EARS-Net Belgium Data call for 2016: Instructions for participating laboratories, including data definition. (version 4, 20/3/2017)

Transcription

1 EARS-Net Belgium Data call for 2016: Instructions for participating laboratories, including data definition. (version 4, 20/3/2017) Questions on this document can be directed towards: Karl Mertens Scientific Institute for Public Health (WIV-ISP) Rue Juliette Wytsmanstraat Brussels Tel , 1

2 Introduction This document gives instructions to laboratories within Belgium to submit data for 2016 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 (Ref 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 for the year 2016 is voluntary. This document relies on the standards and definitions that are laid out by EARS-Net (Ref 2) and summarizes these for participating laboratories. Differences with previous versions of the annual EARS- Net data call for BE are as follows: Addition of objectives; Addition of case definition for AMR and inclusion criteria for tests, samples, isolates; Addition of Data definition following the one of EARS-Net; Removal of the MS Excel template for submitting data, this is replaced by general instructions on the file format and description of variables and code values. Addition of procedure for submitting EARS-Net data by national reference laboratories; Addition of procedure for External Quality Assessment. EARS-Net Case definition for AMR and inclusion criteria EARS-Net uses the following case definition for AMR (see Ref 2 pages for full details). The bacterial species under surveillance are Streptococcus pneumonia (STRPNE), Staphylococcus aureus (STAAUR), Enterococcus faecalis (ENCFAE), Enterococcus faecium (ENCFAI), Escherichia coli (ESCCOL), Klebsiella pneumonia (KLEPNE), Pseudomonas aeruginosa (PSEAER), 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 a susceptibility test has been performed, have to be included. 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, Ref 3) clinical breakpoints, 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 37 ReferenceGuidelinesSIR of Table 3). The combinations of microorganisms x sample types x AMR tests that should be included in EARS-Net data are given in Table 1, these 2

3 combinations serve the full set of microorganism/antimicrobial group combinations that are under regular surveillance by EARS-Net as displayed in Table 2. Following the above case definition for AMR, the participating laboratory should prepare and submit annual EARS-Net data for 2016 in the form of an electronic data file in which each individual observation holds info on a particular isolate x sample x AMR test result on a sample that was taken in All results belonging to a combination of isolates (pathogens), sample types and AMR tests given in Table 1 should be submitted. Next to these AMR tests, see also variables 20, 21, 22, 23, 24 of Table 3 collecting supplementary info on confirmation tests for selected pathogens. All laboratories in BE that performed AMR susceptibility tests corresponding to the above defined sample types, isolates and AMR tests are invited to participate. EARS-Net defines no other inclusion criteria besides the ones of the two previous paragraphs. Importantly, no restrictions are placed on the type of patients to include. te however 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 15, 16, 17, 19 of Table 3). EARS-Net 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. Variables are numbered and named according to the EARS-Net reporting protocol (Ref 2). Sometimes, old variable names are given as well. Participating laboratories should only submit data on variables for which information can be collected and submitted. Variables 7 (sample date), 9 (laboratory code), 10 (sample type), 11 (patient id), 18 (pathogen), 25 (AMR test) and 26 (test result) are mandatory variables (= Yes ), files without at least these variables cannot be processed by IPH/NSIH. Next to these mandatory variables, other variables are labeled recommended (=, but recommended ) because they contain important characteristics of the patient or the hospital stay if the sample was taken in a hospital. The rest of the variables in Tables 3 and 4 specify information on supplementary tests on the isolate and on quantitative susceptibility of the AMR test or guidelines used to perform this test, and are optional. The data definition of Tables 3 and 4 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. The use of uppercase and lowercase characters in variable names and code values should be ignored, as everything will be converted to lowercase. 3

