TESSy - The European
Surveillance System
Antimicrobial resistance (AMR)
reporting protocol 2019
European Antimicrobial Resistance Surveillance Network
(EARS-Net) surveillance data for 2018
February 2019
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Contents
How to use this document ..................................................................................................... 2
Finding further information.................................................................................................... 2
Copyright ............................................................................................................................. 2
Reporting to TESSy .................................................................................................... 3
Checking the data collection schedule .................................................................................... 3
Preparing data ...................................................................................................................... 3
Checking metadata ............................................................................................................... 3
Checking your data source profile .......................................................................................... 4
Submitting your data ............................................................................................................ 4
Finalising your submission ..................................................................................................... 4
TESSy HelpDesk ................................................................................................................... 5
Changes to current AMR metadata .............................................................................. 6
Annex 1 AMR metadata .............................................................................................. 7
AMR metadata set ................................................................................................................ 7
Overview of EARS-Net AMR surveillance metadata ............................................................. 7
Current record type versions ............................................................................................. 7
Isolate-based reporting .................................................................................................... 7
Coverage and representativeness ................................................................................... 17
AMR metadata change history ............................................................................................. 21
Previous metadata changes ............................................................................................ 21
Annex 2 AMR-specific material................................................................................... 22
Contacts ............................................................................................................................ 22
Microbiological guidelines for EARS-Net ................................................................................ 22
Implementation of AMR case definitions for TESSy ............................................................... 22
Objectives for AMR surveillance ........................................................................................... 26
Preparing national AMR datasets ......................................................................................... 27
Checking for duplicate records ........................................................................................ 27
Data management and analysis ...................................................................................... 28
Data analysis and presentation ....................................................................................... 29
Isolate forms ...................................................................................................................... 32
Isolate Record Form Streptococcus pneumoniae .............................................................. 33
Isolate Record Form Staphylococcus aureus .................................................................... 34
Isolate Record Form Escherichia coli ............................................................................... 35
Isolate Record Form Klebsiella pneumoniae ..................................................................... 36
Isolate Record Form Pseudomonas aeruginosa ................................................................ 37
Isolate Record Form □ Enterococcus faecium □ Enterococcus faecalis ...................... 38
Isolate Record Form Acinetobacter spp. .......................................................................... 39
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AMR Reporting Protocol 2019
Introduction
This reporting protocol is for the 2019 data call for antimicrobial resistance (AMR) surveillance data
collected by the European Antimicrobial Resistance Surveillance Network (EARS-Net) for 2018.
The Reporting Protocols are data collection guidelines for reporting countries’ data managers, and the
new Reporting Protocol design is intended to improve user-friendliness by:
Introducing a uniform structure to make it easier for data managers to find data collection
information across different subjects.
Removing information not relevant to data managers.
The Reporting Protocols are supplemented by the
Technical Annex, which contains updated generic
information for each data collection.
Likewise, the Surveillance Protocol will contain some of the generic information previously contained in
the Reporting Protocols.
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 sort of material 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 The metadata set for the subject(s) covered by this Reporting Protocol.
o A history of metadata changes for the subject(s) covered by this Reporting Protocol.
Annex 2 – contains subject-specific material relevant for distribution with the Reporting
Protocol.
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
Technical Annex, including links to:
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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AMR Reporting Protocol 2019
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 complies with the metadata.
4.
Check that your data source profile is up-to-date.
5.
Submit your file(s) to TESSy.
6.
Finalise and approve your submission.
Checking the data collection schedule
An updated link to the current data collections schedule is provided in the
Technical Annex.
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.
AMR-specific guidelines for data collection and preparation for TESSy are provided in
Annex 1 and
Annex 2.
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
Contact Points, the Network 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 metadata – changes since the last Reporting Protocol.
Annex 1 – 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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AMR Reporting Protocol 2019
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.
The
Technical Annex provides an overview of how you work with the metadata file, and the TESSy
user documentation provides in-depth details on metadata.
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 is submitted through the TESSy web interface (go to
Upload).
The
Technical Annex provides an overview of how you submit files to TESSy, and the TESSy user
documentation provides in-depth descriptions of all the upload methods.
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.
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AMR Reporting Protocol 2019
TESSy HelpDesk
Email:
xxxxx@xxxx.xxxxxx.xx
Telephone number:
+46-(0)8-5860 1601
Availability: 9:00 – 16:00 Stockholm time, Monday to Friday (except ECDC
Holidays)
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AMR Reporting Protocol 2019
Changes to current AMR metadata
No changes to AMRTEST metadata have been made since 2014.
AMRDENOM metadata was discontinued in 2018 and replaced by AMRCOVER.
Previous metadata changes to AMRTEST and AMRCOVER 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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AMR Reporting Protocol 2019
Annex 1 AMR metadata
This section describes:
The AMR metadata set
Changes to the AMR metadata
AMR metadata set
The AMR metadata is described in two sections:
Overview of EARS-Net AMR surveillance metadata
Isolate-based reporting
Coverage and representativeness
Overview of EARS-Net AMR surveillance metadata
The metadata set for
isolate based AMR reporting (RecordType
AMRTEST) consists of 8 technical
variables and 29 epidemiological variables, which are further classified as variables at the
patient/isolate level and variables at the AMR test level. The first level includes data referring to the
isolate which are repeated in all records reporting the antimicrobial susceptibility tests performed for
that isolate (See the following table).
The variables used for
reporting coverage and representativeness (RecordType
AMRCOVER)
according to aggregated format include: RecordType; RecordTypeVersion; Subject; DataSource;
ReportingCountry; DateUsedForStatistics; SameMicrSampleCov ; PathogenCov; PropPopulationLabCov;
PopulationReprCov; NumBedsHospCov; NumPatDaysHospCov; HospitalReprCov;
NumCultureSetsHospCov; NumPatDaysForRateCov; IsolateReprCov.
The variables of
AMRTEST and
AMRCOVER RecordTypes are described in more detail, including the
validation rules, in
Isolate-based reporting on page
7 an
d Coverage and representativeness on page 17
Current record type versions
Table 1 shows the record type versions to be used when reporting 2017 AMR surveillance data to
TESSy.
Table 1: AMR record version types for 2017 data
Record type
Record type version
AMRCOVER
AMRCOVER.1
AMRTEST
AMRTEST.2
Isolate-based reporting
The following set of variables applies for isolate-based reporting of AMR. The dataset is sub-divided into
a common set of system related variables (technical variables) and epidemiological variables. The
epidemiologic variables can be classified in two levels: isolate information and susceptibility test
information. The first level includes data referring to the specific isolate, which are repeated for each
antimicrobial agent for which the susceptibility of that isolate has been tested.
The variables are described in the following tables:
Table 2: Technical VariablesTable 3: Epidemiological variables at isolate level
Table 4: Epidemiological variables at AMR test level
Variables #1,2,4,5,6,7,9,10,11,18,25,26 are technically mandatory; TESSy will not accept the data
submission unless these fields have been completed.
However, if you enter data that does not meet the requested combination of “Pathogen”, “Specimen”
and “Antibiotic”, the record is ignored but the batch is NOT rejected. By ignored, TESSy does not insert
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AMR Reporting Protocol 2019
the data for this record into the database. The ignored records are kept as original data but are not
available for analysis or report.
Table 2: Technical Variables
VariableName
1 – RecordID
Description
Unique anonymised identifier for each record within and across the
national surveillance system and subject – MS selected and generated.
Recommended format: "[ReportingCountry][LaboratoryCode]
[Patient Counter][Pathogen]
[Specimen][Antibiotic][DateUsedForStatistics]"
Required (what happens if not
Yes (Error)
submitted)
Data type
String (Max length: 80)
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
2 - RecordType
Description
Structure and format of the data.
Required (what happens if not
Yes (Error)
submitted)
Data type
Coded Value
Code
AMRTEST
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
3 – RecordTypeVersion
Description
There may be more than one version of a recordType. This element
indicates which version the sender uses when generating the message.
Required when no metadata set is provided at upload.
Required
No
Data type
Numeric
Code
See Metadata
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
4 - Subject
Description
Subject of the data to report.
