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8/18/2019 Data Dictionaries Guidelines
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Supporting Publications 2013:EN-409
TECHNICAL REPORT
Data dictionaries/guidelines for reporting data on zoonoses, antimicrobial
resistance and food-borne outbreaks using the EFSA Data models for the
Data Collection Framework (DCF) in the Reporting Year 2012
1
European Food Safety Authority
2,3
European Food Safety Authority (EFSA), Parma, Italy
SUMMARY
These data dictionaries provide guidance for reporting on quantitative, qualitative, and isolate-based quantitativeantimicrobial resistance data in food, animals, and feed, on prevalence data on zoonoses, on Salmonella serovarsand phagetypes, on food-borne outbreak data, on animal population data, on disease status data, text forms, aswell as sample based data in food under the framework of Directive 2003/99/EC. The objective is to explain indetail the individual fields that are included in the European Food Safety Authority Data models to be used forthe transmission of these data through the Data Collection Framework tool using XML/Excel/CSV datatransfers. This manual is specifically aimed to guide the reporting of the information deriving from the year2012.
© European Food Safety Authority, 2013
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TABLE OF CONTENTS
Summary ................................................................................................................................................. 1
Table of contents ..................................................................................................................................... 2
Introduction ............................................................................................................................................ 3
References ............................................................................................................................................... 4
Appendices
I. Data dictionary/guidelines for reporting isolate-based antimicrobial resistance quantitative data
using the EFSA Data model for the Data Collection Framework in the Reporting Year 2012
II. Data dictionary/guidelines for reporting qualitative data on antimicrobial resistance in zoonotic
and indicator bacteria from food and animals using the EFSA Data model for the DataCollection Framework in the Reporting Year 2012
III. Data dictionary/guidelines for reporting quantitative antimicrobial resistance data from zoonotic
and indicator bacteria from animals, food and feed using the EFSA Data model for the Data
Collection Framework in the Reporting Year 2012
IV. Data dictionary/guidelines for reporting aggregated prevalence data on zoonoses and food-borne
pathogens in food, animals and feed using the EFSA Data model for the Data Collection
Framework in the Reporting Year 2012
V. Data dictionary/guidelines for reporting aggregated Salmonella serovar and phagetype data usingthe EFSA Data model for the Data Collection Framework in the Reporting Year 2012
VI. Data dictionary/guidelines for reporting food-borne outbreak data using the EFSA Data model
for the Data Collection Framework in the Reporting Year 2012
VII. Data dictionary/guidelines for reporting aggregated animal population data using the EFSA Data
model for the Data Collection Framework in the Reporting Year 2012
VIII. Data dictionary/guidelines for reporting disease status data using the EFSA Data model for the
Data Collection Framework in the Reporting Year 2012
IX. Data dictionary/guidelines for reporting text forms using the EFSA Data model for the Data
Collection Frame ork in the Reporting Year 2012
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INTRODUCTION
The Directive 2003/99/EC
4
lays down the European Union (EU) system for monitoring andreporting of information on zoonoses, which obligates the EU Member States to collect data on
zoonoses, zoonotic agents, antimicrobial resistance and food-borne outbreaks. The European Food
Safety Authority is assigned the tasks of examining the data collected and preparing the European
Union Summary Reports in collaboration with the European Centre for Disease Prevention and
Control (ECDC).
For the reporting of the annual data, EFSA has created a web-based reporting application as well
as the possibility of submitting data in XML/ Excel/ CSV formats. In particular, for datasubmission through XML/ Excel/ CSV formats, new data models have been created and provided tothe reporting countries before the start of the 2013 reporting period.
To support the Member States in data submission, the existing reporting manuals for zoonoses,
antimicrobial resistance and food-borne outbreak data have been updated to take into account the
latest recommendations on reporting (EFSA, 2013a and 2013b).
To further support the reporting countries in data submission using XML/ Excel/ CSV datatransfer, specific guidelines are given in this report, including data dictionaries and the data
models.
The data dictionaries cover the reporting of qualitative, quantitative and isolate-based quantitative
antimicrobial resistance data in food, animals, and feed as well as of prevalence data on zoonoses and
food-borne contaminants, Salmonella serovar sand phagetypes, food-borne outbreak data, animal
population data, disease status data and sample-based food data and text forms. These data dictionaries
are specifically aimed to guide the reporting of the information deriving from the year 2012 under the
frame ork of Directi e 2003/99/EC
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R EFERENCES
EFSA (European Food Safety Authority), 2012a Technical specifications for the analysis andreporting of data on antimicrobial resistance (AMR) in the European Union Summary Report. The
EFSA Journal 10(2) 2587.
EFSA (European Food Safety Authority), 2012b Technical specifications on the harmonised
monitoring and reporting of antimicrobial resistance in Salmonella, Campylobacter and indicator
Escherichia coli and Enterococcus spp. bacteria transmitted through food. The EFSA Journal
10(6), 2742.
EFSA (European Food Safety Authority), 2012c Technical specifications for the harmonisedmonitoring and reporting of antimicrobial resistance in MRSA in food-producing animals and food.
The EFSA Journal 10 (10), 2897.
EFSA (European Food Safety Authority), 2013a. Manual for Reporting on Zoonoses, Zoonotic Agents
and Antimicrobial Resistance in the framework of Directive 2003/99/EC and of some other
pathogenic microbiological agents for information derived from the year 2012. Supporting
publication 2013: EN-408. [4 pp.] Available online: www.efsa.europa.eu/publications
EFSA (European Food Safety Authority), 2013b. Manual for Reporting on food-borne outbreaks in
the framework of Directive 2003/99/EC from the year 2012. Supporting publication 2013:EN-410
[4 pp]. .Available online: www.efsa.europa.eu/publications
http://www.efsa.europa.eu/en/publications/supporting.htmhttp://www.efsa.europa.eu/en/publications/supporting.htmhttp://www.efsa.europa.eu/en/publications/supporting.htmhttp://www.efsa.europa.eu/en/publications/supporting.htmhttp://www.efsa.europa.eu/en/publications/supporting.htmhttp://www.efsa.europa.eu/en/publications/supporting.htmhttp://www.efsa.europa.eu/en/publications/supporting.htmhttp://www.efsa.europa.eu/en/publications/supporting.htm
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APPENDIX I
Data dictionary/guidelines for reporting quantitative antimicrobial
resistance isolate-based data using the EFSA Data model for the Data
Collection Framework in the Reporting Year 2012
TABLE OF CONTENTS
Table of contents ...................................................................................................................................... 5
Data dictionary/Guidelines for Reporting ................................................................................................ 7
Introduction .............................................................................................................................................. 7
1. General information and identification of the isolate ................................................................. 8
1.1. Result Code (resultCode AMR.01) .......................................................................................... 8
1.2.
Reporting Year (repYear AMR.02) ......................................................................................... 8
1.3.
Reporting Country (repCountry AMR.03) .............................................................................. 8
1.4.
Language (lang AMR.04) ........................................................................................................ 8
2. Information about type and source of samples and isolates ...................................................... 8
2.1.
Zoonotic agent ( zoonosis AMR.05) ......................................................................................... 8
2.2. Matrix (matrix AMR.06 ) ......................................................................................................... 9
3. Information about the sampling performed .............................................................................. 10
3.1.
