The European Antimicrobial Resistance Surveillance … · • recommendation to report the applied reference guidelines ... (STRPNE), Staphylococcus aureus (STAAUR), Enterococcus

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The European Antimicrobial Resistance Surveillance Network

Belgium (EARS-Net BE) protocol 2017:

Including data call, instructions for participating laboratories, data

definition, reporting procedure.

_______________________________________________________

(Version 3, 26/02/2018)

Questions regarding this document can be directed towards:

Thomas Struyf; Tel 02 642 57 68, email: [email protected]

Karl Mertens; Tel 02 642 57 95, email: [email protected]

Scientific Institute for Public Health (WIV-ISP)

Rue Juliette Wytsmanstraat 14 1050 Brussels

mailto:[email protected]


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Introduction

This document gives instructions to laboratories within Belgium to submit data for 2017

to the European Antimicrobial Resistance Surveillance Network (EARS-Net). EARS-Net

is the main EU epidemiologic surveillance system for Anti-Microbial Resistance (AMR),

and data reported from the network serve as important indicators on the occurrence and

spread of AMR in European countries (1). On a yearly basis, EARS-Net collects and

reports across European countries data on AMR against relevant agents within

commonly occurring pathogens isolated from clinical invasive samples in humans.

National data collection and submitting to EU for BE is organized by the Healthcare-

associated infections and antimicrobial resistance service of the Scientific Institute of

Public Health (IPH/NSIH, Brussels, BE). Participation to EARS-Net BE 2017 is voluntary.

This document relies on the standards and definitions that are laid out by EARS-Net (2)

and summarizes these for participating laboratories, adding some extensions. Additions

with respect to the EARS-Net BE 2016 data call and before are as follows:

Additions in version 1:

• recommendation to report quantitative susceptibility test data as much as

possible, with the objective of improved standardization of SIR results

(susceptible, intermediate susceptible, resistant) interpreted according to

EUCAST guidelines (see ‘EARS-Net case definition’);

• inclusion of isolates originating from urine samples (see ‘EARS-Net case

definition’);

• use of laboratory-specific codebooks (see ‘EARS-Net BE data definition’);

• recommendation to report the applied reference guidelines (added in 2016 data

call, see ‘EARS-Net case definition’);

• validation of the laboratory report (added in 2016 data call, see ‘Reporting and

validation’);

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• Addition to External Quality Assessment (EQA), page 12: automatic invitation

sent to National Reference Laboratories

• Removal of the AMR test for Daptomycin from table 1&2

• Addition to footnote table 1: information regarding AMR test for Temocillin

• Addition to table 3: clarification of the variable “Specimen” regarding

URI_CAT


• Update of the section “reporting and validation of laboratory results”

EARS-Net case definition for AMR and inclusion criteria

EARS-Net uses the following EU case definition for AMR (see Ref (2) pages 26-28 for

full details). The bacterial species under surveillance are Streptococcus pneumoniae

(STRPNE), Staphylococcus aureus (STAAUR), Enterococcus faecalis (ENCFAE),

Enterococcus faecium (ENCFAI), Escherichia coli (ESCCOL), Klebsiella pneumoniae

(KLEPNE), Pseudomonas aeruginosa (PSEAER) and Acinetobacter spp. (ACISPP). All

isolates from blood (STRPNE, STAAUR, ENCFAE, ENCFAI, ESCCOL, KLEPNE,

PSEAER, ACISPP) and/or cerebrospinal fluid (STRPNE, ESCCOL, KLEPNE, PSEAER,

ACISPP), for which an Antimicrobial susceptibility test (AST) has been performed, are

included.

From 2017, isolates originating from urine samples will be optionally included as well.

Those can be taken from either a catheter or an alternative sample strategy. Samples

taken for both clinical and screening purposes will be included and differentiation is

based upon a new variable ‘Screening’ (Table 3 variable 4) to the list of epidemiological

variables at isolate level. Results from isolates originating from urine samples are not

required for the European EARS-Net surveillance, but including them will give the

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opportunity to monitor antimicrobial resistance among uropathogens at a national level

(3). Uropathogens under surveillance are the pathogens stated above (except for

STRPNE) supplemented with Proteus mirabilis (PRTMIR).

The combinations of microorganisms x sample types x AMR tests that should be

included in EARS-Net BE data for 2017 are given in Table 1, these combinations serve

the full set of microorganism/antimicrobial group combinations that are under regular

surveillance by EARS-Net BE as displayed in Table 2. From 2017, AMR tests to

“Temocillin” (TEM), “Trimethoprim/sulfamethoxazol” (SXT) and “Nitrofurantoin” (NIT) are

additionally included for the relevant pathogens. As there are no EUCAST clinical

breakpoints for Temocillin susceptibility in enterobacteriaceae yet, please indicate which

guidelines are used for these test combinations. A pathogen is defined as clinically

susceptible, clinically intermediate or clinically resistant to an antibiotic agent according

to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) clinical

breakpoints (4), i.e. clinical MIC breakpoints and their inhibition zone diameter

correlates. Although EARS-Net encourages the use of EUCAST clinical breakpoints,

laboratories using other guidelines are still welcome to submit data if the use of clinical

guidelines is specified on the level of the AMR test (variable 23

‘ReferenceGuidelinesSIR’ of Table 4). The required variable ‘Result_lab’ (variable 15 of

