Genomic Research Laboratory
Division of Infectious Diseases
University of Geneva Hospitals
Rue Gabrielle-Perret-Gentil, 4
CH-1211 Geneva 14 - Switzerland

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The Swiss Federal Council approved “Antibiotic Resistance”, National Research Programme 49 (NRP-49), in June of 1999, appropriating funds of 12 million CHF for a five-year period.

Project A - Rapid molecular characterization of MRSA for improved infection control

Project led by Dr P. Francois

The aim is to develop and apply molecular methods -some of which are already fully validated in our laboratory- to rapidly characterize S. aureus clinical isolates. A comprehensive and rapid description of S. aureus isolates in terms of resistance and virulence markers with feedback to the clinicians within 6 hours should improve antibiotic prescription and provide critical epidemiologic information in real-time, via a web-distributed dynamic database. Such genotyping could nicely combine with our rapid MRSA screening assay.

We have developed a series of qPCR assays for detecting the presence of genes encoding the following toxins: Panton-Valentine Leukocidine1 (PVL), exfoliatins A (etA) and B (etA), and the toxin of the staphylococcal toxic shock syndrome: TSST-1. Multiplexed qPCR assays were developed and validated to genotype the staphylococcal chromosomal cassette: SCCmec2 or the agr group. Interestingly, identification of type IV or type V SCCmec cassettes reveals a better marker than PVL for identifying community-acquired MRSA (CA-MRSA2).

Finally, this work led to the development of a high-throughput MLVA method3 for the rapid and affordable genotyping of MSSA and MRSA. This method determines the number of dinucleotide repeats in several genes (currently 10 different targets within a single tube), and separates them using rapid capillary electrophoresis. This approach is coupled to a dedicated interface for peak detection and data analysis providing very high strain discrimination, applicable for outbreak analysis, evaluation of CA-MRSA genetic relationship 4 or prolonged follow-up5.

Project B - Functional Genomics to Study Glycopeptide Resistance in S. aureus

Project led by Dr P. Vaudaux

The recent emergence of glycopeptide resistant strains of S. aureus is a major problem for hospital infection control. Glycopeptides antimicrobial agents are used for treatment of hospital-or community-acquired infections due to methicillin resistant S. aureus. Vancomycin and teicoplanin glycopeptides exert their antimicrobial effects by inhibiting the cell wall synthesis. The mechanism of vancomycin resistance has been extensively studied by biochemical examinations and transmission electron microscopy. These studies suggested that resistant cells produce increased amounts of peptidoglycan, thus thickening the cell wall. The genetic basis for glycopeptide resistance has not been elucidated yet.

We are interested in identifying and characterising genes involved in glycopeptide resistance in S. aureus. Recently our laboratory has developed a genome-wide S. aureus microarray. Using this technology we were able to identify genes absent from a susceptible-revertant strain derived from a teicoplanin-resistant strain. We are currently evaluating if the susceptibility is correlated to the absence of these genes. In parallel, novel genes whose expression is increased or decreased in resistant strains compared to susceptible ones have been identified. The exact contribution of these genes to the mechanism of glycopeptide resistance is under investigation.

In collaboration with the Geneva Biomedical Proteomics Research Group, we have recently set-up the stage for correlating transcriptomic and proteomic data6, and streamlined the process of peptide identification7.

Project C - Molecular Epidemiology of Antimicrobial Resistance in E. coli

Project led by Prof JC. Piffaretti

The aim of the project is to understand the adaptation of Escherichia coli lineages to specific hosts (humans or animals such as dogs, cats, bovines, etc.). The key question is whether specific genetic lineages exist for a particular host. Particularly, we will analyze whether there is an evolutionary divergence between antibiotic resistance determinants observed in E. coli collected from humans and various animal hosts. Alternatively, this study might reveal significant genetic exchanges of these elements between E. coli and distinct hosts.

The investigation techniques applied here are Multi Locus Sequence Typing (MLST), Pulse Field Gel Electrophoresis (PFGE) or Genotyping on Microarrays, the latter being performed in the Genomic Research Lab.

  1. NRP49 Website
  2. Swiss National Science Foundation

Research Projects
  qMRSA: Detection of MRSA
  MagRSA: Automated Diagnosis of MRSA
  S. aureus biofilms
  S. aureus Intracellular Survival
  S. aureus Proteomics
  NRP-49 Projects: Antimicrobial Resistance
  GESNOMA: Noma disease
  MLVA: S. aureus Genotyping
  MIF Knock-Out Mouse Macrophages
  Patho-adaptation of S. aureus
  Phylogenetic Microarray
  High Throughput Sequencing

Revised Mar 08, 2006 - © 2003-2017 Genomic Research Laboratory, Geneva