Sampling unit type ( sampUnitType AMR.45) ....................................................................... 10
3.2. Total number of sampling units tested (totSampUnitsTested AMR.44) ................................ 10
3.3. Sampling Stage ( sampStage AMR.08) .................................................................................. 10
3.4. Sample origin ( sampOrig AMR.46 ) ...................................................................................... 11
3.5. Sample Type ( sampType AMR.09) ....................................................................................... 11
3 6 T t l b f l t t d (t tU itT t d AMR 07) 11
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9. Information about further isolate characterisation .................................................................. 15
9.1. ESBL phenotype (esbl AMR.38) ........................................................................................... 15
9.2.
AMPC phenotype (ampC AMR.39) ...................................................................................... 15
9.3.
Carbapenemase phenotype (carbapenem AMR.40) .............................................................. 15
9.4. Ceftazidime synergy test ( synTestCAZ AMR.41) .................................................................. 15
9.5. Cefotaxime synergy test ( synTest CTX AMR.42) .................................................................. 15
9.6. Cefepime synergy test ( synTest FEP AMR.43) ..................................................................... 15
9.7. Performed CC MRSA characterisation ( perCC AMR.47 ) .................................................... 15
9.8. Performed MLST MRSA characterisation ( perMLST AMR.48) ........................................... 16
10.
Additional information ........................................................................................................... 16
10.1.
Comment (comment AMR.37 )............................................................................................... 16
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DATA DICTIONARY/GUIDELINES FOR R EPORTING
Introduction
This data dictionary provides guidance for reporting on antimicrobial resistance (AMR) in animals and
food at isolate level pursuant to Article 9 of Directive 2003/99/EC1. The objective is to explain in
detail the individual fields/variables that are included in the EFSA Data model to be used for the
XML/Excel/CSV transmission of isolate-based data on antimicrobial resistance through the EFSA
Data Collection Framework (DCF) tool. This data dictionary is specifically aimed to guide the
reporting of the information deriving from the year 2012.
Compared with the data model used to report isolate-based AMR data from the year 2011, some
changes have been made to enable the reporting via the DCF tool of -lactam resistant phenotypes in
Salmonella and indicator E. coli, as well as further characterisation data for methicillin-resistant
S. aureus (MRSA). Isolate-based data to be submitted to the DCF as part of national reports are to be
used to generate XML/Excel files. More in depth information on the data to be reported can be found
in the ‘Manual for Reporting on Zoonoses, Zoonotic Agents and Antimicrobial Resistance in the
framework of Directive 2003/99/EC and of some other pathogenic microbiological agents for
information derived from the year 2012’ (EFSA, 2013a). The EFSA data model for isolate basedantimicrobial resistance data is summarised in Table 4 and the business rules are presented in Table 5.
Isolate-based data and information to be reported is outlined in the following sections for AMR results
deriving from the use of either dilution or diffusion methods. Member States (MSs) are, however,
strongly encouraged to report quantitative Minimum Inhibitory Concentration (MIC) data from
dilution methods.
S d t t b t d d t b i hil th d t h ld b t d l t
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1.
GENERAL INFORMATION AND IDENTIFICATION OF THE ISOLATE
1.1. Result Code (resul tCode AMR.01 )
This variable is mandatory. It should be unique for the sender and allows the identification of the
record. It will be used by EFSA should an update be needed in a future data transmission or additional
clarifications required.
1.2. Reporting Year (repYear AMR.02 )
This variable is mandatory. It is a numerical field consisting of four digits. It is the reporting year,
which is the year to which reported data refer.
1.3. Reporting Country (repCountry AMR.03 )
This variable is mandatory. It contains codes linked to a pick list (ZOO_CAT_COUNTRY, domain:
D_ALL_repCountry). The list includes the 27 European Union (EU) MSs as well as Norway, Iceland
and Switzerland.
1.4. Language (lang AMR.04 )
This variable is mandatory. It contains codes linked to a pick list (ZOO_CAT_LANG, domain:D_ALL_lang). It is the EEA language used to fill in the free text fields notably those foreseen under
variables AMR.14 ‘sampling details’ and AMR.37 ‘comment’. Only ‘en’ for English is accepted.
2. INFORMATION ABOUT TYPE AND SOURCE OF SAMPLES AND ISOLATES
2.1. Zoonotic agent (zoonosis AMR.05 )
This variable is mandatory. It contains codes linked to a pick list (ZOO_CAT_PARAM_ZOO,
d i D AMR i ) It bl ti f th b t i l t t t d f ti i bi l
http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_ZOO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_ZOO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1
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Table 1: Salmonella serovars of public health importance and relative codes for DCF
Animal species/food Salmonella serovar (Level 2 term) Code for DCF
All animal species and derived meatS . Typhimurium RF-00002265-MCG
S . Typhimurium, monophasic RF-00003051-MCG
Gallus gallus (fowl): Breeders of egg production line, breeders of meat production
line, laying hens, broilers and broiler meat
S . Enteritidis RF-00002135-MCG
S. Agona RF-00001667-MCG
S . Virchow RF-00001152-MCG
S . Hadar RF-00001843-MCGS. Kentucky RF-00000640-MCG
S . Infantis RF-00001894-MCG
Broilers and broiler meat S . Javaa RF-00001325-MCG
Turkeys and turkey meat
S . Enteritidis RF-00002135-MCG
S. Agona RF-00001667-MCG
S. Kentucky RF-00000640-MCG
S. Newport RF-00000960-MCG
S . Saintpaul RF-00001234-MCG
Pigs: breeding pigs, suckling piglets, weanerto growers, fattening pigs, and swine meat
S . Derby RF-00001592-MCG
S. Agona RF-00001667-MCG
Cattle: dairy cattle, beef cattle and bovinemeat
S . Dublin RF-00001517-MCG
S . Infantis RF-00001894-MCGa
Pre io sl kno n as S Parat phi B ar Ja a
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Table 2: Recommended categories to be used for the reporting of the origin of the isolates
Bacteria Animal species/Food categories
Salmonella
Laying hens, broilers, fattening turkeys, fattening pigs, calves (under 1
year)a, young bovines (1-2 years) and adult cattle (>2 years)
Broiler meat, turkey meat, pig meat and bovine meat
Campylobacter
Broilers, fattening turkeys, fattening pigs, calves (under 1 year) a, young bovines (1-2 years) and adult cattle (>2 years)
Broiler meat, turkey meat
Indicator E. coli
Laying hens, broilers, fattening turkeys, fattening pigs, calves (under 1
year)a, young bovines (1-2 years) and adult cattle (>2 years)
Broiler meat, turkey meat, pig meat and bovine meat
Indicator enterococci
Laying hens, broilers, fattening pigs, fattening turkeys, calves (under 1year)a, young bovines (1-2 years) and adult cattle (>2 years)
Broiler meat, turkey meat, pig meat and bovine meat
(a): Those MSs monitoring AMR in fattening calve populations that are older than 12 months of age, and typically raised for
the production of rosé veal, may report data under the category ‘veal calves (at or above 1 year)’ [code A0CHK].
If relevant information is available, AMR data may as well be reported separately for isolates from
breeding flocks of Gallus gallus for egg production line and for meat production line. AMR data in
young and adult cattle may also be distinguished between dairy and meat production sectors.