Table 4) encodes the final result of the laboratory according to these interpretations. Use

of different guidelines (eg. CLSI vs EUCAST) currently limits the comparison of results

for particular ASTs between laboratories, as well as the interpretation of national results

for such tests (5). We therefore recommend participating laboratories from 2017

onwards, next to the ‘Result_lab’ variable, to include the quantitative results on ASTs as

much as possible. These results are encoded through the results of Zone-, MIC-

(minimal inhibitory concentration) and E-tests from recommended variables 16 to 23 of

Table 4. WIV-ISP will create a new variable “SIR_eucast”, based on the application of

EUCAST guidelines on the reported quantitative AST results. Both laboratory results

(SIR_eucast, and the reported result from the dedicated laboratory) remain consultable;

and the laboratory will keep the final decision on which of the two SIR variables is to be

used for national and EU reporting (see ‘Reporting and validation’).

Following the above case definitions for AMR, the participating laboratory should

prepare and submit EARS-Net BE data for 2017 in the form of an electronic data file in

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which each individual observation holds info on a particular isolate x sample x AMR test

result on a sample that was taken in 2017. All results belonging to a combination of

isolates (pathogens), sample types and AMR tests given in Table 1 should be submitted.

Next to ASTs, supplementary info on confirmation tests for selected pathogens is

collected as well. These are tests for detection of PCR mecA-gene and detection of

PBP2a-agglutination of Staphylococcus aureus isolates, for serotype of Streptococcus

pneumoniae isolates, and for detection of Extended-spectrum beta-lactamase (ESBL)

and detection of Carbapenemases (CP) of Escherichia coli, Klebsiella pneumoniae and

Proteus mirabilis isolates. Particularly the inclusion of tests for ESBL and/or CP is

recommended for national follow-up of carbapenem resistance in Gram-negative

bacteria (5).

All laboratories in BE (including non-hospital laboratories) that performed routine

susceptibility tests in 2017 corresponding to the above defined sample types, isolates

and AMR (or confirmation) tests are invited to participate. EARS-Net BE defines no other

inclusion criteria besides the ones of the previous paragraphs. Importantly, no

restrictions are placed on the type of patients to include. Samples originating from

unknown patients should be excluded (e.g. samples from quality assessments). Note

that several variables are collected describing sample and patient characteristics such

as a patient’s hospitalization status or the ward in the hospital in which a sample was

taken (see variables 9,10,11,13 of Table 3).

EARS-Net BE data definition

The data file of a particular laboratory will contain variables on the isolate and AMR test

level. That is, it will include the info on a particular AMR test as a separate observation,

and repeat all info on the level of the isolate over all included AMR tests. Tables 3 and 4

give the data collection definition for isolate and AMR test info, respectively. Participating

laboratories should only submit data on variables for which information can be collected

and submitted. Variables 1 (sample date), 2 (laboratory code), 3 (specimen), 5 (patient

id), 12 (pathogen), 14 (AMRtest) and 15 (Result_lab), are mandatory variables

(Required=’Yes’). Files without at least these variables cannot be processed by

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IPH/NSIH. Variable 4 (screening) is recommended if the sample type is urine. Next to

these mandatory variables, other variables are labeled ‘recommended’ (Required=’No,

but recommended’) because they contain values needed for the interpretation of

quantitative results. The rest of the variables in Tables 3 and 5 specify information on the

date of hospitalization, on the identifier for the acute care hospital where the sample was

taken and on the number of blood culture sets performed in the hospital that year, and

are optional.

The data definition of Tables 3, 4 and 5 should be taken as a guideline, and does not

need to be followed 100% strictly. Possible alterations that are accepted:

• Participating laboratories are free to use any of these variable names or code

values, or use their own nomenclature providing they can provide

correspondence with this data definition. Laboratory-specific codebooks

document how each laboratory’s specific nomenclature corresponds with EARS-

Net BE codification. These codebooks are included in the annual laboratory

report. Their validation by the laboratory is an essential step in obtaining correct

results (see further ‘Reporting and validation’). For 2017 data, these codebooks

will be extended with variables encoding patient and unit types for specific

specialties (for example intensive care), such that results for more specific

patient types can be reported.

• The use of uppercase and lowercase characters in variable names and code

values may be ignored, as everything will be converted to lowercase.

• No rules to avoid duplicate observations are defined for the data submitted by the

laboratory; these will be implemented by IPH/NSIH during preparation of national

EARS-Net data. See also ‘Reporting and validation’.

• ASTs for which results are submitted need not be limited to the ones shown in

Table 1; after conversion, IPH/NSIH will only keep the ones belonging to the

requested combinations.

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Instructions for national reference laboratories

During preparation of national EARS-Net BE data, IPH/NSIH will try to merge the AMR

test data from a local laboratory with the data provided by the national reference

laboratory and obtained from the same isolate. To make this possible, the local and

reference laboratories need to submit EARS-Net BE data in which identifiers of

exchanged isolates are constructed exactly the same; these are variables ‘Patient ID’

(variable 5) and ‘Isolate ID’ (variable 8). Furthermore, the national reference laboratory

needs to submit EARS-Net BE data containing a clear identifier of the local laboratory

(variable 2) providing the isolate.

