TESSy - The European
Surveillance System
STI Reporting Protocol 2019
Sexually Transmitted Infections
Surveillance data for 2018
February 2019
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STI Reporting Protocol 2019
Introduction
Contents
Introduction ............................................................................................................... 4
How to use this document ..................................................................................................... 4
Finding further information .................................................................................................... 4
Copyright ............................................................................................................................. 4
Reporting to TESSy .................................................................................................... 5
Checking the data collection schedule .................................................................................... 5
Preparing data ...................................................................................................................... 5
Checking metadata ............................................................................................................... 5
Checking your data source profile .......................................................................................... 6
Submitting your data ............................................................................................................ 6
Finalising your submission ..................................................................................................... 6
Changes to current STI metadata ................................................................................ 7
Annex 1 STI metadata ................................................................................................ 8
Current record type versions ................................................................................................. 8
STI metadata set .................................................................................................................. 8
STI epidemiological variables ............................................................................................ 9
STI metadata change history ............................................................................................... 10
Annex 2 Subject-specific material .............................................................................. 11
STI data collection .............................................................................................................. 11
Historical data (1990-2017) ............................................................................................ 11
STI data analysis plan ......................................................................................................... 11
Completeness and origin of reporting .............................................................................. 11
Preparing datasets for analyses ...................................................................................... 12
Descriptive epidemiology ................................................................................................ 12
© ECDC February 2019 All rights reserved.
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STI Reporting Protocol 2019
Introduction
Introduction
This reporting protocol is for the 2019 data call for sexually transmitted infections surveillance data
for 2018.
ECDC’s Reporting Protocols are data collection guidelines for reporting countries’ data managers; the
Reporting Protocol is intended to improve user-friendliness by providing a uniform structure to make
it easier for data managers to find data collection information across different subjects.
Because reporting countries’ data managers sometimes play multiple roles, it is sometimes relevant to
distribute subject-specific material together with a Reporting Protocol. To maintain the uniform
structure, this information is now included in
Annex 2.
How to use this document
This Reporting Protocol provides information for reporting countries’ data managers in three main
sections:
Reporting to TESSy – contains guidelines on how to prepare data for submission to TESSy,
deadlines, subject-specific information (e.g. new changes to metadata), and links to further
information.
Annex 1 – contains:
o A history of metadata changes for the subject(s) covered by this Reporting Protocol.
o The metadata set for the subject(s) covered by this Reporting Protocol.
Annex 2 – contains subject-specific material relevant for distribution with the Reporting
Protocol, for example:
o Guidelines for data collection.
o Analysis plan.
Finding further information
Paragraphs denoted by the information icon tell where you can find further information.
Updated links to all the schedules, documentation and training materials mentioned in this Reporting
Protocol are included in the
TESSy document section, including:
Metadata sets and history.
Tutorials for data transformation using respectively Excel and Access.
TESSy user documentation.
CSV and XML transport protocols.
Copyright
© European Centre for Disease Prevention and Control, 2019. Reproduction is authorised, provided
the source is acknowledged.
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STI Reporting Protocol 2019
Reporting to TESSy
Reporting to TESSy
This section provides both an overview of the TESSy reporting process and tips on where you can find
useful information.
The overall process is:
1.
Familiarise yourself with the data collection deadlines.
2.
Prepare (export and transform) your data.
3.
Check that your data comply with the metadata.
4.
Check that your data source profile is up-to-date.
5.
Submit your file(s) to TESSy.
6.
Finalise your submission.
Checking the data col ection schedule
The latest data collection schedule is available in the
TESSy website.
The deadline for reporting 2018 STI surveillance data is 30 September 2019.
Preparing data
After you have exported the data from your national database, you need to ensure that the data are
in a format that TESSy can accept. This applies both to the type of file submitted to TESSy (only CSV
and XML files can be submitted) and to the format of the data in certain fields.
Tutorials covering how you can transform your data to the correct TESSy format using Excel or
Access are available on the TESSy documents website. Information on the file formats is available in
the CSV Transport Protocol and XML Transport Protocol.
Checking metadata
The TESSy metadata define the fields and data formats that are valid as input to TESSy for a given
subject.
As requirements to the data to be shared among TESSy users change, the data changes needed to
support the new requirements are identified and agreed upon between the National Surveillance
Focal Points, the surveillance networks and their coordination groups and ECDC’s disease experts,
and then implemented as changes to the TESSy metadata.
In order to ensure that your data can be saved correctly in TESSy, you therefore need to check that
your data are correctly formatted according to the most recent metadata set.
Changes to the metadata for the subject of this Reporting Protocol are described in:
Changes to current STI metadata – changes since the last Reporting Protocol.
Annex 1 STI metadata change history – all preceding changes.