For the food and animal origins, the pick list categories at level 1 provide for a high-level
categorisation of animal species/foodstuffs, whereas levels 2, 3 and 4 allow for the reporting of more
detailed information. It is recommended that relevant animal populations/food categories
( di t l l 2 3 d 4 t ) l t d f th il bl i f ti k it
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3.4.
Sample origin (sampOri g AMR.46 )
This variable is optional but recommended to be reported to EFSA as well. It contains codes linked
to a pick list (ZOO_CAT_COUNTRY). Sample origin is used to indicate the country of origin for the
animal, food or feed sampled (ISO 3166-1-alpha-2 country code). If the exact country of origin of the
sampled item is not known, the following terms may be reported: ‘European Union’ (code EU), ‘Non
EU’ (code XE), ‘Non EEA’ (code XC) or ‘Unknown’ (code XX).
3.5. Sample Type (sampType AMR.09 )
This variable is optional but recommended to be reported to EFSA as well. It contains codes linked
to a pick list (ZOO_CAT_SMPTYP). It describes the biological source of the sample and allows forcharacterisation of the sample category (i.e. animal, food or environmental sample) and the sample
type (e.g. faeces, caecal content, boot swabs, neck skin): e.g. ‘animal sample – nasal swab’ (code
S015A); ‘food sample – carcass swab’ (code S021A).
3.6.
Total number of samples tested (totUn itTested AMR.07 )
This variable is optional but recommended to be reported to EFSA as well. Its type is integer and
the data values are numeric. It is the total number of samples tested for the presence of the bacteria in
question from a given matrix (i.e. animal population or food category)/sample type, whether positiveor negative, in order to collect the bacterial isolates tested for antimicrobial susceptibility, within a
specific reporting MS and during the whole 2012 exercise of the AMR monitoring programme. These
data may be used to assess the prevalence of resistant bacteria.
3.7. Sampling Context (sampContext AMR.10 )
This variable is optional but recommended to be reported to EFSA as well. It contains codes linked
to a pick list (ZOO_CAT_SRCTYP, domain: D_ALL_sampContext). It identifies the type of
i th f k f hi h l d i l t h b ll t d It i ibl t
http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SRCTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SRCTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1
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3.11.
Sampling details (sampDetails AMR.14 )
This variable is optional. This is a free text of maximum 2,000 alphanumerical characters. It can be
used to give more information on the sampling design, stage or context, when needed. It should becompleted in English (see element ‘lang AMR.04’).
3.12. Area of Sampling (sampArea AMR.15 )
This variable is optional but recommended to be reported to EFSA as well. It contains codes linked
to a pick list (ZOO_CAT_NUTS). It indicates the area, or region, or province in the country (in
accordance to the NUTS standard) in which the animal/food sample has been collected. The reporting
of the area of sampling is encouraged so that, for example, geographical spreading of some multi-resistant clones may be studied.
4. INFORMATION ABOUT THE LABORATORY
4.1.
Laboratory Identification Code (labCode AMR.16 )
This variable is optional but recommended to be reported at national level. The codes in this field
identify the laboratory performing AMR testing for the combination ‘isolate/antimicrobial’ in
question. This code is reported at the isolate level as MSs may have more than one laboratory performing the susceptibility tests. The code is to be unique in a given Member State.
4.2. Laboratory Isolate Code (labI solCode AMR.17 )
This variable is mandatory. The codes in this field are to uniquely identify the isolate for which AMR
testing was performed.
4.3.
Total number of isolates available in the laboratory (labTotIsol AMR.18)
Thi i bl i d t Thi i i l fi ld ( t d 1 if k ) It th t t l
http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_NUTS!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_NUTS!A1
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5.3.
Susceptibility Test Year/Month/Day (analysisY/analysisM /analysisD AMR.25/AMR.26/
AMR.27 )
These variables are optional. These are numerical fields allowing a maximum of four digits for the
variable year and maximum two digits for the variables month and day. It corresponds to the date
when the AMR testing was performed.
6. INFORMATION ABOUT THE METHOD AND THE ANTIMICROBIAL
6.1. Method (anMethCode AMR.28 )
This variable is mandatory. It contains codes linked to a pick list (ZOO_CAT_ANLYMD, domain:D_AMR_anMethCode). It indicates the test method used for AMR testing. Different types of diffusion
or dilution methods are available for reporting, e.g. ‘dilution’ (code F128A), ‘dilution – micro dilution
method’ (code F131A).
6.2. Antimicrobial substance (substance AMR.29 )
This variable is mandatory. It contains codes linked to a pick list (ZOO_CAT_PARAM_SUB). It
indicates the antimicrobial substance against which the isolates were tested. Antimicrobial substances
are listed within the pick list according to antimicrobial families. For Salmonella, Campylobacter ,
indicator E. coli and indicator enterococci, it is recommended that results are reported at least for theset of antimicrobial substances listed in Table 3. It is noteworthy that the lists have been extended to include all substances recommended for susceptibility testing in the ‘Technical specifications on the
harmonised monitoring and reporting of antimicrobial resistance in Salmonella, Campylobacter and
indicator Escherichia coli and Enterococcus spp. bacteria transmitted through food’ (EFSA, 2012b)
and in ‘Technical specifications on the harmonised monitoring and reporting of antimicrobial
resistance in methicillin-resistant Staphylococcus aureus in food-producing animals and food’ (EFSA,
2012c).
http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_ANLYMD!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_SUB!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_SUB!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_ANLYMD!A1
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more in detail at the level of the actual substances tested, e.g. sulfamethoxazole (code RF-00000612-VET) ortetracycline (code RF-00000670-VET). If known, it is recommended to report the substance for the sake of consistency.
6.3.
Cut-off value (cutoffValue AMR.30 )
This variable is mandatory. This field allows for numeric data values with decimal numbers. The
variable indicates the cut-off value for the dilution or disk diffusion methods that should be used,
according to the reporting Member States, for defining resistant isolates in the National Report. In any
case, the EFSA will use harmonised epidemiological cut-off (ECOFF) values for the analysis of the
data to be included in the EU Summary Report. Nevertheless, MSs might prefer to use an ad hoc cut-
off value for the interpretation of their national data.
It should be avoided to report in duplicate AMR data using different ECOFFs for the same isolates(e.g. harmonised ECOFF and ad hoc ECOFF).
7. INFORMATION ABOUT DILUTION METHOD
7.1. Lowest (limit) (lowest AM R.31 )
This variable is mandatory for dilution method data. However, in the data model, it is marked as
optional because in case of diffusion data, this field must be left empty. It contains codes linked to a
pick list (ZOO_CAT_FIXMEAS, domain: D_AMR_NUMBER). It is the lowest concentration of theconcentration range used to test AMR in the laboratory. It is foreseen that the lowest concentration
should lie between ‘0.002’ and ‘4096’ and Lowest < Highest . Only numerical values should be used
(no ‘
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8.2.
Disc diameter (mm) (diskDi am AMR.35 )
This variable is mandatory for diffusion method data. However, in the data model, it is marked as
optional because in case of dilution data, this field must be left empty. The variable allows enteringnumeric data values with floating-point decimal numbers. It corresponds to the diameter of the disc
used in the testing, which is reported by default in millimeter.
8.3.