Submitting EARS-Net BE 2017 data

Data needs to be submitted to IPH/NSIH in the form of a flat-text data file, in Comma

Separated Value (CSV) format or similar. If MS Excel is used, the use of formatting such

as calculated fields or hiding of columns or rows should be avoided. MS Access files are

not accepted. Data files may not exceed 40Mb. Please spread the data over multiple

files if this is the case. If preferred by the laboratory, submission of EARS-Net BE data in

separate parts (for example by period, pathogen, etc.) is possible.

Submitting EARS-Net BE data proceeds by sending an email with attachment to

[email protected] . A laboratory that tested zero isolates in 2017 for a particular

pathogen or series of pathogens (with no resulting AMR data), is invited to report this in

the mail message as well. Information that pertains to the participation, such as the full

laboratory name, contact person and address, the laboratory code, hospital code, the

number of blood culture sets performed in the hospital that year, and, if applicable for all

ASTs, the guideline applied to interpret AST results (variables 24-30, table 5), should be

completed in the empty Excel table that will be sent in attachment to this data-call.

Please refer to the EARS-NET BE webpage on http://www.nsih.be for the deadline for

submitting laboratory data.


http://www.nsih.be/

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Reporting and validation of laboratory results

Conversion and standardization

Upon reception, laboratory data will be converted and standardized by the IPH-NSIH unit

to the EARS-NET BE 2017 data definition. In an intermediate step, the laboratory may

be contacted for validation of unclear test (and other) codes should these occur. Only

laboratory data standardized towards the (Pathogen, Specimen, Antimicrobial test)

combinations of Table 1 of this protocol are kept for further treatment and analysis.

De-duplication of laboratory data:

De-duplication of annual laboratory data goes as follows: For each laboratory and

pathogen:

(1) Aggregation of all test results (variable AMRtest) within the same isolate (variable

IsolateId) into their respective antimicrobial groups, prioritizing test results, as interpreted

by the laboratory (variable Result_lab), according to the most resistant result (R>I>S)

(2) In case of multiple samples on the same date for the same patient, prioritization is

done on sample type (CSF>BLOOD), and then on test results (R>I>S)

(2) For each patient (variable PatientCounter), results on the first occurring specimen

(variables SampleDate, Specimen) within the study year are then kept

The same de-duplication steps are performed separately for urine samples.

Reporting

De-duplicated laboratory data is then analyzed and reported in the form of a MS Excel

(XLS) file. Analysis occurs always for a particular pathogen, results of which are given in

the relevant worksheet of the report file. These pathogen specific worksheets present

the results for the sample types “Blood/CSF” and “Urine”. Both indicators on sample or

patient characteristics as well as on resistance (or non-susceptibility) rate for relevant

antibiotic groups are presented.

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Pathogen specific results

Indicators for sample characteristics are similar for each pathogen, these are “Number of

Samples”, “Percentage of BLOOD samples”, “Percentage of Female Patients”,

“Percentage of Patients Aged>75”, “Percentage of Patients Aged>85” and “Percentage

of Hospitalized Patients”. For urine samples, the “Percentage of samples from catheters”

and the “Percentage of clinical samples” is reported as well. For each indicator, the

annual result for the laboratory is given in the column named “Result”, with further

specification of the number of samples corresponding to the particular indicator and the

total number of samples in brackets, and the binomial 95% confidence interval in case

the indicator is a proportion (column “95% CI”).

Indicators for antimicrobial resistance follow those of Table 2. This table follows the EU

EARSNET protocol (2) as a basis, and is updated with following supplementary

indicators that take into account results of confirmation tests for specific pathogens. The

supplementary indicators are “MRSA accounting for detection of MecA-gene and/or

PBP2a-agglutination” (Staphylococcus aureus), “% Positive ESBL within samples

Resistant to Third-Generation Cephalosporins” (Escherichia coli, Klebsiella pneumoniae,

Proteus mirabilis), “% Positive Carbapenemase within samples Resistant to

Carbapenems” (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa,

Acinetobacter spp, Proteus mirabilis). National results for these last two indicators are

only calculated within the group of laboratories that submitted results for confirmation

tests “ESBL” and/or “Carbapenemases”.

Rates for antimicrobial resistance are always reported in the form of a percentage

(column “% (I)R/SIR”), that is the extrapolated number of samples that tested

“R=Resistant” (or “IR=Non-Susceptible” if specified in the antimicrobial group) over 100

samples that were tested for the antimicrobials of a particular antimicrobial group, with

the number of tested samples and the number of resistant or non-susceptible samples in

brackets. The binomial 95 % Confidence Interval (“% 95% CI”), as well as the

percentage of EUCAST utilization (% EUCAST) is also reported in separate columns

(Figure 1).

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Validation

Inspection and validation by the laboratory of the results displayed in the XLS Laboratory

file is a crucial step in obtaining reliable national results on Antimicrobial resistance. We

therefore encourage laboratories to suggest any corrections of errors they may

encounter and, if deemed necessary, to re-submit a corrected laboratory data to WIV-

ISP. One important error that might occur is that not all tests for which results were

submitted by the laboratory are accounted for in the XLS report and this due to improper

or insufficient standardization of laboratory-specific antimicrobial test codes. For

example, a wrong standard test code might be assigned to a particular laboratory-

specific test description, which can result in susceptibility results becoming unavailable

for the specific Pathogen x Antimicrobial group combination relying on this specific test.

