Update from the EURL-AR...Update from the EURL-AR Rene S. Hendriksen, PhD Research group of Genomic Epidemiology National Food Institute, Technical University of Denmark Annual …

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

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


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



The development of the EURL protocol for quantification of ESBL/AmpC-producing Escherichia coli in caecal content and fresh meat samples

4



• The revision of the EURL protocol for isolation of ESBL, ampC and carbapenemase-producing E. coli from caecal samples and fresh meat

5



• 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

6

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


• 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



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

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−√







Colistin−√Note and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)






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√√√√


VancomycinE. faecalis√√√√

Sheet2

Sheet3


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−√







Colistin−√






Salmonella spp.Azithromycin−√







Colistin−√Note and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)






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√√√√


VancomycinE. faecalis√√√√

Sheet2

Sheet3



Conducted a MIC reading survey to test the ability to read MIC’s


• 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 others

GLASS / GAP• Advise• Guidance• Resources• Capacity

building• “One Health”

15

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


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)


Co-ordination of National Reference Laboratories and provision of technical

support

17

• 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


Evaluation and development of analytic methods

Multi-plex PCR for surveillance of colistin, mcr-genes 1 to 5


Co-ordination of National Reference Laboratories and provision of technical

support417 unique visitors / month according to Google analytics


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

20


• 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)


E-learning

• In 2017, included a lecture on colistin• 46.773 participants from > 150 countries


Annual Workshop / Training courses


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

[email protected]

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

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Update from the EURL-AR...Update from the EURL-AR Rene S. Hendriksen, PhD Research group of Genomic Epidemiology National Food Institute, Technical University of Denmark Annual …