4 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. AMR tests 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. A participating laboratory can submit its results on the AMR test level in horizontal format as opposed to the vertical manner of the data definition of Table 4. In such horizontal format, the AMR test results for a particular isolate will be displayed in columns side-by side (each column representing an AMR test), instead of as separate observations. Also, when submitting horizontal AMR test data, please make sure to indicate info on variable 37 ReferenceGuidelinesSIR separately should a particular AMR test not follow EUCAST guidelines. During preparation of national EARS-Net 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 done on the same sample isolate. To make this possible, the local and reference laboratories need to submit EARS-Net data in which identifiers of exchanged isolates are constructed exactly the same; these are variables Patient ID (variable 11) and Isolate ID (variable 14). Furthermore, the national reference laboratory needs to submit EARS-Net data containing a clear identifier of the local laboratory (variable 7) providing each sample. Submitting EARS-Net data for 2016 and further treatment of 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 formatting such as calculated fields or hiding of columns or rows should be avoided. Submitting EARS-Net data proceeds by sending an with attachment to nsihdata@wiv-isp.be. Please make sure to indicate the full laboratory name and address in the mail message. A laboratory that tested zero isolates in 2016 for a particular pathogens or series of pathogens (with no resulting AMR data), is invited to report this in the mail message as well. Deadline for submitting EARS-Net data for 2016 is 16/5/2017. 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. The annual procedure for this EQA is as follows: 4

5 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. 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 2016 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 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. References Ref 1. European Centre for Disease Prevention and Control. Antimicrobial resistance surveillance in Europe Annual Report of the European Antimicrobial Resistance Surveillance Network (EARS-Net). Stockholm: ECDC; ( ) 5

6 Ref 2. European Centre for Disease Prevention and Control. TESSy - The European Surveillance System. Antimicrobial resistance (AMR) reporting protocol Stockholm: ECDC; ( ) Ref 3. European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines and breakpoints to determine clinical antimicrobial susceptibility (available at ). 6

7 Table 1: Microorganism, specimen source and antimicrobial agent combinations under surveillance by EARS-Net Microorganism Specimen source Antimicrobial agent Streptococcus pneumoniae (STRPNE) blood (BLOOD); cerebrospinal fluid (CSF) Azithromycin (AZM) Cefotaxime (CTX) Ceftriaxone (CRO) Clarithromycin (CLR) Erythromycin (ERY) Levofloxacin (LVX) Moxifloxacin (MFX) rfloxacin (NOR) Oxacillin (OXA) Penicillin (PEN) Staphylococcus aureus (STAAUR) blood (BLOOD) Cefoxitin (FOX) Cloxacillin (CLO) Ciprofloxacin (CIP) Daptomycin (DAP) Dicloxacillin (DIC) Flucloxacillin (FLC) Levofloxacin (LVX) Linezolid (LNZ) Meticillin (MET) rfloxacin (NOR) Ofloxacin (OFX) Oxacillin (OXA) Rifampin (RIF) Vancomycin (VAN) Enterococcus faecalis (ENCFAE) blood (BLOOD) Ampicillin (AMP) Amoxicillin (AMX) Gentamicin-High (GEH) Linezolid (LNZ) Teicoplanin (TEC) Vancomycin (VAN) Enterococcus faecium (ENCFAI) blood (BLOOD) Ampicillin (AMP) Amoxicillin (AMX) Gentamicin-High (GEH) Linezolid (LNZ) Teicoplanin (TEC) Vancomycin (VAN) Escherichia coli (ESCCOL) blood (BLOOD); cerebrospinal fluid (CSF) Amikacin (AMK) Amoxicillin-clavulanic acid (AMC) Ampicillin (AMP) Amoxicillin (AMX) 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) rfloxacin (NOR) Ofloxacin (OFX) Piperacillin-tazobactam (TZP) Polymyxin B (POL) Tigecycline (TCG) 7

8 Microorganism Specimen source Antimicrobial agent Tobramycin (TOB) Klebsiella pneumoniae (KLEPNE) blood (BLOOD); cerebrospinal fluid (CSF) 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) rfloxacin (NOR) Ofloxacin (OFX) Piperacillin-tazobactam (TZP) Polymyxin B (POL) Tigecycline (TCG) Tobramycin (TOB) Pseudomonas aeruginosa (PSEAER) Acinetobacter spp. (ACISPP) blood (BLOOD); cerebrospinal fluid (CSF) blood (BLOOD); cerebrospinal fluid (CSF) 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) Amikacin (AMK) Ciprofloxacin (CIP) Colistin (COL) Gentamicin (GEN) Imipenem (IPM) Levofloxacin (LVX) Meropenem (MEM) Netilmicin (NET) Polymyxin B (POL) Tobramycin (TOB) 8

