “meditec2” in the subdirectory c:\whonet5\machines. If you do not know how to upload an NPR report into your Meditech system, consult with your IT support staff or contact John Ucci directly at the above e-mail. Most users with sufficient access will utilize the “Upload Reports from PC” option on the “NPR Customization Menu”, as illustrated in the figures below.

   

2. Selecting the Meditech data
   Select the “BacLink NPR download” to run from either a menu or directly through the NPR Customization Process Reports routine. The date selection window appears:
   BACLINK DOWNLOAD
   From Collection Date
   Thru Collection Date
   Note that the date range selection is by specimen Collection Date

3. Creating the data file After entering the date range selection, the Print On window appears. There are three options at this point: DOWNLOAD, SPOOL and SCHED. Alternatively, automated transfer to an FTP site is also possible.

   1. Download
      If DOWNLOAD is selected, a Suppress: Nothing, Page banners, Form feeds, or Both? window may appear. Select N.

      The Save As window opens. Direct the report to the location you wish to store the downloaded data. This location will vary from site to site. Important: Remember the location you save the download file to and be consistent in using the same location. The location can be on the local hard drive (C:\) or on a network (\\servername\) where “servername” represents the local server storing the data.

      The downloaded files are conveniently saved to the WHONET data directory or another directory of the users choice. For example: C:\whonet5\data or \\servername\whonet5\data or \\servername\whonet5\download.

      Once the file location is selected, enter a valid Windows file name. Since the export files will have a text file structure, you may wish to include the extension “.txt”, “.csv” or “.dat”. Try to use a consistent naming convention. For example, if the data are downloaded monthly, appropriate names for the January 2003 data file include: jan2003.txt, w0103.txt, micro_2003.01, etc.

      Click “Save” to save the file to the selected location. Note: Be careful that an existing file name is not used. There is no warning message provided and previously saved data can be overwritten. Depending on the selected date range, the report will take a few seconds to a few minutes to complete.

   Once the data are downloaded to a file, End Of Report appears.

   2. Spool or Sched>
      If a download file is printed to SPOOL (saved as a spool file) or SCHED (assigned to a print schedule) consult the MEDITECH information systems contact for your department to help in configuring these options.

   3. FTP
      A data file can be scheduled to download directly to a specified location on a local hard drive or network server by configuring a FTP host in MEDITECH (Version 4.9 and higher). Again, discuss this option with the MEDITECH IS analyst.

Now that you have created a data file with the desired data from the Meditech system, BacLink can be used to convert this export file to the WHONET file format. The below instructions are meant as a quick guide. Detailed instructions can be found in the BacLink manual, baclink2manual.doc, by default in the folder: c:\whonet5\docs.

Start the BacLink program by double-clicking on the BacLink shortcut icon installed on your desktop. The BacLink program screen appears.

1. Configuring BacLink for Meditech data
   The first time that you use BacLink, you will the tell the software what kind of data file you would like to import, as well as the name and a code for your laboratory.

   Click on the New Format button. The File Format screen opens. From the drop down box, select the Country: for example, United States. Enter the Laboratory Name – the name of your laboratory, for example Boston General Hospital. If you will potentially import data from a number of different sources (Meditech, Excel, etc.), you may wish to indicate this in the laboratory name, for example Boston General Hospital (Meditech). Enter up to three characters for the Laboratory Code, for example BGH. The laboratory code that you indicate will be used by BacLink and WHONET as the default file extension for your WHONET data files.

   Click on the File Structure button, and the below screen will appear. Set the selections as follows:

   File Structure – Meditech
   File Location – Indicate the folder where you plan to save your downloaded Meditech files. c:\whonet5\data is the default location suggested by BacLink, but any convenient location can be used. In many institutions, data files are placed in a folder on a central server.

   File Name – If your downloaded data files will generally end in “.txt”, then leave the default response as “*.txt”. Otherwise, indicate an appropriate filter which will facilitate finding your data files, for example: “*.*”, “*.csv”, “micro*.*”, etc. If the name of the downloaded data file will not change over time, you may indicate the fixed name, for example: “download.txt”
   File Origin – DOS (ASCII)

   Click on the OK button.

   

   Though not required, you may wish to click on the New data file button. On this screen, you can indicate the default data File location for your new WHONET files. By default, BacLink will put the WHONET files in the same location as your original Meditech files. You can also indicate the name of the WHONET file that you will create, though it is generally more convenient to give a file name later, just before a file conversion, and not here on this screen. The default WHONET file name will have the three-letter laboratory code as the file extension. Click on the OK button.

