Samples

Selecting the Samples menu item in the blue ribbon takes you to the sample directory. The directory has two possible views: Human (A) and Environment (B). You can switch between the two views by clicking on the respective button at the top right. The active view is highlighted in dark blue.

Here you will find for the selected view a list of all samples documented in SORMAS, regardless of whether they were recorded under cases, contacts or event participants (in the view ‘human’) as well as all documented environment-related samples for the ‘environment’ view. However, samples that belong to archived entities can no longer be edited (provided no other active entity is linked). Here you can get an overview of all available samples, filter, sort and export the overview according to certain criteria and edit existing samples, for example to add new test results.

Sample directory for the “human” view

Open

In the upper area you will find the available filter options for the sample directory (A). You can combine the filters as required, for example to determine all positive samples from a specific laboratory. All selected filters must be activated using the "Apply filters" button or ENTER; the set filters are discarded using the "Reset filters" button.

You can use the predefined filters "Shipped", "Not shipped", "Received" and "Referred to other lab" with a light blue background to filter the list according to the status of the sample (B). You also have the option of filtering the list according to active or archived samples or according to their context (Case samples / Contact samples / Event participant samples) (C).

To edit an existing sample, click on the sample ID in the first column of the table (D). Editing an existing sample is not only possible via the sample directory, but also via opening a person (click on the pencil symbol in the sample which is displayed in the ‘Samples’ box on the right side of the window).

Opening and editing the sample information

To edit an existing sample, click on the sample ID in the sample directory or on the pencil icon of a sample that is displayed in the "Samples" box on the first page of a case, contact or event participant. All the information available for this sample is then displayed.

Open

In the upper area (A) you will find the ID assigned by the system for this sample, the date on which the sample was taken and the ID of the associated case/contact/event participant.

The most important information and mandatory details for a sample are:

• Purpose of the sample is usually "External lab testing " and preset accordingly

• Date sample was collected is the date on which the sample was taken, whereby the time can also be specified

• Type of sample: chosen from a standardised specimen list aligned to SNOMED-CT, for example Nasopharyngeal swab or Oropharyngeal (throat) swab. The list is filtered by the disease of the associated case, contact or event participant, so you only see specimen types that are meaningful for that disease. If you select Clinical Sample (Other), a free-text field appears so you can name the specimen.

• Laboratory is the name of the laboratory to which the sample is/was sent

• Date sample was sent and date sample received at lab: if any of the fields "Sent/dispatched" or "Received" is checked, the respective date must be specified

• Final laboratory result: one of Pending, Positive, Negative, Indeterminate, Not done or Not applicable

Note:

The Sample source field is no longer shown on the sample form. Existing values are retained in the database and in exports but are not editable through the user interface.

Using the tabs (B), you can either go back to the sample directory or directly open the case, contact or event participant associated with the sample. The following options are offered in three boxes on the right-hand side of the screen:

• In addition to the ID, the top box (C) contains the most important information on the case, contact or event participant to which the sample belongs.

• The Pathogen tests box (D) shows the results of the pathogen tests already performed. You can use the "New test result" button to enter new test results, e.g. a new Covid-19 pathogen test.

• The Additional tests box (E) records non-pathogen laboratory values such as haemoglobin in urine. This box only appears when your administrator has enabled the Additional tests feature, which is switched off by default.

Visualization of samples in the sample and pathogen test area: The laboratory messages are displayed in the Messages menu item as follows: The menu item Messages is displayed as follows: An eye symbol is displayed for sample and pathogen test listings if a laboratory message is pending. Clicking on this symbol opens the corresponding laboratory message if it was previously processed in SORMAS. The arrows (bottom/center) can be used to switch between the stored laboratory messages.

Sample types

The Type of sample list follows SNOMED-CT, so specimen types recorded in SORMAS map onto an international terminology and can be exchanged with laboratory systems. Where a canonical SNOMED-CT code exists it is stored with the sample and included in the detailed export.

The list you see is filtered three ways:

• By disease. Specimen types that are not clinically meaningful for the disease of the associated case, contact or event participant are hidden. A stool sample, for example, is not offered for a Measles case.

• By country. Some specimen types are hidden on Luxembourg servers.