9 Table 2: Microorganism and antimicrobial group combinations under regular EARS-Net surveillance Microorganism Antimicrobial group Antimicrobial agents Escherichia coli (ESCCOL) Aminopenicillins AMX, AMP Fluoroquinolones CIP, OFX, LVX, MFX, NOR Third-generation cephalosporins CTX, CRO, CAZ Aminoglycosides GEN, TOB, NET Carbapenems IPM, MEM Polymyxins POL, COL Klebsiella pneumoniae (KLEPNE) Fluoroquinolones CIP, OFX, LVX, MFX,NOR Third-generation cephalosporins CTX, CRO, CAZ Aminoglycosides GEN, TOB, NET Carbapenems IPM, MEM Polymyxins POL, COL Pseudomonas aeruginosa Piperacillin-tazobactam TZP (PSEAER) Ceftazidime CAZ Fluoroquinolones CIP, LVX Aminoglycosides GEN, TOB, NET Carbapenems IPM, MEM Amikacin AMK Polymyxins POL, COL Acinetobacter spp (ACISPP) Fluoroquinolones CIP, LVX Aminoglycosides GEN, TOB, NET Carbapenems IPM, MEM Amikacin AMK Polymyxins POL, COL Streptococcus pneumoniae Penicillins PEN, OXA (STRPNE) Macrolides ERY, CLR, AZM Fluoroquinolones LVX, NOR, MFX Third-generation cephalosporins CTX, CRO Staphylococcus aureus (STAAUR) MRSA MET, OXA, FOX, FLC, CLO, DIC Rifampicin RIF Fluoroquinolones CIP, OFX, LVX, NOR Linezolid LNZ Vancomycin VAN Daptomycin DAP Enterococcus faecalis (ENCFAE) High-level aminoglycoside resistance GEH and Enterococcus faecium Vancomycin VAN (ENCFAI) Aminopenicillins AMX, AMP Teicoplanin TEC Linezolid LNZ 9

10 Table 3: Epidemiological variables at isolate level (variables in grey are mandatory) 7 SampleDate (SamplingDate) Date when sample was taken. This date should fall in Yes Date Exact date only, YYYY-MM-DD 9 - Laboratory (LabId) Laboratory code unique for each laboratory within the country, assigned by national EARS-Net coordinator within IPH te: this is not the IPH/NSIH hospital code; Contact the national EARS-Net coordinator within IPH if unknown. need to provide this code if fixed for the entire file, in this case please provide the code as part of the exchange For data submitted by a national reference laboratory: this is the code of the local laboratory that provided the sample. Yes d Value 10 - Specimen (SampleType) Isolate source The source of the isolate (i.e. blood) Yes. d Value Enter data corresponding to the requested combination of Pathogen, Specimen and Antibiotic in Table 1 Microorganism, specimen source and antimicrobial agent combinations under surveillance by EARS-Net. BLOOD = blood CSF = Cerebrospinal fluid 11 PatientId used by the lab to specify patient. te: this code identifies the patient, not the admission within a hospital. Upon processing by IPH/NSIH, this code will be converted to an anonymous (patientcounter) numeric code. Yes Text 12 - Gender Gender, but recommended d Value M = Male F = Female O = Other UNK = Unknown 13 - Age (DateBirth) Age of the patient when the sample was taken, Alternatively, provide that patient s birth date. 10