   Click on Save. Give a name to the BacLink configuration file, which will save the above-indicated user selections, for example “bwh.cfg” or “meditech download.cfg”. You may give any valid Windows file name. BacLink will add “.cfg” as a file extension to indicate to BacLink that this is a configuration file.

   Click on Exit. This will return you to the main BacLink screen. Your newly defined file format will appear on the list of formats available to you.

2. Converting data with BacLink

   Original data file
   From the main BacLink screen, click on the File Format configured in the previous step. On the BacLink 2 screen under “Original data file”, “File name”, select the download file to be converted. Example c:\whonet5\data\jan2003.txt.

   New data file
   Enter a name for the new WHONET data file that you wish to create with your converted data. Example: c:\whonet5\data\jan2003.xxx, where ‘xxx’ refers to your three-letter laboratory code. Your screen should then look similar to the following:

   

   Click on Begin Conversion. BacLink begins converting the downloaded delimited file to a WHONET 5 file. BacLink will show you the first three isolates to permit a visual inspection of the accuracy of the conversion. The information from your data file, as read by BacLink, appears to the left of the screen. The information which will be saved in the WHONET file appears to the right of the screen. Where appropriate, WHONET will change your codes and formats to those used by WHONET.

   

   If you notice any discrepancies or errors in the field mappings, you may correct these from the main BacLink screen using “Edit format”. Click “Next” to advance through the first three isolates. BacLink will then continue until the file is completely converted.

   If BacLink does not understand some of the data codes in your file, the program asks whether you would like to define the unrecognized codes. If you answer Yes, you will be shown a list of the various organism, antibiotic, specimen type, location, gender, and test result codes that could not be understand. Click on a variable of interest, such as “Organism”, and click Define codes.

   You will subsequently be shown a list of each of the unrecognized code. Select a code and click Define code. For most variables (except Location), you will be asked to select the matching or closest term from a list of WHONET codes. For Location, you will have the option of defining the patient department and type (inpatient, outpatient, ICU, etc.). Continue defining codes until you have defined all, or at least the most important and frequent, data elements. When finished, click “OK”, “OK” to return to the main BacLink screen.

   If you have defined some additional codes, you should then convert the same file a second time in order to include the new code matchings in the converted data file. When finished with BacLink, click Exit.

Now that you have created a valid WHONET file using BacLink and your Meditech data, you can proceed to WHONET. For details on the use of WHONET, consult the manual WHONET 5.0 whonet5manual.doc, as well as available update pages describing the enhancements of further versions of the software.

1. Creating a laboratory configuration
   To begin using WHONET, you must first create a “Laboratory configuration” with descriptive information about your laboratory -- antibiotics, breakpoints, patient locations, etc. For laboratories not using BacLink, this is typically done with a feature called New laboratory. However, for users of BacLink, there is a shortcut available called Create a laboratory from a data file.

   Double-click on the WHONET icon. You will be shown a list of WHONET laboratories defined on your computer (with the default installation, you will see a single laboratory – “USA Test Hospital”). To access the aforementioned shortcut, click on Cancel. Then click File from the main WHONET menu, and then the option Create a laboratory from a data file.

   You will be requested to indicate your country, laboratory name, and laboratory code. Enter the responses using the same country and laboratory code which you selected in BacLink.

   You will then be requested to select a valid WHONET data file. Search and select for the file which you created above using BacLink. Then click OK. At this point, WHONET will scan the contents of this file – antibiotics, location codes, etc. – and create a valid WHONET laboratory configuration. When requested, you can click Yes if you want to review the details of the configuration. Otherwise, click No, and you can continue with Data analysis.

   Note: After creating the configuration utilizing the here-described shortcut, further edits, such as any modifications to the antibiotic breakpoints, can be done with Modify laboratory.

2. Using WHONET
   Once you have defined a laboratory configuration, it will appear in the list of laboratories when you enter WHONET. Click on your laboratory name. For data entry or data analysis options, click on Open laboratory. If you wish to modify the laboratory information in the configuration, click on Modify laboratory. For use of the WHONET analysis features, explore the screen display and/or consult the manual.

The WHONET and BacLink softwares are available free-of-charge from the World Health Organization website: www.who.int/drugresistance/whonetsoftware You will see a file called: whonet54setup.exe

Double-click on this file, and select “Run”, and follow the installation instructions. This process will install both the WHONET and BacLink softwares, by default into the c:\whonet5 folder. When you complete the installation, you will see icons for WHONET and BacLink on your desktop. Manuals for both softwares can be found in c:\whonet5\docs.