Required (what happens if not
Yes (Error)
submitted)
Data type
Coded Value
Code
AMR
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
5 - DataSource
Description
The data source (surveillance system) that the record originates from.
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AMR Reporting Protocol 2019
Required (what happens if not
Yes (Error)
submitted)
Data type
Coded Value
Code
See Metadata
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
6 - ReportingCountry
Description
The country reporting the record.
Required (what happens if not
Yes (Error)
submitted)
Data type
Coded Value
Code
See Metadata
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
7 - DateUsedForStatistics
Description
The reference date used for standard reports that is compared to the
reporting period. Recommended: Date when sample was taken.
Required (what happens if not
Yes (Error)
submitted)
Data type
Date
Code
Exact date only, “YYYY-MM-DD”
Corresponding variable in the
Date of sample collection
(new format)
previous EARSS Dataset
(notes)
VariableName
8 - Status
Description
Status of reporting NEW/UPDATE or DELETE (inactivate). Default if left
out: NEW/UPDATE. If set to DELETE, the record with the given recordId
will be deleted from the TESSy database (or better stated, invalidated). If
set to NEW/UPDATE or left empty, the record is newly entered into the
database.
Required
No
Data type
Coded Value
Code
NEW/UPDATE OR DELETE
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
Table 3: Epidemiological variables at isolate level
VariableName
9 - LaboratoryCode
Description
Laboratory code unique for each laboratory within the country.
Required (what happens if not
Yes (Error)
submitted)
Data type
Coded Value
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AMR Reporting Protocol 2019
Code
See Metadata
If a country has a need for additional codes in the list, they must contact
TESSy Helpdesk to get the code added. Recommended format:
[ReportingCountry]-[code of three characters]
Corresponding variable in the
Laboratory code
previous EARSS Dataset
VariableName
10 - Specimen
Description
Isolate source
The source of the isolate (i.e. blood)
Required
Yes (Ignore): data entry is required. However, if you enter data that does
not meet the requested combination of “Pathogen”, “Specimen” and
“Antibiotic”, the record is ignored but the batch is NOT rejected. By ignored,
we mean that TESSy does not insert the data for this record into the
database. The ignored records are kept as original data but are not available
for analysis or report.
Data type
Coded Value
Code
BLOOD = blood
CSF = Cerebrospinal fluid
Corresponding variable in the
Isolate source
(new codes)
previous EARSS Dataset
(notes)
VariableName
11 - PatientCounter
Description
Numeric Code for each patient, unique within lab.
Anonymous code by lab to specify patient.
Required (what happens if not
Yes (Error)
submitted)
Data type
Numeric
Code
Require that the labs anonymize the PatientCounter.
Corresponding variable in the
Patient ID / Code
(it must be anonymous. It was a string now it is a
previous EARSS Dataset
number.)
(notes)
VariableName
12 - Gender
Description
Gender
Required (what happens if not
Yes (Warning)
submitted)
Data type
Coded Value
Code
M = Male
F = Female
O = Other
UNK = Unknown
Corresponding variable in the
Sex
(new codes)
previous EARSS Dataset
(notes)
VariableName
13 - Age
Description
Age of the patient when the sample was taken.
Required (what happens if not
Yes (Warning)
submitted)
Data type
Numeric
Code
Integer
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AMR Reporting Protocol 2019
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
14 - IsolateId
Description
Isolate ID; Code for each isolate, unique within lab and year
Text code assigned by lab to specify isolate
Required (what happens if not
Yes (Warning)
submitted)
Data type
Text
Corresponding variable in the
Isolate sample number
previous EARSS Dataset
VariableName
15 - HospitalId
Description
Unique identifier for the hospital within each laboratory.
Required (what happens if not
Yes (Warning)
submitted)
Data type
Text
Code
Unique identifier for the hospital within each laboratory. Recommended
format: [LaboratoryCode]-[letter assigned to a hospital – starting from A,
B, C, etc.]
Corresponding variable in the
Hospital code
(new recommended format)
previous EARSS Dataset
(notes)
VariableName
16 - PatientType
Description
Origin of patient. Is the patient at the moment the sample is taken
admitted in a hospital (inpatient), or not (outpatient). Patients that go to
the hospital for Dialysis, other Day Hospital Care and to Emergency room
should be classified as “O” for the field “PatientType”. All other patient
that are admitted in the hospital as inpatients should be classified as
“INPAT”.
Required (what happens if not
Yes (Warning)
submitted)
Data type
Coded Value
Code
INPAT= Admitted (Inpatient)
OUTPAT= Outpatient
O =Other (e.g. emergency room)
UNK=Unknown
Corresponding variable in the
Origin of patient
(new codes)
previous EARSS Dataset
(notes)
VariableName
17 - HospitalUnitType
Description
Hospital department (at time of sample collection)
Required (what happens if not
Yes (Warning)
submitted)
Data type
Coded Value
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AMR Reporting Protocol 2019
Code
INTMED =Internal Medicine
PEDS =Paediatrics/neonatal
PEDSICU=Paediatrics/neonatal ICU
SURG =Surgery
ONCOL=Haematology/Oncology
OBGYN=Obstetrics/Gynaecology
ICU=Intensive Care Unit
ED=Emergency Department
URO=Urology Ward
INFECT=Infectious Disease Ward
O =Other
UNK=Unknown
Corresponding variable in the
Hospital department
(new codes)
previous EARSS Dataset
(notes)
VariableName
18 - Pathogen
Description
Pathogen
Species and genus of the pathogen which has been isolated from the
sample.
Required (what happens if not
Yes (Error)
submitted)
Data type
Coded Value
Code
STRPNE=
Streptococcus pneumoniae
STAAUR=
Staphylococcus aureus
ENCFAE=
Enterococcus faecalis ENCFAI=
Enterococcus faecium
ESCCOL=
Escherichia coli
KLEPNE=
Klebsiella pneumoniae
PSEAER=
Pseudomonas aeruginosa ACISPP=
Acinetobacter spp.
Corresponding variable in the
Pathogen code
(new codes)
previous EARSS Dataset
(notes)
VariableName
19 - DateOfHospitalisation
Description
Date of admission in hospital
Required
No
Data type
Date
Code
Exact date only, “YYYY-MM-DD”
Corresponding variable in the
Date of admission
(new format)
previous EARSS Dataset
(notes)
VariableName
20 - ResultPCRmec
Description
Detection of PCR mecA-gene
Required
No
Data type
Coded Value
Code
POS=positive
NEG=negative
UNK=unknown
Corresponding variable in the
PCR mec-gene
(new codes)
previous EARSS Dataset
(notes)
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AMR Reporting Protocol 2019
Validation rule
To be reported only if Pathogen=STAAUR.
VariableName
21 - ResultPbp2aAggl
Description
Detection of PBP2a-agglutination
Required
No
Data type
Coded Value
Code
POS=positive;
NEG=negative;
UNK=unknown
Corresponding variable in the
PBP2a-agglutination
(new codes)
previous EARSS Dataset
(notes) Validation rule
To be reported only if Pathogen=STAAUR.
VariableName
22 - Serotype
Description
Serotype/group of the pathogen isolated from the sample.
Reference: Danish Kauffman-Lund scheme from the WHO Collaborating
Centre for Reference and Research on Pneumococci at the Danish Serum
Institute.
Required
No
Data type
Coded Value
Code
See Metadata
Corresponding variable in the
Serotype
previous EARSS Dataset
(notes) Validation rule
To be reported only if Pathogen=STRPNE.
VariableName
23 - ESBL
Description
Detection of ESBL
Required
No
Data type
Coded Value
Code
POS=positive
NEG=negative
UNK=unknown
Corresponding variable in the
ESBL present
(new codes)
previous EARSS Dataset
(notes) Validation rule
To be reported only if Pathogen= ESCCOL or KLEPNE.
VariableName
24 - ResultCarbapenemases
Description
Detection of Carbapenemases. This refers to phenotypic test for
carbapenemase activity (e.g. the Modified Hodge Test - MHT).
