EFSA Scientific Validation of data supported by the … · DTU Food, Technical University of Denmark Term of Reference; EURL AR Confirmatory testing • Provide confirmatory testing

EFSA Scientific Validation of data supported by the EURL Reference Testing

6 April 2018

EURL-AR Network

DTU Food, Technical University of Denmark

Term of Reference; EURL AR

Confirmatory testing Provide confirmatory testing for NRLs on bacterial isolates of

particular relevance or on request by the European Commission and EFSA

Provide reference testing of putative Salmonella and E. coli isolates producing beta-lactamases with extended spectrum, and carbapenemases

To support the activities related with the implementation of the new monitoring methods

To offer relevant legal Material Transfer Agreements (MTAs) between the EURL and MSs to ensure the legal aspects of strain and publication ownership

To assure the quality of results for MS, confirm the presumptive phenotypes observed, determine the respective corresponding genotypes and detect resistance mechanisms

2 9 April 2018

3

EUSR-AMR REFERENCE TESTING

Selection of isolates: Discrepancies ESBL/AmpC/Carba-phenotypes Emerging resistance /clones

Confirmation of results Ask MSs for the isolates Perform: MIC re-testing, WGS

Usefulness of WGS to support AMR surveillance

EFSA Scientific validation- Ref. testing

Carbapenem resistance P1 and/or P2: MERO, IMI, ETP

Comparison P1 and P2: FOT, TAZ and MERO Discrepancies (including AMP) Inferred phenopypes: ESBL, AmpC, ESBL/AmpC, CPs

Selected antimicrobials P1: AZI, TIG, COL

Possible clones

SELECTION OF ISOLATES

CONFIRM MECHANISM INFERRED FROM PHENOTYPE

Scientific validation- Ref. testing

CTX-M-15

VIM-1

SHV-12

cAMPc

CMY-2

DETECT EMERGING CLONES MECHANISMS


S. Para B dT+

S. Kentucky

S. Infantis mcr-1

blaVIM-1

blaCTX-M-15

blaCMY-2


Intepretation of the genotypic results

7 9 April 2018

Color codes GENOTYPE

Agreement phenotype-genotype at both labs (if data from only one lab are provided, this is indicated in the comments field)

Agreement phenotype-genotype at EURL only

Agreement phenotype-genotype at MS only

The gene detected does not explain (fully) the phenotype

Not detected phenotypically (antimicrobial not in the panel/panel not tested)

In parenthesis, next to each gene, there is a value showing if the hit is partial or has less than 100% identity to the reference gene

Incorrect serovar identification


Individual results

8 9 April 2018

EFSA/EURL-AR reference testing PHENOTObtained MIC data NA / >64>2 >0.064 >8 >0.125 NA >16 >16 >05/ >0. >1 >2 >2 / >0.5>8

Country Organism Country Organism Isolate c Panel Working Date SMX TMP CIP TET MERO AZI NAL CHL FOT TGC COL TAZ AMP

EFSA Salmonella - S. En AMR MON 64 0,5 0,03 4 0.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA

CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM

EFSAAustriaSalmonella - S. Enteritidis - PT 4344814AMR MON161024>32>8>64128128320.25>640.034>12880.250.2510.510.5

BulgariaSalmonella - S. Infantisnot EFSA

Beatriz Guerra: Beatriz Guerra:after Restesting no cefalosp/carba resistance)EURLBulgariaSalmonella - S. Infantisiso_949EUVSEC2231/20/160.030.25180.060.250.250.25/41/48

EFSACroatiaSalmonella - S. InfantisHRSAL1347/1/14AMR MON320.5141281632>8>6412816>4164320.256412840.58>641

EFSACyprusEscherichia coli, non-pathogenic1342/1AMR MON pnl26432640.060.25>324816

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEURLCyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified1342/1EUVSEC22712/10/150.03>6432640.060.12>324/48/416

EFSACyprusEscherichia coli, non-pathogenic1699/1AMR MON>1024>3286412832640.032>128160.250.2510.5640.5

EFSACyprusEscherichia coli, non-pathogenic1699/1AMR MON pnl2640.5

SwitzerlandSalmonella - S. Typhimurium14/ MHK1959_S18812/8/15640.250.0320.068480.250.2540.520.5

SwitzerlandSalmonella - S. Typhimurium14/ MHK2020_S18912/8/151280.50.0340.064480.250.2540.520.5

Omitted due to mixed morfologies

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC552121 - 112/17/156410.2520.0381288>40.2518>641