IZD value (mm) (I ZD AMR.36 )
This variable is mandatory for diffusion data. However, in the data model, it is marked as optional
because in case of dilution data, this field must be left empty. It contains codes linked to a pick list
(ZOO_CAT_FIXMEAS, domain: D_AMR_IZD). It represents the inhibition zone diameter values
deriving from the AMR testing of the isolate, which is reported by default in millimeter.
9. INFORMATION ABOUT FURTHER ISOLATE CHARACTERISATION
9.1. ESBL phenotype (esbl AMR.38 )
This variable is optional and contains codes linked to a pick list (ZOO_CAT_ESBL). It is a new
feature of the 2012 data collection exercise. It allows MSs to report ESBL phenotypes in isolates of
Salmonella and E. coli through enzyme formulas (e.g. TEM-52, SHV-2, CTX-M-1), when these are
known.
9.2. AMPC phenotype (ampC AMR.39 )
This variable is optional and contains codes linked to a pick list (ZOO_CAT_AMPC). It is a new
feature of the 2012 data collection exercise. It allows MSs to report AmpC phenotypes in isolates of
Salmonella and E. coli through enzyme formulas (e.g. CMY-2, AAC-1), when these are known.
9.3. Carbapenemase phenotype (carbapenem AMR.40 )
Thi i bl i ti l d t i d li k d t i k li t (ZOO CAT CARBAPENEM) It
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9.8.
Performed MLST MRSA characterisation (perMLST AMR.48 )
This is a new feature of the 2012 data collection exercise: this variable is optional and contains codes
linked to a pick list (ZOO_CAT_YESNO). It allows MSs to report whether the determination of theMRSA multi-locus sequence type results from an actually performed genetic test (YES) or has been
inferred from other tests/online databases (NO).
10. ADDITIONAL INFORMATION
10.1. Comment (comment AMR.37 )
This free text variable is optional. This is a free text of maximum 2,000 alphanumerical characters.
This is an additional comment for the row (= a set of information). It should be completed in English(see element ‘lang AMR.04’ ).
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Table 4: The EFSA data model for isolate based antimicrobial resistance data reporting
Element
CodeElement Name
Short Element name for
XML/Excel/CSV transfer
XML Schema
TypeMandatory Pick lists Current
AMR.01 Result Code resultCode xs:String(60) Mandatory
AMR.02 Reporting Year repYear xs:integer(4) Mandatory
AMR.03 Reporting Country repCountry xs:string(2) Mandatory ZOO_CAT_COUNTRY
AMR.04 Language lang xs:string(2) Mandatory ZOO_CAT_LANG
AMR.05 Zoonotic Agent zoonosis xs:string(15) Mandatory ZOO_CAT_PARAM_ZOO
AMR.06 Matrix matrix xs:string(4000) Mandatory ZOO_CAT_MATRIX
AMR.07 Total number of samples tested totUnitTested xs:integer Optional
AMR.44 Total number of sampling units tested totSampUnitsTested xs:integer Optional
AMR.45 Sampling unit type sampUnitType xs:string(5) Optional ZOO_CAT_UNIT
AMR.08 Sampling Stage sampStage xs:string(5) Optional ZOO_CAT_SMPNT
AMR.46 Sample origin sampOrig xs:string(2) Optional ZOO_CAT_COUNTRY
AMR.09 Sample Type sampType xs:string(5) Optional ZOO_CAT_SMPTYPAMR.10 Sampling Context sampContext xs:string(5) Optional ZOO_CAT_SRCTYP
AMR.11 Sampler sampler xs:string(5) Optional ZOO_CAT_SMPLR
AMR.12 Program Code progCode xs:string(20) Optional
AMR.13 Sampling Strategy progSampStrategy xs:string(5) Optional ZOO_CAT_SAMPSTR
AMR.14 Sampling Details sampDetails xs:string(2000) Optional
AMR.15 Area of Sampling sampArea xs:string(5) Optional ZOO_CAT_NUTS
AMR.16 Laboratory Identification Code labCode xs:string(100) Optional
AMR.17 Laboratory Isolate Code labIsolCode xs:string(20) Mandatory
AMR.18 Total number of isolates available in the laboratory labTotIsol xs:integer Mandatory
AMR.19 Sampling Year sampY xs:integer(4) MandatoryAMR.20 Sampling Month sampM xs:integer(2) Mandatory
AMR.21 Sampling Day sampD xs:integer(2) Optional
AMR.22 Isolation Year IsolY xs:integer(4) Optional
AMR.23 Isolation Month IsolM xs:integer(2) Optional
http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_ZOO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_MATRIX!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPNT!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SRCTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPLR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPLR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SAMPSTR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_NUTS!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_NUTS!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SAMPSTR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPLR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SRCTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPNT!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_MATRIX!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_ZOO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1
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Table 4 (continued): The EFSA data model for isolate based antimicrobial resistance data reporting
Element
CodeElement Name
Short Element name for
XML/Excel/CSV transfer
XML Schema
TypeMandatory Pick lists Current
AMR.24 Isolation Day IsolD xs:integer(2) Optional
AMR.25 Susceptibility Test Year analisysY xs:integer(4) OptionalAMR.26 Susceptibility Test Month analisysM xs:integer(2) Optional
AMR.27 Susceptibility Test Day analisysD xs:integer(2) Optional
AMR.28 Method anMethCode xs:string(5) Mandatory ZOO_CAT_ANLYMD
AMR.29 Antimicrobial Substance substance xs:string(15) Mandatory ZOO_CAT_PARAM_SUB
AMR.30 Cut-off value cutoffValue xs:double Mandatory
AMR.31 Lowest (limit) lowest xs:string(5) Optional ZOO_CAT_FIXMEAS
AMR.32 Highest (limit) highest xs:string(5) Optional ZOO_CAT_FIXMEAS
AMR.33 MIC values (mg/L) MIC xs:string(5) Optional ZOO_CAT_FIXMEAS
AMR.34 Disk concentration (microg) diskConc xs:double Optional
AMR.35 Disk diameter (mm) diskDiam xs:double Optional
AMR.36 IZD values (mm) IZD xs:string(5) Optional ZOO_CAT_FIXMEAS
AMR.38 ESBL phenotype esbl xs:string(5) Optional ZOO_CAT_ESBL
AMR.39 AMPC phenotype ampC xs:string(5) Optional ZOO_CAT_AMPC
AMR.40 Carbapenemase phenotype carbapenem xs:string(5) Optional ZOO_CAT_CARBAPENEM
AMR.41 Ceftazidime synergy test synTestCAZ xs:string(3) Optional ZOO_CAT_POSNEG
AMR.42 Cefotaxime synergy test synTestCTX xs:string(3) Optional ZOO_CAT_POSNEG
AMR.43 Cefepime synergy test synTestFEP xs:string(3) Optional ZOO_CAT_POSNEG
AMR.47 Performed CC MRSA characterisation perCC xs:string(1) Optional ZOO_CAT_YESNO
AMR.48 Performed MLST MRSA characterisation perMLST xs:string(1) Optional ZOO_CAT_YESNOAMR.37 Comment resComm xs:string(2000) Optional
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Table 5: EFSA business rules for isolate based antimicrobial resistance data reporting
Error code Error type Element
Rule
AMR01 E AMR01 Reporting year has to be >=1995 and 0AMR04 E AMR19 Sampling year has to be >=1995 and =1995 and =1995 and =0 and 0
AMR13E
AMR34If analytical method in (‘diffusion’,’diffusion - disk ’,’diffusion - Etest’,’diffusion - paper disk ’) then Disk concentration(microg) value must be Not NULL
AMR14E
AMR35If analytical method in (‘diffusion’,’diffusion - disk ’,’diffusion - Etest’,’diffusion - paper disk ’) then Disk diameter value must be Not NULL
AMR15E
AMR36If analytical method in (‘diffusion’,’diffusion - disk ’,’diffusion - Etest’,’diffusion - paper disk ’) then IZD (mm) value must be Not NULL
AMR08 E AMR02 Value of language has to be =‘en’
AMR17 E AMR18 Value of total number of isolates in the lab has to be >=-1
AMR18 E AMR33 If MIC contains ‘‘ then MIC must be = HIGHEST
AMR20 E AMR33 MIC must not contains ‘>=‘ or ‘LOWEST AND MIC must be =‘,’=‘,’= lowest AND < HIGHEST