It is especially important to focus on:
Field formats
Many fields require that data are formatted in a specific way. For example, dates must be in the
YYYY-MM-DD format; dates in the DD/MM/YYYY format will be rejected.
Coded values
Some fields only permit the use of specific values (coded values). For example,
M,
F,
UNK, or
Other are the
coded values for Gender and any other value in a Gender field will be rejected.
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STI Reporting Protocol 2019
Reporting to TESSy
A single metadata set file contains all the definitions and rules you need to comply with to format
your data correctly for every subject (usually a disease). The file can be downloaded as an Excel file
from the TESSy documents website.
By filtering the fields in the file by subject, you can see the fields required for your subject and the
rules applying to these fields.
Checking your data source profile
Before submitting your file(s), please review the profile for your data source(s) in TESSy (go to
Data
Sources), and update the information, if necessary.
Complete and up-to-date data source information for each subject is important for improving
interpretation of data - each surveillance system has different features that need to be taken into
account when comparing data at an international level.
If your data source information is out-of-date and you do not have access rights to update it, please
request your National Focal Point for Surveillance or National Coordinator to do so.
In-depth information on the data source variables is available in the TESSy user documentation.
Submitting your data
Data are submitted through the TESSy web interface (go to
Upload).
Finalising your submission
The compliance of your data with the validation rules in the metadata is checked automatically during
the data upload process.
The result of your upload – i.e. rejected or validated – is displayed immediately after the conclusion
of the check in the
Validation details webpage. Please review the result carefully:
If your file has been rejected, there will be a message explaining each instance of non-
compliance with the metadata that you need to correct.
If your file has been validated, there might be warnings and remarks relating to possible data
quality issues or to potential overwriting of existing records that you should consider.
When you file has been validated and you are satisfied that all corrections have been made, please
ensure prompt approval – unapproved uploads can block for the approval of other uploads.
The TESSy user documentation provides information on reviewing validation results and adjusting
reporting periods to avoid overwriting existing records.
Following submission, further validation checks are performed by ECDC disease experts. If issues are
identified, experts may contact you for clarification and/or to upload corrected data.
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STI Reporting Protocol 2019
Changes to current STI metadata
Changes to current STI metadata
The coded value list for the variable SiteOfInfection has been changed to include NA. This is because
some validation rules require the value NA.
The previous metadata changes are described in
Annex 1.
Information on changes to the metadata for other subjects is available on the TESSy
documentation website.
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STI Reporting Protocol 2019
Annex 1 STI metadata
Annex 1 STI metadata
This section describes:
The STI metadata set
Changes to the STI metadata since 2015
Current record type versions
Table 1 shows the record type versions to be used when reporting 2018 STI surveillance data to
TESSy.
Table 1: STI record type versions for 2018 data
Disease
Case-based
Aggregated record type
record type version
version
Chlamydia
CHLAM.3
STIAGGR.1
Gonorrhoea
GONO.3
STIAGGR.1
LGV
LGV.2
STIAGGR.1
Congenital Syphilis
CONSYPH.2
AGGR.1
Syphilis
SYPH.3
STIAGGR.1
STI metadata set
Table 2 lists the metadata variables for STI.
The common variables apply to reporting case-based data for all STI and consist of 20 variables.
These variables can be divided into system-related and epidemiological variables.
The variables used for reporting aggregated data include age class, gender, case classification, date
used for statistics, reporting country and the number of cases. The hierarchy for aggregated reporting
is as follows:
1. Gender
2. Age class
3. Transmission
Table 2: STI metadata variables
Variable Name
Syphilis
Gonorrhoea Chlamydia LGV
Congenital
Syphilis
Common variables
1. RecordID
√
√
√
√
√
2. RecordType
√
√
√
√
√
3. RecordTypeVersion
√
√
√
√
√
4. Subject
√
√
√
√
√
5. Status
√
√
√
√
√
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STI Reporting Protocol 2019
Annex 1 STI metadata
6. DataSource
√
√
√
√
√
7. Age
√
√
√
√
√
8. Gender
√
√
√
√
√
9. Outcome
NA
NA
NA
NA
√
10. DateofOnset
√
√
√
√
√
11. DateOfDiagnosis
√
√
√
√
√
12. DateOfNotification
√
√
√
√
√
13. DateUsedForStatistics
√
√
√
√
√
14. ReportingCountry
√
√
√
√
√
15. Classification
√
√
√
√
√
16. ClinicalCriteria
NA
NA
NA
NA
NA
17. LaboratoryResult
√
√
√
√
√
18. EpiLinked
NA
NA
NA
NA
NA
19. PlaceOfNotification
√
√
√
√
√
20. PlaceOfResidence
√
√
√
√
√
Disease-specific variables
21. ClinicalServiceType
√
√
√
√
22. CountryOfBirth
√
√
√
√
23. CountryOfNationality
√
√
√
24. ProbableCountryOfInfection
√
√
√
25. Transmission
√
√
√
√
26. HIVStatus
√
√
√
√
27. SexWorker
√
√
√
28. ContactSW
√
√
√
29. SiteOfInfection
√
√
√
√
30. StageSYPH
√
31. StageSYPHdetailed
√
32. CountryOfBirthOfMother
√
33. CountryOfNationalityOfMother
√
34. AgeMonth
√
STI epidemiological variables
•
In the Annual Epidemiological Report (AER), the date of diagnosis (as a proxy for date of
consultation) is used for all analyses. If possible, please report this date as the Date used
for Statistics.
