Analysis performed by the NRC


  • Confirmation of bacterial identification to species level using MALDI-TOF MS and/or whole-genome sequencing (including 16S rRNA, rpoB sequencing)

  • In vitro susceptibility testing to antimicrobial drugs by disc diffusion according to EUCAST guidelines
  • Determination of MICs by broth microdilution method according the EUCAST guidelines and interpretative breakpoints

  • Carbapenem hydrolysis-based tests
  • Inhibitors-based combination disk tests:
    • For the detection of ESBL and/or hyperproduced AmpC
    • For the detection of carbapenemase
  • Extended susceptibility disk diffusion testing against aminoglycosides for the detection of 16S rRNA methylases

  • Immunochromatographic detection of carbapenemase (OXA-48, KPC, VIM, NDM, IMP, OXA-23)
  • Simplex or multiplex PCR targeting
    • carbapenemases (NDM, VIM, KPC, IMP, OXA-48, OXA-427, BES, IMI, SIM, GIM, DIM, FIM, SMB, SME, SPM)
    • ESBL (TEM, SHV, CTX-M group 1,  2 and 9 )
    • minor ESBL (GES, VEB, PER, BEL, PME)
    • plasmidic cephalosporinases (MOX, CMY, DHA, ACC, ACT/MIR, FOX)
    • OXA-carbapenemases (OXA-group23, -24 and -58, OXA-198)
    • other oxacillinases groups (OXA-1, OXA-2, OXA-9, OXA-10, OXA-18, OXA-20)
    • 16S rRNA methylases (ArmA, Rmt A-B-C-D-E-F-G, NpmA)
    • plasmid-borne quinolone resistance genes (QnrA, QnrB, QnrS)
    • Plasmid-mediated colistin resistance genes (MCR-1 to MCR-5)
  • Other genetic characterization methods:
    • Target-amplified or whole-genome sequencing for the determination of virulence factors, resistance genes and the genetic environment
    • Plasmid extraction by Kieser method
    • Conjugation, transformation and cloning
    • PCR-based replicon typing : method based on replicons (Inc/rep PCR) of the major plasmid incompatibility groups (Caratolli A. et al , JAC. 2010 Dec;65(12):2518-29)
    • Multiplex End-point PCR detecting capsular types (K1, K2, K5, K20, K54 and K57) and virulence factors (rmpA, wcaG, terW, iutA, repA and silS) in K.pneumoniae
    • Quadruplex End-point PCR assigning E.coli to the following phylo-groups (A,B1,B2,C,D,E and F)

MLST typing  : PCR and sequencing of 7 house keeping genes and definition of ST according the website

coreMLST typing: sequencing of 629 house keping genes and definition of cgST according the website


Whole-genome sequencing with phylogenetic analysis for outbreak investigation

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