To export the data from LabPro, you will take advantage of LabPro’s interface utility. If you do not have this utility installed, please contact your Dade-Behring representative. In most low-resource countries, this software is available free-of-charge from company representatives.

LabPro’s interface utility is usually used to transfer test results across a cable to a central laboratory information system. Fortunately, it is also possible to use this same utility for transferring data to a text file on the computer’s hard drive. The below instructions describe: 1. how to configure the interface so that the results go to a local text file; and 2. how to run the interface so that the data are “transmitted” to the text file.

Configuring the “interface”

Open LabPro.
Click on the icon for “Utilities”.
Click on “Configuration”. Double-click on “Interface”.

If the system does not respond or if the icon is disabled, it is possible that the “Interface” software is not installed on your instrument. Contact your local MicroScan representative for assistance.

You will see the screen for “Configure Communication Devices”. You will now create a new interface which directs the data output to a file on your computer’s hard drive.

Click on “Device”, “Add”, “LIS”.
On the screen “Device Configuration”, you will see the following options:
Device name – Type a name for the interface, for example the name of your hospital or “WHONET export” or other name of your choosing.
Physical – Change the option “Serial” to the option “File”.
Data Link – LabPro will automatically change the selection to “Null”
Message – LabPro will set this option to “MicroScan”
Click on the row for “Physical”, and then “Configure”.
Under “File Settings”, you can indicate the name of the “Import File Name” and the “Export File Name”.

Since you will be exporting data, the “Export File Name” is of greater importance. The default name suggested by LabPro is “Export.exp”. The default location is the MicroScan\LabPro subdirectory. You may use these defaults or change them to a name of your choice, for example: c:\whonet5\data\export.exp, c:\whonet5\data\MicroScan.txt, etc. When you have indicated the desired name, click “OK”, “OK”.

On the list of devices, your new interface should now appear.

“Transmitting” the data

From the main LabPro screen, click on the icon for the “Interface Monitor”.

You will see the list of devices including the columns “Device Name”, “Status”, “Next Send Time”, “Next Request Time”, and “Error Conditions”.

Click on the file export interface that you have configured. Then click on “Device”, “Transmit Patient Data”. A screen for “Manual Transmit” will appear.

You have the option of selecting the isolates to transmit from the following list of variables: “Admission #”, “Collect Date”, “Individual Specimens with Isolate”, “Isolate Status Date”, “Patient ID”, “Specimen #”, “Specimen Status Date”, “Test Group Status Date”.

Choose the variable that you wish to use for selecting the isolates. Unfortunately, if you select a date field, you cannot select a “From” and “To” date. You may only select isolates from a given date up to the present date using the option “Days prior to transmission date”. If you choose “Specimen #” or “Patient ID”, you may indicate “From” and “To” values.

If you have possibly exported or transmitted these data previously, you should click on the “Retransmit data previously sent” option to ensure that all records are transmitted.

When finished with your selections, click on “Data”, “Transmit”. The system will begin sending the isolates. You can follow the progress of the transmission on the “Interface Monitor” as the Status of the interface changes from “Idle” to “Waiting” to “Sending” and eventually back to “Idle”. During the transfer, you will see the message “Transmitting Data” at the bottom of the window. If you then use “My Computer” or the “Windows Explorer” to look for the file, you will be able to verify that LabPro has created the requested file.

Important Note: If the export file already exists, you will receive a small screen “Confirm” indicating that the file already exists, for example “D:\Microscan\LabPro\Export.exp contains data. Erase?” Unfortunately, this screen may be hidden by the “Interface Monitor” screen with “Status” set to “Waiting”. In this case, the user should either click on the “Confirm” icon which appears at the bottom of the screen on the Windows Task Bar or move the “Interface Monitor” screen so that the question can be seen. To replace the existing file, click on “OK”.

If you do not want to replace the previously existing file, you should rename your file, for example “Export.january2003.exp”. Renaming the file will thus permit you to create a permanent backup of your MicroScan export files.

If you have installed WHONET and BacLink on a different computer, then copy the exported data file to the other computer using a diskette, CD, or USB memory stick.

Other LabPro options

Active Specimen Range
By default, LabPro may only transmit or export “active” specimens. By default, the active specimen range is set to 30 days prior to the current date. To change this option, click on the “Utilities” option, “System”, “Active Specimen Range”. By default, the “Enable Active Specimen Range” option is selected. To remove this feature, remove the check mark. If you wish to use the Active Range feature, you may change the length of the active period by indicating the number of “Preceding Days”. By default, this is set to 30 days.