• By retirement. Eight older specimen types have been retired: Nasal swab, Oropharyngeal (throat) swab (old), Throat aspirate, Cornea p.m, Urine p.m, Soft tissue sample, Bone and joint specimen and Other. They are no longer offered when creating a sample, but any sample already recorded with one keeps it, still displays it, and still exports it.

Clinical Sample (Other) replaces the retired Other entry. Selecting it reveals a free-text field so the specimen can be named; unlike the old Other, filling this field is optional.

Indicators in the Pathogen tests box

Each entry in the Pathogen tests box can carry small icons in its top-right corner:

Create new test results manually

To enter a new test result manually, either select the "New test result" in the "Pathogen tests" box on the sample page in the Samples menu or directly in the corresponding (already created) case using "New sample" (in the Samples box on the right-hand side). A new window will open in both situations.

If you create a new sample, the following information must be entered before entering the data for a new test result:

A      Purpose of the sample: “external lab testing” or “internal/in-house testing” have to be selected. In case of “external lab testing” the field laboratory has to be specified, and the boxes ‘Request pathogen tests to be performed?’, ‘Sent/dispatched’, ‘Received’ ticked according to the actions taken.

B       Date of sample was collected: the date has to be specified, the specification of the time is optional.

C       Type of sample has to be chosen from the drop-down menu.

D      Laboratory appears if the purpose of the sample is “external lab testing” and must be specified.

E Final laboratory result,  with one of the following values: Pending, Positive, Negative, Indeterminate, Not done or Not applicable.

The Add pathogen test button in the Create new sample window is only shown when your administrator has enabled the Allow adding pathogen tests from a sample feature. It is enabled by default.

Open

Via the Add pathogen test button in the Create new sample window, a new pathogen test can be entered.
When adding a new test result via the Samples menu and the Pathogen tests box, a window opens with the same information to be specified.

The information to be entered for a new pathogen test result is the following:

A      Test category: Required. Narrows the Type of test list to one of seven groups: Molecular Assays, Serological Tests, Antigen Detection, Culture & Isolation, Microscopy & Staining, Antimicrobial Susceptibility Testing, Functional Immune Assays. Only categories that contain at least one method relevant to the tested disease are offered. Selecting a Type of test first will fill in its category automatically.

B       Type of test: The laboratory method used. The list is filtered by the chosen category and by the tested disease, so a Measles test and a Tuberculosis test offer different methods. If you select PCR / RT-PCR the corresponding test specifications can be entered directly. Selecting Other reveals a free-text field for the method name.

C       Date and time of test: The date is required. A date in the future is rejected.

D      Tested disease: Selected from the diseases configured on the server.

E      Test result: Which result fields appear depends on the method you selected in Type of test. In the common case you will see the familiar Test result dropdown with Pending, Positive, Negative, Indeterminate, Not done or Not applicable.

F      Result verified by lab supervisor: Indication of whether verification has taken place. Unchanged.

G      Performed by reference laboratory: Tick when the test was carried out by a reference laboratory rather than the primary one. Tests flagged this way carry an institution icon in the Pathogen tests box.

H      Retest requested: Tick when a repeat of this test has been requested. Flagged tests carry a refresh icon in the Pathogen tests box.

I      Preliminary: Preliminary results. for example an antigen test later confirmed by PCR can be marked using the Preliminary checkbox. After the confirmatory result is entered, the checkbox can be cleared. Unchanged.

Depending on the tested disease, an additional section appears below the standard fields with disease-specific laboratory data i.e serogroup and serotype for meningococcal and pneumococcal infection, genotype for Measles and Cryptosporidiosis, RSV subtype for RSV, drug susceptibility for Tuberculosis and so on.

Open

If the test result entered is “Positive”, a window opens and a new case for the selected disease can be created.

If you have created the sample in the Case ribbon directly within the case, it will be displayed inthesamples box on the right-hand side. You can use the pencil icon to edit further information about thissample afterwards.

Open

If you have clicked on the pencil icon, you will automatically be directed to the sample itself within the Sample ribbon. You will then see the corresponding case on the left-hand side.

Open

Recording results

A pathogen test no longer always asks for a simple Positive/Negative answer. Each laboratory method declares what kind of result it produces, and the form shows only the matching fields. A method can produce more than one kind, in which case you will see more than one field.