To prevent this error, the laboratory should carefully verify the correspondence between

the total number of samples that were submitted for a particular pathogen and the total

number of tests that were done for a particular Antimicrobial group, as shown in cells

“C9” and “C19:C27” of the XLS report respectively (Figure 1). Please note that these

results are calculated based on de-duplicated data.

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Figure 1: Example of an XLS lab report: total number of samples that were submitted for

a particular pathogen and the total number of tests that were done for a particular

Antimicrobial group, in brackets, as shown in cells “C9” and “C19:C27” (indicated with a

red circle)

Any difference between these should be verified to be due to laboratory policy, data not

yet submitted, or the possibility of wrongly standardized test codes. To facilitate this

verification, the “Standardisation” worksheet of the XLS report shows all test codes

isolated from the laboratory data (column D “LaboratoryCode”) and how these were

standardized to the EARS NET BE 2017 definition (Figure 2).

Fictitious data

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Figure 2: Example of a “Standardisation” worksheet of the XLS lab report

Any errors in this standardisation should be reported back to EARSNET BE coordinator

at IPH/NSIH for immediate correction and subsequent re-creation of the XLS laboratory

report.

Data worksheet

Note also that the “Data” worksheet shows the laboratory data, standardized according

to the EARS NET 2017 definition, with addition of a set of “_*” variables identifying the

original patient variables used by the laboratory (Figure 3). This data worksheet does not

show the original laboratory data, but the de-duplicated data.

Fictitious data

XXX

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Figure 3: Example of a “Data” worksheet in the XLS lab report

Reporting of national data

Next to the results of a particular laboratory, the relevant results of the national

distribution of laboratory resistance rates is given under heading “BE”, and this in the

form of number of laboratories submitting samples, total number of samples (“# SIR”) ,

total number of resistant or non-susceptible samples (“# (I)R”), the database mean (“%

Mean (db)”), mean of laboratory means (“% Mean (of LAB means)”), and percentiles 10,

25, 50 (median), 75 and 90. These results are also available for the indicators on sample

characteristics.

Finally, the results on antimicrobial resistance for each pathogen and its relevant

antimicrobial groups are shown visually as well, and this in form of the Laboratory

resistance rate and its 95% Confidence interval (in red), and a ‘modified’ Box&Whisker

(BW) plot of the national distribution of the Laboratory means and percentiles (in grey).

After sending the final statistical lab reports, NSIH will also produce a national

descriptive report for the year 2017. National data for 2017 with anonymized laboratory,

hospital and patient identifiers will be submitted to the European Centre for Disease

Fictitious data

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prevention and Control (ECDC) via The European Surveillance System (TESSy, (2)) for

inclusion in the ECDC annual report on AMR (1).

External Quality Assessment (EQA)

All laboratories reporting data to EARS-Net will be invited to participate in the annual

EQA. This is a service contracted by ECDC with United Kingdom National External

Quality Assessment Service (UK NEQAS) at Public Health England. National Reference

Laboratories for EARS-Net pathogens will be invited to the annual EQA regardless of

their participation.

The annual procedure for this EQA is as follows:

• UK NEQAS contacts the coordinator of EARS-Net BE at NSIH/IPH once a year,

to update the contact details of participating laboratories and compile a final list

of addresses of laboratories to be included in the EQA for BE.

• UK NEQAS then contacts the potential EQA participants with information on EQA

reporting requirements and timelines, the provisions for intellectual property, data

ownership and sharing, and planned post-EQA activities such as reports and

publications.

• At the time of the actual EQA (most often early autumn), UK NEQAS prepares

one package for each laboratory, containing a set of at least 6 bacterial isolates,

safety instructions, and detailed information about routines for reporting of

results. In addition to collection of EQA results, information on the use of

methods (i.e. automated systems, disc diffusion, E-test etc.) and guidelines for

clinical breakpoints as well as on the availability of and the requirement and/or

obligation to participate to a national EQA scheme should be collected from the

laboratories (type of EQA, mandatory, voluntary etc.). The packages (already

labeled with the specific local laboratory address) are sent to the coordinator of

EARS-Net BE. Laboratories register their results in an on-line database provided

by UK NEQAS.

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• The results will be compiled and analyzed by UK NEQAS, which will provide

individual feed-back of the results to each participating laboratory; country

reports to each national EQA coordinator providing all EQA results from the

laboratories in the country. The report should include the results from all

participating laboratories (including a national summary and results for each

individual laboratory) and include a short conclusion on the capacity of

participating laboratories and if needed, recommendations for improvement.

Restrictions and confidentiality measures

IPH/NSIH applies the same restrictions and confidentiality measures to EARS-Net data

for 2017 of a particular laboratory and its contents as done with all other IPH/NSIH

surveillances. This means that a particular laboratory’s data (or its contents) will only

serve the objectives stated in the EARS-Net BE 2017 protocol. When institute

(laboratory or hospital)-specific results are reported or presented, the identity of a

particular institute will be only disclosed to the designated contact person(s) of the

institute itself.

