In the following section the variables of the GLASS minimal configuration laboratory are described. Most of them are required for generating the GLASS exchange format (GLASS aggregated data files). If the user has configured the laboratory to requirements different from the GLASS protocol, additional data entry fields may appear.
Note: GLASS is collecting data not only on “positive” results (GLASS priority pathogens) but also on the overall number of clinical specimens submitted to the laboratory for species isolation and identification. That means, for example for blood specimens, information on isolates other than the GLASS priority pathogens and also “negative” results should be included in the aggregated GLASS data submission. WHONET has implemented this approach in the GLASS sample file, providing the information is entered on site; the overall number of samples for the respective specimen is aggregated in the sample file. For more details on data entry in WHONET see below under “Pathogen”. More information on the approach and methodology can be found in the GLASS Manual for Early Implementation and the GLASS guide to preparing aggregated AMR data files.
Unique patient identifier
Enter a unique patient identifier (ID) for each patient with a maximum of 12 characters. Several specimens and isolates can be assigned to each patient and corresponding unique ID. The unique patient ID is required for de-duplication that is automatically done by WHONET software when generating the GLASS exchange format (see also section 6.3).
Date of birth
To enter the date of birth see instructions on the previous page regarding the format. Alternatively the user may wish to enter the patient’s age (see “Age”). When generating the GLASS exchange format, age will be aggregated into the GLASS pre-defined age group category.
Enter “m” for male and “f” for female. Missing values will be reported in the GLASS aggregated data file as unknown.
The option of entering the patient’s age exists. However, if the patient’s date of birth has been entered, the patient’s age will automatically be calculated and inserted in the age field when the specimen date is entered. When generating the GLASS exchange format, age will be grouped in the GLASS pre-defined age group category.
Date of admission
Enter the date of hospital (inpatient) admission (see previous page for date format). Date of admission is a field required to calculate “hospital origin”.
Select the location type (ward type). It is important to indicate the patient’s location as the calculation of the GLASS variable “origin” (community or hospital, see “infection origin” below) is based on an algorithm in the WHONET software that requires the variable’s location type. As a minimum enter outpatient or inpatient respectively. For hospitalized patients, the “date of admission” and “specimen date” are also required. Missing values will result in unknown “origin” in the GLASS aggregated data file.
The GLASS protocol defines “origin” as community- or hospital-acquired infection (see also the GLASS Manual for Early Implementation and the GLASS document “ A guide to preparing aggregated AMR data files” for more details). WHONET software calculates “Infection origin” using a combination of data entry fields. In order for the software to calculate this field, three data fields are needed: location type; and for hospitalized patients - specimen date and the date of admission. The rules for calculating the “Infection origin” (corresponding to the GLASS “origin”) are as follows: All location types of “out” (coded value for outpatient) will result in the isolate being reported to GLASS as “Community”. If admission date and specimen date are provided, and location type is “in” (coded value for inpatient), the system will verify that the admission date occurred more than two days prior to the specimen’s collection. If this is true, the isolate will be marked “Hospital”, otherwise it will be marked “Community”. If the system cannot determine the “Infection origin”, usually due to missing data, it will be reported as “Unknown” to GLASS.
Enter the surveillance site (maximum 3 letters laboratory code) or choose “other” in the event that the patient has not been cared for at the surveillance site.
Enter a number for each specimen with a maximum of 12 characters.
The specimen number may be helpful for data validation purposes when, for example, several isolates from the same patient are entered.
Enter the date the specimen was taken (see previous page for date format). This field is required to calculate the “Infection origin”.
Enter the specimen type from the GLASS list that is displayed on the right half of the screen. Two lists are available to the user – the short “GLASS list” with four specimen types (“Blood”, “Genital”, “Stool” and “Urine”); or the “Standard WHONET list” with a much larger number of specimen types e.g. “Cerebrospinal fluid”, “Sputum”, “Joint fluid”, etc. Choose the list that is most appropriate for your needs.
The 3-character WHONET organism code should be entered here, or selected from the GLASS pathogen list on the right half of the screen that is displayed by default for the minimal GLASS configuration. To view the standard or extended list and to enter information on isolates other than the GLASS priority pathogens, select ”standard” or “extended” respectively from the drop down option. To enter data for specimens submitted to the laboratory but with “negative” results (“no isolate growth”) leave the pathogen field blank or use the WHONET code “xxx” signifying “No growth”, and press the “Save isolate” button on the upper right screen and proceed as prompted. The specimen will be correctly included in the GLASS sample file. More information on the approach and methodology can be found in the GLASS Manual for Early Implementation and the GLASS document “A guide to preparing aggregated AMR data files”.
The antibiotic panel displayed by default shows the antibiotics for the selected organism proposed by GLASS for reporting. If the user changes the panel to “All antibiotics”, then it is possible to select from any of the antibiotics on the list.
Susceptibility results and the list of antibiotics
To enter susceptibility results, first click on the appropriate test method – disk diffusion, MIC or ETest. The list of antibiotics for that test method appears. Each time a result is entered press : the cursor then jumps to the next antibiotic on the antibiotic panel for the organism tested.
Entering susceptibility results
WHONET allows the entry of quantitative results (e.g. 13 mm, 64 µg/ml) or the entry of qualitative results (R = resistant, I = intermediate, S = susceptible).
The lowest possible zone diameter is 6 mm. If 0 mm is entered (indicating no inhibition), WHONET will automatically change this to 6 mm.
For off-scale MIC values the following, for example, may be entered: <=.5, >64.
If MIC results from the test of a drug combination are being entered (e.g. trimethoprim/sulfamethoxazole), enter the result of the first or principal agent. These concentrations usually follow the 1, 2, 4, 8 … doubling-dilution series.
Saving the isolate information
When all the data for an isolate have been entered, click on “Save isolate” (or press Alt-S). The data will be saved and the “Data entry” screen will be cleared so that the data for the next isolate can be entered.
WHONET will ask whether the user wants to:
- Save the isolate
- Save and continue with the same isolate
- Save and continue with the same patient
Click on one of these options to save or on “Cancel”, if the decision is not to save the record.
Exit data entry
When all data have been entered, click on “Exit” to return to the main WHONET screen.