Introduction
The European Surveillance System (TESSy) is a web service hosted by European Center for Disease Prevention and Control (ECDC) that is a highly flexible metadata-driven system for collection and analysis of data. It gives privilege to nominated individuals and organizations to submit their infectious disease surveillance data and let them access aggregated submitted data. TESSy supports uploading of a specific XML files containing surveillance data. The submission can be done automatically by using an encrypted Web Service API or manually through a secure web-based user interface.
SeqSphere+ TESSy Submission
Important: The current SeqSphere+ version only supports the export of a TESSyDataUpload XML file. This file has to be submitted manually by the user through the TESSy web-based user interface.
The TESSy XML file exporting can be invoked through the menu function File | Export Samples to TESSy XML File. In the upcoming dialog samples can be selected by projects, by a database search, or from the currently loaded samples. After selecting samples the dialog can be confirmed by pressing OK.
If the TESSy XML export is called for the first time the TESSy Datasource and Reporting Country must be defined in an upcoming dialog. They are stored for the SeqSphere+ user account and can later be changed in the menu Options | Account Details and tab TESSy Account. After entering the two fields the dialog can be confirmed by pressing OK.
The values for the TESSy submission are now retrieved from the SeqSphere+ database. If mandatory fields are missing or values do not match the coded values defined by TESSy, the resulting errors/warnings are shown. Samples that caused errors cannot be submitted. However, it is possible to skip those samples and submit only the ones without errors.
If no errors/warnings occur or if the errors/warning dialog is confirmed with Continue, the TESSy Export Preview is shown. It contains a table with all field values that will be exported to the XML. The table is only a preview and cannot be edited.
When the preview dialog is confirmed, the file path of the XML can be chosen and the TESSy XML file is written.
Hint: As the created TESSy XML file contains also the assembly contigs (FASTA), the file size is around 1 MB per sample. According to ECDC it is not recommended to submit TESSy XML files that are larger than 20 MB. Therefore, a maximum of around 20 samples should be exported into a single XML file.
Mapping between TESSy Fields and SeqSphere+ Fields
The following TESSy RecordTypes and versions are currently supported by SeqSphere+:
- CAMPISO v3 (Campylobacteriosis isolate)
- ECOLIISO v3 (E. coli isolate)
- LISTISO v3 (Listeria isolate)
- SALMISO v4 (Salmonella isolate)
The mapping between the submitted TESSy fields and the SeqSphere+ database fields is predefined. The following table lists the submitted TESSy fields, the mapped SeqSphere+ fields, the mandatory state, a description, and the RecordTypes in which the field is available.
| TESSy Field1) | SeqSphere+ Field(s) | Mandatory | Description | C2) | E2) | L2) | S2) |
|---|---|---|---|---|---|---|---|
| RecordId | Sample ID | yes (error) | Unique identifier for each isolate within the data source / lab system. The exact Sample ID field is used for this. | x | x | x | x |
| RecordType | Genus | yes (error) | Structure and format of the data (case based reporting or aggregate reporting). Can be one of the types CAMPISO, ECOLIISO, LISTISO, or SALMISO based on the Genus field of the sample. | x | x | x | x |
| RecordTypeVersion | n/a | no | Indicates the version of the Record type used in the reported batch. The versions are predefined in SeqSphere+ and cannot be changed. | x | x | x | x |
| Subject | Genus | yes (error) | Equal to RecordType TESSy field. | x | x | x | x |
| dataSource | TESSy DataSource specified by the SeqSphere+ user | yes (error) | The data source (laboratory) that the record originates from. It consists of two parts, first the ISO code for country of laboratory and second the unique code of the lab. Like DE-XXXX. This information is entered by user in TESSy Account tab of Account Details dialog in SeqSphere+. | x | x | x | x |
