Ecology and Evolution of microorganisms (EMI-E0339)

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Olivier Clermont
Research Engineer
email : olivier.clermont@inserm.fr

Inserm U722

Ecology and evolution of microorganisms

Contact information - Inserm U722
Faculté de Médecine Xavier Bichat
16, rue Henri Huchard -- 75018 Paris (France)

Tel: 33 (0)1 57 27 77 43 -- Fax: 33 (0)1 57 27 77 24
3ème étage - ascenseur B - pièce 396

Research interest

Education

List of the 10 main publications

Exhaustive list of publications

Research interest

Ingénieur en Biologie Moléculaire, mon but est de trouver et d'appliquer de nouvelles méthodes d'analyse moléculaire. Mon parcours m'a ainsi mené de l'analyse médicale en microbiologie jusqu'à une thèse en génétique microbienne en passant par une formation en biochimie et en génétique humaine. Cette dernière expérience m'a permis de faire partie de l'équipe qui a identifié le gène responsable des amyotrophies spinales infantiles (SMA) dans laquelle je me suis d'abord intéressé à la mise au point de la carte génétique haute résolution de la région contenant le gène puis, après l'identification de celui-ci (gène SMN1), à la délicate caractérisation de ses mutations ponctuelles. Du coté bactérien, je me suis donc spécialisé sur la génétique de Escherichia coli et, en particulier, son épidémiologie, sa phylogénie, la caractérisation de ses îlots de pathogénicité (PAI) et la relation entre phylogénie et virulence.

Education

Degrees

2002	Thèse de Doctorat de l'Ecole Pratique des Hautes Etudes (EPHE). Titre : « Etude génétique et épidémiologique de Escherichia coli responsable de méningite néonatale »
1996	Diplôme de l'Ecole Pratique des Hautes Etudes (EPHE). Titre : « Les Amyotrophies Spinales Infantiles : De la localisation chromosomique au diagnostic génétique »
1992	Diplôme de Premier Cycle Technique (DPCT) du Conservatoire National des Arts et Métiers, option Biochimie.
1988	Brevet de Technicien Supérieur (BTS), option Analyses Biologiques.

Academic positions

2003-present	Research Engineer
1998-2003	Research Engineer in EA3105 in "Laboratoire d'études de génétique bactérienne dans les infections de l'enfant", directed by Pr. Edouard Bingen

List of the 10 main publications

CLERMONT O., BURLET P., BURGLEN L., LEFEBVRE S., PASCAL F., Mc PHERSON J., WASMUTH J.J., COHEN D., LE PASLIER D., WEISSENBACH J., LATHROP M., MUNNICH A., MELKI J. (1994).
Use of genetic and physical mapping to locate the spinal muscular atrophy locus between two new highly polymorphic DNA markers. Am. J. Hum. Genet. 54: 687-94.

MELKI J., LEFEBVRE S., BURGLEN L., BURLET P., CLERMONT O., MILLASSEAU P., REBOULLET S., BENICHOU B., ZEVIANI M., LE PASLIER D., COHEN D., WEISSENBACH J., MUNNICH A. (1994).
De novo and inherited deletions of the 5q13 region in spinal muscular atrophies. Science 264: 1474-7.

LEFEBVRE S., BURGLEN L., REBOULLET S., CLERMONT O., BURLET P., VIOLLET L., BENICHOU B., CRUAUD C., MILLASSEAU P., ZEVIANI M., LE PASLIER D., FREZAL J., COHEN D., WEISSENBACH J., MUNNICH A., MELKI J. (1995).
Identification and characterization of a spinal muscular atrophy-determining gene. Cell 80: 155-65.

BUSSAGLIA E., CLERMONT O., TIZZANO E., LEFEBVRE S., BURGLEN L., URTIZBEREA J.A., COLOMER J., MUNNICH A., BAIGET M., MELKI J. (1995).
A frame-shift deletion in the survival motor neuron gene in Spanish spinal muscular atrophy patients. Nat. Genet. 11: 335-7.

CLERMONT O., BONACORSI S., BINGEN E. (2000).
Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66: 4555-8.

DURIEZ P., CLERMONT O., BONACORSI S., BINGEN E., CHAVENTRE A., ELION J., PICARD B., DENAMUR E. (2001).
Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiology.147: 1671-6.

CLERMONT O., CORDEVANT C., BONACORSI S., MARECAT A., LANGE M., BINGEN E. (2001).
Automated ribotyping provides rapid phylogenetic subgroup affiliation of clinical extraintestinal pathogenic Escherichia coli strains. J. Clin. Microbiol. 39: 4549-53.

BONACORSI S., CLERMONT O., HOUDOIN V., CORDEVANT C., BRAHIMI N., MARECAT A., TINSLEY C., NASSIF X., LANGE M., BINGEN E. (2003).
Molecular analysis and experimental virulence of french and north american Escherichia coli neonatal meningitis isolates: identification of a new virulent clone. J. Infect. Dis. 187: 1895-906.

ESCOBAR-PARAMO P., CLERMONT O., BLANC-POTARD A.B., BUI H., LE BOUGUENEC C., DENAMUR E. (2004).
A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol. Biol. Evol. 21: 1085-94.