Export the LabPro code lists
LabPro permits the export of the list of system- and user-defined codes (organisms, anibiotics, specimens, etc.), for example for use in Excel. To export the codes, click on the “Interface Monitor” icon. Click on the “Device” you have configured for file exports. Click on “Device”, “Transmit Custom Data”. You will be given the following choices for the export: “Institutions”, “Isolate Comments”, “Organisms”, “Patient Comments”, “Physicians”, “Services”, “Sources”, “Specimen Comments”, “Techs”, “Drug Tests”, and “Wards”. Click on the desired options, and then on “Transmit”. The data will be transmitted to the export file which you have configured.

Automatic transmissions
Go to “Device Monitor”. Click on Device.
“Device”, “Auto-Communication”
“Enable Auto-Transmit”
Indicate the time or times for the daily transmissions. (To delete a time, use right-button on the time.)
“Search Type”: Admission #, Collect Date, “Isolate Status Date”, “Patient ID”, “Specimen #, “Specimen Status Date”, “Test Group Status Date”.
For dates: “Days prior to transmission date”.
For others: “From”, “To”
Options: “Active specimen only”, “Retransmit data previously sent”

Now that you have created a data file with the desired data, BacLink can be used to convert this export file to the WHONET file format. The below instructions are meant as a quick guide. Detailed instructions can be found in the BacLink manual, baclink2manual.doc, by default in the folder: c:\whonet5\docs.

Start the BacLink program by double-clicking on the BacLink shortcut icon installed on your desktop. The BacLink program screen appears.

1. Configuring BacLink The first time that you use BacLink, you will the tell the software what kind of data file you would like to import, as well as the name and a code for your laboratory.

   Click on the New Format button. The File Format screen opens. From the drop down box, select the Country: for example, United States. Enter the Laboratory Name – the name of your laboratory, for example Boston General Hospital. If you will potentially import data from a number of different sources (LabPro, Cerner, Excel, etc.), you may wish to indicate this in the laboratory name, for example Boston General Hospital (LabPro). Enter up to three characters for the Laboratory Code, for example BGH. The laboratory code that you indicate will be used by BacLink and WHONET as the default file extension for your WHONET data files.

   Click on the File Structure button, and the below screen will appear. Set the selections as follows:

   File Structure – Microscan (Interface)

   File Location – Indicate the folder where you plan to save your LabPro files. c:\whonet5\data is the default location suggested by BacLink, but any convenient location can be used. In many institutions, data files are placed in a folder on a central server.

   File Name – If your downloaded data files will generally end in “.txt”, then leave the default response as “*.txt”. Otherwise, indicate an appropriate filter which will facilitate finding your data files, for example: “*.*”, “*.csv”, “micro*.*”, etc. If the name of the downloaded data file will not change over time, you may indicate the fixed name, for example: “download.txt”

   File Origin – Windows (ANSI)

   Click on the OK button.

   

   Though not required, you may wish to click on the New data file button. On this screen, you can indicate the default data File location for your new WHONET files. By default, BacLink will put the WHONET files in the same location as your original LabPro files. You can also indicate the name of the WHONET file that you will create, though it is generally more convenient to give a file name later, just before a file conversion, and not here on this screen. The default WHONET file name will have the three-letter laboratory code as the file extension.
   Click on the OK button.

   Click on Save. Give a name to the BacLink configuration file, which will save the above-indicated user selections, for example “bwh.cfg” or “labpro.cfg”. You may give any valid Windows file name. BacLink will add “.cfg” as a file extension to indicate to BacLink that this is a configuration file.

   Click on Exit. This will return you to the main BacLink screen. Your newly defined file format will appear on the list of formats available to you.

2. Converting data with BacLink

   Original data file
   From the main BacLink screen, click on the File Format configured in the previous step. On the BacLink 2 screen under “Original data file”, “File name”, select the download file to be converted. Example c:\whonet5\data\jan2003.txt.

   New data file
   Enter a name for the new WHONET data file that you wish to create with your converted data. Example: c:\whonet5\data\jan2003.xxx, where ‘xxx’ refers to your three-letter laboratory code. Your screen should then look similar to the following:

   

   Click on Begin Conversion. BacLink begins converting the downloaded delimited file to a WHONET 5 file. BacLink will show you the first three isolates to permit a visual inspection of the accuracy of the conversion. The information from your data file, as read by BacLink, appears to the left of the screen. The information which will be saved in the WHONET file appears to the right of the screen. Where appropriate, WHONET will change your codes and formats to those used by WHONET.