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC552121 - 212/17/156410.2520.0381288>40.25missing2>640.5

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC614124 - 112/17/1580.258missing0.03216>128>40.518>640.5

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC614124 - 212/17/1580.25420.038>1288>40.518>640.5

RomaniaSalmonella - S. Kentucky10687-5DB156 - 112/17/15>10240.25>8>640.038>12880.250.511>64>32

RomaniaSalmonella - S. Kentucky10687-5DB156 - 212/17/15>10240.25>8>640.038>12880.250.511>64>32

RomaniaSalmonella - S. Kentucky10687-5DB156 - 312/17/15>10240.50.015640.038>12880.250.512>6432

EUVSEC2

EFSA/EURL-AR reference testing EUVSEC2 panels

Obtained MIC data

CountryOrganismIsolate codeWorking #DateFOXETPIMIMEROTAZFEPF/CT/CFOTTRM

BelgiumSalmonella - Not typeable1418199 1STR1312/10/15160.030.250.06440.12/40.5/4416

BelgiumSalmonella - S. 4,5:b1415511 1STR1412/10/15160.030.250.06440.25/40.5/4416

BelgiumSalmonella - S. ParatyphiS14FP0113091/29/16320.030.120.0332>320.5/41/4>6432

BelgiumSalmonella - S. ParatyphiS14FP01131101/29/16>640.2520.2532>3264/432/4>64>128

BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-103192/12/1640.150.120.030.250.060.06/40.12/40.254

BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-104202/12/1620.150.120.030.250.060.06/40.12/40.254

BulgariaSalmonella - S. Infantisiso_649221/20/1640.150.120.030.250.120.06/40.25/40.254

BulgariaSalmonella - S. Infantisiso_949231/20/1680.060.250.0310.250.25/41/40.258

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified1242/12612/10/1580.060.250.034160.12/40.25/4>644

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified1342/12712/10/15640.060.120.0332>324/48/4>6416

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified1699/1282/12/1640.150.120.030.250.060.06/40.12/40.254




CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified194/E/C/1322/12/1640.150.120.030.250.060.06/40.12/40.254




CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified3018/13612/10/1540.150.250.030.5160.06/40.12/4644

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified455/1372/12/1640.150.250.03140.06/40.25/4328

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified817/13812/10/1540.150.250.030.580.06/40.12/4644

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified889/1392/12/1640.150.250.030.580.06/40.25/40.254

CyprusSalmonella - S. Infantis301-3024112/10/15160.030.50.068>320.25/40.5/4>648



CyprusSalmonella - S. Virchow328844812/10/1540.030.250.068>320.25/40.5/4>648

EstoniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEST2014-131552/12/1640.150.120.030.250.060.06/40.12/40.258


EstoniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEST2014-3285712/16/15160.150.250.0320.061/41/418

EstoniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEST2014-4625812/10/15160.150.250.0320.060.5/41/418


GermanyEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified14-AB00564_0631/7/1680.150.120.030.250.120.12/40.12/40.258

GermanyEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified14-AB02549_0641/7/1640.150.250.030.2540.06/40.12/414

GermanyEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified15-AB00353_0651/19/1540.150.120.030.250.060.06/40.12/40.254

GreeceSalmonella - S. Havana51937112/10/15320.150.50.0340.250.5/44/41>128

HungaryEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedM2014-10008815722/2/1680.150.120.030.250.060.06/40.12/40.254

HungaryEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedM2014-10044842732/3/1640.030.120.03280.06/40.25/41616

HungarySalmonella - S. EnteritidisM2014-ETBI-050198/01752/2/1620.150.250.030.250.060.06/40.12/40.254

HungarySalmonella - S. EnteritidisM2014-ETBI-051017/01762/3/1620.150.250.030.250.060.12/40.25/40.258

HungarySalmonella - S. HadarM2014-ETBI-048890/01772/2/1640.150.120.030.250.060.12/40.12/40.258

HungarySalmonella - S. InfantisM2014-ETBI-012461/01802/3/16160.150.120.0310.250.25/40.5/40.258

HungarySalmonella - S. NewportM2014-ETBI-000864/01902/2/1620.150.250.030.250.120.06/40.12/40.254

ItalyEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified14051236QM4DJ19112/10/15320.030.250.030.250.250.12/40.25/40.2516

ItalySalmonella - S. Infantis6157L7RQ319412/16/15160.150.250.038320.5/41/46416

LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 36991/20149612/16/1580.150.250.030.250.120.06/40.12/40.58




LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 54235/2/201410012/16/1540.150.120.030.250.120.06/40.12/40.258


LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 55174/201410312/16/1580.150.120.03320.50.06/40.25/448


LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 68727/201410512/16/15640.030.120.0380.254/48/484



LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 74413/20141082/12/1640.150.120.03820.06/40.12/488


LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 79915/201411012/16/1580.150.120.031320.06/40.12/4>648



LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC11211512/16/1540.150.120.031620.06/40.12/4832

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC15811612/16/15>640.250.250.0364132/464/46432

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC37511812/16/1580.150.120.0380.50.06/40.12/448

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC38411912/16/15320.030.120.0380.124/48/484

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC55012012/16/15>640.060.250.06320.258/48/488



LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC9812512/16/1580.150.250.03280.06/40.25/4648

NetherlandsSalmonella - S. HeidelbergSAL RIVM 381.141271/7/16320.030.50.06160.58/48/484

NetherlandsSalmonella - S. HeidelbergSAL RIVM 381.251281/7/16320.030.250.0680.58/48/484

NorwaySalmonella - S. Infantis2014-01-7699-1-1-1-11301/7/16320.150.120.0310.250.5/40.5/40.516

PolandEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedU14/123813212/16/15160.150.250.030.520.12/40.25/40.58

PolandSalmonella - S. MbandakaS14/06911352/12/1640.150.250.030.50.060.06/40.25/40.258

PortugalSalmonella - S. EnteritidisPAT-14-29155SA13812/16/15640.030.250.06320.516/416/4328

RomaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified10579-1 VS EC1412/12/1680.150.120.030.250.060.06/40.12/40.258



RomaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified13343-1.2 SM EC14512/16/15>640.120.250.0380.254/44/488

RomaniaSalmonella-S. Glostrup10219-2 DB1471/21/1640.150.250.030.250.060.06/40.25/40.258

RomaniaSalmonella - S. Infantis11155-1 VS1511/21/1680.150.120.030.50.120.25/40.5/40.258

SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedIsol10215812/16/1580.150.120.030.250.060.06/40.12/40.254

SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedIsol10415912/16/1540.150.120.030.520.06/40.12/4>644

SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedIsol10516012/16/1540.150.120.030.520.06/40.12/4>644


SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedIsol11616212/16/1580.030.250.034>320.12/40.25/4>648


SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedIsol1501642/12/16160.060.120.032320.12/40.24/4>644

SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedISOl1511651/19/1640.150.120.030.250.060.06/40.12/40.254



SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedIsol1811691/7/16>640.120.250.06320.516/432/41616

SpainEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedZTA14/00120EC1721/7/16160.150.120.0316>320.12/40.12/4>648

SpainEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedZTA14/00134EC1731/7/16160.150.250.032320.12/40.25/4>648

SpainEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedZTA14/00895EC1741/7/16160.150.120.03140.12/40.25/4>648

SpainSalmonella - S. Cerro1405951751/7/16>640.030.50.0664132/464/43216

SpainSalmonella - S. Infantis236921771/21/1640.150.250.030.50.060.12/40.5/40.258

SwedenEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedECT111841/7/16160.150.250.0340.121/42/418

SwitzerlandEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified14/ MHK0477_Ec1851/7/16>640.120.250.03160.58/416/41616

SwitzerlandEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified14/MHK0493_Ec1861/19/1640.150.120.0340.50.06/40.25/4116

SwitzerlandEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified14/ MHK1815_Ec1871/7/1640.150.120.030.2540.06/40.12/4324

Omitted due to mixed morfologies

LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 55171/2014101 - 112/16/15640.030.120.03160.254/44/484

LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 55171/2014101 - 212/16/15640.030.250.06160.54/48/43216

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC1054114 - 112/16/1580.060.120.03280.12/40.25/4>648

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC1054114 - 212/16/1580.030.250.03280.12/40.25/4648

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC281117 - 112/16/1580.150.120.031620.06/40.25/41616

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC281117 - 212/16/15160.150.120.033242/41/41616

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC55212112/16/1540.150.120.03820.06/40.25/488see also EUVSEC

LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC614124see also EUVSEC

Total strains

CountryNo total (AMR MON) No Total AMR MON P2No selected Ref. testingNo Analysed by EURLNo Analysed by EURL P1No Analysed by EURL P2No Analysed by EURL P1+P2No of no discrepancies Number of Discrepancies Number of Discrepancies SMX

