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Accueil > Equipes de Recherche > Bactéries Pathogènes Opportunistes et Environnement > Opportunistic bacterial pathogens and environment

Opportunistic bacterial pathogens and environment

Team Leaders : COURNOYER Benoit & SERGENTET Delphine

Team :

Permanent Members

BLAHA Didier Lecturer (MCF), UCB
BOIRON Patrick Professor (PR), UCB
COURNOYER Benoit Research Director (DR), CNRS
DOLEANS-JORDHEIM Anne Lecturer (MCF), UCB
FRENEY Jean Professor (PR), UCB
LOUKIADIS Estelle ISPV VetAgroSup
RODRIGUEZ-NAVA Véronica Lecturer (MCF), UCB
THEVENOT SERGENTET Delphine Lecturer (MCF), VetAgroSup
BERGERON Emmanuelle Engineer (IE), UCB
COMMUN Carine Technician (T), UCB
MARJOLET Laurence Engineer (IE), VetAgroSup
GANET Sarah Engineer (IE), VetAgroSup
BOUVIER-CROZIER Marion Sarah Engineer (IE), VetAgroSup
MAZUY-CRUCHAUDET Christine Engineer (IE), VetAgroSup

Non permanent members

GLEIZAL Audrey Assistant Engineer CDD
RIBUN Sébastien Engineer (IE)
GALIA Wessam Post-doctoral researcher
MARTI Romain Post-doctoral researcher
MISZCZYCHA Stéphane Post-doctoral researcher
BOUKAREB Amine PhD Student (2012-2015)
KERANGART Stéphane PhD Student (2012-2015)
PAGES Laurence PhD Student (2012-2015)
BERNARDIN Claire PhD Student (2013-2016)
DOUELLOU Thomas PhD Student (2013-2016)
VOISIN Jérémy PhD Student (2013-2016)
RANNOU Emilie PhD Student (visiteur)

Research field and main goals

Our research activities are dedicated to the understanding of the ecology and evolution of opportunistic bacterial pathogens. The originality of our approaches is in part our ability at integrating social (urbanization, behavior) and environmental issues in the understanding of the factors and forces leading to opportunistic infections and epidemic outbreaks. The notions of invasiveness and expology are investigated, with a particular emphasis on the impact of the biotopes (physico-chemical components, structure, etc) and related biocenosis on the fate of bacterial opportunistic pathogens (BOP) and their virulence. The incidences of environmental filters including agricultural (food, crops, etc) and urban practices (wastewater treatments, management of urban waters) on the dissemination of BOP and their ability at colonizing certain individuals (e. g. people with cystic fibrosis, children and seniors) are investigated. These studies are done without a priori on the BOP species likely to be encountered in the investigated outdoor contexts. However, the most significant populations representing human health hazards among these sites tend to belong to proteobacteria such as Pseudomonas aeruginosa, Burkholderia of the cepacia complex (Bcc), Stenotrophomonas maltophilia, E. coli shiga-toxin producers, and Actinobacteria such as Nocardia. These bacteria are responsible for community-acquired infections, and some, are well-known etiological agents of nosocomial infections.
Fig. 6.1 shows an organizational chart of our research activities. The team’s research activities are divided into four themes : (i) Bio-geography and matrices (sources, transfers, dynamics), (ii) Population diversity and structure (phenotype, genotype, genome), (iii) Expology (exposure, colonization), and (iv) Genetic adaptations towards environmental constraints (virulence, outdoor functions).

PNG - 63.5 ko

Fig. 6.1 : Main research areas of the BPOE team. 1, 2 and 6 indicate our contributions in the understanding of the incidences of various outdoor contexts on BOP prevalence and dissemination. 3 indicates our contributions in the understanding of properties (metabolic activities, adherence, etc) explaining the success of some BOP genotypes in particular outdoor contexts. 4 concerns the expology issues including the investigations of factors that can contribute at exacerbating/reducing BOP virulence among matrices exposing human populations to these organisms. 5 concerns our research activities on clinical cases including the incidence of a human colonization on the selection or loss of particular genetic/genomic elements among BOP.