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References

1. European Centre for Disease Prevention and Control. Antimicrobial resistance surveillance in Europe 2016. Annual Report of the European Antimicrobial Resistance Surveillance Network (EARS-Net) [Internet]. ECDC. 2017 [cited 2017 Nov 28]. p. 1–88. Available from: https://ecdc.europa.eu/sites/portal/files/documents/AMR 2016_Final-with-cover-for-web-2017.pdf

2. European Centre for Disease Prevention and Control. TESSy - The European Surveillance System. EARS-Net reporting protocol 2017 [Internet]. ECDC. 2017 [cited 2017 Nov 28]. Available from: https://ecdc.europa.eu/sites/portal/files/documents/EARS-Net-reporting-protocol-2017.pdf

3. Flores-Meireles A, Walker J, Caparon M, Hultgren S. Urinary tract infections: epidemiology, mechanisms of infection and treatment options. Nat Rev Microbiol [Internet]. 2015;13(5):269–84. Available from: http://dx.doi.org/10.1038/nrmicro3432

4. European Committee on antimicrobial susceptibility testing. Guidelines and breakpoints to determine clinical antimicrobial susceptibility [Internet]. EUCAST. 2017 [cited 2017 Nov 28]. Available from: http://www.eucast.org/clinical_breakpoints/

5. Struyf T, Mertens K. European Antimicrobial Resistance Surveillance Network (EARS-Net) Belgium. Annual report 2017 (data referring to 2016) [Internet]. WIV-ISP. 2017 [cited 2017 Nov 29]. Available from: http://www.nsih.be/download/2017_EARS_NationalReport_Belgium.pdf

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Table 1: Microorganism, specimen source and antimicrobial resistance test

combinations under surveillance by EARS-Net.

Microorganism Specimen source Antimicrobial test Streptococcus pneumoniae (STRPNE)

blood (BLOOD); cerebrospinal fluid (CSF)

Azithromycin (AZM) Cefotaxime (CTX) Ceftriaxone (CRO) Clarithromycin (CLR) Erythromycin (ERY) Levofloxacin (LVX) Moxifloxacin (MFX) Norfloxacin (NOR) Oxacillin (OXA) Penicillin (PEN) Serotype (ST)1

Staphylococcus aureus (STAAUR)

blood (BLOOD); urine (URI_NONSP, URI_NONCAT, URI_CAT)

Cefoxitin (FOX) Cloxacillin (CLO) Ciprofloxacin (CIP) Dicloxacillin (DIC) Flucloxacillin (FLC) Levofloxacin (LVX) Linezolid (LNZ) Meticillin (MET) Nitrofurantoin (NIT) Norfloxacin (NOR) Ofloxacin (OFX) Oxacillin (OXA) Rifampicin (RIF) Trimethoprim/sulfamethoxazol (SXT)) Vancomycin (VAN) MecA-gene (MECA)2

PBP2A-agglutination (PB2A)3

Enterococcus faecalis (ENCFAE) blood (BLOOD); urine (URI_NONSP, URI_NONCAT, URI_CAT)

Ampicillin (AMP) Amoxicillin (AMX) Gentamicin-High (GEH) Linezolid (LNZ) Nitrofurantoin (NIT) Teicoplanin (TEC) Trimethoprim/sulfamethoxazol (SXT)

Vancomycin (VAN) Enterococcus faecium (ENCFAI) blood (BLOOD);

urine (URI_NONSP, URI_NONCAT, URI_CAT)

Ampicillin (AMP) Amoxicillin (AMX) Gentamicin-High (GEH) Linezolid (LNZ) Nitrofurantoin (NIT) Teicoplanin (TEC) Trimethoprim/sulfamethoxazol (SXT)

Vancomycin (VAN) Escherichia coli (ESCCOL) blood (BLOOD);

cerebrospinal fluid (CSF); urine (URI_NONSP, URI_NONCAT, URI_CAT)

Amikacin (AMK) Amoxicillin-clavulanic acid (AMC) Amoxicillin (AMX) Ampicillin (AMP) Cefepime (FEP) Cefotaxime (CTX) Ceftazidime (CAZ) Ceftriaxone (CRO) Ciprofloxacin (CIP) Colistin (COL) Ertapenem (ERT) Gentamicin (GEN) Imipenem (IPM) Levofloxacin (LVX) Meropenem (MEM) Moxifloxacin (MFX)

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Microorganism Specimen source Antimicrobial test Netilmicin (NET) Nitrofurantoin (NIT) Norfloxacin (NOR) Ofloxacin (OFX) Piperacillin-tazobactam (TZP) Polymyxin B (POL) Temocillin (TEM)4

Tigecycline (TCG) Tobramycin (TOB) Trimethoprim/sulfamethoxazol (SXT) Extended Spectrum Beta Lactamase (ESBL)5

Carbapenemase (CP)6

Klebsiella pneumoniae (KLEPNE) blood (BLOOD); cerebrospinal fluid (CSF); urine (URI_NONSP, URI_NONCAT, URI_CAT)