11 , but recommended Numeric Integer 14 IsolateId Isolate ID; for each isolate, unique within lab and year Text code assigned by lab to specify isolate, but recommended Text 15 Hospital Identifier for the 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. te: this is not the laboratory code!, but recommended Text 16 - PatientType (AdmissionType) Origin of patient. Is the patient at the moment the sample is taken admitted in a hospital (inpatient), or not (outpatient). Patients that go to the hospital for Dialysis, other Day Hospital Care and to Emergency room should be classified as O for the field PatientType. All other patient that are admitted in the hospital as inpatients should be classified as INPAT., but recommended d Value INPAT= Admitted (Inpatient) OUTPAT= Outpatient O =Other (e.g. emergency room) UNK=Unknown 17 - HospitalUnitType Hospital department (at time of sample collection), but recommended d Value INTMED =Internal Medicine PEDS =Paediatrics/neonatal PEDSICU=Paediatrics/neonatal ICU SURG =Surgery ONCOL=Haematology/Oncology OBGYN=Obstetrics/Gynaecology ICU=Intensive Care Unit ED=Emergency Department URO=Urology Ward INFECT=Infectious Disease Ward O =Other UNK=Unknown 18 - Pathogen Pathogen Species and genus of the pathogen which has been isolated from the sample. Yes 11

12 Validation rule Validation rule Validation rule Validation rule d Value Provide data corresponding to the requested combination of Pathogen, Specimen and Antibiotic of Table 1 Microorganism, specimen source and antimicrobial agent 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 DateOfHospitalisation (AdmissionDate) Date of admission in hospital Date Exact date only, YYYY-MM-DD 20 - ResultPCRmec Detection of PCR meca-gene d Value POS=positive NEG=negative UNK=unknown To be reported only if Pathogen=STAAUR ResultPbp2aAggl Detection of PBP2a-agglutination d Value POS=positive; NEG=negative; UNK=unknown To be reported only if Pathogen=STAAUR Serotype 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. d Value Contact the national EARSNet BE coordinator within IPH/NSIH for a detailed list of codes To be reported only if Pathogen=STRPNE ESBL Detection of ESBL d Value POS=positive NEG=negative UNK=unknown To be reported only if Pathogen= ESCCOL or KLEPNE ResultCarbapenemases Detection of Carbapenemases. This refers to phenotypic test for carbapenemase activity (e.g. the Modified Hodge Test - MHT). 12

13 Validation rule d Value POS=positive NEG=negative UNK=unknown To be reported only if Pathogen= ESCCOL or KLEPNE or PSEAER or ACISPP 13

14 Table 4: Epidemiological variables at AMR test level (variables in grey are mandatory) 25 - Antibiotic (AntibioticECDC) Antimicrobial code Yes d Value, Provide data corresponding to the requested combination of Pathogen, Specimen and Antibiotic of Table 1 Microorganism, specimen source and antimicrobial agent combinations under surveillance by EARS-Net SIR (TestResult) Final interpretation result of all different susceptibility tests performed Yes d Value S=susceptible; I=intermediate; R=resistant 27 - ResultZoneSign Zone test operator (> < =). This field can indicate if a value of the zone diameter of the disk test is less than" (<); equal to or less than (< =); "equal to" (=); equal to or greater than (>=); or "greater than" (>) the value indicated in the following field. d Value < <= = >= > 28 - ResultZoneValue Zone test Value in mm. Numeric Integer 29 - ResultZoneSIR Zone test interpretation. d Value S=susceptible; I=intermediate; R=resistant 30 - ResultMICSign MIC test operator (> < =). type < <= = >= This field can indicate if a value of the zone diameter of the MIC test is less than" (<); equal to or less than (< =); "equal to" (=); equal to or greater than (>=); or "greater than" (>) the value indicated in the following field. d Value 14

15 > 31 - ResultMICValue MIC test value in mg/l. Text If <1 then float, if >=1 then integer 32 - ResultMICSIR MIC test interpretation. d Value S=susceptible; I=intermediate; R=resistant 33 - ResultEtestSign 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 in the following field. d Value < <= = >= > 34 - ResultEtestValue Gradient strip test value (Value in mg/l). Text If <1 then float, if >=1 then integer. The value 1.5 is also allowed ResultEtestSIR Gradient strip test interpretation. d Value S=susceptible; I=intermediate; R=resistant 36 - DiskLoad 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). Text Value and units: i.e. UI, mcg ReferenceGuidelinesSIR To differentiate use of CSLI and EUCAST guidelines for determining clinical breakpoint for antimicrobial susceptibility of the isolate 15

16 d value EUCAST = European Committee on Antimicrobial Susceptibility Testing CLSI = Clinical and Laboratory Standards Institute NAT = National O = Other 16