Required
No
Data type
Coded Value
Code
POS=positive
NEG=negative
UNK=unknown
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
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AMR Reporting Protocol 2019
Validation rule
To be reported only if Pathogen= ESCCOL or KLEPNE or PSEAER or ACISPP
Table 4: Epidemiological variables at AMR test level
VariableName
25 - Antibiotic
Description
Antimicrobial code
Required
Yes (Ignore): data entry is required. However, if you enter data that does
not meet the requested combination of “Pathogen”, “Specimen” and
“Antibiotic”, the record is ignored but the batch is NOT rejected. By
ignored, we mean that TESSy does not insert the data for this record into
the database. The ignored records are kept as original data but are not
available for analysis or report.
Data type
Coded Value,
Code
See
Implementation of AMR case definitions for TESSy where a list of all
antimicrobial agent codes are provided
Corresponding variable in the
Antibiotic code
previous EARSS Dataset
VariableName
26 - SIR
Description
Final interpretation result of all different susceptibility tests performed
Required (what happens if not
Yes (Error)
submitted)
Data type
Coded Value
Code
S=susceptible;
I=intermediate;
R=resistant
Corresponding variable in the
S/I/R
previous EARSS Dataset
VariableName
27 - ResultZoneSign
Description
Zone (> < =)
This field can indicate if a value of the zone diameter of the disk test is
“less than" (<); “equal to or less than” (< =); "equal to" (=); “equal to or
greater than” (>=); or "greater than" (>) the value indicated in the
following field.
Required
No
Data type
Coded Value
Code
<
<=
=
>=
>
Corresponding variable in the
Zone (> < =)
(new codes)
previous EARSS Dataset
(notes)
VariableName
28 - ResultZoneValue
Description
Zone (Value in mm)
Required
No
Data type
Numeric
Code
Integer
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Corresponding variable in the
Zone (Value in mm)
(only Zone diameter in millimetres;
previous EARSS Dataset
(notes)
VariableName
29 - ResultZoneSIR
Description
Interpretation of the zone test.
Required
No
Data type
Coded Value
Code
S=susceptible;
I=intermediate;
R=resistant
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
30 - ResultMICSign
Description
MIC (> < =)
This field can indicate if a value of the zone diameter of the MIC test is
“less than" (<); “equal to or less than” (< =); "equal to" (=); “equal to or
greater than” (>=); or "greater than" (>) the value indicated in the
following field.
Required
No
Data type
Coded Value
Code
<
<=
=
>=
>
Corresponding variable in the
MIC (> < =)
(new codes)
previous EARSS Dataset
(notes)
VariableName
31 - ResultMICValue
Description
MIC (Value in mg/l)
Required
No
Data type
Text
Code
If <1 then float, if >=1 then integer
Corresponding variable in the
MIC (Value in mg/l)
(only MIC values in mg/l; in the EARSS Dataset it also
previous EARSS Dataset
could contain the S/I/R results)
(notes)
VariableName
32 - ResultMICSIR
Description
Interpretation of the MIC test.
Required
No
Data type
Coded Value
Code
S=susceptible;
I=intermediate;
R=resistant
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
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VariableName
33 - ResultEtestSign
Description
Gradient strip (> < =)
This field can indicate if a value of the zone diameter of the gradient strip
is “less than" (<); “equal to or less than” (< =); "equal to" (=); “equal to or
greater than” (>=); or "greater than" (>) the value indicated in the
following field.
Required
No
Data type
Coded Value
Code
<
<=
=
>=
>
Corresponding variable in the
E-test (> < =)
(new codes)
previous EARSS Dataset
(notes)
VariableName
34 - ResultEtestValue
Description
Gradient strip value (Value in mg/l)
Required
No
Data type
Text
Code
If <1 then float, if >=1 then integer. The value 1.5 is also allowed.
Corresponding variable in the
E-test (Value in mg/l)
(only E-test values in mg/l; in the EARSS Dataset it
previous EARSS Dataset
also could contain the S/I/R results)
(notes)
VariableName
35 - ResultEtestSIR
Description
Interpretation of the gradient strip test.
Required
No
Data type
Coded Value
Code
S=susceptible;
I=intermediate;
R=resistant
Corresponding variable in the
(new variable)
previous EARSS Dataset
(notes)
VariableName
36 - DiskLoad
Description
Disk content (only if Zone)
This field can be used to mention the load of the antimicrobial disk used.
Please mention the value and the Units (e.g. mcg, Units or IU).
Required
No
Data type
Text
Code
Value and units: i.e. UI, mcg.
Corresponding variable in the
Disk load
previous EARSS Dataset
VariableName
37 - ReferenceGuidelinesSIR
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Description
To differentiate use of CSLI and EUCAST guidelines for determining clinical
breakpoint for antimicrobial susceptibility of the isolate
Required
No
Data type
Coded value
Code
EUCAST = European Committee on Antimicrobial Susceptibility Testing
CLSI = Clinical and Laboratory Standards Institute
NAT = National
O = Other
Corresponding variable in the
New variable 2012
previous EARSS Dataset
Coverage and representativeness
The following set of variables applies for country aggregate reporting of coverage and
representativeness of laboratories participating in EARS-Net. The dataset is sub-divided into a
common set of system related variables (technical variables) and epidemiological variables. The
epidemiological variables have to be provided at microorganism level if coverages and
representativeness differ by species. Otherwise, if coverages and representativeness are the same
for all species, one AMRCOVER record per DataSource and year is expected.
The variables are described in the following tables:
Table 5: Technical variables
Table 6: Epidemiological variables
Variables #1,3,4,5,6,7,8, 9,10,13,16 are technically mandatory; TESSy will not accept the data
submission unless these fields have been completed.
Table 5: Technical variables
VariableName
1 - RecordType
Description
Structure and format of the data.
Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
AMRCOVER
VariableName
2 - RecordTypeVersion
Description
There may be more than one version of a recordType. This element
indicates which version the sender uses when generating the message.
Required when no metadata set is provided at upload.
Required
No
Data type
Numeric
Code
See Metadaset
VariableName
3 - Subject
Description
Subject of data to report.
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Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
AMRCOVER
VariableName
4 - DataSource
Description
The data source (surveillance system) that the record originates from.
Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
See Metadaset
VariableName
5 - ReportingCountry
Description
The country reporting the record.
Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
See Metadata
VariableName
6 - DateUsedForStatistics
Description
The reference year for which the data are valid.
Required (what happens if not Yes (Error)
submitted)
Data type
Date
Code
"YYYY"
Table 6: Epidemiological variables
VariableName
7 - SameMicrSampleCov
Description
Estimated coverages and representativeness are the same for all
microorganism species under surveillance.
If coverages and representativeness are the same for all microorganism
species, one AMRCOVER record per DataSource and year is expected (the
code "PATAMR" should be used for the variable "PathogenCov"). If
coverages and representativeness differ by species, eight AMRCOVER
records per DataSource and year are expected (all codes other than
"PATAMR" should be used for the variable "PathogenCov").
Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
Y = Yes
N = No
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VariableName
8 - PathogenCov
Description
Pathogen.
The code "PATAMR" should be used if coverage is the same for all
pathogens. The other eight codes are specific for each microorganism
under surveillance.
Required
Yes (Error)
Data type
Coded Value
Code
PATAMR= All EARS-Net pathogens (to be used if coverage is the same for
all pathogens)
ACISPP =
Acinetobacter species
ENCFAE =
Enterococcus faecalis ENCFAI =
Enterococcus faecium ESCCOL =
Escherichia coli KLEPNE =
Klebsiella pneumoniae PSEAER =
Pseudomonas aeruginosa STAAUR =
Staphylococcus aureus STRPNE =
Streptococcus pneumoniae
VariableName
9 - PropPopulationLabCov
Description
Best available estimate for the proportion of the national population
covered by the laboratories reporting to EARS-Net in the specific year. Use
'.' as decimal delimiter, e.g. 0.32.
Required (what happens if not Yes (Error)
submitted)
Data type
Text
Code
Float
VariableName
10 - PopulationReprCov
Description
Population sample representativeness.
Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
HIGH = all main geographical regions are covered and data are considered
representative of the national epidemiology;
MEDIUM = most geographical regions are covered and data are
considered of medium representativity of the national epidemiology;
POOR = only a few geographical areas are covered and data are poorly
representative of the national epidemiology.
VariableName
11 - NumBedsHospCov
Description
Total number of beds of hospitals served by laboratories reporting to
EARS-Net.
Required (what happens if not No
submitted)
Data type
Numeric
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Code
Integer
VariableName
12 - NumPatDaysHospCov
Description
Total number of patient-days of hospitals served by laboratories reporting
to EARS-Net.
Required (what happens if not Yes (Warning)
submitted)
Data type
Numeric
Code
Integer
VariableName
13 - HospitalReprCov
Description
Hospital sample representativeness.
Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
HIGH = the hospital sample is representative of the acute care hospital
distribution in the country;
MEDIUM = the hospital sample is partly representative of the acute care
hospital distribution in the country;
POOR = the hospital sample is poorly representative of the acute care
hospital distribution in the country.
VariableName
14 - NumCultureSetsHospCov
Description
Total number of blood culture sets performed in hospitals served by
laboratories reporting to EARS-Net. The provided data should be suitable
for calculating the blood culture rate in the specific year: number of sets
refers to the hospital sample for which the aggregated denominator
(NumPatDaysForRateCov) is provided.
Required (what happens if not Yes (Warning)
submitted)
Data type
Numeric
Code
Integer
VariableName
15 - NumPatDaysForRateCov
Description
Total number of patient-days of hospitals served by laboratories which
provided the Number of blood culture sets performed. This number can
be equal to "NumPatDaysHospCov " or lower if only part of the
laboratories provided the number of blood sets performed.
Required (what happens if not Yes (Warning)
submitted)
Data type
Numeric
Code
Integer
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VariableName
16 - IsolateReprCov
Description
Isolate sample representativeness.
Required (what happens if not Yes (Error)
submitted)
Data type
Coded Value
Code
HIGH = the isolate sample is representative of microorganisms causing
invasive infections and of patient casemix of the included hospitals;
MEDIUM = the isolate sample is partly representative of microorganisms
causing invasive infections and of patient casemix of the included
hospitals;
POOR = the isolate sample is poorly representative of microorganisms
causing invasive infections and of patient case-mix of the included
hospitals.
AMR metadata change history
Metadata changes prior to 2014 can be found on the TESSy documents website.
Previous metadata changes
Table 7: Summary of implemented changes in case-based record types for Antimicrobial Resistance
(AMR)
Year
Subject
Description
2018
AMRDENOM
The metadata subject was discontinued.
2019
AMRCOVER
The new metadata subject was introduced in place of AMRDENOM.
2015-
AMRTEST
No changes to AMR metadata.
2019
2014
AMRTEST
Addition of new codes to coded value list for antibiotics.
AMRTEST
Update of validation rules associated to these new antibiotics.
All
Update NUTS codes according to the NUTS Codes 2010 classification from EUROSTAT
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Annex 2 AMR-specific material
Contacts
Questions regarding coding, upload of data etc. should be directed to the
TESSy helpdesk at
xxxxx@xxxx.xxxxxx.xx
Questions regarding the AMR reporting and content will be dealt with by the ECDC EARS-Net contact:
E-mail:
xxxxxxxx@xxxx.xxxxxx.xx
Questions regarding the use of WHONET to prepare data for TESSy upload can be directed to ECDC
contractor
John Stelling:
E-ma
il xxxxxxxxx@xxxxxx.xxx (kee
p xxxxxxxx@xxxx.xxxxxx.xx in Cc)
Microbiological guidelines for EARS-Net
EARS-Net encourages the use of The European Committee on Antimicrobial Susceptibility Testing
(EUCAST) guidelines and breakpoints to determine clinical antimicrobial susceptibility (available at
http://www.eucast.org/). In 2012, the EUCAST steering committee established a subcommittee for
detection of resistance mechanisms and specific resistances of clinical and/or epidemiological
importance. The sub-committee was established partly in response to frequently asked questions from
users of EUCAST guidelines on this issue, and partly on request from the ECDC, as expert microbiology
guidance was needed for EARS-Net participants.
The remit of the subcommittee was to develop practical guidelines for detection of specific antimicrobial
resistance mechanisms of clinical and/or epidemiological importance. The document was developed by
conducting systematic literature searches, and most recommendations are based on multi-centre
studies, as these provide the best measure of robustness of the methods. Prior to publication of
these guidelines, they were subjected to wide consultation through the EUCAST consultation contact
lists, the EUCAST website and ECDC focal point contacts. An updated version of the result of this work
can be found in the EUCAST guidelines for detection of resistance mechanisms and specific resistances
of clinical and/or epidemiological importance1. This document replaces the previous EARSS
microbiology manual.
The guideline describes the definition of the mechanisms of resistances, an outline description of
recommended methods of detection, and references to detailed descriptions of the methods for:
1. Carbapenemase-producing Enterobacteriaceae
2. Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae
3. Acquired AmpC β-lactamase-producing Enterobacteriaceae
4. Meticillin-resistant Staphylococcus aureus (MRSA)
5. Glycopeptide non-susceptible Staphylococcus aureus
6. Vancomycin resistant enterococci
7. Penicillin non-susceptible Streptococcus pneumoniae
Implementation of AMR case definitions for TESSy
Given the typology of data for AMR surveillance, which refers to laboratory isolates rather than to cases
of disease, the following case definition has been implemented in the RecordType “AMRTEST”, for
reporting to TESSy:
The bacterial species under surveillance are:
1. EUCAST. 2017. EUCAST guidelines for detection of resistance mechanisms and specific resistances of clinical
and/or epidemiological importance. Version 2.0 of July 2017 Available at
http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Resistance_mechanisms/EUCAST_detection_of_res
istance_mechanisms_170711.pdf
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Streptococcus pneumoniae (STRPNE)
Staphylococcus aureus (STAAUR)
Enterococcus faecalis (ENCFAE)
Enterococcus faecium (ENCFAI)
Escherichia coli (ESCCOL)
Klebsiella pneumoniae (KLEPNE)
Pseudomonas aeruginosa (PSEAER)
Acinetobacter species (ACISPP).
All isolates from blood (STRPNE, STAAUR, ENCFAE, ENCFAI, ESCCOL, KLEPNE, PSEAER, ACISPP)
and/or cerebrospinal fluid (STRPNE, ESCCOL, KLEPNE, PSEAER, ACISPP), for which a susceptibility test
has been performed, have to be included.
The generic case definition of antibiotic resistance defined in the Commission implementing decision
laying down case definitions for reporting communicable diseases to the Community network.1Although
EARS-Net encourages the use of EUCAST clinical breakpoints in line with the EU case definitions,
countries and laboratories using other guidelines are still welcome to report data if the use of clinical
guidelines is specified unde
r Variable 37 (ReferenceGuidelinesSIR). Reporting of quantitative
susceptibility data is strongly encouraged.
Duplicates from the same patients should be eliminated taking only the first by date of sample
collection and isolate source
. Table 8 lists all microorganism/source and antibiotic agent combinations
under surveillance by EARS-Net.
If records referring to additional combinations are uploaded, they will be filtered out by the system -
see
TESSy Filter 1.
Table 8: Microorganism, specimen source and antimicrobial agent combinations under surveillance by
EARS-Net
Microorganism
Specimen source
Antimicrobial agent
Streptococcus pneumoniae (STRPNE)
blood (BLOOD);
Azithromycin (AZM)
cerebrospinal fluid (CSF)
Cefotaxime (CTX)
Ceftriaxone (CRO)
Clarithromycin (CLR)
Erythromycin (ERY)
Levofloxacin (LVX)
Moxifloxacin (MFX)
Norfloxacin (NOR)
Oxacillin (OXA)
Penicillin (PEN)
Staphylococcus aureus (STAAUR)
blood (BLOOD)
Cefoxitin (FOX)
Cloxacillin (CLO)
Ciprofloxacin (CIP)
Daptomycin (DAP)
Dicloxacillin (DIC)
Flucloxacillin (FLC)
Levofloxacin (LVX)
Linezolid (LNZ)
Meticillin (MET)
Norfloxacin (NOR)
Ofloxacin (OFX)
Oxacillin (OXA)
Rifampin (RIF)
Vancomycin (VAN)
Enterococcus faecalis (ENCFAE)
blood (BLOOD)
Ampicillin (AMP)
Amoxicillin (AMX)
1. Commission Implementing Decision on the communicable diseases and related special health issues
to be covered by epidemiological surveillance – Annex 1 (replacing Commission Decision No
2000/96/EC).