Austria7634

Austria

EFSA/EURL-AR reference testing PHENOTYPE EUVSEC panelsECOFFS Salmonella/E. coli

Obtained MIC data EUVSEC2 panelsNA / >64>2>0.064>8>0.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSAAustriaSalmonella - S. Enteritidis - PT 4344814AMR MON1616>0.5/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSAnot EURLBelgiumSalmonella1418199 1STR1AMR MON64>320.5412816216416>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSABulgariaEscherichia coli, non-pathogeniciso_865-103AMR MON10240.58>641281612880.250.2510.5>640.5

BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiednot EFSA

Beatriz Guerra: Beatriz Guerra:after Restesting no cefalosp/carba resistance)EURLBulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-103EUVSEC2192/12/160.030.250.2540.0150.120.060.06/40.12/44

EFSABulgariaEscherichia coli, non-pathogeniciso_865-104AMR MON>1024>324>6412812880.250.510.5640.5

BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedAfter checking MIC reading sheets, modified ETP 321>640.12>12864161644

BulgariaSalmonella - S. InfantisCHECKED, EURL values as obtained, and in agreement with genotype. After checking MIC reading sheets, modified ETP 320.25>640.064>12880.250.2510.510.5


Beatriz Guerra: Beatriz Guerra:after Restesting no cefalosp/carba resistance)EURLBulgariaSalmonella - S. Infantisiso_649EUVSEC2221/20/160.030.250.2540.0150.120.120.06/40.25/44

EFSABulgariaSalmonellaiso_949AMR MON>1024>32>8>64128128320.25>640.034>12880.250.2510.510.5


Beatriz Guerra: Beatriz Guerra:after Restesting no cefalosp/carba resistance)EURLBulgariaSalmonella - S. Infantisiso_949EUVSEC2231/20/160.030.25180.060.250.250.25/41/48

EFSA/EURL-AR reference testing GENOTYPE

CountryOrganismsample_namecollection_dategenome_sizecontigsn50speciesserovarmlstmlst_genesvirulenceplasmids_schemedplasmids_unschemedpmlstsResistance genes stratified by antimicrobial classes

Isolate codeAminoglycosideTrimethoprimFluoroquinoloneMLS - Macrolide-Lincosamide-StreptograminBBeta-lactamSulphonamideTetracyclinesPhenicolColistin

DTU2016_430_PRJ1050_Eschericha_coli_iso_865_10320145034369107166897Escherichia coliecoli[ST-162]ecoli[ADK-9,FUMC-65,GYRB-5,ICD-1,MDH-9,PURA-13,RECA-6]astA,gad,iroN,iss,lpfA,mchFIncFIC(FII),IncFIB(AP001918)Col(MG828),ColRNAIIncF[F18:A-:B1]strA (99,88 %) (contig 18); strB (99,88) (contig 18)dfrA14 (99,59 %)gyrA S83L, D87N / parC S80InoneblaTEM-1Bsul2tet(A)nonenone

BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-103OBS: also -18 mutation at chromosomal ampC promoterCOMMENTS

DTU2016_431_PRJ1050_Eschericha_coli_iso_865_10420145027329136133675Escherichia coliecoli[ST-2607]ecoli[ADK-6,FUMC-4,GYRB-22,ICD-18,MDH-11,PURA-8,RECA-7]astA,iss,lpfAIncI1ColRNAI,Col156,Col(MG828)IncI1[Unknown ST]nonedfrA1gyrA S83L, D87N / parC S80InoneblaTEM-1Bsul2tet(A)nonenone

BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-104OBS: also -18 mutation at chromosomal ampC promoterCOMMENTS

DTU2016_432_PRJ1050_Salmonella_infantis_iso_6492014494232588203916Salmonella entericaN/A (7:r:-)senterica[ST-32]senterica[AROC-17,DNAN-18,HEMD-22,HISD-17,PURE-5,SUCA-21,THRA-19]NAColRNAI,Col(MG828)NAaadA1dfrA14 (99,79)gyrA S83Ynonenonesul1tet(A)nonenone

BulgariaSalmonella - S. Infantisiso_649COMMENTS

DTU2016_433_PRJ1050_Salmonella_infantis_iso_9492014493967387203916Salmonella entericaN/A (7:r:-)senterica[ST-32]senterica[AROC-17,DNAN-18,HEMD-22,HISD-17,PURE-5,SUCA-21,THRA-19]NAColpVC,Col(MG828)NAaadA1dfrA14 (99,79)gyrA S83Ynonenonesul1tet(A)nonenone