Amikacin (AMK) Amoxicillin-clavulanic acid (AMC) Cefepime (FEP) Cefotaxime (CTX) Ceftazidime (CAZ) Ceftriaxone (CRO) Ciprofloxacin (CIP) Colistin (COL) Ertapenem (ERT) Gentamicin (GEN) Imipenem (IPM) Levofloxacin (LVX) Meropenem (MEM) Moxifloxacin (MFX) Netilmicin (NET) Norfloxacin (NOR) Ofloxacin (OFX) Piperacillin-tazobactam (TZP) Polymyxin B (POL) Temocillin (TEM)4

Tigecycline (TCG) Tobramycin (TOB) Trimethoprim/sulfamethoxazol (SXT) Extended Spectrum Beta Lactamase (ESBL)5

Carbapenemase (CP)6

Pseudomonas aeruginosa (PSEAER)

blood (BLOOD); cerebrospinal fluid (CSF); urine (URI_NONSP, URI_NONCAT, URI_CAT)

Amikacin (AMK) 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) Tobramycin (TOB) Carbapenemase (CP)6

Acinetobacter spp. (ACISPP) blood (BLOOD); cerebrospinal fluid (CSF); urine (URI_NONSP, URI_NONCAT, URI_CAT)

Amikacin (AMK) Ciprofloxacin (CIP) Colistin (COL) Gentamicin (GEN) Imipenem (IPM) Levofloxacin (LVX) Meropenem (MEM) Netilmicin (NET) Polymyxin B (POL) Tobramycin (TOB) Trimethoprim/sulfamethoxazol (SXT) Carbapenemase (CP)6

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Microorganism Specimen source Antimicrobial test Proteus mirabilis (PRTMIR) urine (URI_NONSP,

URI_NONCAT, URI_CAT)

Amoxicillin (AMX) Ampicillin (AMP) Cefotaxime (CTX) Ceftazidime (CAZ) Ceftriaxone (CRO) Ciprofloxacin (CIP) Gentamicin (GEN) Imipenem (IPM) Levofloxacin (LVX) Meropenem (MEM) Netilmicin (NET) Norfloxacin (NOR) Ofloxacin (OFX) Temocillin (TEM)4

Tobramycin (TOB) Trimethoprim/sulfamethoxazol (SXT) Extended Spectrum Beta Lactamase (ESBL)5

Carbapenemase (CP)6

1Serotype: 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. Code: Contact the national EARS-Net BE coordinator within IPH/NSIH for a detailed list of

codes. To be reported only if available and Microorganism=STRPNE.

2mecA-gene: Detection of PCR mecA-gene (positive, negative or unknown). To be reported only if

available and Microorganism=STAAUR.

3PBP2aAggl: Detection of PBP2a-agglutination (positive, negative or unknown). To be reported only if

available and Microorganism=STAAUR.

4Temocillin (TEM): EUCAST breakpoints are still under consideration. Please make sure to indicate the

guideline that was used (e.g. BSAC).

5Extended Spectrum Beta Lactamase (ESBL): Detection of ESBL (positive, negative or unknown). Reporting

recommended. To be reported only if available and Microorganism= ESCCOL or KLEPNE or PRTMIR.

6Carbapenemase (CP): Detection of Carbapenemases. This refers to phenotypic test for carbapenemase

activity (e.g. the Modified Hodge Test - MHT) (positive, negative or unknown). Reporting recommended. To

be reported only if available and Microorganism= ESCCOL or KLEPNE or PSEAER or ACISPP or PRTMIR.

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Table 2: Microorganism and antimicrobial group combinations under EARS-Net BE

surveillance

Microorganism Antimicrobial group Antimicrobial tests Escherichia coli (ESCCOL)

Aminopenicillins AMX, AMP Carboxypenicillins TEM Fluoroquinolones CIP, OFX, LVX, MFX, NOR Third-generation cephalosporins CTX, CRO, CAZ Third-generation cephalosporins, ESBL+ CTX, CRO, CAZ, ESBL Aminoglycosides - Amikacin GEN, TOB, NET Aminoglycosides + Amikacin GEN, TOB, NET, AMK Carbapenems IPM, MEM Carbapenems, CP+ IPM, MEM, CP Polymyxins POL, COL Trimethoprim/sulfamethoxazol SXT Nitrofuran derivatives NIT

Klebsiella pneumoniae (KLEPNE)

Carboxypenicillins TEM Fluoroquinolones CIP, OFX, LVX, MFX,NOR Third-generation cephalosporins CTX, CRO, CAZ Third-generation cephalosporins, ESBL+ CTX, CRO, CAZ, ESBL Aminoglycosides - Amikacin GEN, TOB, NET Aminoglycosides + Amikacin GEN, TOB, NET, AMK Carbapenems IPM, MEM Carbapenems, CP+ IPM, MEM, CP Polymyxins POL, COL Trimethoprim/sulfamethoxazol SXT

Pseudomonas aeruginosa (PSEAER)

Piperacillin-tazobactam TZP Ceftazidime CAZ Fluoroquinolones CIP, LVX Aminoglycosides - Amikacin GEN, TOB, NET Aminoglycosides + Amikacin GEN, TOB, NET, AMK Carbapenems IPM, MEM Carbapenems, CP+ IPM, MEM, CP Polymyxins POL, COL

Acinetobacter spp (ACISPP)