Available at : https://eur-lex.europa.eu/legal-
content/EN/TXT/PDF/?uri=CELEX:32018D0945&from=EN#page=72
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Gentamicin-High (GEH)
Linezolid (LNZ)
Teicoplanin (TEC)
Vancomycin (VAN)
Enterococcus faecium (ENCFAI)
blood (BLOOD)
Ampicillin (AMP)
Amoxicillin (AMX)
Gentamicin-High (GEH)
Linezolid (LNZ)
Teicoplanin (TEC)
Vancomycin (VAN)
Escherichia coli (ESCCOL)
blood (BLOOD);
Amikacin (AMK)
cerebrospinal fluid (CSF)
Amoxicillin-clavulanic acid (AMC)
Ampicillin (AMP)
Amoxicillin (AMX)
Cefepime (FEP)
Cefotaxime (CTX)
Ceftazidime (CAZ)
Ceftriaxone (CRO)
Ciprofloxacin (CIP)
Colistin (COL)
Ertapenem (ETP)
Gentamicin (GEN)
Imipenem (IPM)
Levofloxacin (LVX)
Meropenem (MEM)
Moxifloxacin (MFX)
Netilmicin (NET)
Norfloxacin (NOR)
Ofloxacin (OFX)
Piperacillin-tazobactam (TZP)
Polymyxin B (POL)
Tigecycline (TCG)
Tobramycin (TOB)
Klebsiella pneumoniae (KLEPNE)
blood (BLOOD);
Amikacin (AMK)
cerebrospinal fluid (CSF)
Amoxicillin-clavulanic acid (AMC)
Cefepime (FEP)
Cefotaxime (CTX)
Ceftazidime (CAZ)
Ceftriaxone (CRO)
Ciprofloxacin (CIP)
Colistin (COL)
Ertapenem (ETP)
Gentamicin (GEN)
Imipenem (IPM)
Levofloxacin (LVX)
Meropenem (MEM)
Moxifloxacin (MFX)
Netilmicin (NET)
Norfloxacin (NOR)
Ofloxacin (OFX)
Piperacillin-tazobactam (TZP)
Polymyxin B (POL)
Tigecycline (TCG)
Tobramycin (TOB)
Pseudomonas aeruginosa (PSEAER)
blood (BLOOD);
Amikacin (AMK)
cerebrospinal fluid (CSF)
Cefepime (FEP)
Ceftazidime (CAZ)
Ciprofloxacin (CIP)
Colistin (COL)
Gentamicin (GEN)
Imipenem (IPM)
Levofloxacin (LVX)
Meropenem (MEM)
Netilmicin (NET)
Piperacillin (PIP)
Piperacillin/Tazobactam (TZP)
Polymyxin B (POL)
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Tobramycin (TOB)
Acinetobacter species (ACISPP)
blood (BLOOD);
Amikacin (AMK)
cerebrospinal fluid (CSF)
Ciprofloxacin (CIP)
Colistin (COL)
Gentamicin (GEN)
Imipenem (IPM)
Levofloxacin (LVX)
Meropenem (MEM)
Netilmicin (NET)
Polymyxin B (POL)
Tobramycin (TOB)
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Objectives for AMR surveillance
Surveillance of AMR within the European Union (EU) has been assured by European law: AMR is listed
as a special health issue in the Commission Implementing Decision (EU) 2018/945 of 22 June 2018 on
the communicable diseases and related special health issues to be covered by epidemiological
surveillance.1
EARS-Net is based on a network of representatives from the Member States collecting routine clinical
antimicrobial susceptibility data from national AMR surveillance initiatives. Scientific guidance and
support to the network is provided by the EARS-Net Coordination Committee. This group is composed
of individual experts selected from among the nominated disease-specific contact points and experts
from other organisations that are involved in surveillance of antimicrobial resistance.
The objective of EARS-Net is to collect, analyse and report data on AMR, across EU/EEA Member States
and as defined in the EARS-Net protocol, to enable action to address AMR.
1 Decision No 1082/2013/EU of the European Parliament and of the Council of 22 October 2013 on serious cross-
border threats to health and repealing Decision No 2119/98/EC.
http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2013:293:0001:0015:EN:PDF
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Preparing national AMR datasets
The data collection at laboratory level can be performed both electronically and manually by filling out
the corresponding Isolate Records Forms per pathogen (see
Isolate forms). If the data collection at
laboratory level has been performed manually by filling the Isolate Records, the Country Data Manager
should create the fields “Age” and “PatientCounter” starting from the available information in the paper
forms (“Year of birth” and “Patient ID / Code”).
The data collection for EARS-Net is supported by WHONET (Microbiology Laboratory Database
Software) which is a useful tool for processing and analysis of antimicrobial resistance data. It provides
a routine procedure to perform data entry and to export data in EARS-Net exchange format and can be
used locally by participating laboratories and centrally by country data managers. The software and
manual can be downloaded from http://www.whonet.org/
If a new laboratory joins the surveillance network the country disease specific contact points must
communicate the new code of the new laboratory to the Helpdesk at xxxxx@xxxx.xxxxxx.xx by e-mail
before uploading data; otherwise the system will not recognise the new code and will reject the entire
file.
Checking for duplicate records
Before uploading a file to TESSy, the country data manager has to revise the laboratory data and check
for duplicates (records with the same RecordId). If there are duplicates, TESSy will reject the upload.
Duplicates should be eliminated by merging/selecting records.
Recommendations for merging and selecting records:
In the TESSy metadata set the recommended format of the RecordId is the combination of the
following fields: ReportingCountry; LaboratoryCode; PatientCounter; Pathogen; Specimen;
Antibiotic; DateUsedForStatistics.
Identify multiple isolates within the same day (using the field IsolateId when available) and
select the first one per day (DateUsedForStatistics).
If there are still duplicates, further merging/selection of records should be done according to
the recommended method summarized in the following examples 1, 2 and 3.
Example 1 – Duplicates: same microorganism/antimicrobial agent combination but
different microbiological tests
Pathogen Antibiotic SIR
ResultZoneSIR
ResultMICValue ResultMICSIR
ESCCOL
CTX
R
R
ESCCOL
CTX
S
0.5
S
The two records above refer to the same patient and the same microorganism/antimicrobial
agent combination from the same source (blood) in the same day.
According to the metadata set specifications, they are considered as
duplicates and will
generate an error in the uploading process to TESSy with the subsequent rejection of the
entire batch of records.
To avoid this unsuccessful outcome, it is possible to
merge the reported data in one row.
For the final interpretation of the susceptibility test (SIR), the MIC result will prevail.
Pathogen Antibiotic SIR
ResultZoneSIR
ResultMICValue ResultMICSIR
ESCCOL
CTX
S
R
0.5
S
Example 2 – Duplicates: same microorganism/antimicrobial agent combination, same
test, different SIR results
Pathogen
Antibiotic
SIR
ResultZoneSIR
ResultMICValue
ResultMICSIR
ESCCOL
CTX
R
R
8
R
ESCCOL
CTX
S
S
0.5
S
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Select the first in this order R→I→S (therefore the most resistant is selected). This is a rare occurrence
and this rule is implemented to have a standard algorithm for filtering the duplicates.
Example 3 – Duplicates: same microorganism/antimicrobial agent combination, same
test, same SIR results
Pathogen
Antibiotic
SIR
ResultZoneSIR
ResultMICValue
ResultMICSIR
ESCCOL
CTX
S
S
0.5
S
ESCCOL
CTX
S
S
0.5
S
If the records have the same SIR result (true duplicates) just select one of them, taking into account
the completeness of the other variables.