BulgariaSalmonella - S. Infantisiso_949COMMENTS

Color codes GENTOYPE

Agreement phenotype-genotype at both labs (if data from only one lab are provided, this is indicated in the comments field)

Agreement phenotype-genotype at EURL only

Agreement phenotype-genotype at MS only

The gene detected does not explain (fully) the phenotype

Not detected phenotypically (antimicrobial not in the panel/panel not tested)

In parenthesis, next to each gene, there is a value showing if the hit is partial or has less than 100% identity to the reference gene

Incorrect serovar identification

Strains selected at EFSA for testing but not received at EURL

YEARCountryBacterialabIsolCode

2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_1121

2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_1133-145



Reasons for selection

YEARCountryBacterialabIsolCodeESBL_Sel1ESBL_Sel2Discr_Sel1Colistin_Sel1Colistin_Sel2Azithr_Sel1Azithr_Sel2Kentucky_Sel1Infantis_Sel1






2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-9911ECgeq16

2014BulgariaSalmonella - S. Infantisiso_6491

2014BulgariaSalmonella - S. Infantisiso_9491

Croatia

EFSA/EURL-AR reference testing PHENOTYPE EUVSEC panelsECOFFS Salmonella/E. coli

Obtained MIC data EUVSEC2 panelsNA / >64>2>0.064>8>0.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSACroatiaSalmonella - S. InfantisHRSAL1347/1/14AMR MON320.514128162>0.064>8>0.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSACzech RepublicSalmonellaBA 17761AMR MON640.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSAnot EURLCyprusEscherichia coli, non-pathogenic1242/1AMR MON>1024>32>8>6412816>4164320.256412840.58>641

EFSACyprusEscherichia coli, non-pathogenic1342/1AMR MON pnl26432640.060.25>324816

CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEURLCyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified1342/1EUVSEC22712/10/150.03>6432640.060.12>324/48/416

EFSACyprusEscherichia coli, non-pathogenic1699/1AMR MON>1024>3286412832640.032>128160.250.2510.5>640.5

EFSACyprusEscherichia coli, non-pathogenic1699/1AMR MON pnl264>2>0.064>8>0.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSAGreeceSalmonella - S. Havana5193AMR MON pnl20.064>8>0.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSAHungaryEscherichia coli, non-pathogenicM2014-10008815AMR MON6464>2>0.064>8>0.125NA>16>16>05/ >0.25>1>2>2 / >0.5>8>2>8>0.06>1 / >0.5NA/ >0.125NANANA


EFSAnot EURLSpainEscherichia coli, non-pathogenicZTA14/00120ECAMR MON8>0.06>1 / >0.5NA/ >0.125NANANA


EFSAnot EURLSwitzerlandEscherichia coli, non-pathogenic14/ MHK0477_EcAMR MON16

9

WGS DATA HELPS US TO DETECT.

Emerging Mechanisms?mcr-1, mcr1.6, mcr-3, mcr-4, mcr-5. Colistin-R

Emerging Clones/Plasmids?E. coli [mcr-1/mcr-3] + CTX-M-55 in two countries?

S. Kentucky Cipro-R


Confirmatory testing results, 2015 Exercise

187 strains tested 4488 MIC determinations at EURL-AR5,1% of MIC values with variation over 1 dilution regarding MSresults

AZI: 64 strains MS predicted resistant (89,1% confirmed)Total of 62 EURL resistant strains (33,2% of full collection)

51,6% mph(A)14,6% mph(A) + erm(B)6,5% mph(B)

TIG: 10 strains predicted resistant (0% confirmed)

MERO: 2 strains predicted resistant (0% confirmed)

COL: 41 strains predicted resistant (80,5% confirmed)Total of 34 resistant strains (18,2% of full collection)

61.8% mcr-1 incl. variants11,8% unknown

ESBL/AmpC: 148 strains predicted resistant (96,6% confirmed)Total of 145 resistant strains (77,5% of full collection)

69% CTX-M6,9% CMY-215,2% ampC PM(C42T, T32A, T12G)

EUSR-AMR Reference testing:Validation Monitoring 2016 (exercise 2017)

Data submission

1st Data validation:

MS requested to correct data and re-test if

important issues found

(15 June)

Selection for Ref. testing (ca.

