Update from the EURL-AR...Update from the EURL-AR Rene S. Hendriksen, PhD Research group of Genomic...
Transcript of Update from the EURL-AR...Update from the EURL-AR Rene S. Hendriksen, PhD Research group of Genomic...
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Update from the EURL-AR
Rene S. Hendriksen, PhDResearch group of Genomic EpidemiologyNational Food Institute, Technical University of Denmark
Annual EURL AR workshop 5-6 April 2018
DTU, Kgs. Lyngby, Denmark
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DTU Food, Technical University of Denmark
Objectives of the EURL-AR
• Ensure the quality of antimicrobial susceptibility testing in the Member States (MSs).
– The most optimal phenotypic and genotypic detection methods for AMR
– Implement and harmonize the procedures and methodologies used
• Provisions of monitoring of antimicrobial resistance• Improving and boosting communication• Strengthen education and training• Address knowledge gabs • Ensuring harmonization according to the Commission
Implementing Decision (2013/652/EU)• Assistance to the MSs to reduce the knowledge gaps and raise
the level to that of the highest performing country
• Cooperation with international partners to shaping the global agenda and ensure that EU influences and follows global standards and guidelines to combat AMR2
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DTU Food, Technical University of Denmark
Scientific advice and support to the Commission in 2018
3 4 April 2018
Continued to provide answers and/ or clarifications to specificad hoc questions from Directorate F, Health and Food Auditsand Analysis Unit 5
http://www.google.dk/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAUQjRxqFQoTCPa1kfKzg8kCFUhzcgodH_cFIA&url=http://ec.europa.eu/education/policy/vocational-policy/doc/brugescom_en.pdf&bvm=bv.106923889,d.bGQ&psig=AFQjCNGYaYWLZGcbXKxqgBOJ0yALjfAyIA&ust=1447160707034605
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DTU Food, Technical University of Denmark
Scientific advice and support to the Commission in 2018
The development of the EURL protocol for quantification of ESBL/AmpC-producing Escherichia coli in caecal content and fresh meat samples
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DTU Food, Technical University of Denmark
Scientific advice and support to the Commission in 2018
• The revision of the EURL protocol for isolation of ESBL, ampC and carbapenemase-producing E. coli from caecal samples and fresh meat
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DTU Food, Technical University of Denmark
Scientific advice and support to the Commission in 2018
• Review of the laboratory protocol for validation of selective MacConkey agar plates
– Frequency in use of negative and positive controls for media validation
– Validation of the 96-hour time interval between collection and analysis of samples
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20-21 March 2018 - Parma
Request for scientific and technical assistance on harmonised monitoring of antimicrobial resistance (AMR) in bacteria transmitted through food
1st EFSA WG on AMR monitoring
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DTU Food, Technical University of Denmark
• Revise of the Grant Decision level– Costs of transportation and the cost of the samples in the
reimbursement of costs
– Extending the period for performing AST tests to end February
– Cost of tests
– Defining maximum time to perform a test
– Negative and positive controls and re-tests for unusual phenotypes
Scientific advice and support to the Commission in 2018
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DTU Food, Technical University of Denmark
Future criteria - priority and / or emerging AMR phenotypes that require further action
Gram negativeSpecies Antibiotic with MIC >
ECOFF Further
characteristicConfirm purity
Confirm ID
Re-test Store Further notes
E. coli Azithromycin − √Cefotaxime AMPR √ Test also EUSVEC2Cefotaxime AMPS √ √ √ √ Test also EUSVEC2Cefoxitin FOTR and/or TAZR √Cefoxitin FOTS and TAZS √ √ √ √Ceftazidime AMPR √ Test also EUSVEC2Ceftazidime AMPS √ √ √ √ Test also EUSVEC2Colistin − √Ertapenem FOTR and/or TAZR √Ertapenem FOTSand/or TAZS √ √ √ √Imipenem − √ √ √ √Meropenem − √ √ √ √ Test also EUSVEC2Tigecycline − √ √ Re-test as antibiotic is labile
Salmonella spp. Azithromycin − √Cefotaxime AMPR √ Test also EUSVEC2Cefotaxime AMPS √ √ √ √ Test also EUSVEC2Cefoxitin FOTR and/or TAZR √Cefoxitin FOTS and TAZS √ √ √ √Ceftazidime AMPR √ Test also EUSVEC2Ceftazidime AMPS √ √ √ √ Test also EUSVEC2Colistin − √ Note and store also COL-S
S. Enteritidis and S. Dublin (serogroup 9)
Ertapenem FOTR and/or TAZR √Ertapenem FOTSand/or TAZS √ √ √ √Imipenem − √ √ √ √Meropenem − √ √ √ √ Test also EUSVEC2Tigecycline − √ √ Re-test as antibiotic is labile
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Table. Relevant priority and / or emerging antimicrobial resistance phenotypes that require further action.