Data management and analysis
TESSy filter 1 (case definition) and validation report
TESSy filters the uploaded records according to the list of Microorganism/Specimen/Antimicrobial agent
combinations included in the AMR surveillance (the EARS-Net case definition for TESSy is described in
more detail in
Implementation of AMR case definitions for TESSy). Records referring to additional
Microorganism/Specimen/Antimicrobial agent combinations are discharged.
Shortly after the data uploading, TESSy provides a validation report which should be assessed by the
country user. The report shows summary statistics of the validated data from the uploaded batch.
TESSy filter 2 (preparing dataset for analysis)
This filter aims to obtain one record per patient/microorganism/specimen/antimicrobial agent
combination and year.
STEP 1
Select all records that belong to
Fields to identify the date:
the
first date within the
•
DateUsedForStatistics
considered YEAR for each
Fields to identify the patient/microorganism
patient/microorganism
combination:
combination.
•
ReportingCountry
•
LaboratoryCode
•
PatientCounter
•
Pathogen
STEP 2
If more than
one source (BLOOD,
Field to identify the
source:
CSF) is reported within the first
•
Specimen
date, select only one giving
priority to the CSF.
STEP 3
If the
same antimicrobial is
Field to identify the
antimicrobial:
reported in more than one record
•
Antibiotic
within the first date, make a
Fields to identify
results coming from the gradient
selection giving priority to records
strip test:
with results
coming from the
•
ResultEtestSIR**
gradient strip test*.
•
ResultEtestVALUE**
STEP 4
If the same antimicrobial is still
Fields to identify
results coming from other MIC tests:
reported in more than one record
•
ResultMICSIR*
within the first date, make a
•
ResultMICVALUE*
selection giving priority to records
with
results coming from other
MIC tests.
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STEP 5
If the same antimicrobial is still
Field to identify the
final interpretation of the
reported in more than one record,
susceptibility test:
make a selection according with
•
SIR
the
final interpretation of the
susceptibility test (
priority
sequence R→I→S).
STEP 6
If the same antimicrobial is still
reported in more than one record,
select the first one.
* In the selection process gradient strip test results should prevail over other MIC results since, in the routine labs activity, the
latter are likely to have been obtained through automated systems which are general y considered less reliable than gradient strip
tests.
** At least one among the two fields is not missing.
The TESSy filter includes two additional steps for meticillin-resistant Staphylococcus aureus (between
Step 2 and Step 3 of the main algorithm).
Conditions
Pathogen=“STAAUR”
AND
(Antibiotic=“OXA” OR “MET” OR “FLC” OR “DIC” OR “CLO” OR “FOX”)
Additional
If the same
antimicrobial is reported in more
Field to identify the
antimicrobial:
STEP I
than one record within the first date, make a
•
Antibiotic
selection giving priority to records with the
Fields to identify the
confirmation test
confirmation test results.
results:
•
ResultPCRmec***
•
ResultPbp2aAggl***
Additional
If the same antimicrobial is still reported in
STEP II
more than one record, make a selection
according with the confirmation test result
(priority to records with a positive result).
***At least one among the two fields is not missing.
Data analysis and presentation
For the analysis, an isolate is considered resistant to an antimicrobial agent when tested and
interpreted as resistant (R) in accordance with the clinical breakpoint criteria used by the local
laboratory. An isolate is considered non-susceptible to an antimicrobial agent when tested and found
resistant (R) or with intermediate susceptibility (I) using the same clinical breakpoints as interpretive
criteria. EARS-Net encourages the use of EUCAST breakpoints, however, results based on other
interpretive criteria used by the reporting countries are accepted for the analysis.
As a general rule, data are expressed as a resistance percentage, i.e. the percentage of R isolates out
of all isolates with antimicrobial susceptibility testing (AST) information on that specific microorganism–
antimicrobial agent combination, and for some bacteria as the percentage of non-susceptible (I+R)
isolates out of all isolates with the relevant information. For selected analyses, a 95% confidence
interval is determined for the resistance percentage by applying an exact confidence interval for
binomial data.
In most cases, the percentage resistance is calculated considering an antimicrobial group (instead of a
single antimicrobial agent), which needs other specifications to perform the analysis. The group often
but not always represent an antimicrobial class. An example of an antimicrobial group is the third-
generation cephalosporins for E. coli. This group contains three antimicrobial agents: ceftriaxone
(CRO), cefotaxime (CTX) and ceftazidime (CAZ). If two or more antimicrobials (records) are reported
for the same “microorganism/antimicrobial group” combination, count only one of them; the choice has
to be done according with the final interpretations of the susceptibility test (field=SIR; priority
sequence R→I→S).
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Specific rule for Streptococcus pneumoniae and non-susceptibility to penicillin
The antimicrobial considered for this resistance are penicillin (PEN) and oxacillin (OXA). If both are
reported, give priority to penicillin.
Specific rule to define Meticillin-resistant Staphylococcus aureus (MRSA)
The antimicrobials considered for this resistance are: Oxacillin (OXA), Meticillin (MET), Flucloxacillin
(FLC), Cloxacillin (CLO), Dicloxacillin (DIC) and Cefoxitin (FOX). Other tests (equivalents) are also
considered as confirmation tests: PCR mecA or PBP2a detection.
Hierarchical levels to assess the MRSA
Priority sequence of the results
Confirmation test (PCR mecA and PBP2a)
POS→NEG
Gradient strip test (SIR result of OXA, MET, FLC, DIC, CLO, FOX) R→S
Other MIC tests (SIR result of OXA, MET, FLC, DIC, CLO, FOX)
R→S
Other test (SIR result of OXA, MET, FLC, DIC, CLO, FOX)
R→S
The definition of MRSA is based on the following criteria:
I.
If at least one between ResultPCRmec and ResultPbp2aAggl is positive then MRSA.
II.
If at least one between ResultPCRmec and ResultPbp2aAggl is negative and the other one
is not positive then MSSA (Meticillin-sensitive Staphylococcus aureus)
III.
If both ResultPCRmec and ResultPbp2aAggl are missing then consider SIR to define
susceptibility (if SIR=S then MSSA; if SIR=I or R then MRSA)
The full set of microorganism/antimicrobial group combinations that are under regular surveillance by
EARS-Net (routinely presented in the EARS-Net annual report and the public EARS-Net database) is
displayed in
Table 9. In addition, additional analysis of other single or group of antimicrobial agents will
be performed on an ad hoc basis.
If fewer than 10 isolates are reported for a specific organism–antimicrobial agent combination in a
country, the results for this country are not displayed on the maps presented in the Annual Report and
the interactive database.
The statistical significance of temporal trends of antimicrobial resistance percentages by country is
calculated based on data from the last four years. Countries reporting fewer than 20 isolates per year,
or not providing data for all years within the considered period, are not included in the analysis.
Statistical significance of trends is assessed by the Cochran–Armitage test. An additional sensitivity
analysis is performed by repeating the Cochran–Armitage test only including laboratories which
consistently reported for the full four-year period in order to exclude selection bias when assessing the
significance of the trends.