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Error code Error type Element
Rule
AMR25 E AMR36 IZD must be numeric
AMR28 W AMR08 WARNING. For data interpretation purposes, sample stage ‘sampStage’ must be specified
AMR29 W AMR10 WARNING. For data interpretation purposes, the sampling context ‘sampContext’ must be specified
AMR30 W AMR11 WARNING. For data interpretation purposes, the sampler must be specified
AMR31 W AMR13 WARNING. For data interpretation purposes, the sampling strategy ‘ progSampStrategy’ must be specified
AMR32W
AMR06
WARNING. For data interpretation purposes, its is advised not to use general categories : matrix NOT IN ( 'Gallus gallus
(fowl)','Gallus gallus (fowl) - unspecified','Compound feedingstuffs, not specified')
AMR33 W AMR46 WARNING. For data interpretation purposes, sample origin ‘sampOrig’ must be specified
AMR34E
AMR05
The zoonosis should always be reported at least to the second level of the pickist (using the domain
D_ZOO_CAT_PARAM_ZOO_AMR)
AMR35 E AMR47 If MRSA clonal complex is reported then perCC should be filled in to indicate if result was inferred or tested
AMR36 E AMR48 If MRSA MLST is reported then perCC and perMLST should be filled in to indicate if result was inferred or tested
AMR37 E AMR30 Reported cut-off for a specific substance and zoonotic agent must be unique
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APPENDIX II
Data dictionary/guidelines for reporting qualitative data on antimicrobial
resistance in zoonotic and indicator bacteria from food and animals using
the EFSA Data model for the Data Collection Framework in the Reporting
Year 2012
TABLE OF CONTENTS
Table of contents .................................................................................................................................... 21
Data dictionary/Guidelines for Reporting .............................................................................................. 22
Introduction ............................................................................................................................................ 22
1. General information and identification of the isolate ............................................................... 22
1.1. Reporting Year (repYear AQL.01) ........................................................................................ 22
1.2. Reporting Country (repCountry AQL.02) ............................................................................. 22
1.3.
Language (lang AQL.03) ...................................................................................................... 22
2.
Information about type and source of samples and isolates .................................................... 22
2.1. Zoonotic agent ( zoonosis AQL.04)........................................................................................ 22
2.2. Matrix (matrix AQL.05) ........................................................................................................ 23
3. Information about the sampling performed .............................................................................. 24
3.1. Sampling Stage ( sampStage AQL.06 ) ................................................................................... 24
3.2.
Sample Type ( sampType AQL.07) ........................................................................................ 24
3.3.
Sampling Context ( sampContext AQL.08) ............................................................................ 24
3.4. Sampler ( sampler AQL.09) ................................................................................................... 25
3 5 S li ( S S AQL 10) 25
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DATA DICTIONARY/GUIDELINES FOR R EPORTING
Introduction
This data dictionary provides guidance for reporting on qualitative antimicrobial resistance (AMR)
data from zoonotic and indicator bacteria in animals, food and feed under the framework of Directive
2003/99/EC1. The objective is to explain in detail the individual fields that are included in the EFSA
Data model to be used for the XML transmission of qualitative data on antimicrobial resistance
through the Data Collection Framework (DCF) tool. This data dictionary is specifically aimed to guide
the reporting of the information deriving from the year 2012. More in depth information on the data to
be reported can be found from the ‘Manual for Reporting on Zoonoses, Zoonotic Agents and
Antimicrobial Resistance in the framework of Directive 2003/99/EC and of some other pathogenicmicrobiological agents for information derived from the year 2012’ (EFSA, 2013a). The EFSA data
model for qualitative antimicrobial resistance tables is summarised in Table 4 and the complete set of business rules applied for data validation are presented in Table 5.
1.
GENERAL INFORMATION AND IDENTIFICATION OF THE ISOLATE
1.1. Reporting Year (repYear AQL .01 )
This variable is mandatory. It is a numerical field consisting of four digits. It is the reporting year,
which is the year to which reported data refer.
1.2. Reporting Country (repCountry AQL.02 )
This variable is mandatory. It contains codes linked to a pick list (ZOO_CAT_COUNTRY, domain:
D_ALL_repCountry). The list includes the 27 European Union (EU) Member States (MSs) as well as
Norway, Switzerland and Iceland.
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Table 1: Salmonella serovars of public health importance and relative codes for DCF
Animal species/food Salmonella serovar (Level 2 term) Code for DCF
All animal species and derived meatS . Typhimurium RF-00002265-MCG
S . Typhimurium, monophasic RF-00003051-MCG
Gallus gallus (fowl): Breeders of egg production line, breeders of meat production
line, laying hens, broilers and broiler meat
S . Enteritidis RF-00002135-MCG
S. Agona RF-00001667-MCG
S . Virchow RF-00001152-MCG
S . Hadar RF-00001843-MCG
S. Kentucky RF-00000640-MCG
S . Infantis RF-00001894-MCG
Broilers and broiler meat S . Java a RF-00001325-MCG
Turkeys and turkey meat
S . Enteritidis RF-00002135-MCG
S. Agona RF-00001667-MCG
S. Kentucky RF-00000640-MCG
S. Newport RF-00000960-MCG
S . Saintpaul RF-00001234-MCG
Pigs: breeding pigs, suckling piglets, weanerto growers, fattening pigs, and swine meat
S . Derby RF-00001592-MCG
S. Agona RF-00001667-MCG
Cattle: dairy cattle, beef cattle and bovinemeat
S . Dublin RF-00001517-MCG
S . Infantis RF-00001894-MCG
a Previously known as S . Paratyphi B var. Java
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Table 2: Recommended food and animal categories for AMR reporting
Bacteria Animal species/Food categories
Salmonella
Laying hens, broilers, fattening turkeys, fattening pigs, calves
(under 1 year )a, young bovines (1-2 years) and adult cattle (>2
years)
Broiler meat, turkey meat, pig meat and bovine meat
Campylobacter
Broilers, fattening turkeys, fattening pigs, calves (under 1 year )a,
young bovines (1-2 years) and adult cattle (>2 years)Broiler meat, turkey meat
Indicator E. coli
Laying hens, broilers, fattening turkeys, fattening pigs, calves
(under 1 year )a, young bovines (1-2 years) and adult cattle (>2
years)
Broiler meat, turkey meat, pig meat and bovine meat
Indicator enterococci
Laying hens, broilers, fattening pigs, fattening turkeys, calves
(under 1 year )a
, young bovines (1-2 years) and adult cattle (>2years)
Broiler meat, turkey meat, pig meat and bovine meat
(a): Those MSs monitoring AMR in fattening calve populations that are older than 12 months of age, and typically raised forthe production of rosé veal, may report data under the category ‘veal calves (at or above 1 year)’ (code A0CHK).