CLERMONT O., BURLET P., BENIT P., SAUGIER-VEBER P., CHANTERAU D., MUNNICH A., CUSIN V. (2004).
Molecular analysis of SMA patients without homozygous SMN1 deletion using a new strategy for identification of SMN1 subtle mutations. Hum mutat. 24: 417-27.

Exhaustive list of publications

LE GALL T.*, CLERMONT O.*, GOURIOU S., PICARD B., NASSIF X., DENAMUR E.,
TENAILLON O.
Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains.
Mol. Biol. Evol., 2007, 24, 2373-2384
*The two first authors have equally contributed to the work

CLERMONT O., JOHNSON J.R., MENARD M., DENAMUR E.
Determination of Escherichia coli O types by allele-specific PCR: application to bloodstream isolates.
Diagn. Microbiol. Infect. Dis., 2007, 57, 129-136

DIARD M., BAERISWYL S., CLERMONT O., GOURIOU S., PICARD B., TADDEI F., DENAMUR E., MATIC I.
Caenorhabditis elegans as a simple model to study phenotypic and genetic virulence determinants of extraintestinal pathogenic Escherichia coli.
Microbes Infect., 2007, 9, 214-223

JOHNSON J.R., CLERMONT O., MENARD M., KUSKOWSKI M.A., MENARD M., PICARD B., DENAMUR E.
Experimental mouse lethality of Escherichia coli isolates in relation to accessory raits, physlogenetic group, and clinical source.
J. Infect Dis., 2006, 194, 1141-1150

MELKI J., BURLET P., CLERMONT O., PASCAL F., PAUL B., ABDELHAK S,. NAKAMURA Y., WEISSENBACH J., LATHROP M., MUNNICH A. (1993).
Refined linkage map of chromosome 5 in the region of the spinal muscular atrophy gene. Genomics 15: 521-4.

BURLET P., ABDELHAK S., PASCAL F., CLERMONT O., PAUL B., MUNNICH A., MELKI J. (1993).
Trinucleotide repeat polymorphism at the D5S556 locus. Hum. Mol. Genet. 2: 1328.

MELKI J., LEFEBVRE S., BURGLEN L., BURLET P., CLERMONT O., MILLASSEAU P., REBOULLET S., BENICHOU B., ZEVIANI M., LE PASLIER D., COHEN D., WEISSENBACH J., MUNNICH A. (1994).
Délétions héritées et de novo dans les Amyotrophies Spinales. Médecine/Sciences 10: 889-91.

BURGLEN L., LEFEBVRE S., REBOULLET S., CLERMONT O., BURLET P., VIOLLET L., BENICHOU B., CRUAUD C., MILLASSEAU P., ZEVIANI M., LE PASLIER D., FREZAL J., COHEN D., WEISSENBACH J., MUNNICH A., MELKI J. (1995).
Identification et caractérisation d'un gène déterminant dans les Amyotrophies Spinales. Médecine/Sciences 11: 149-51.

BUSSAGLIA E., CLERMONT O., TIZZANO E., LEFEBVRE S., BURGLEN L., URTIZBEREA J.A., COLOMER J., MUNNICH A., BAIGET M., MELKI J. (1995).
A frame-shift deletion in the survival motor neuron gene in Spanish spinal muscular atrophy patients. Nat. Genet. 11: 335-7.

CLERMONT O., BURLET P., LEFEBVRE S., BURGLEN L., MUNNICH A., MELKI J. (1995).
SMN gene deletion in adult-onset spinal muscular atrophy. Lancet 346: 1712-3.

BURGLEN L., LEFEBVRE S., CLERMONT O., BURLET P., VIOLLET L., CRUAUD C., MUNNICH A., MELKI J. (1996).
Structure and organization of the human survival motor neurone (SMN) gene. Genomics 32: 479-82.

BURLET P., BURGLEN L., CLERMONT O., LEFEBVRE S., VIOLLET L., MUNNICH A., MELKI J. (1996).
Large scale deletions of the 5q13 region are specific to Werdnig-Hoffmann disease. J. Med. Genet. 33: 281-3.

BURGLEN L., AMIEL J., VIOLLET L., LEFEBVRE S., BURLET P., CLERMONT O., RACLIN V., LANDRIEU P., VERLOES A., MUNNICH A., MELKI J. (1996).
SMN gene deletion in the arthrogryposis multiplex congenita-spinal muscular atrophy association. J. Clin. Invest. 98: 1130-2.

BRAHE C., CLERMONT O., ZAPPATA S., TIZIANO F., MELKI J., NERI G. (1996).
Frameshift mutation in the survival motor neuron gene in a severe case of SMA type I. Hum. Mol. Genet. 5: 1971-6.

VIOLLET L., BERTRANDY S., BUENO BRUNIALTI A.L., LEFEBVRE S., BURLET P., CLERMONT O., CRUAUD C., GUENET J.L., MUNNICH A., MELKI J. (1997).
cDNA isolation, expression and chromosomal localization of the mouse survival motor neuron gene (Smn). Genomics 40: 185-8.