SpeciesAntibiotic with MIC > ECOFF Further characteristicConfirm purity Confirm IDRe-testStoreFurther notes
S. aureusCefoxitin−√
Erythromycin−√
Linezolid−√
Quinupristin-dalfopristin −√
Vancomycin−√
Streptococci Cefoxitin−√√√√
Penicillin−√√√√
E. coliAzithromycin−√
CefotaximeAMPR√Test also EUSVEC2
CefotaximeAMPS√√√√Test also EUSVEC2
CefoxitinFOTR and/or TAZR√
CefoxitinFOTS and TAZS√√√√
CeftazidimeAMPR√Test also EUSVEC2
CeftazidimeAMPS√√√√Test also EUSVEC2
Colistin−√
ErtapenemFOTR and/or TAZR√
ErtapenemFOTSand/or TAZS√√√√
Imipenem−√√√√
Meropenem−√√√√Test also EUSVEC2
Tigecycline−√√Re-test as antibiotic is labile
Salmonella spp.Azithromycin−√
CefotaximeAMPR√Test also EUSVEC2
CefotaximeAMPS√√√√Test also EUSVEC2
CefoxitinFOTR and/or TAZR√
CefoxitinFOTS and TAZS√√√√
CeftazidimeAMPR√Test also EUSVEC2
CeftazidimeAMPS√√√√Test also EUSVEC2
Colistin−√Note and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)
ErtapenemFOTR and/or TAZR√
ErtapenemFOTSand/or TAZS√√√√
Imipenem−√√√√
Meropenem−√√√√Test also EUSVEC2
Tigecycline−√√Re-test as antibiotic is labile
Campylobacter spp.CiprofloxacinNALS√√√√
Erythromycin−√√√√
Gentamicin−√
Nalidixic acid CIPS√√√√
EnterococciDaptomycin−√
Gentamicin−√
Linezolid−√
PenicillinAMPS√
Quinupristin-dalfopristin E. faecium√E. faecalis is intrinsically resistant to Q/D
TeicoplaninE. faecalis√√√√
Tigecycline−√√Re-test as antibiotic is labile
VancomycinE. faecalis√√√√
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DTU Food, Technical University of Denmark
Future criteria - priority and / or emerging AMR phenotypes that require further action
Gram positive
12 4 April 2018
Species Antibiotic with MIC > ECOFF
Further characteristic
Confirm purity
Confirm ID
Re-test Store Further notes
S. aureus Cefoxitin − √Erythromycin − √Linezolid − √Quinupristin-dalfopristin − √Vancomycin − √
Streptococci Cefoxitin − √ √ √ √Penicillin − √ √ √ √
Sheet1
Table. Relevant priority and / or emerging antimicrobial resistance phenotypes that require further action.