It is recommended that relevant animal sub-populations (corresponding to the level 2, level 3 and level
4 terms) are selected, as far as the available information makes it possible and as enabled by the
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3.4.
Sampler (sampler AQL.09 )
This variable is optional. It contains codes linked to a pick list (ZOO_CAT_SMPLR). It indicates the
type of the body who performed the sampling, e.g. ‘Industry sampling’ (code CX01A), ‘Officialsampling’ (code CX02A).
3.5.
Sampling strategy (progSampStrategy AQL .10 )
This variable is optional. It contains codes linked to a pick list (ZOO_CAT_SAMPSTR). It is the
sampling strategy performed in the programme or project, e.g. ‘Objective sampling’ (code ST10A),
‘Census’ (code ST50A). Reporting of the sampling strategy is encouraged to enable evaluation of the
representativeness of the AMR monitoring programmes.
3.6. Sampling details (sampDetails AQL .11 )
This variable is optional. This is a free text of maximum 2,000 alphanumerical characters. It can be
used to give more information on the sampling design, stage or context, when needed. It should becompleted in English (see element ‘lang AQ L.03’ ).
3.7.
Monitoring Program (monitProgr AQL.13 )
This variable is optional. It contains codes linked to a pick list, consisting of terms ‘yes’, ‘no’ and
‘unknown’ (ZOO_CAT_YESNO). It indicates whether the tested bacterial isolates originate from amonitoring programme or not.
3.8. Tested (tested AQL .15 )
This variable is mandatory. This is a numerical field (reported as -1 if unknown). The number of
tested (N) indicates the number of isolates tested for AMR.
3.9. Resistant (resistant AQL .16 )
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Table 3: Recommended antimicrobials for susceptibility testing and relative codes for DCF
Salmonella C. jejun i /C. coli
Indicator E. coli
Indicator enterococci
Ampicillin
RF-00000688-VET
Erythromycin
RF-00000589-VET
Ampicillin
RF-00000688-VET
Ampicillin
RF-00000688-VET
CefotaximeRF-00000717-VET
CiprofloxacinRF-00000695-VET
CefotaximeRF-00000717-VET
ChloramphenicolRF-00000525-VET
ChloramphenicolRF-00000525-VET
Tetracyclinesa ChloramphenicolRF-00000525-VET
ErythromycinRF-00000589-VET
Ciprofloxacin
RF-00000695-VET
Streptomycin
RF-0899-001-PPP
Ciprofloxacin
RF-00000695-VET Gentamicin
RF-00000536-VET
GentamicinRF-00000536-VET
GentamicinRF-00000536-VET
GentamicinRF-00000536-VET
LinezolidRF-00000758-VET
Nalidixic acidRF-00000547-VET
- Nalidixic acidRF-00000547-VET
Quinopristin/dalfopristinRF-00000777-VET
Streptomycin
RF-0899-001-PPP
-Streptomycin
RF-0899-001-PPP
Streptomycin
RF-0899-001-PPPSulfonamides
a - Sulfonamides
a Tetracyclines
a
Tetracyclinesa - Tetracyclines
a
VancomycinRF-00000569-VET
TrimethoprimRF-00000562-VET
-TrimethoprimRF-00000562-VET
-
(a): In the case of sulphonamides and tetracyclines, these are classes of substances. Information can be reported at either the
level of the class of substances, e.g. sulfonamides (code RF-00000690-VET), tetracyclines (code RF-00000672-VET) or
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Table 4: The EFSA data model for qualitative antimicrobial resistance tables
Element
CodeElement Name
Short Element name for
XML/Excel transferType Mandatory Pick lists Current
AQL.01 Reporting Year repYear xs:integer(4) Mandatory
AQL.02 Reporting Country repCountry xs:string(2) Mandatory ZOO_CAT_COUNTRY
AQL.03 Language lang xs:string(2) Mandatory ZOO_CAT_LANG
AQL.04 Zoonotic Agent zoonosis xs:string(15) Mandatory ZOO_CAT_PARAM_ZOO
AQL.05 Matrix matrix xs:string(4000) Mandatory ZOO_CAT_MATRIX
AQL.06 Sampling Stage sampStage xs:string(5) Optional ZOO_CAT_SMPNT
AQL.07 Sample Type sampType xs:string(5) Optional ZOO_CAT_SMPTYP
AQL.08 Sampling Context sampContext xs:string(5) Optional ZOO_CAT_SRCTYP
AQL.09 Sampler sampler xs:string(5) Optional ZOO_CAT_SMPLR
AQL.10 Sampling Strategy progSampStrategy xs:string(5) Optional ZOO_CAT_SAMPSTR
AQL.11 Sampling Details sampDetails xs:string(2000) Optional
AQL.12 Total Number of isolates in the laboratory labTotIsol xs:integer Mandatory
AQL.13 Monitoring Program monitProgr xs:string(1) Optional ZOO_CAT_YESNO
AQL.14 Antimicrobial Substance substance xs:string(15) Mandatory ZOO_CAT_PARAM_SUB
AQL.15 Tested tested xs:integer Mandatory
AQL.16 Resistant resistant xs:integer Mandatory
http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_LANG!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_ZOO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_MATRIX!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPNT!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SRCTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPLR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SAMPSTR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_YESNO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_SUB!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_SUB!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_YESNO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SAMPSTR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPLR!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SRCTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPTYP!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_SMPNT!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_MATRIX!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_PARAM_ZOO!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_LANG!A1http://d/DATA/IE/Temporary%20Internet%20Files/Content.Outlook/S6RSI9N8/Zoonoses%20Data%20Models%20and%20Picklists%20(2).xls%23ZOO_CAT_COUNTRY!A1
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Table 5: The EFSA business rules for qualitative antimicrobial resistance
Error code Error type Element
Rule
AQL01 E AQL01 Reporting year has to be >=1995 and 0
AQL03 E AQL15 Value of total units tested has to be = to value of resistant
AQL05 E AQL12 Value of total isolates in the laboratory has to be >= -1
AQL06 E AQL16 Value of resistant units has to be >= 0
AQL07 E AQL02 Value of language has to be ="en"
AQL08 E AQL04The zoonosis should always be reported at least to the second level of the pickist (using the domain
D_ZOO_CAT_PARAM_ZOO_AMR)
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APPENDIX III
Data dictionary/guidelines for reporting quantitative aggregated
antimicrobial resistance data from zoonotic and indicator bacteria from
animals, food and feed using the EFSA Data model for the Data Collection
Framework in the Reporting Year 2012
TABLE OF CONTENTS
Table of contents .................................................................................................................................... 29
Data dictionary/Guidelines for Reporting .............................................................................................. 30
Introduction ............................................................................................................................................ 30
1.