Fluoroquinolones CIP, LVX Aminoglycosides - Amikacin GEN, TOB, NET Aminoglycosides + Amikacin GEN, TOB, NET, AMK Carbapenems IPM, MEM Carbapenems, CP+ IPM, MEM, CP Amikacin AMK Polymyxins POL, COL Trimethoprim/sulfamethoxazol SXT

Streptococcus pneumoniae (STRPNE)

Penicillins PEN, OXA Macrolides ERY, CLR, AZM Fluoroquinolones LVX, NOR, MFX Third-generation cephalosporins CTX, CRO

Staphylococcus aureus (STAAUR)

MRSA MET, OXA, FOX, FLC, CLO, DIC MRSA, CON+ MET, OXA, FOX, FLC, CLO, DIC, MECA,

PBP2A Rifampicin RIF Fluoroquinolones CIP, OFX, LVX, NOR Linezolid LNZ Vancomycin VAN Trimethoprim/sulfamethoxazol SXT Nitrofuran derivatives NIT

Enterococcus faecalis (ENCFAE) Enterococcus faecium (ENCFAI)

High-level aminoglycoside resistance GEH Vancomycin VAN Aminopenicillins AMX, AMP Teicoplanin TEC Linezolid LNZ Trimethoprim/sulfamethoxazol SXT Nitrofuran derivatives NIT

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Proteus mirabilis (PRTMIR)

Aminopenicillins AMX, AMP Carboxypenicillins TEM Aminoglycosides - Amikacin GEN, TOB, NET Aminoglycosides + Amikacin GEN, TOB, NET, AMK Fluoroquinolones CIP, OFL, LVX, NOR Third-generation cephalosporins CTX, CRO, CAZ Third-generation cephalosporins, ESBL+ CTX, CRO, CAZ, ESBL Carbapenems IPM, MEM Carbapenems, CP+ IPM, MEM, CP Trimethoprim/sulfamethoxazol SXT

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Table 3: Epidemiological variables at isolate level (variables in dark grey are required,

variables in light grey are recommended)

VariableName 1 – SampleDate

Description Date when sample was taken. This date should fall in 2017.

Required Yes

Data type Date

Code Exact date only, “YYYY-MM-DD”

VariableName 2 - LaboratoryCode

Description Laboratory code unique for each laboratory BE, assigned by national EARS-Net BE coordinator within IPH/NSIH Note: this is not the IPH/NSIH hospital code; Contact the national EARS-Net coordinator within IPH if unknown. No need to provide this code if fixed for the entire file, in this case please provide the code as part of the email exchange For data submitted by a national reference laboratory: this is the code of the local laboratory that provided the sample.

Required Yes

Data type Coded Value

VariableName 3 - Specimen

Description Isolate source The source of the isolate (i.e. blood/CSF/urine)

Required Yes.


Code Enter data corresponding to the requested combination of “Pathogen”, “Specimen” and “AMR test” in Table 1 ‘Microorganism, specimen source and antimicrobial resistance test combinations under surveillance by EARS-Net’. BLOOD = blood CSF = Cerebrospinal fluid URI_NONSP = Urine (non-specified) URI_NONCAT = Urine (Other than catheter) URI_CAT = Catheter urine (at least 24h catheterized)

VariableName Description Required Data type Code

4 – Screening Reason for urine sampling (screening or clinical (e.g. diagnosis)) no, but recommended if urine sample Coded value S = Screening C = Clinical UNK = Unknown

VariableName 5 – PatientId

Description Code used by the lab to specify patient. Note: A patient ID is crucial for the de-duplication of the data. This code should identify the patient, not the admission within a hospital. Upon processing by IPH/NSIH, this code will be converted to an anonymous (patient counter) numeric code. If there is no Patient ID available, IPH/NSIH will produce one based on the patient’s personal

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information: Surname/First name/Postal code/Domicile/Date of birth. These data are required, if there is no patient ID available.

Required Yes

Data type Text

VariableName 6 - Gender

Description Gender

Required No, but recommended


Code M = Male F = Female O = Other UNK = Unknown

VariableName 7 - Age

Description Age of the patient when the sample was taken, Alternatively, provide that patient’s birth date.


Data type Numeric

Code Integer

VariableName 8 – IsolateId

Description Isolate ID; Code for each isolate, unique within lab and year Text code assigned by lab to specify isolate


Data type Text

VariableName 9 - PatientType

Description Origin of patient. Is the patient at the moment the sample is taken admitted in an acute care 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”.



Code

INPAT= Admitted (Inpatient) OUTPAT= Outpatient O =Other (e.g. emergency room) UNK=Unknown

VariableName 10 – Hospital

Description Identifier for the acute care hospital where the sample was taken. Use a national hospital code (NSIH or RIZIV/INAMI for example), or simply the name of the hospital if unknown. Note: this is not the laboratory code!


Data type Text

Code Text

VariableName 11 - HospitalUnitType

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Description Hospital department (at time of sample collection)



Code INTMED =Internal Medicine PEDS =Paediatrics/neonatal PEDSICU=Paediatrics/neonatal 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

VariableName 12 - Pathogen

Description Pathogen Species and genus of the pathogen which has been isolated from the sample.