   

   If you notice any discrepancies or errors in the field mappings, you may correct these from the main BacLink screen using “Edit format”. Click “Next” to advance through the first three isolates. BacLink will then continue until the file is completely converted.

   If BacLink does not understand some of the data codes in your file, the program asks whether you would like to define the unrecognized codes. If you answer Yes, you will be shown a list of the various organism, antibiotic, specimen type, location, gender, and test result codes that could not be understand. Click on a variable of interest, such as “Organism”, and click Define codes.

   You will subsequently be shown a list of each of the unrecognized code. Select a code and click Define code. For most variables (except Location), you will be asked to select the matching or closest term from a list of WHONET codes. For Location, you will have the option of defining the patient department and type (inpatient, outpatient, ICU, etc.). Continue defining codes until you have defined all, or at least the most important and frequent, data elements. When finished, click “OK”, “OK” to return to the main BacLink screen.

   If you have defined some additional codes, you should then convert the same file a second time in order to include the new code matchings in the converted data file. When finished with BacLink, click Exit.

Now that you have created a valid WHONET file using BacLink and your LabPro data, you can proceed to WHONET. For details on the use of WHONET, consult the manual WHONET 5.0 whonet5manual.doc, as well as available update pages describing the enhancements of further versions of the software

1. Creating a laboratory configuration
   To begin using WHONET, you must first create a “Laboratory configuration” with descriptive information about your laboratory -- antibiotics, breakpoints, patient locations, etc. For laboratories not using BacLink, this is typically done with a feature called New laboratory. However, for users of BacLink, there is a shortcut available called Create a laboratory from a data file.

   Double-click on the WHONET icon. You will be shown a list of WHONET laboratories defined on your computer (with the default installation, you will see a single laboratory – “USA Test Hospital”). To access the aforementioned shortcut, click on Cancel. Then click File from the main WHONET menu, and then the option Create a laboratory from a data file.

   You will be requested to indicate your country, laboratory name, and laboratory code. Enter the responses using the same country and laboratory code which you selected in BacLink.

   You will then be requested to select a valid WHONET data file. Search and select for the file which you created above using BacLink. Then click OK. At this point, WHONET will scan the contents of this file – antibiotics, location codes, etc. – and create a valid WHONET laboratory configuration. When requested, you can click Yes if you want to review the details of the configuration. Otherwise, click No, and you can continue with Data analysis.

   Note: After creating the configuration utilizing the here-described shortcut, further edits, such as any modifications to the antibiotic breakpoints, can be done with Modify laboratory.

2. Using WHONET Once you have defined a laboratory configuration, it will appear in the list of laboratories when you enter WHONET. Click on your laboratory name. For data entry or data analysis options, click on Open laboratory. If you wish to modify the laboratory information in the configuration, click on Modify laboratory. For use of the WHONET analysis features, explore the screen display and/or consult the manual.

The WHONET and BacLink softwares are available free-of-charge from the World Health Organization website: www.who.int/drugresistance/whonetsoftware You will see a file called: whonet54setup.exe

Double-click on this file, and select “Run”, and follow the installation instructions. This process will install both the WHONET and BacLink softwares, by default into the c:\whonet5 folder. When you complete the installation, you will see icons for WHONET and BacLink on your desktop. Manuals for both softwares can be found in c:\whonet5\docs.

The Vitek system is a UNIX-based system with an interface option which allows the transfer of individual, pending, and final results. The most recent upgrade of the Vitek BioLiaison software ncludes a simple, configurable routine for exporting selected isolates to a DOS-formated diskette.

7.6.1 Vitek export

BASIC
From the bioMérieux – bioLIAISON Main Menu, select Reports, DataTrac, Logbook Report. Enter the selection criteria. Dates, codes, select ‘List…’ (will appear in Black). Uses the local Vitek date format. “Collection date…”

Select Format, Pick, Click on ‘logbook_132.format’. ‘OK’

Click on:
Export…
“Export to floppy” screen
“Please choose a delimiter between fields for the exported file:” choose “|”. “Please give the DOS filename of the export file:” File name: _______ . TXT
Insert diskette
Click on “Export”.
When finished “Export succeeded!”. Click on “OK”.
Click on “Quit” to return to the previous screen.
“File”, “Quit”