General information and identification of the isolate ............................................................... 30
1.1.
Reporting Year (repYear AQT.01) ........................................................................................ 30
1.2.
Reporting Country (repCountry AQT.02) ............................................................................. 30
1.3.
Language (lang AQT.03) ...................................................................................................... 30
2. Information about type and source of samples and isolates .................................................... 30
2.1.
Zoonotic agent ( zoonosis AQT.04)........................................................................................ 30
2.2.
Matrix (matrix AQT.05) ........................................................................................................ 32
3. Information about the sampling ................................................................................................. 32
3.1.
Sampling Stage ( sampStage AQT.06 ) ................................................................................... 32
3.2.
Sample origin ( sampOrig AQT.22) ....................................................................................... 33
3.3.
Sample Type ( sampType AQT.07) ........................................................................................ 33
3.4.
Total number of samples tested (totUnitTested AQT.23) ...................................................... 33
3.5.
Sampling unit type ( sampUnitType AQT.25) ........................................................................ 33
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DATA DICTIONARY/GUIDELINES FOR R EPORTING
Introduction
This data dictionary provides guidance for reporting on quantitative antimicrobial resistance (AMR)
data from zoonotic and indicator bacteria in animals, food and feed under the framework of Directive
2003/99/EC1.
Quantitative AMR data are being defined for the purpose of the reporting exercise as AMR data
obtained using either diffusion or dilution methods and that are being reported in an aggregated
manner (conversely to isolate-based AMR data).
The objective is to explain in detail the individual fields that are included in the EFSA Data model to
be used for the XML transmission of quantitative data on antimicrobial resistance through the Data
Collection Framework (DCF) tool. This data dictionary is specifically aimed to guide the reporting of
the information deriving from the year 2012. More in depth information on the data to be reported can
be found from the ‘Manual for Reporting on Zoonoses, Zoonotic Agents and Antimicrobial Resistance
in the framework of Directive 2003/99/EC and of some other pathogenic microbiological agents for
information derived from the year 2012’ (EFSA, 2013a). The EFSA data model for quantitativeantimicrobial resistance tables is summarised in Table 4 and the complete set of business rules applied
for data validation are presented in Table 5.
1. GENERAL INFORMATION AND IDENTIFICATION OF THE ISOLATE
1.1. Reporting Year (repYear AQT.01 )
This variable is mandatory. It is a numerical field consisting of four digits. It is the reporting year,
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It is expected that AMR data are reported for Salmonella, preferentially at serovar level, for
Campylobacter jejuni, Campylobacter coli, indicator Escherichia coli, indicator Enterococcus faecium
and indicator Enterococcus faecalis.
For Salmonella, the reporting of AMR data at the serovar level (level 2 term) is encouraged to be
performed consistently, as it is scientifically relevant to analyse resistance at this level, in particular
for the serovars of public health significance and emerging serovars and serovars exhibiting particular
combinations of resistance. Certain serovars of public health importance are listed in Table 1. If
desired, susceptibility data can be reported at an even greater level of detail than the recommended
level 2 term, e.g. 'Salmonella - S . Typhimurium - DT 137’ (code RF-00002322-MCG).
Table 1: Recommended Salmonella serovars of public health importance and codes for DCF
Animal species/food Salmonella serovar (Level 2 term)
Code for DCF
All animal species and derived meatS . Typhimurium RF-00002265-MCG
S . Typhimurium, monophasic RF-00003051-MCG
Gallus gallus (fowl): Breeders of egg production line, breeders of meat productionline, laying hens, broilers and broiler meat
S . Enteritidis RF-00002135-MCG
S. Agona RF-00001667-MCG
S . Virchow RF-00001152-MCG
S . Hadar RF-00001843-MCG
S. Kentucky RF-00000640-MCG
S . Infantis RF-00001894-MCG
Broilers and broiler meat S . Javaa RF-00001325-MCG
S . Enteritidis RF-00002135-MCG
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2.2.
Matrix (matrix AQT.05 )
This variable is mandatory. It contains codes linked to a pick list (ZOO_CAT_MATRIX). It
represents the food/feed category or the animal species which the isolate tested for AMR derives from.Also more detailed breakdown information is included at levels 2-4, such as the type of animals (wild,
farmed, pet), production category (breeding, fattening animals), subcategory of food (minced meat,
hard cheese), and type of food (frozen, ready-to-eat, etc). For example: ’Gallus gallus (fowl) / laying
hens / day-old chicks’ (code A007081A) or ‘meat from bovine animals – minced meat – intended to
be eaten cooked’ (code A034861A).
As regards the reporting of food-producing animal species investigated, it is recommended that, where
appropriate, the AMR data reported are stratified by animal age/production stage and/or production
type, as levels of resistance may be quite distinct between these groups, reflecting the widely differing
treatment regimes, management practices and hygienic conditions encountered. It is, therefore,
recommended that AMR data are reported for the animal species/food categories listed in Table 2.
Table 2: Recommended food and animal categories for AMR reporting
Bacteria Animal species/Food categories
Salmonella
Laying hens, broilers, fattening turkeys, fattening pigs, calves (under 1
year)a, young bovines (1-2 years) and adult cattle (>2 years)
Broiler meat, turkey meat, pig meat and bovine meat
Campylobacter
Broilers, fattening turkeys, fattening pigs, calves (under 1 year)a, young
bovines (1-2 years) and adult cattle (>2 years)
Broiler meat, turkey meat
Laying hens, broilers, fattening turkeys, fattening pigs, calves (under 1a
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3.2.
Sample origin (sampOri g AQT.22 )
This variable is optional. It contains codes linked to a pick list (ZOO_CAT_COUNTRY). Sampling
origin is used to indicate the country of origin for the animal, food or feed sampled (ISO 3166-1-alpha-2 country code). If the exact country of origin of the sampled item is not known, the following
terms may be reported: ‘European Union’ (code EU), ‘Non EU’ (code XE), ‘Non EEA’ (code XC) or
‘Unknown’ (code XX).
3.3. Sample Type (sampType AQT.07)
This variable is optional. It contains codes linked to a pick list (ZOO_CAT_SMPTYP). It describes
the biological source of the sample, e.g. ‘animal sample – nasal swab’ (code S015A); ‘food sample – carcase swab’ (code S021A).
3.4. Total number of samples tested (totUn itTested AQT.23 )
This variable is optional. Its type is integer and the data values are numeric. It is the total number of
samples tested for the presence of the bacteria in question from a given matrix (i.e. animal population
or food category)/sample type, whether positive or negative, in order to collect the bacterial isolates
tested for antimicrobial susceptibility, within a specific reporting MS and during the whole 2012
exercise of the AMR monitoring programme. These data may be used to assess the prevalence ofresistant bacteria.
3.5. Sampling unit type (sampUni tType AQT.25 )
This variable is optional. It contains codes linked to a pick list (ZOO_CAT_UNIT, domain:
D_AMR_sampUnitType). It defines the type of sampling unit taken in the sampling event: animal,
flock, herd, batch etc.
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3.10.