SpeciesAntibiotic with MIC > ECOFF Further characteristicConfirm purity Confirm IDRe-testStoreFurther notes
S. aureusCefoxitin−√
Erythromycin−√
Linezolid−√
Quinupristin-dalfopristin −√
Vancomycin−√
Streptococci Cefoxitin−√√√√
Penicillin−√√√√
E. coliAzithromycin−√
CefotaximeAMPR√Test also EUSVEC2
CefotaximeAMPS√√√√Test also EUSVEC2
CefoxitinFOTR and/or TAZR√
CefoxitinFOTS and TAZS√√√√
CeftazidimeAMPR√Test also EUSVEC2
CeftazidimeAMPS√√√√Test also EUSVEC2
Colistin−√
ErtapenemFOTR and/or TAZR√
ErtapenemFOTSand/or TAZS√√√√
Imipenem−√√√√
Meropenem−√√√√Test also EUSVEC2
Tigecycline−√√Re-test as antibiotic is labile
Salmonella spp.Azithromycin−√
CefotaximeAMPR√Test also EUSVEC2
CefotaximeAMPS√√√√Test also EUSVEC2
CefoxitinFOTR and/or TAZR√
CefoxitinFOTS and TAZS√√√√
CeftazidimeAMPR√Test also EUSVEC2
CeftazidimeAMPS√√√√Test also EUSVEC2
Colistin−√Note and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)
ErtapenemFOTR and/or TAZR√
ErtapenemFOTSand/or TAZS√√√√
Imipenem−√√√√
Meropenem−√√√√Test also EUSVEC2
Tigecycline−√√Re-test as antibiotic is labile
Campylobacter spp.CiprofloxacinNALS√√√√
Erythromycin−√√√√
Gentamicin−√
Nalidixic acid CIPS√√√√
EnterococciDaptomycin−√
Gentamicin−√
Linezolid−√
PenicillinAMPS√
Quinupristin-dalfopristin E. faecium√E. faecalis is intrinsically resistant to Q/D
TeicoplaninE. faecalis√√√√
Tigecycline−√√Re-test as antibiotic is labile
VancomycinE. faecalis√√√√
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DTU Food, Technical University of Denmark
Scientific advice and support to the Commission in 2018
Conducted a MIC reading survey to test the ability to read MIC’s
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DTU Food, Technical University of Denmark
• Inter-EURLs Working Group on WGS– Proficiency Testing (Chaired by EURL AR)
– WGS laboratory procedures
– Bioinformatics tools
– WGS Cluster Analysis
– Benchmarking
– Trainings on WGS
– Reference and confirmatory testing using WGS
Scientific advice and support to the Commission in 2018
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DTU Food, Technical University of Denmark
Scientific advice and support to others
GLASS / GAP• Advise• Guidance• Resources• Capacity
building• “One Health”
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AGISAR• Update surveillance manual• NGS (AMR genes)• TriCycle, ESBL in Africa – EU
style• CIA list
New activities:
• Setting up PTs for the United Nations Secretary-General´s Mechanism for Investigation of Alleged Use of Chemical and Biological Weapons (UNSGM)
• FAO Reference Centre for AMR – work prog discussions initiated
http://www.google.dk/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCJj354Wzg8kCFUWmcgod-9AKtw&url=http://www.ema.europa.eu/ema/index.jsp?curl%3Dpages/about_us/general/general_content_000221.jsp&psig=AFQjCNERLapLd5zQ8MutAEKYN5ducObiOQ&ust=1447160461100688https://www.google.dk/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCOSiiJWzg8kCFWIQcgodV5sDPg&url=https://twitter.com/who&psig=AFQjCNF0Z2C_ZuwKTCpCFTV7hr2Y9Yi0HA&ust=1447160512234882https://www.google.dk/url?sa=i&rct=j&q=&esrc=s&source=imgres&cd=&cad=rja&uact=8&ved=0ahUKEwif2JyyrvXXAhVkDZoKHV4jBTMQjRwIBw&url=https://dan.wikitrans.net/FN:s_livsmedels-_och_jordbruksorganisation&psig=AOvVaw2io5_pktj4Sqk56x6qZ7cz&ust=1512648895750244
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DTU Food, Technical University of Denmark
Ring trials (EQAS), comparative testing and quality assurance
• Trial 1 (October)– Salmonella – Campylobacter– Genotypic characterization also including detection of ESBL,
carbapenem, and ampC genes
• Trial 2 (June)– Escherichia coli– Enterococci– Staphylococci incl. MRSA
• Trial 3 (November)– Matrix EQAS, including qualitative detection of ESBL and AmpC
producing E. coli from a matrix of caecal and food samples (cattle swine, and chicken/ beef pork, and chicken meat)
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DTU Food, Technical University of Denmark
Co-ordination of National Reference Laboratories and provision of technical
support
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• Meetings on standardization of monitoring of antimicrobial resistance
• Maintaining the network of NRL’s
• Dissemination and collection of knowledge and information
• Improve and extend databases of primers, reference material and antimicrobial resistance geneshttp://www.antimicrobialresistance.dk/