300 isolates)

EURL-asked for isolates

Comparison MIC

EFSA/EURL, contact MSSubmission changed, re-testing

EURL to provide MIC data

comparison EFSA/EURL

WGS

3rd. Ref. Testing: Monitoring 2016

05 06 07-9 9-10 4Q 1Q

2017 2018

EUSR-2016

TIMELINE EXERCISE 2017

2-3Q06-09

MS re-tested/re-corrected reported data

MS re-tested/corrected reported data

MS change data according to EURL results


Carbapenem-R P1 and/or P2: MERO, IMI, ETP

Comparison P1 and P2: FOT, TAZ and MERO

Not solved discrepancies

Inferred phenopypes: ESBL, AmpC, ESBL/AmpC, CPs

Presumptive AmpC/ESBL-phenotype

AmpC phenotype MIC= 16

ESBLs, AmpC

Selected antimicrobials P1: TIG, COL, AZI;

Country specific issues Possible clones: S. Enteritidis COL-R vs. COL-S: R-mechanism unknown

SELECTION OF ISOLATES 2017 EXERCISE

Selection not statistically representative, mostly problematic isolates


CP: MERO, IMI, ETP: Not confirmed in 2 cases; 11 not sent to EURL

FOX not confirmed in 17: TAZ not confirmed in 2.

Inferred phenopypes: ESBL, AmpC, ESBL/AmpC,

Presumptive AmpC: AmpC, 11 out of 95 not confirmed.

Selected antimicrobials P1:

TIG: 2 (0 out of 13 selected for this),

COL: 3 (out of 53 selected for this)

AZI: 3 (1 out of 9 selected for this);

Posible clones: S. Enteritidis COL-R vs. COL-S:all results confirmed

RESULTS AFTER CHANGING DATA FOLLOWING EURL TEST

Selection not statistically representative, mostly problematic isolates


Future criteria - priority and / or emerging AMR phenotypes that require further action

Gram negative

15 9 April 2018

Species Antibiotic with MIC > ECOFF

Further characteristic

Confirm 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

CefotaximeAMPRTest also EUSVEC2

CefotaximeAMPSTest also EUSVEC2

CefoxitinFOTR and/or TAZR

CefoxitinFOTS and TAZS

CeftazidimeAMPRTest also EUSVEC2

CeftazidimeAMPSTest also EUSVEC2

Colistin

ErtapenemFOTR and/or TAZR

ErtapenemFOTSand/or TAZS

Imipenem

MeropenemTest also EUSVEC2

TigecyclineRe-test as antibiotic is labile

Salmonella spp.Azithromycin







ColistinNote and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)



Imipenem



Campylobacter spp.CiprofloxacinNALS

Erythromycin

Gentamicin

Nalidixic acid CIPS

EnterococciDaptomycin

Gentamicin

Linezolid

PenicillinAMPS

Quinupristin-dalfopristin E. faeciumE. 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

16 9 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



Imipenem



Salmonella spp.Azithromycin







ColistinNote and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)



Imipenem



Campylobacter spp.CiprofloxacinNALS

Erythromycin

Gentamicin

Nalidixic acid CIPS

EnterococciDaptomycin

Gentamicin

Linezolid

PenicillinAMPS

Quinupristin-dalfopristin E. faeciumE. faecalis is intrinsically resistant to Q/D

TeicoplaninE. faecalis


VancomycinE. faecalis

Sheet2

Sheet3

17

Thanks for your attention!B. Guerra, R. Garcia Fierro, K. Nagy, A. Stoicescu, I. Mangone, P-A Beloeil

Dr. Beatriz Guerra Romn, PhDSenior Scientific OfficerUnit on Biological Hazards and Contaminants (BIOCONTAM)Department of Risk Assessment and Scientific Assistance (RASA)

e-mail: [email protected]


Acknowledgement

Jette Sejer Kjeldgaard

Ana Rita Rebelo

Pimlapas Leekitcharoenphon

Valeria Bortolaia

Susanne Karlsmose Pedersen

Inge Hansen

Thank you for your attention

Rene S. Hendriksen, PhD

Research group of Bacterial Genomics and Antimicrobial ResistanceWHO 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]

Slide Number 1Term of Reference; EURL ARSlide Number 3Slide Number 4Slide Number 5Slide Number 6Intepretation of the genotypic results Individual resultsSlide Number 9Slide Number 10Slide Number 11Slide Number 12Slide Number 13Slide Number 14Future criteria - priority and / or emerging AMR phenotypes that require further actionFuture criteria - priority and / or emerging AMR phenotypes that require further actionSlide Number 17AcknowledgementSlide Number 19

EFSA Scientific Validation of data supported by the … · DTU Food, Technical University of Denmark Term of Reference; EURL AR Confirmatory testing • Provide confirmatory testing

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