CEA CHRU CNRS CPU INRA INRIA INSERM INSTITUT PASTEUR IRD

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33rdrd meeting international research - June 10, 2011 meeting international research - June 10, 2011

Infectious disease and MicrobiologyIgnorance, speculative deductions, unconfirmed predictions

- H factor

- Highest grant = 73 M€- I.H.U

Didier Raoult - Didier Raoult - didier.raoult@gmail.comdidier.raoult@gmail.com - - Marseille - FranceMarseille - France

ObjectiveObjectiveCompleting the Genes repertoire- Microorganisms- Genomes

Where- In environnement (water, goil, animals, vectors plants)- Healthy humans- Patients

Comparing repertoires to identify links with diseases -Microbes- Genomes- Genes

Tools for diagnostic

Unknown genosphere by metagenomics Unknown genosphere by metagenomics studiesstudies

10-15% organisms with Ribosomes

15-30% known viruses

55-70% ???

DNA sequences of the living in the XXIDNA sequences of the living in the XXIth th

centurycentury

Edwards RA, Rohwer F. Viral metagenomics. Nature Rev Microbiol. 2005;3:504-510. U

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• TABASCO, Hot Ketchup and human stool

• Positive detection by RT-PCR

TEM ~ 109/ml

• Is it multiplying in humans?

• Is it causing something?P.Colson.Pepper Mild Mottle Virus, a Plant Virus Associated with Specific Immune Responses, Fever, Abdominal Pains, and Pruritus in Humans.Plos one.2010

Tools Culture- introducing culturomics

Free-living bacterial community

264 lost COGs

Facultative host-associatedBacteria

GS 2.92 ± 1.6GC 43.0 ± 11.7Op 3.36 ± 2.6

TR 65.7 ± 56.0

615 lost COGs

Core of lost genesMetabolismCellular processes

↑ Atypical rDNA operon

↓ Growth rate

Merhej V, et al. Biol Direct. 2009 Apr 10;4:13.

Genome sequencing and analysis

In point of care for diagnostic and treatment POC

Timone Senegal

Molecular diagnostic Molecular diagnostic

ResultsResults1) Giant viruses2) Microbiota and obesity3) Repertoire of causes fever in Africa (45%)4) New culture media (TB, T.whipplei, Coxiella burnetii for vaccine)5) Reversion of pathogenocity paradigm more pathogenic less genes

(except toxins) => vaccine interest6) New antibiotics (pentamidine)7) Multiplexed serologic microaray