http://www.antimicrobialresistance.dk/http://www.eucast.org/https://www.google.dk/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCNyxseu6g8kCFaj8cgod_zACGA&url=https://twitter.com/oieanimalhealth&psig=AFQjCNGnXfdgKCBh90ekPp-UdgkGKFCIfw&ust=1447162571238927https://www.google.dk/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCLyft8ezg8kCFaGqcgodQGUFCg&url=https://en.wikipedia.org/wiki/European_Centre_for_Disease_Prevention_and_Control&psig=AFQjCNGlWMOYMMLPenD0Yc1B8BTw1ixemg&ust=1447160616443648http://www.google.dk/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCJSpzNm6g8kCFYifcgodGysImQ&url=http://community.clsi.org/&psig=AFQjCNG7Mj5-20eCSEHq6vFHy-MbGlPgIA&ust=1447162535815616https://www.google.dk/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&uact=8&ved=0CAcQjRxqFQoTCOSiiJWzg8kCFWIQcgodV5sDPg&url=https://twitter.com/who&psig=AFQjCNF0Z2C_ZuwKTCpCFTV7hr2Y9Yi0HA&ust=1447160512234882
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DTU Food, Technical University of Denmark
Evaluation and development of analytic methods
Multi-plex PCR for surveillance of colistin, mcr-genes 1 to 5
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DTU Food, Technical University of Denmark
Co-ordination of National Reference Laboratories and provision of technical
support417 unique visitors / month according to Google analytics
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DTU Food, Technical University of Denmark
Confirmatory testing
• The EURL-AR will provide confirmatory testing on bacterial isolates of particular relevance upon request by the NRLs, the European Commission and EFSA:
• This specific targeted confirmatory testing will be offered by the EURL-AR to support the activities related to the implementation of Decision 2013/652/EU
• This confirmatory testing will be used to assure the quality of results submitted by MSs, to detect resistance mechanisms and to determine correspondence between phenotypes and genotypes
• The EURL-AR will offer Material Transfer Agreements (MTAs) between the EURL-AR and MSs to define the legal aspects of strain and data ownership
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DTU Food, Technical University of Denmark
• Some NRL’s and 3rd countries such as candidate countries might have a need for special assistance in the implementation of the EC action plan on AMR
– 1 - 2 visits per year since 2006– 3 days agenda – lab / theoretical lectures– Summary report shared with MS and EC– Follow up on corrective actions
Missions for specific assistance to individual laboratories (site visits)
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DTU Food, Technical University of Denmark
E-learning
• In 2017, included a lecture on colistin• 46.773 participants from > 150 countries
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DTU Food, Technical University of Denmark
Annual Workshop / Training courses
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DTU Food, Technical University of Denmark
Thank you for your attention
Rene S. Hendriksen, PhD
Research group of Bacterial Genomics and Antimicrobial Resistance
WHO Collaborating Centre for Antimicrobial Resistance in Food borne Pathogens
European Union Reference Laboratory for Antimicrobial Resistance
National Food Institute, Technical University of Denmark
mailto:[email protected]
Update from the EURL-AR���Objectives of the EURL-AR�Scientific advice and support to the Commission in 2018�Scientific advice and support to the Commission in 2018�Scientific advice and support to the Commission in 2018�Scientific advice and support to the Commission in 2018Request for scientific and technical assistance on harmonised monitoring of antimicrobial resistance (AMR) in bacteria transmitted through food�Scientific advice and support to the Commission in 2018Future criteria - priority and / or emerging AMR phenotypes that require further action�Future criteria - priority and / or emerging AMR phenotypes that require further action��Scientific advice and support to the Commission in 2018�Scientific advice and support to the Commission in 2018�Scientific advice and support to othersRing trials (EQAS), comparative testing and �quality assurance�Co-ordination of National Reference Laboratories and provision of technical supportEvaluation and development of �analytic methods�Co-ordination of National Reference Laboratories and provision of technical supportConfirmatory testingMissions for specific assistance to individual laboratories (site visits)�E-learningAnnual Workshop / Training coursesSlide Number 24