ADVANCED
Setup, Formatting, Logbook Report Format
“Formatting Logbook Report Format”
“Setup” or “Report format” Include duplicates Yes/No, Include Test results Yes/No
“File” “New” “Open” “Save” “Selected format” (no spaces) “OK”
L = label
C = code
T = text
watch screen width
if more space needed:
-- remove unneeded fields
-- move fields closer together
-- replace ‘text’ fields by ‘code fields’

Now that you have created a data file with the desired data, BacLink can be used to convert this export file to the WHONET file format. The below instructions are meant as a quick guide. Detailed instructions can be found in the BacLink manual, baclink2manual.doc, by default in the folder: c:\whonet5\docs.

Start the BacLink program by double-clicking on the BacLink shortcut icon installed on your desktop. The BacLink program screen appears.

1. Configuring BacLink
   The first time that you use BacLink, you will the tell the software what kind of data file you would like to import, as well as the name and a code for your laboratory.

   Click on the New Format button. The File Format screen opens. From the drop down box, select the Country: for example, United States.

   Enter the Laboratory Name – the name of your laboratory, for example Boston General Hospital. If you will potentially import data from a number of different sources (LabPro, Cerner, Excel, etc.), you may wish to indicate this in the laboratory name, for example Boston General Hospital (LabPro). Enter up to three characters for the Laboratory Code, for example BGH. The laboratory code that you indicate will be used by BacLink and WHONET as the default file extension for your WHONET data files.

   Click on the File Structure button, and the below screen will appear. Set the selections as follows:

   File Structure – Vitek (Export)
   File Location – Indicate the folder where you plan to save your LabPro files. c:\whonet5\data is the default location suggested by BacLink, but any convenient location can be used. In many institutions, data files are placed in a folder on a central server.
   File Name – If your downloaded data files will generally end in “.txt”, then leave the default response as “*.txt”. Otherwise, indicate an appropriate filter which will facilitate finding your data files, for example: “*.*”, “*.csv”, “micro*.*”, etc. If the name of the downloaded data file will not change over time, you may indicate the fixed name, for example: “download.txt”
   File Origin – Windows (ANSI)

   Click on the OK button.

   

   Though not required, you may wish to click on the New data file button. On this screen, you can indicate the default data File location for your new WHONET files. By default, BacLink will put the WHONET files in the same location as your original LabPro files. You can also indicate the name of the WHONET file that you will create, though it is generally more convenient to give a file name later, just before a file conversion, and not here on this screen. The default WHONET file name will have the three-letter laboratory code as the file extension. Click on the OK button.

   Click on Save. Give a name to the BacLink configuration file, which will save the above-indicated user selections, for example “bwh.cfg” or “labpro.cfg”. You may give any valid Windows file name. BacLink will add “.cfg” as a file extension to indicate to BacLink that this is a configuration file.

   Click on Exit. This will return you to the main BacLink screen. Your newly defined file format will appear on the list of formats available to you.

2. Converting data with BacLink

   Original data file
   From the main BacLink screen, click on the File Format configured in the previous step. On the BacLink 2 screen under “Original data file”, “File name”, select the download file to be converted. Example c:\whonet5\data\jan2003.txt.

   New data file
   Enter a name for the new WHONET data file that you wish to create with your converted data. Example: c:\whonet5\data\jan2003.xxx, where ‘xxx’ refers to your three-letter laboratory code. Your screen should then look similar to the following:

   

   Click on Begin Conversion. BacLink begins converting the downloaded delimited file to a WHONET 5 file. BacLink will show you the first three isolates to permit a visual inspection of the accuracy of the conversion. The information from your data file, as read by BacLink, appears to the left of the screen. The information which will be saved in the WHONET file appears to the right of the screen. Where appropriate, WHONET will change your codes and formats to those used by WHONET.

   

   If you notice any discrepancies or errors in the field mappings, you may correct these from the main BacLink screen using “Edit format”. Click “Next” to advance through the first three isolates. BacLink will then continue until the file is completely converted.

   If BacLink does not understand some of the data codes in your file, the program asks whether you would like to define the unrecognized codes. If you answer Yes, you will be shown a list of the various organism, antibiotic, specimen type, location, gender, and test result codes that could not be understand. Click on a variable of interest, such as “Organism”, and click Define codes.

   You will subsequently be shown a list of each of the unrecognized code. Select a code and click Define code. For most variables (except Location), you will be asked to select the matching or closest term from a list of WHONET codes. For Location, you will have the option of defining the patient department and type (inpatient, outpatient, ICU, etc.). Continue defining codes until you have defined all, or at least the most important and frequent, data elements. When finished, click “OK”, “OK” to return to the main BacLink screen.