Required Yes


Code Provide data corresponding to the requested combination of “Pathogen”, “Specimen” and “AMR test” of Table 1 ‘Microorganism, specimen source and antimicrobial resistance test combinations under surveillance by EARS-Net’. STRPNE=Streptococcus pneumoniae STAAUR=Staphylococcus aureus ENCFAE=Enterococcus faecalis ENCFAI=Enterococcus faecium ESCCOL=Escherichia coli KLEPNE=Klebsiella pneumoniae PSEAER=Pseudomonas aeruginosa ACISPP=Acinetobacter spp. PRTMIR= Proteus mirabilis

VariableName 13 - DateOfHospitalisation

Description Date of admission in hospital

Required No

Data type Date

Code Exact date only, “YYYY-MM-DD”

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Table 4: Epidemiological variables at AMR test level (variables in dark grey are required,

variables in light grey are recommended)

VariableName 14 - AMRtest

Description Antimicrobial resistance test code, can refer to code for a antimicrobial susceptibility test or a confirmation test

Required Yes

Data type Coded Value,

Code Provide data corresponding to the requested combination of “Pathogen”, “Specimen” and “AMR test” of Table 1 ‘Microorganism, specimen source and antimicrobial resistance test combinations under surveillance by EARS-Net’.

VariableName 15 – Result_lab

Description Result of the test specified in ‘AMRtest’. Either this is the final SIR interpretation by the lab, based on results of all different susceptibility tests performed. An extra variable called “SIR_eucast” will be added by IPH/NSIH, based on application of EUCAST guidelines on the provided quantitative AST results for this test. Either, this is the result of the confirmation test.

Required Yes


Code S=susceptible; I=intermediate; R=resistant; POS=positive NEG=negative UNK=unknown Serotype if Pathogen=STRPNE

VariableName 16 – ResultZone

Description Zone test Value in mm, possibly accompanied by Zone test operator (><=) This zone test operator 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


Data type Numeric + coded value

Code Integer, possibly accompanied by: < or <= or = or >= or >

VariableName 17 - ResultZoneSIR

Description Zone test interpretation, as interpreted by the lab



Code S=susceptible; I=intermediate; R=resistant

VariableName 18 – ResultMIC

Description MIC test value in mg/l, possibly accompanied by MIC test operator (><=) This MIC test operator can indicate if a value 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



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Code Numeric, possibly accompanied by: < or <= or = or >= or >

VariableName 19 - ResultMICSIR

Description MIC test interpretation, as interpreted by the lab.




VariableName 20 – ResultEtest

Description Gradient strip test value (Value in mg/l), possibly accompanied by gradient strip test operator (><=) 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

Required

No, but recommended


Code Numeric, possibly accompanied by: < or <= or = or >= or >

VariableName 21 - ResultEtestSIR

Description Gradient strip test interpretation, as interpreted by the lab.




VariableName 22 - DiskLoad

Description Disk content (only if Zone test). 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).


Data type Text

Code Value and units: i.e. UI, mcg.

VariableName 23 - ReferenceGuidelinesSIR

Description To differentiate use of CSLI and EUCAST guidelines for determining clinical breakpoint for antimicrobial susceptibility of the isolate


Data type Coded value

Code EUCAST = European Committee on Antimicrobial Susceptibility Testing CLSI = Clinical and Laboratory Standards Institute NAT = National BSAC = British Society for Antimicrobial Chemotherapy O = Other

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Table 5: Epidemiological variables at hospital level

VariableName 24 - LaboratoryCode

Description Laboratory code unique for each laboratory BE, assigned by national EARS-Net BE coordinator within IPH/NSIH Note: this is not the IPH/NSIH hospital code; Contact the national EARS-Net coordinator within IPH if unknown. No need to provide this code if fixed for the entire file, in this case please provide the code as part of the email exchange For data submitted by a national reference laboratory: this is the code of the local laboratory that provided the sample.

Required Yes


VariableName 25 – Hospital

Description Identifier for the acute care hospital where the sample was taken. Use a national hospital code (NSIH or RIZIV/INAMI for example), or simply the name of the hospital if unknown. Note: this is not the laboratory code!

Required No

Data type Text

Code Text

VariableName 26 – LaboratoryAddress

Description Full laboratory address

Required

Yes

Data type Text

Code Text

VariableName 27 – ContactPerson

Description Contact person in the laboratory

Required Yes

Data type Text

Code Text

VariableName Description Required Data type Code

28 – Email Email address of the contact person Yes Text Text

VariableName 29 - GlobalReferenceGuidelinesSIR

Description If applicable for all AST tests in the laboratory: To differentiate use of CSLI and EUCAST guidelines for determining clinical breakpoint for antimicrobial susceptibility of the isolate.

Required Yes

Data type Coded value

Code EUCAST = European Committee on Antimicrobial Susceptibility Testing

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CLSI = Clinical and Laboratory Standards Institute NAT = National BSAC = British Society for Antimicrobial Chemotherapy O = Other

VariableName 30 -NumCultureSetsHosp

Description Number of blood culture sets performed in the hospital that year. These need to be specified for any hospital (code) declared under variable ‘Hospital’

Required No

Data type Numeric

Code Exact number

Documents

The European Antimicrobial Resistance Surveillance … · • recommendation to report the applied reference guidelines ... (STRPNE), Staphylococcus aureus (STAAUR), Enterococcus