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