HANASH A., LEGUERN E., BIROUK N., CLERMONT O., POUGET J., BOUCHE P., MUNNICH A., BRICE A., MELKI J. (1997). SMN gene analysis of the spinal form of Charcot-Marie-Tooth disease. J. Med. Genet. 34: 507-8.

LEFEBVRE S., BURLET P., LIU Q., BERTRANDY S., CLERMONT O., MUNNICH A., DREYFUSS G., MELKI J. (1997). Correlation between severity and SMN protein level in spinal muscular atrophy. Nat. Genet. 16: 265-9.

BURLET P., HUBER C., BERTRANDY S., LUDOSKY M.A., ZWAENEPOEL I., CLERMONT O., ROUME J., DELEZOIDE A.L., CARTAUD J., MUNNICH A., LEFEBVRE S. (1998).
The distribution of SMN protein complex in human fetal tissues and its alteration in spinal muscular atrophy. Hum. Mol. Genet. 7: 1927-33.

BERTRANDY S., BURLET P., CLERMONT O., HUBER C., FONDRAT C., THIERRY-MIEG D., MUNNICH A., LEFEBVRE S. (1999).
The RNA-binding properties of SMN: deletion analysis of the zebrafish orthologue defines domains conserved in evolution. Hum. Mol. Genet. 8: 775-82.

BONACORSI S., CLERMONT O., TINSLEY C., LE GALLI., BEAUDOIN J.C., ELION J., NASSIF X., BINGEN E. (2000).
Identification of regions of the Escherichia coli chromosome specific for neonatal meningitis associated strains. Infect. Immun. 68: 2096-101.

CLERMONT O., BONACORSI S., BINGEN E. (2000).
Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66: 4555-8.

LE THOMAS I., MARIANI-KURKDJIAN P., COLLIGNON A., GRAVET A., CLERMONT O., BRAHIMI N., GAUDELUS J., AUJARD Y., NAVARRO J., BEAUFILS F., BINGEN E. (2001).
Breast milk transmission of a Panton-Valentine leukocidin-producing Staphylococcus aureus strain causing infantile pneumonia. J. Clin. Microbiol. 39: 728-9.

CLERMONT O., BONACORSI S., BINGEN E. (2001).
The Yersinia high-pathogenicity island is highly predominant in virulence-associated phylogenetic groups of Escherichia coli. FEMS Microbiol. Lett.196: 153-7.

FITOUSSI F., LOUKIL C., GROS I., CLERMONT O., MARIANI P., BONACORSI S., LE THOMASI., DEFORCHE D., BINGEN E. (2001).
Mechanisms of macrolide resistance in clinical group B streptococci isolated in France. Antimicrob. Agents Chemother. 45: 1889-91.

LE THOMAS I., COUETDIC G., CLERMONT O., BRAHIMI N., PLESIAT P., BINGEN E. (2001).
In vivo selection of a target/efflux double mutant of Pseudomonas aeruginosa by ciprofloxacin therapy. J. Antimicrob. Chemother. 48: 553-5.

LEFLON-GUIBOUT V., BONACORSI S., CLERMONT O., TERNAT G., HEYM B., NICOLAS-CHANOINE M.H. (2002).
Pyelonephritis caused by multiple clones of Escherichia coli, susceptible and resistant to co-amoxiclav, after a 45 day course of co-amoxiclav. J. Antimicrob. Chemother. 49: 373-7.

BINGEN-BIDOIS M., CLERMONT O., BONACORSI S., TERKI M., BRAHIMI N., LOUKIL C., BARRAUD D., BINGEN E. (2002).
Phylogenetic analysis and prevalence of urosepsis strains of Escherichia coli bearing pathogenicity island-like domains. Infect. Immun. 70: 3216-26.

HOUDOIN V., BONACORSI S., BRAHIMI N., CLERMONT O., NASSIF X., BINGEN E. (2002).
A uropathogenicity island contributes to the pathogenicity of Escherichia coli strains that cause neonatal meningitis. Infect. Immun. 70: 5865-9.

CUSIN V., CLERMONT O., GERARD B., CHANTERAU D., ELION J. (2003).
Prevalence of SMN1 deletion and duplication in carrier and normal populations: implication for genetic counselling. J. Med. Genet. 40: e39.

CLERMONT O., BONACORSI S., BINGEN E. (2004).
Characterization of an anonymous marker strongly linked to E. coli strains causing neonatal meningitis. J. Clin. Microbiol. 42: 1770-2.

ESCOBAR-PARAMO P., CLERMONT O., BLANC-POTARD A.B., BUI H., LE BOUGUENEC C., DENAMUR E. (2004).
A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol. Biol. Evol. 21: 1085-94.

BONACORSI S., LEFEVRE S., CLERMONT O., HOUDOIN V., BOURRILLON A., LOIRAT C., AUJARD Y., BINGEN E. (2005).
Escherichia coli strains causing urinary tract infection in uncircuncised infants resemble urosepsis-like adult strains. J. Urol. 173:195-197.