Because of this, some methods deliberately show no Test result dropdown. Typing and sequencing methods i.e Serotyping, Serogrouping, MLST, cgMLST, SNP Typing, Genotyping, Whole-Genome Sequencing, Sanger Sequencing do report an identity, not a positive/negative outcome, so they ask only for Test result details. Records saved with such a method carry a Not applicable test result.

A separate Antibody titre field is available for serological methods that report a titre.

Antimicrobial susceptibility testing

Selecting Antibiotic Susceptibility Testing (AST) as the type of test opens a Drug Susceptibility grid. The grid is available for Tuberculosis, Latent Tuberculosis, Invasive Meningococcal Infection, Invasive Pneumococcal Infection and Shigellosis.

Each antibiotic occupies one row with three entries:

Approximately twenty two antibiotics are covered and the full list will be linked.

Leave a row blank for any antibiotic that was not tested.

Disease-specific laboratory data

Below the standard pathogen-test fields, an additional section appears whose content depends on the tested disease:

Changing the tested disease on an unsaved test swaps this section and clears the selected method, because the available methods differ by disease.

Positive test results for contact persons

If you change a contact's pending test result to "positive", a prompt to automatically convert the person into a case is displayed. Confirm with "Yes" to convert the contact into a case.

Sample directory for the environment view

The Environment view lists environmental samples i.ei.e water, soil, air and vector samples taken from a sampling site rather than from a person. It is the counterpart to the Human view and is reached with the same view switch at the top right of the sample directory.

The Environment button only appears when your administrator has enabled Environment management and your user role carries the right to view environment samples. On servers without environment management, the switch is not shown and the directory opens directly in the Human view.The Environment button only appears when your administrator has enabled Environment management and your user role carries the right to view environment samples. On servers without environment management, the switch is not shown and the directory opens directly in the Human view.

Status filters. Above the table, four buttons filter by dispatch status: All, Not shipped, Shipped and Received.

Active / archived / deleted. A dropdown to the right filters by lifecycle: Active environment samples, Archived environment samples, All active and archived environment samples, and for users allowed to see them, Deleted environment samples. Choosing Deleted reveals a Deletion reason column.

Filters (A). The filter bar offers:

A Show more filters area adds a GPS bounding box i.e latitude and longitude from / to for restricting the list to a geographic area.

As in the human view, filters are applied with Apply filters or ENTER and cleared with Reset filters.

Columns. The table shows: Sample ID, Field sample ID, Date of sampling, Environment, Location of sampling site, District (hidden by default), Sent/dispatched, Dispatchment date, Received, Laboratory, Sample material, Positive pathogen tests, Latest pathogen test, Number of tests. The Sample material of an environment sample is one of Water, Soil, Air, Vectors or Other.

Opening an environment sample. Click the sample ID in the first column to open it. An environment sample carries its own Pathogen tests box, so test results are recorded against it in the same way as for a human sample.

Export sample directory

Export sample directory for the ‘human’ view

The data in the sample directory for the view ‘human’ can be exported. To do this, there is an "Export" button in the top right-hand corner of the overview, which can be used to start a basic or detailed export.

Open

In both cases, a CSV file is downloaded. The basic export contains all columns that are displayed in the standard view of the sample directory. The detailed export includes all information that can be recorded for a sample. The export also includes the newer laboratory fields i.e test category, quantitative value and unit, smear grade, antibody titre, reference-laboratory and retest flags inclusive of the SNOMED-CT identifier of the sample type where one is mapped.

As this export takes a little longer, users are notified of this with a notification window.

Export sample directory for the ‘environment' view

The data in the sample directory for the view ‘environment’ can be exported. To do this, there is an "Export" button in the top right-hand corner of the overview, which can be used to start the export.

A CSV file is downloaded. The export contains all columns of the sample directory.

Delete test results (only for administrators)

The administrator user role has the authorization to delete test results in SORMAS. To do this, open the test result and select the red "Delete" button in the window.

Deletion of samples in mass editing mode is also possible. The mass editing mode can be selected  in the sample directory. (Further information on the mass editing mode can be found in the admin manual).

Open

Administrator settings

Two settings under Configuration → Feature configuration change how the sample and pathogen-test forms behave. Both are server-wide and both are on by default.

A third, older setting is relevant here: Additional tests controls the Additional tests box on the sample page. It is off by default.

Sample dashboard

The sample dashboard filter bar now includes Test results and Disease variant. The No disease option was removed from the disease filter, and the disease list now matches the one offered when creating a case.