Sampling strategy (progSampStrategy AQT.10 )
This variable is optional. It contains codes linked to a pick list (ZOO_CAT_SAMPSTR). It is the
sampling strategy performed in the programme or project identified by program code, e.g. ‘Objectivesampling’ (code ST10A), ‘census’ (code ST50A). Reporting of the sampling strateg y is encouraged to
enable evaluation of the representativeness of the AMR monitoring programmes.
3.11.
Sampling details (sampDetails AQT.11 )
This variable is optional. This is a free text of maximum 2,000 alphanumerical characters. It can be
used to give more information on the sampling design, stage or context, when needed. It should becompleted in English (see element ‘lang AQT.03’).
3.12. Monitoring Program (monitProgr AQT.14 )
This variable is optional. It contains codes linked to a pick list, consisting of terms ‘yes’, ‘no’ and
‘unknown’ (ZOO_CAT_YESNO). It indicates whether the tested bacterial isolates originate from a
monitoring programme or not.
4.
INFORMATION ABOUT THE LABORATORY
4.1.
Total number of isolates available in the laboratory (labTotIsol AQT.12 )
This variable is mandatory. Its type is integer and the data values are numeric (reported as -1 if
unknown). This is the total number of isolates stored per specific bacterial species (serotype/or
serovar/ spa-type) in the laboratory, for a given reporting year and as far as possible broke down per
animal population (e.g. laying hen or broilers) / food category
5. INFORMATION ABOUT THE METHOD AND THE ANTIMICROBIALS
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Table 3: List or recommended antimicrobials for susceptibility testing and relative codes for
DCF
Salmonella C. jejun i /C. coli
Indicator E.coli
Indicator enterococci
AmpicillinRF-00000688-VET
ErythromycinRF-00000589-VET
AmpicillinRF-00000688-VET
AmpicillinRF-00000688-VET
Cefotaxime
RF-00000717-VET
Ciprofloxacin
RF-00000695-VET
Cefotaxime
RF-00000717-VET Chloramphenicol
RF-00000525-VET
Chloramphenicol
RF-00000525-VET
Tetracyclines
a
Chloramphenicol
RF-00000525-VET
Erythromycin
RF-00000589-VET
CiprofloxacinRF-00000695-VET
StreptomycinRF-0899-001-PPP
CiprofloxacinRF-00000695-VET
GentamicinRF-00000536-VET
Gentamicin
RF-00000536-VET
Gentamicin
RF-00000536-VET
Gentamicin
RF-00000536-VET
Linezolid
RF-00000758-VET
Nalidixic acidRF-00000547-VET
- Nalidixic acidRF-00000547-VET
Quinopristin/dalfopristinRF-00000777-VET
StreptomycinRF-0899-001-PPP - StreptomycinRF-0899-001-PPP StreptomycinRF-0899-001-PPP
Sulfonamidesa - Sulfonamides
a Tetracyclines
a
Tetracyclinesa - Tetracyclines
a
VancomycinRF-00000569-VET
TrimethoprimRF-00000562-VET
-TrimethoprimRF-00000562-VET
-
(a): In the case of sulphonamides and tetracyclines, these are classes of substances. Information can be reported at either the
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6.2.
Highest (limit) (highest AQT.18 )
This variable is mandatory for dilution method data. However, in the data model, it is marked as
optional because in case of diffusion data, this field must be left empty. It contains codes linked to a pick list (ZOO_CAT_FIXMEAS, domain: D_AMR_MIC). It is the highest concentration of the
concentration range used to test AMR in the laboratory. In any case, the highest concentration should
be between ‘0.002’ and ‘4096’ and Highest > Lowest . Only numerical values should be used (no ‘
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Table 4: The EFSA data model for quantitative antimicrobial resistance tables
Element
CodeElement Name
Short Element name for
XML/Excel transferXML Schema Type Mandatory Pick lists Current
AQT.01 Reporting Year repYear xs:integer(4) Mandatory
AQT.02 Reporting Country repCountry xs:string(2) Mandatory ZOO_CAT_COUNTRYAQT.03 Language lang xs:string(2) Mandatory ZOO_CAT_LANG
AQT.04 Zoonotic Agent zoonosis xs:string(15) Mandatory ZOO_CAT_PARAM_ZOO
AQT.05 Matrix matrix xs:string(4000) Mandatory ZOO_CAT_MATRIX
AQT.06 Sampling Stage sampStage xs:string(5) Optional ZOO_CAT_SMPNT
AQT.22 Sample Origin sampOrigin xs:string(2) Optional ZOO_CAT_COUNTRY
AQT.07 Sample Type sampType xs:string(5) Optional ZOO_CAT_SMPTYP
AQT.23 Total number of samples tested totUnitsTested xs:integer Optional
AQT.24Total number of sampling unitstested
totSampUnitsTested xs:integerOptional
AQT.25 Sampling unit type sampUnitType xs:string(5) Optional ZOO_CAT_UNIT
AQT.08 Sampling Context sampContext xs:string(5) Optional ZOO_CAT_SRCTYP
AQT.09 Sampler sampler xs:string(5) Optional ZOO_CAT_SMPLR
AQT.26 Program Code progCode xs:string(20) Optional
AQT.10 Sampling Strategy progSampStrategy xs:string(5) Optional ZOO_CAT_SAMPSTR
AQT.11 Sampling Details sampDetails xs:string(2000) Optional
AQT.12 Total Number of isolates in the lab labTotIsol xs:integer Mandatory
AQT.13 Method anMethCode xs:string(5) Mandatory ZOO_CAT_ANLYMD
AQT.14 Monitoring Program monitProgr xs:string(1) Optional ZOO_CAT_YESNO
AQT.15 Antimicrobial Substance substance xs:string(15) Mandatory ZOO_CAT_PARAM_SUB
AQT.16 Cut-off value cutoffValue xs:double MandatoryAQT.17 Lowest limit lowest xs:string(5) Optional ZOO_CAT_FIXMEAS
AQT.18 Highest limit highest xs:string(5) Optional ZOO_CAT_FIXMEAS
AQT.19 Range range xs:string(5) Mandatory ZOO_CAT_FIXMEAS
AQT.20 Number of inhibited inhibited xs:integer Mandatory
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Table 5: The EFSA business rules for quantitative antimicrobial resistance
Error code Error type Element
Rule
AQT01 E AQT01 Reporting year has to be >=1995 and =0 and =-1
AQT08 E AQT20 Value of inhibited units in the lab has to be >=0
AQT09 E AQT17 LOWEST must be numeric (no ‘‘,’>=‘,’=‘,’ 0
AQT19 E AQT16 CUTOFF must be >= lowest AND < HIGHEST
AQT20 W AQT05WARNING. For data interpretation purposes, it is advised not to use general categories : matrix NOT IN ('Gallus gallus (fowl)',
'Gallus gallus (fowl) - unspecified', 'Compound feedingstuffs, not specified')
AQT23 E AQT19If analytical method in (‘diffusion’,’diffusion - disk ’,’diffusion - Etest’,’diffusion - paper disk ’) then range (IZD) must be
numeric
AQT24 E AQT19 If analytical method in (‘dilution’,’dilution - agar ’,’dilution - broth’,’dilution - micro-dilution method’,’dilution - sensititre’)and
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Data dictionary for reporting zoonoses, antimicrobial resistance and food-borne outbreak datausing the EFSA data model
Supporting publications 2013:EN-409 39
Error code Er