| ReportingCountry | Reporting Country specified by the SeqSphere+ user | yes (error) | The country reporting the record. Is entered by user in TESSy Account tab of Account Details dialog in SeqSphere+. | x | x | x | x |
| ContactPerson | Firstname, Lastname, and Phone of the SeqSphere+ user | no | Contact person for the data upload. Is entered by user in Account Details dialog in SeqSphere+. | x | x | x | x |
| dateUsedForStatistics | Collection Date, Receipt Date | yes (error) | The most epidemiological relevant date for the isolate. Equal to the date of sampling if available (Collection Date). If not, equal to the date of receipt in the reference lab (Receipt Date). | x | x | x | x |
| Status | n/a | no | Status of reporting NEW/UPDATE or DELETE (inactivate). SeqSphere+ currently only supports NEW/UPDATE which is the predefined value. | x | x | x | x |
| Age | Host Age (years) | yes (warning) | Age of patient in years as received or at the date of sampling. | x | x | x | x |
| DateOfReceiptReferenceLab | Receipt Date | yes (error) | Date of receipt in reference laboratory or typing laboratory with reference function. | x | x | x | x |
| DateOfSampling | Collection Date | yes (warning) | Date the sample from which the isolate was derived, was taken. It should be an exact date. | x | x | x | x |
| Gender | Host Sex | yes (warning) | Gender of the reported case. The following values are allowed to be entered in SeqSphere+: male, m, female, w, f, Other and different forms of unknown. | x | x | x | x |
| SampleId | Sample ID | no | Unique identifier for each sample within the lab system, allowing to link isolates derived from the same sample. The same as the TESSy Record ID field. | x | x | x | x |
| SampleOrigin | Source Subtype | yes (error) | Sample source: human, food, feed, animal, environment. In SeqSphere+ only samples with Source Subtype "human" are supported for TESSy Export currently. | x | x | x | x |
| ECDCCaseId | ECDC Case ID | no | TESSy globally unique identifier assigned upon upload of the case, so that isolate records can be linked to case records. The ECDC Case ID field in SeqSphere+ is used. | x | x | x | x |
| CaseId | Case ID | no | Unique identifier for each case within the data source / surveillance system related to the isolate, so that isolate records can be linked to case records. The Case ID field in SeqSphere+ is used. | x | x | x | x |
| Specimen | Isolation Source | no | The relevant specimen type used for diagnosis of the case. The Isolation Source field in SeqSphere+ is used. | x | x | x | |
| Pathogen | Species | yes (error) | Species or genus of the pathogen which is the cause of the reported disease. It is only available for CAMPISO samples and only coli, fetus, jejuni and lari species would be converted to CAMCOL, CAMFET, CAMJEJ and CAMLAR. | x | |||
| Serotype | Serotype | no | Serotype of the pathogen which is the cause of the reported disease. The exact value of the Serotype field in SeqSphere+ is used. | x | x | ||
| WgsAssembler | Assembler | no | The assembler used for sequencing, optionally including parameter settings. | x | x | x | x |
| WgsAssembly | Assembly file content | no | The assembled genome, as a gzipped FASTA file. The file contents are subsequently converted into a Base64-encoded string for inclusion into XML. This string does not appear in preview dialog, instead the base count number is shown there. | x | x | x | x |
| WgsEnaId | Nucleotide Accession (which starts with E) | no | European Nucleotide Archive (ENA) identifier, based on which the raw read data can be accessed. | x | x | x | x |
| WgsProtocol | Sequencing Protocol, Sequencing Length, Sequencing Vendor, Sequencing Platform | if WgsAssembly is given | Protocol used for sequencing, limited to the sequencing technology used (today Illumina or IonTorrent) and the read length (e.g., MISEQ_2X150). | x | x | x | x |
| WgsSequenceId | Nucleotide Accession (which starts with S) | no | Sequence Read Archive (SRA) identifier, based on which the raw read data can be accessed. | x | x | x | x |
| PCRserogroup | Result from L.monocytogenes 5-plex PCR Serogroup task | no | Serogroup of L. monocytogenes based on molecular serotyping. Listeria 5-plex PCR Serogroup typing result is used if available. | x |
1) Fields according to TESSy metadata report (v42)
2) C=CAMPISO; E=ECOLIISO; L=LISTISO; S=SALMISO