•
For chlamydia, gonorrhoea, syphilis, congenital syphilis and LGV, only confirmed cases
should be reported at EU level. Cases must be classified according to EU case definitions.
If different case definitions are used, please specify this in the Data Source data.
•
When reporting the age-class for aggregated data, please use the following categories:
0-4, 5-14, 15-19, 20-24, 25-34, 35-44, 45-64, ≥ 65. This is coded in TESSy as
AGECLASS2 (coded value list name), subset of codes 5_ (codes for age categories are
preceded by 5_). If this age grouping is not applied, it might not be possible to use the
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STI Reporting Protocol 2019
Annex 1 STI metadata
country data for parts of the analysis. If this coding is not possible, please contact the
TESSy team to identify possible alternative options.
STI metadata change history
Metadata changes prior to 2015 can be found on the TESSy documents website.
Table 3: Summary of implemented changes to STI metadata
Year
Subject Description
2015
STI
There were no STI metadata changes in 2015.
2016
STI
There were no STI metadata changes in 2016.
2017
STI
There were no STI metadata changes in 2017.
2018
SYPH
Coded value list for “SiteOfInfection” was changed to include the value NA. The value NA is required for a
validation rule.
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STI Reporting Protocol 2019
Annex 2 Subject-specific material
Annex 2 Subject-specific material
STI data collection
STI data analysis plan
Contact information (disease experts and others)
STI data collection
The surveillance data on five STIs are collected as part of the enhanced surveillance for STIs and
concern cases that were diagnosed in 2018.
Case-based data are preferred. If case-based data
are not available, the aggregate format (RecordType: STIAGGR) broken down by 1) gender, 2) age
class and 3) transmission may be used. Please note that reporting in aggregated format means that
your country’s data might not be used for some of the more detailed analyses.
Historical data (1990-2017)
Data for 1990-2017 has been collected in previous data collections and have been published in
previous STI surveillance reports and the ECDC surveillance atlas. Historical data can be corrected by
re-uploading to TESSy. These updates are taken into account for the AER and reflected in updates of
the surveillance atlas if done before the deadline.
Historical data should be uploaded in the following ways:
1990-1999: annual data in
aggregated data format broken down by 1) gender – 2) age
class (preferred category) – 3) transmission. This means that ‘Date of Statistics’ is YYYY
(1990-1999) only for the inclusion of historical data.
2000 onwards:
case-based data is preferred. If case-based data are not available the
aggregate format broken down by 1) gender, 2) age class and 3) transmission may be used.
STI data analysis plan
This data analysis plan describes the analyses performed for the STI chapters of the Annual
Epidemiological Report. All analyses described below will be performed, however a selection will be
used in the report. Conversely, additional analyses which are data-driven will be performed. Analyses
that are considered to be useful for future inclusion in the AER will be included in future versions of
this document. All analyses except where otherwise specified are based on the variable Date of
Diagnosis as the date field.
The STI surveillance data will be presented as a chapter of the AER in an online report
(https://ecdc.europa.eu/en/annual-epidemiological-reports) linked to the ECDC surveillance atlas of
infectious disease
s (http://ecdc.europa.eu/en/data-tools/atlas/Pages/atlas.aspx). A selection of
analyses will be presented in the report and atlas.
Completeness and origin of reporting
The completeness of data will be analysed overall. Completeness by country will also be analysed and
fed back to countries to show how they fare compared to the overall EU/EEA average. An analysis of
the ‘Datasource’ variables will give an overview by country of the availability of data in 2018 and
provides an overview of the origin of the data. The information is needed to be able to interpret the
actual data on STIs. The main characteristics which will be assessed include: type of system
(comprehensive, sentinel), type of reporting (clinical, laboratory), legal framework (compulsory,
voluntary).
Data will be presented in the following in tables:
Overview of reported (aggregated or case-based) data per country and time period by STI.
Aggregate and case-based datasets need to be merged for the analyses.
Overview of country data sources per country by STI.
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STI Reporting Protocol 2019
Annex 2 Subject-specific material
Overview of completeness (value versus unknown or not reported) per variable overall and by
reporting country per STI.