   If you have defined some additional codes, you should then convert the same file a second time in order to include the new code matchings in the converted data file. When finished with BacLink, click Exit.

Now that you have created a valid WHONET file using BacLink and your LabPro data, you can proceed to WHONET. For details on the use of WHONET, consult the manual WHONET 5.0 whonet5manual.doc, as well as available update pages describing the enhancements of further versions of the software.

1. Creating a laboratory configuration
   To begin using WHONET, you must first create a “Laboratory configuration” with descriptive information about your laboratory -- antibiotics, breakpoints, patient locations, etc. For laboratories not using BacLink, this is typically done with a feature called New laboratory. However, for users of BacLink, there is a shortcut available called Create a laboratory from a data file.

   Double-click on the WHONET icon. You will be shown a list of WHONET laboratories defined on your computer (with the default installation, you will see a single laboratory – “USA Test Hospital”). To access the aforementioned shortcut, click on Cancel. Then click File from the main WHONET menu, and then the option Create a laboratory from a data file.

   You will be requested to indicate your country, laboratory name, and laboratory code. Enter the responses using the same country and laboratory code which you selected in BacLink.

   You will then be requested to select a valid WHONET data file. Search and select for the file which you created above using BacLink. Then click OK. At this point, WHONET will scan the contents of this file – antibiotics, location codes, etc. – and create a valid WHONET laboratory configuration. When requested, you can click Yes if you want to review the details of the configuration. Otherwise, click No, and you can continue with Data analysis.

   Note: After creating the configuration utilizing the here-described shortcut, further edits, such as any modifications to the antibiotic breakpoints, can be done with Modify laboratory.

2. Using WHONET
   Once you have defined a laboratory configuration, it will appear in the list of laboratories when you enter WHONET. Click on your laboratory name. For data entry or data analysis options, click on Open laboratory. If you wish to modify the laboratory information in the configuration, click on Modify laboratory. For use of the WHONET analysis features, explore the screen display and/or consult the manual.

The WHONET and BacLink softwares are available free-of-charge from the World Health Organization website: www.who.int/drugresistance/whonetsoftware

Create a WHONET account and download the latest WHONET setup file. Double-click the setup file, and select “Run” and follow the installation instructions. This process will install both the WHONET and BacLink softwares by default into the c:\whonet5 folder When you complete the installation you will see icons for WHONET and BacLink on your desktop. Manuals for both softwares can be found in c:\whonet5\docs.

The BD EpiCenterTM is clinical data management software which allows the export of BD PhoenixTM AST results to WHONET. BD EpiCenterTM software version 6.60 or above is required for this process to work.
BD EpiCenterTM data export

- Launch BD EpiCenterTM (V6.60 or above) and log in.
- Select the “DataView” reporting module from Toolbar.

- Select the predefined data filter in the following location “Predefined3-WHONET Data ExportWHONET Data Export” and press “Run”.

- Enter the appropriate filter criteria to limit the data returned, and press “Run”.

- When the result data has been displayed, click the “Print Preview” option and then select the option to export data to Tab separated text file. File name and export file location will be suggested but can be modified before saving.

For more assistance, refer to the BD EpiCenterTM online help.

Now that you have created a data file with the desired data, BacLink can be used to convert this export file to the WHONET file format. The instructions below are a quick guide.
Start the BacLink program by double-clicking on the BacLink shortcut icon installed on your desktop. The BacLink program screen appears.

1. Configuring BacLink
   The first time BacLink is used, choose the kind of data file you would like to import, as well as the name and a code for your laboratory.

   Click on the New Format button. The File Format screen opens. From the drop down box, select the Country: for example, United States. Enter the Laboratory Name – the name of your laboratory, for example Boston General Hospital. If data could be imported from a number of different sources you may wish to indicate this in the laboratory name, for example Boston General Hospital (Phoenix). Enter up to three characters for the Laboratory Code, for example BGH. The laboratory code entered will be used by BacLink and WHONET as the default file extension for your WHONET data files.

   Click on the File Structure button, and the below screen will appear. Set the selections as follows:

   

   File Structure – BD EpiCenter

   File Location – Indicate the folder where the WHONET files will be saved. c:\whonet5\data is the default location suggested by BacLink, but any convenient location can be used. In many institutions, data files are placed in a folder on a central server.

