• Confirmation of bacterial identification to species level using MALDI-TOF MS

• Screening of antimicrobial resistance mechanisms by in vitro susceptibility testing to 16 antimicrobial drugs using disc diffusion
• 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 and OXA-23)
• End-point PCR simplex or multiplex targetting
  
  • Class A and class B carbapenemases (NDM, VIM, KPC, IMP, IMI, SIM, GIM, DIM, FIM, SMB, SME, SPM)  
  • Class D carbapenemases (OXA-48, OXA-427, OXA-198, OXA-23, OXA-24, OXA-58)
  • Major ESBL families (TEM, SHV and PME )
  • minor ESBL families (GES, VEB, PER and BEL)
  • oxacillinase group (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)
• Other genetic characterization methods:
  
  • Sequencing of resistance genes  and the genetic environment by NGS
  • 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)

Serotyping of Pseudomonas eruginosa by NGS

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

core MLST typing: sequencing of 629 house keeping genes and definition of cgST according the website

A. baumannii  : http://pubmlst.org/abaumannii

P. aeruginosa  : http://pubmlst.org/paeruginosa