Preparing datasets for analyses
Case-based and aggregate datasets are merged for each STI.
Country population denominators used to calculate rates are based on data from the Eurostat
database. Rates are not calculated for countries with sentinel surveillance systems unless the
countries have provided ECDC with denominator data and coverage for the specific
surveillance system.
Recode age into age class: <15, 15-19, 20-24, 25-34, 35-44, 45+; if data on age are
unavailable or coded in the wrong age-class, the country will be excluded from the analysis;
Total numbers in tables include unknowns; total numbers in graphs exclude unknowns except
where specified.
Country of birth, country of nationality and reporting country: these variables are explored by
country/region and to be recoded after this exercise to describe the origin of the reported
cases. Country of nationality is the most important variable, if not available the country of
birth should be used instead.
Probable country of infection will be recoded into ‘acquired abroad’ and ‘acquired in home
country’.
HIV status: tabulate HIV status including the unknowns; recode into HIV positive, HIV
negative, HIV unknown/ NA.
Site of infection: tabulate site of infection per STI including the unknowns.
Descriptive epidemiology
The analyses will describe the occurrence of STI by time, place and population across countries and
group countries and variables if possible.
Overall numbers and rates
•
Present number of STI cases for the last 10 years, overall and by country.
•
Rates are calculated per 100 000 population for chlamydia, gonorrhoea and syphilis;
rates for congenital syphilis are calculated per 100 000 live births.
•
Present STI rates for the last 10 years, overall and by country (only for countries with
comprehensive surveillance systems or where an adjustment can be made).
•
Calculate the change in STI rates (and number of cases) over the previous five years and
compared to the previous year. Other comparisons will be done based on the
epidemiology of the infection.
Gender
•
Present number of STI cases by gender for the last 10 years, overall and by country.
•
Present STI rates by gender for the last 10 years, overall and by country.
•
Calculate the increase by gender by STI over the last five years and compared to the
previous year.
•
Gender distribution: male-to-female ratio by reporting country per STI for the report
year; compare the trend in male-to-female ratio by STI.
Age
•
Age distribution: present the age distribution by STI for the report year.
•
Age-specific rates: present age-specific rates for the report year and compare with age-
specific rates for the previous nine years. Describe trends in age-specific rates.
Age-Gender
•
Present the age distribution by gender and by STI in the report year. Describe recent
trends in age and gender specific rates.
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STI Reporting Protocol 2019
Annex 2 Subject-specific material
Transmission
•
Present proportion of cases reported in the report year by transmission category.
Describe trends, changes in distribution over the last year, five years, ten years.
•
For men who have sex with men (MSM) (Transmission=MSM): trends in STI by year, for
age groups ≤ and > 35 years of age; calculate rates based on number of men with MSM
transmission with denominator being male population; explore grouping of countries; for
case-based data only (possibly include aggregate dataset if ‘transmission’ is provided).
•
Transmission: present percentage of MSM by country per STI for the report year;
compare with the trend in percentage MSM by STI over last five and ten years; (except
for congenital syphilis). (Case-based data only; possibly include aggregate dataset if
‘transmission’ is provided).
Geographical information
•
Present the country of nationality (home country versus other) by country per STI in the
report year; present the probable country of infection (as percentage acquired abroad)
per STI in the report year.
•
For congenital syphilis: present the country of birth/nationality of mother by country
(home country versus other).
•
Examine the completeness of subnational data – provide examples for countries where
completeness is higher than 80%.
HIV Status
•
Present the proportion of HIV positive by country per STI for the report year; present
percentage HIV positive by gender and transmission category per STI over the last ten
years.
•
Compare proportion of HIV positive cases with overall HIV rates taken from HIV report,
by country.
Sex work
•
Percentages of SW/CSW by country per STI by gender (and in total numbers) (except for
chlamydia), if completeness allows.
Site of infection
•
Proportion of cases by site of infection, by transmission category for chlamydia,
gonorrhoea and primary syphilis for the report year.
Clinical Service
•
Clinical service: present the distribution of clinical services in percentage by country per
STI for the report year (except for congenital syphilis). Present by grouping similar
services. Analyse any changes over time.
Chlamydia – analysis by level of chlamydia control activities
•
Present overall rates of chlamydia by country grouped according to level of chlamydia
control (as presented in “Chlamydia Control in Europe - A survey in the Member States
2012”).
•
Analyse overall rates of gonorrhoea and syphilis by level of chlamydia control to identify
any associations.
Syphilis – infectiousness
•
Syphilis: present the percentage in infectious syphilis and by stage of infection for the
report year and investigate any changes over last five and ten years.
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STI Reporting Protocol 2019
Annex 2 Subject-specific material
Depending on the interpretation of the above results more detailed analyses may be suggested
regarding specific STI, risk group or countries.
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