EFSA Scientific Validation of data supported by the … · DTU Food, Technical University of...
Transcript of EFSA Scientific Validation of data supported by the … · DTU Food, Technical University of...
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EFSA Scientific Validation of data supported by the EURL Reference Testing
6 April 2018
EURL-AR Network
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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
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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
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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
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CONFIRM MECHANISM INFERRED FROM PHENOTYPE
Scientific validation- Ref. testing
CTX-M-15
VIM-1
SHV-12
cAMPc
CMY-2
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DETECT EMERGING CLONES MECHANISMS
Scientific validation- Ref. testing
S. Para B dT+
S. Kentucky
S. Infantis mcr-1
blaVIM-1
blaCTX-M-15
blaCMY-2
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DTU Food, Technical University of Denmark
Intepretation of the genotypic results
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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
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DTU Food, Technical University of Denmark
Individual results
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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, unspecified1780/1292/12/1640.150.120.030.250.060.06/40.12/40.254
CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified1812/13012/10/15160.150.250.030.250.060.06/40.12/40.258
CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified1917/1312/12/1640.150.120.030.250.060.06/40.12/40.254
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, unspecified2213/13312/10/1540.150.250.030.250.060.06/40.12/40.258
CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified2231/1342/12/1680.150.250.030.250.060.06/40.12/40.254
CyprusEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified2289/1352/12/1680.150.250.030.250.250.06/40.12/40.254
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. Infantis303-3044212/10/15160.030.250.038>320.5/40.5/4>648
CyprusSalmonella - S. Infantis307-3084312/10/1540.030.250.068>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, unspecifiedEST2014-1395612/10/1540.150.120.030.250.120.06/40.12/40.54
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
EstoniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEST2014-7592/12/1640.150.120.030.250.060.06/40.12/40.258
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 39322/20149712/16/1580.150.120.030.250.120.06/40.12/40.254
LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 39323/20149812/16/1540.150.120.030.250.120.06/40.12/40.254
LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 44870/20149912/16/1540.150.120.030.250.120.06/40.12/40.254
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 55172/201410212/16/1580.150.120.030.250.120.06/40.12/40.254
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 67358/1/20141042/12/1680.150.120.030.250.060.06/40.12/40.252
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 70765/2/20141062/12/1680.150.120.030.250.060.06/40.12/40.258
LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 74412/20141072/12/16160.150.120.030.250.250.12/40.25/40.254
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 76207/2/20141092/12/1640.150.120.030.250.060.06/40.12/40.252
LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 79915/201411012/16/1580.150.120.031320.06/40.12/4>648
LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 79917/201411112/16/1540.150.120.031320.06/40.25/4648
LatviaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC 84347/201411212/16/1580.150.120.03180.06/40.25/4328
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, unspecifiedEC59412212/16/15>640.060.250.03320.516/432/41632
LithuaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedEC59712312/16/15>640.060.50.03160.58/416/4648
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, unspecified10904-2 VS EC1422/12/1680.150.120.030.250.060.06/40.12/40.254
RomaniaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecified11559-2 VS EC14412/16/1540.150.250.030.250.060.06/40.12/40.254
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, unspecifiedIsol11516112/16/15160.150.250.030.50.060.12/40.25/40.2516
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, unspecifiedIsol1331632/12/1640.150.120.030.250.060.06/40.25/40.254
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, unspecifiedIsol1611661/7/1640.150.250.030.250.060.06/40.12/40.254
SlovakiaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiedIsol1631671/7/1680.150.120.030.250.060.06/40.12/40.254
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
EFSAnot EURLBelgiumSalmonella1418199 1STR1AMR MON64>320.5412816216416>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
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
BulgariaSalmonella - S. Infantisnot EFSA
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
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
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
2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_261
2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-99
Reasons for selection
YEARCountryBacterialabIsolCodeESBL_Sel1ESBL_Sel2Discr_Sel1Colistin_Sel1Colistin_Sel2Azithr_Sel1Azithr_Sel2Kentucky_Sel1Infantis_Sel1
2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_11211
2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_1133-1451
2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_2611
2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-1031
2014BulgariaEscherichia coli, non-pathogenic - E.coli, non-pathogenic, unspecifiediso_865-1041
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
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
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
EFSAnot EURLSpainEscherichia coli, non-pathogenicZTA14/00120ECAMR MON8>0.06>1 / >0.5NA/ >0.125NANANA
CountryOrganismCountry Organism Isolate codePanelWorking #DateSMXTMPCIPTETMEROAZINALCHLFOTTGCCOLTAZAMPGENFOXETPIMIFEPF/CT/CTRM
EFSAnot EURLSwitzerlandEscherichia coli, non-pathogenic14/ MHK0477_EcAMR MON16
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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
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DTU Food, Technical University of Denmark
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)
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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
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Scientific validation- Ref. testing
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
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Scientific validation- Ref. testing
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
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DTU Food, Technical University of Denmark
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
CefotaximeAMPRTest also EUSVEC2
CefotaximeAMPSTest also EUSVEC2
CefoxitinFOTR and/or TAZR
CefoxitinFOTS and TAZS
CeftazidimeAMPRTest also EUSVEC2
CeftazidimeAMPSTest also EUSVEC2
ColistinNote and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)
ErtapenemFOTR and/or TAZR
ErtapenemFOTSand/or TAZS
Imipenem
MeropenemTest also EUSVEC2
TigecyclineRe-test as antibiotic is labile
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
TigecyclineRe-test as antibiotic is labile
VancomycinE. faecalis
Sheet2
Sheet3
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DTU Food, Technical University of Denmark
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
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
CefotaximeAMPRTest also EUSVEC2
CefotaximeAMPSTest also EUSVEC2
CefoxitinFOTR and/or TAZR
CefoxitinFOTS and TAZS
CeftazidimeAMPRTest also EUSVEC2
CeftazidimeAMPSTest also EUSVEC2
ColistinNote and store also COL-S S. Enteritidis and S. Dublin (serogroup 9)
ErtapenemFOTR and/or TAZR
ErtapenemFOTSand/or TAZS
Imipenem
MeropenemTest also EUSVEC2
TigecyclineRe-test as antibiotic is labile
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
TigecyclineRe-test as antibiotic is labile
VancomycinE. faecalis
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Sheet3
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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]
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DTU Food, Technical University of Denmark
Acknowledgement
Jette Sejer Kjeldgaard
Ana Rita Rebelo
Pimlapas Leekitcharoenphon
Valeria Bortolaia
Susanne Karlsmose Pedersen
Inge Hansen
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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
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