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AMR Reporting Protocol 2019
Table 9: Microorganism and antimicrobial group combinations under regular EARS-Net surveillance
Microorganism
Antimicrobial group
Antimicrobial agents
Escherichia coli (ESCCOL)
Aminopenicillins
AMX, AMP
Fluoroquinolones
CIP, OFX, LVX
Third-generation cephalosporins
CTX, CRO, CAZ
Aminoglycosides
GEN, TOB, NET
Carbapenems
IPM, MEM
Polymyxins
POL, COL
Klebsiella pneumoniae
Fluoroquinolones
CIP, OFX, LVX
(KLEPNE)
Third-generation cephalosporins
CTX, CRO, CAZ
Aminoglycosides
GEN, TOB, NET
Carbapenems
IPM, MEM
Polymyxins
POL, COL
Pseudomonas aeruginosa
Piperacillin+/- tazobactam
TZP, PIP
(PSEAER)
Ceftazidime
CAZ
Fluoroquinolones
CIP, LVX
Aminoglycosides
GEN, TOB, NET
Carbapenems
IPM, MEM
Amikacin
AMK
Polymyxins
POL, COL
Acinetobacter species (ACISPP)
Fluoroquinolones
CIP, LVX
Aminoglycosides
GEN, TOB, NET
Carbapenems
IPM, MEM
Amikacin
AMK
Polymyxins
POL, COL
Streptococcus pneumoniae
Penicillins
PEN, OXA
(STRPNE)
Macrolides
ERY, CLR, AZM
Fluoroquinolones
LVX, NOR, MFX
Third-generation cephalosporins
CTX, CRO
Staphylococcus aureus
MRSA
MET, OXA, FOX, FLC, CLO, DIC
(STAAUR)
Rifampicin
RIF
Fluoroquinolones
CIP, OFX, LVX, NOR
Enterococcus faecalis (ENCFAE)
High-level aminoglycoside resistance
GEH
and Enterococcus faecium
Vancomycin
VAN
(ENCFAI)
Aminopenicillins
AMX, AMP
Page 31 of 39
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AMR Reporting Protocol 2019
Isolate forms
To be filled in by the laboratories without electronic system
The following isolate forms are included:
Isolate Record Form Streptococcus pneumoniae
Isolate Record Form Staphylococcus aureus
Isolate Record Form Escherichia coli
Isolate Record Form Klebsiella pneumoniae
Isolate Record Form Pseudomonas aeruginosa
Isolate Record Form □ Enterococcus faecium □ Enterococcus faecalis
Isolate Record Form Acinetobacter spp.
Page 32 of 39
Isolate Record Form Streptococcus pneumoniae
Instructions: Please send data of the first blood and/or cerebrospinal fluid isolate of every patient with an invasive
S.
pneumoniae infection. Send data on resistant and susceptible isolates; use 1 form per isolate.
[n] Indicates variable number in reporting protocol
[9] Laboratory Code
□
□
[7] Date of sample collection (yyyy-mm-dd )
[14] Isolate Id
[10] Specimen
Blood
CSF
□ □
□
□
[11] Patient counter
[12] Gender
Man
Female
Other
Unknown
[13] Age (years)
□
□
□
□
[15] Hospital Id
[16] Patient type
Inpatient
Outpatient
Other
[19] Date of Hospitalisation (yyyy-mm-dd)
Unknown
[17] Hospital Department
□
□
□
□
□
□
Internal medicine
Paediatrics/neonatal
Paediatrics/neonatal ICU
Surgery
Haematology/Oncology
Obstetrics/Gynaecology
□
□
□
□
□
□
Intensive care unit
Emergency department
Urology department
Infectious disease ward
Other Unknown
Antibiotic susceptibility testing (S/I/R, zone and/or MIC)
[26 ] SIR
Zone diameter
MIC
Gradient strip results
[37] Reference
guidelines
(final
[28]
[29]
[36]
[31]
[32]
[34]
[35]
Fill in EUCAST,
interpretation
Result
Interpretation
Result
Interpretation
Result
Interpretation
CLSI, National,
result of all
Disk load
(mm)
(SIR)
(mg/l)
(SIR)
(mg/l)
(SIR)
Other
different
(specify
susceptibility
unit))
test performed)
[25]
Antibiotic
Oxacillin
Penicillin
Erythromycin
Clarithromycin
Azithromycin
Cefotaxime
Ceftriaxone
Norfloxacin
Levofloxacin
Moxifloxacin
[22] Serotype:
Send this form to (Name/Institute/Contact details):
Isolate Record Form Staphylococcus aureus
Instructions: Please send data of the first blood and/or cerebrospinal fluid isolate of every patient with an invasive
S.
pneumoniae infection. Send data on resistant and susceptible isolates; use 1 form per isolate.
[n] Indicates variable number in reporting protocol
[9] Laboratory Code
□
□
[7] Date of sample collection (yyyy-mm-dd )
[14] Isolate Id
[10] Specimen
Blood
CSF
□ □
□
□
[11] Patient counter
[12] Gender
Man
Female
Other
Unknown
[13] Age (years)
□
□
□
□
[15] Hospital Id
[16] Patient type
Inpatient
Outpatient
Other
[19] Date of Hospitalisation (yyyy-mm-dd)
Unknown
[17] Hospital Department
□
□
□
□
□
□
Internal medicine
Paediatrics/neonatal
Paediatrics/neonatal ICU
Surgery
Haematology/Oncology
Obstetrics/Gynaecology
□
□
□
□
□ □
Intensive care unit
Emergency department
Urology department
Infectious disease ward
Other
Unknown
MRSA confirmation tests
□
□
□
[20] PCR mec
Positive
Negative Unknown
□
□
□
[21] Pbp2a agg lutination
Positive Negative Unknown
Antibiotic susceptibility testing (S/I/R, zone and/or MIC)
[26 ] SIR
Zone diameter
MIC
Gradient strip results
[37] Reference
guidelines
(final
[28]
[29]
[36]
[31]
[32]
[34]
[35]
Fill in EUCAST,
interpretation
Result
Interpretation
Result
Interpretation
Result
Interpretation
CLSI, National,
result of all
Disk load
(mm)
(SIR)
(mg/l)
(SIR)
(mg/l)
(SIR)
Other
different
(specify
susceptibility
unit))
test performed)
[25] Antibiotic
Cefoxitin
Oxacillin
Meticillin
Flucloxacillin
Cloxacillin
Dicloxacillin
Ciprofloxacin
Ofloxacin
Levofloxacin
Norfloxacin
Rifampicin
Linezolid
Vancomycin
Daptomycin
Send this form to (Name/Institute/Contact details):
Isolate Record Form Escherichia coli
Instructions: Please send data of the first blood and/or cerebrospinal fluid isolate of every patient with an invasive
S.
pneumoniae infection. Send data on resistant and susceptible isolates; use 1 form per isolate.
[n] Indicates variable number in reporting protocol
[9] Laboratory Code
□
□
[7] Date of sample collection (yyyy-mm-dd )
[14] Isolate Id
[10] Specimen
Blood
CSF
□ □
□
□
[11] Patient counter
[12] Gender
Man
Female
Other
Unknown
[13] Age (years)
□
□
□
[15] Hospital Id
[16] Patient type
Inpatient
Outpatient
Other
[19] Date of Hospitalisation (yyyy-mm-dd)
□ Unknown
[17] Hospital Department
□
□
□
□
□
□
Internal medicine
Paediatrics/neonatal
Paediatrics/neonatal ICU
Surgery
Haematology/Oncology
Obstetrics/Gynaecology
□
□
□
□
□ □
Intensive care unit
Emergency department
Urology department
Infectious disease ward
Other
Unknown
Phenotypic detection of resistance
□
□
□
[20] ESBL
Positive
Negative
Unknown
□
□
□
[21] Carbapenemase
Positive
Negative
Unknown
Antibiotic susceptibility testing (S/I/R, zone and/or MIC)
[26 ] SIR
Zone diameter
MIC
Gradient strip results
[37] Reference
guidelines
(final interpretation
result of all different
susceptibility test
[28]
[29]
[36]
[31]
[32]
[34]
[35]
Fill in EUCAST,
[25] Antibiotic
performed)
Result
Interpretation
Result
Interpretation
Result
Interpretation
CLSI, National,
Disk load
(mm)
(SIR)
(mg/l)
(SIR)
(mg/l)
(SIR)
Other
Amoxicillin
Ampicillin
Amoxicillin-
clavulanic acid
Piperacillin -
tazobactam
Gentamicin
Tobramycin
Netilmicin
Amikacin
Ciprofloxacin
Ofloxacin
Levofloxacin
Moxifloxacin
Cefotaxime
Ceftriaxone
Ceftazidime
Cefepime
Imipenem
Meropenem
Doripenem
Ertapenem
Colistin
Tigecycline
Send this form to (Name/Institute/Contact details):
Isolate Record Form Klebsiella pneumoniae
Instructions: Please send data of the first blood and/or cerebrospinal fluid isolate of every patient with an invasive
S.
pneumoniae infection. Send data on resistant and susceptible isolates; use 1 form per isolate.