   File Name – *.txt

   File Origin – Windows (ANSI)

   Click on the OK button.

   

   Though not required, you may wish to click on the New data file button. On this screen, you can indicate the default data File location for your new WHONET files. You can indicate the name of the WHONET file that you will create, though it is generally more convenient to give a file name later, just before a file conversion, and not here on this screen. The default WHONET file name will have the three-letter laboratory code as the file extension.
   Click on the OK button.

   Click on Save. Give a name to the BacLink configuration file, which will save the above-indicated user selections, for example “bgh.cfg”. You may give any valid Windows file name. BacLink will add “.cfg” as a file extension to indicate to BacLink that this is a configuration file.

   Click on Exit. This will return you to the main BacLink screen. Your newly defined file format will appear on the list of formats available to you.

2. Converting data with BacLink
   Original data file
   From the main BacLink screen, click on the File Format configured in the previous step. For “File name”, browse and select the file to be converted. Example c:\whonet5\data\WHONET Export20150319.txt.

   New data file
   Enter a name for the new WHONET data file that you wish to create with your converted data. Example: c:\whonet5\data\ WHONET Export20150319.xxx, where ‘xxx’ refers to your three-letter laboratory code. Your screen should look similar to the following:

   

   Click on Begin Conversion. BacLink begins converting the selected Tab delimited text file to a WHONET 5 file. BacLink will display the first three isolates to permit a visual inspection of the accuracy of the conversion. The information from your data file, as read by BacLink, appears to the left of the screen. The information which will be saved in the WHONET file appears to the right of the screen. Where appropriate, WHONET will change your codes and formats to those used by WHONET.

   

   If you notice any discrepancies or errors in the field mappings, you may correct these from the main BacLink screen using “Edit format”. Click “Next” to advance through the first three isolates. BacLink will then continue until the file is completely converted.

   If BacLink does not understand some of the data codes in your file, the program asks whether you would like to define the unrecognized codes. If you answer Yes, you will be shown a list of the various organism, antibiotic, specimen type, location, gender, and test result codes that could not be understand. Click on a variable of interest, such as “Organism”, and click Define codes.

   You will subsequently be shown a list of each of the unrecognized code. Select a code and click Define code. For most variables (except Location), you will be asked to select the matching or closest term from a list of WHONET codes. For Location you will have the option of defining the patient department and type (inpatient, outpatient, ICU, etc.). Continue defining codes until you have defined all, or at least the most important and frequent, data elements. When finished click “OK”, then “OK” again to return to the main BacLink screen.

   If you have defined some additional codes, you should then convert the same file a second time in order to include the new code matchings in the converted data file. When finished with BacLink, click Exit.

Now that you have created a valid WHONET file using BacLink and your BD EpiCenterTM data, you can proceed to WHONET. For details on the use of WHONET, consult the manual WHONET 5.0 whonet5manual.doc, as well as available update pages describing the enhancements of further versions of the software.

1. Creating a laboratory configuration
   To begin using WHONET, you must first create a “Laboratory configuration” with descriptive information about your laboratory -- antibiotics, breakpoints, patient locations, etc. For laboratories not using BacLink, this is typically done with a feature called New laboratory. However, for users of BacLink, there is a shortcut available called Create a laboratory from a data file.

   Double-click on the WHONET icon. You will be shown a list of WHONET laboratories defined on your computer (with the default installation, you will see a single laboratory – “USA Test Hospital”). To access the aforementioned shortcut, click on Cancel. Then click File from the main WHONET menu, and then the option Create a laboratory from a data file.

   You will be asked to indicate your country, laboratory name, and laboratory code. Enter the responses using the same country and laboratory code which you selected in BacLink

   You will then be requested to select a valid WHONET data file. Search for and select the file created above using BacLink. Then click OK. At this point, WHONET will scan the contents of this file – antibiotics, location codes, etc. – and create a valid WHONET laboratory configuration. When requested, you can click Yes if you want to review the details of the configuration. Otherwise, click No, and continue with Data analysis.

   Note: After creating the configuration utilizing the here-described shortcut, further edits, such as any modifications to the antibiotic breakpoints, can be done with Modify laboratory.

2. Using WHONET Once you have defined a laboratory configuration, it will appear in the list of laboratories when you enter WHONET. Click on your laboratory name. For data entry or data analysis options, click on Open laboratory. If you wish to modify the laboratory information in the configuration, click on Modify laboratory. For use of the WHONET analysis features, explore the screen display and/or consult the manual.