* Mandatory variable, [n] Indicates variable number in reporting protocol
[9] Laboratory Code
□
□
[7] Date of sample collection (yyyy-mm-dd )
[14] Isolate Id
[10] Specimen
Blood
CSF
□ □
□
□
[11] Patient counter
[12] Gender
Man
Female
Other
Unknown
[13] Age (years)
□
□
□
[15] Hospital Id
[16] Patient type
Inpatient
Outpatient
Other
[19] Date of Hospitalisation (yyyy-mm-dd)
□ Unknown
[17] Hospital Department
□
□
□
□
□
□
Internal medicine
Paediatrics/neonatal
Paediatrics/neonatal ICU
Surgery
Haematology/Oncology
Obstetrics/Gynaecology
□
□
□
□
□ □
Intensive care unit
Emergency department
Urology department
Infectious disease ward
Other
Unknown
Phenotypic detection of resistance
□
□
□
[20] ESBL
Positive
Negative
Unknown
□
□
□
[21] Carbapenemase
Positive
Negative
Unknown
Antibiotic susceptibility testing (S/I/R, zone and/or MIC)
[26 ] SIR
Zone diameter
MIC
Gradient strip results
[37] Reference
guidelines
(final interpretation
result of all different
susceptibility test
[28]
[29]
[36]
[31]
[32]
[34]
[35]
Fill in EUCAST,
[25] Antibiotic
performed)
Result
Interpretation
Result
Interpretation
Result
Interpretation
CLSI, National,
Disk load
(mm)
(SIR)
(mg/l)
(SIR)
(mg/l)
(SIR)
Other
Amoxicillin
clavulanic acid
Piperacillin -
tazobactam
Gentamicin
Tobramycin
Amikacin
Netilmicin
Ciprofloxacin
Ofloxacin
Levofloxacin
Moxifloxacin
Nalidixic acid
Cefotaxime
Ceftriaxone
Ceftazidime
Cefepime
Imipenem
Meropenem
Doripenem
Ertapenem
Colistin
Tigecycline
Send this form to (Name/Institute/Contact details):
Isolate Record Form Pseudomonas aeruginosa
Instructions: Please send data of the first blood and/or cerebrospinal fluid isolate of every patient with an invasive
S.
pneumoniae infection. Send data on resistant and susceptible isolates; use 1 form per isolate.
[n] Indicates variable number in reporting protocol
[9] Laboratory Code
□
□
[7] Date of sample collection (yyyy-mm-dd )
[14] Isolate Id
[10] Specimen
Blood
CSF
□ □
□
□
[11] Patient counter
[12] Gender
Man
Female
Other
Unknown
[13] Age (years)
□
□
□
[15] Hospital Id
[16] Patient type
Inpatient
Outpatient
Other
[19] Date of Hospitalisation (yyyy-mm-dd)
□ Unknown
[17] Hospital Department
□
□
□
□
□
□
Internal medicine
Paediatrics/neonatal
Paediatrics/neonatal ICU
Surgery
Haematology/Oncology
Obstetrics/Gynaecology
□
□
□
□
□ □
Intensive care unit
Emergency department
Urology department
Infectious disease ward
Other
Unknown
Phenotypic detection of resistance
□
□
□
[21] Carbapenemase
Positive
Negative
Unknown
Antibiotic susceptibility testing (S/I/R, zone and/or MIC)
[26 ] SIR
Zone diameter
MIC
Gradient strip results
[37] Reference
guidelines
(final
[28]
[29]
[36]
[31]
[32]
[34]
[35]
Fill in EUCAST,
interpretation
Result
Interpretation
Result
Interpretation
Result
Interpretation
CLSI, National,
result of all
Disk load
(mm)
(SIR)
(mg/l)
(SIR)
(mg/l)
(SIR)
Other
different
(specify
susceptibility
unit))
test performed)
[25] Antibiotic
Piperacillin
Piperacillin-
tazobactam
Gentamicin
Tobramycin
Netilmicin
Amikacin
Ciprofloxacin
Levofloxacin
Ceftazidime
Cefepime
Imipenem
Meropenem
Doripenem
Colistin
Send this form to (Name/Institute/Contact details):
Isolate Record Form □ Enterococcus faecium
□ Enterococcus faecalis
Instructions: Please send data of the first blood and/or cerebrospinal fluid isolate of every patient with an invasive
S.
pneumoniae infection. Send data on resistant and susceptible isolates; use 1 form per isolate.
* Mandatory variable, [n] Indicates variable number in reporting protocol
[9] Laboratory Code
□
□
[7] Date of sample collection (yyyy-mm-dd )
[14] Isolate Id
[10] Specimen
Blood
CSF
□ □
□
□
[11] Patient counter
[12] Gender
Man
Female
Other
Unknown
[13] Age (years)
□
□
□
[15] Hospital Id
[16] Patient type
Inpatient
Outpatient
Other
[19] Date of Hospitalisation (yyyy-mm-dd)
□ Unknown
[17] Hospital Department
□
□
□
□
□
□
Internal medicine
Paediatrics/neonatal
Paediatrics/neonatal ICU
Surgery
Haematology/Oncology
Obstetrics/Gynaecology
□
□
□
□
□ □
Intensive care unit
Emergency department
Urology department
Infectious disease ward
Other
Unknown
Antibiotic susceptibility testing (S/I/R, zone and/or MIC)
[26 ] SIR
Zone diameter
MIC
Gradient strip results
[37] Reference
guidelines
(final
[28]
[29]
[36]
[31]
[32]
[34]
[35]
Fill in EUCAST,
interpretation
Result
Interpretation
Result
Interpretation
Result
Interpretation
CLSI, National,
result of all
Disk load
(mm)
(SIR)
(mg/l)
(SIR)
(mg/l)
(SIR)
Other
different
(specify
susceptibility
unit))
test performed)
[25] Antibiotic
Amoxicillin
Ampicillin
Gentamicin -
High
Vancomycin
Teicoplanin
Linezolid
Send this form to (Name/Institute/Contact details):
Isolate Record Form Acinetobacter spp.
Instructions: Please send data of the first blood and/or cerebrospinal fluid isolate of every patient with an invasive
S.
pneumoniae infection. Send data on resistant and susceptible isolates; use 1 form per isolate.
* Mandatory variable, [n] Indicates variable number in reporting protocol
[9] Laboratory Code
□
□
[7] Date of sample collection (yyyy-mm-dd )
[14] Isolate Id
[10] Specimen
Blood
CSF
□ □
□
□
[11] Patient counter
[12] Gender
Man
Female
Other
Unknown
[13] Age (years)
□
□
□
[15] Hospital Id
[16] Patient type
Inpatient
Outpatient
Other
[19] Date of Hospitalisation (yyyy-mm-dd)
□ Unknown
[17] Hospital Department
□
□
□
□
□
□
Internal medicine
Paediatrics/neonatal
Paediatrics/neonatal ICU
Surgery
Haematology/Oncology
Obstetrics/Gynaecology
□
□
□
□
□ □
Intensive care unit
Emergency department
Urology department
Infectious disease ward
Other
Unknown
Phenotypic detection of resistance
□
□
□
[21] Carbapenemase
Positive
Negative
Unknown
Antibiotic susceptibility testing (S/I/R, zone and/or MIC)
[26 ] SIR
Zone diameter
MIC
Gradient strip results
[37] Reference
guidelines
(final
[28]
[29]
[36]
[31]
[32]
[34]
[35]
Fill in EUCAST,
interpretation
Result
Interpretation
Result
Interpretation
Result
Interpretation
CLSI, National,
result of all
Disk load
(mm)
(SIR)
(mg/l)
(SIR)
(mg/l)
(SIR)
Other
different
(specify
susceptibility
unit)
test performed)
[25] Antibiotic
Ciprofloxacin
Levofloxacin
Gentamicin
Tobramycin
Netilmicin
Amikacin
Imipenem
Meropenem
Doripenem
Colistin
Send this form to (Name/Institute/Contact details):