Bibliography :

2018


  • Kosova-Maali, D., Bergeron, E., Maali, Y., Durand, T., Gonzalez, J., Mouniée, D., Sandoval Trujillo, H., Boiron, P., Salinas-Carmona, M.-C., Rodriguez-Nava, V., 2018. High Intraspecific Genetic Diversity of Nocardia brasiliensis, a Pathogen Responsible for Cutaneous Nocardiosis Found in France: Phylogenetic Relationships by Using sod and hsp65 Genes [WWW Document]. BioMed Research International. URL https://www.hindawi.com/journals/bmri/2018/7314054/ (consulté 6.6.2018).


  • Radix, S., Jordheim, A.D., Rocheblave, L., N'Digo, S., Prignon, A.-L., Commun, C., Michalet, S., Dijoux-Franca, M.-G., Mularoni, A., Walchshofer, N., 2018. N,N′ -disubstituted cinnamamide derivatives potentiate ciprofloxacin activity against overexpressing NorA efflux pump Staphylococcus aureus 1199B strains. European Journal of Medicinal Chemistry. https://doi.org/10.1016/j.ejmech.2018.03.028


  • Voisin, J., Cournoyer, B., Vienney, A., Mermillod-Blondin, F., 2018. Aquifer recharge with stormwater runoff in urban areas: Influence of vadose zone thickness on nutrient and bacterial transfers from the surface of infiltration basins to groundwater. Science of The Total Environment 637-638, 1496-1507. https://doi.org/10.1016/j.scitotenv.2018.05.094

2017



  • Bernardin Souibgui, C., Zoropogui, A., Voisin, J., Ribun, S., Vasselon, V., Pujic, P., Rodriguez-Nava, V., Belly, P., Cournoyer, B., Blaha, D., 2017. Virulence test using nematodes to prescreen <i>Nocardia</i> species capable of inducing neurodegeneration and behavioral disorders. PeerJ 5, e3823. https://doi.org/10.7717/peerj.3823


  • Bertin, Y., Habouzit, C., Dunière, L., Laurier, M., Durand, A., Duchez, D., Segura, A., Thévenot-Sergentet, D., Baruzzi, F., Chaucheyras-Durand, F., Forano, E., 2017. Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? PLOS ONE 12, e0187229. https://doi.org/10.1371/journal.pone.0187229


  • Canouï, E., Blanc, K., Loubinoux, J., Valade, S., Hamard, C., Lefebvre, A., Amorim, S., Bébéar, C., Rodriguez-Nava, V., Lebeaux, D., Launay, O., Alifano, M., Rabbat, A., Kernéis, S., 2017. The value of molecular techniques to diagnose Ureaplasma urealyticum and Nocardia farcinica pleuropneumonia in a patient with diffuse large B-cell lymphoma. International Journal of Infectious Diseases 64, 93-95. https://doi.org/10.1016/j.ijid.2017.09.015


  • Chonova, T., Lecomte, V., Bertrand-Krajewski, J.-L., Bouchez, A., Labanowski, J., Dagot, C., Lévi, Y., Perrodin, Y., Wiest, L., Gonzalez-Ospina, A., Cournoyer, B., Sebastian, C., 2017. The SIPIBEL project: treatment of hospital and urban wastewater in a conventional urban wastewater treatment plant. Environmental Science and Pollution Research 1-10. https://doi.org/10.1007/s11356-017-9302-0


  • Douëllou, T., Delannoy, S., Ganet, S., Fach, P., Loukiadis, E., Montel, M.-C., Sergentet-Thevenot, D., 2017. Molecular characterization of O157:H7, O26:H11 and O103:H2 Shiga toxin-producing Escherichia coli isolated from dairy products. International Journal of Food Microbiology 253, 59-65. https://doi.org/10.1016/j.ijfoodmicro.2017.04.010


  • Eymery, M., Reix, P., Morfin, F., Doleans-Jordheim, A., Vrielynck, S., Jubin, V., Perceval, M., 2017. 164 Are viral respiratory infections a real issue in infants with cystic fibrosis: preliminary results of a prospective cohort study. Journal of Cystic Fibrosis, Abstracts of the 40th European Cystic Fibrosis Conference 16, Supplement 1, S108. https://doi.org/10.1016/S1569-1993(17)30528-3


  • Galia, W., Leriche, F., Cruveiller, S., Garnier, C., Navratil, V., Dubost, A., Blanquet-Diot, S., Thevenot-Sergentet, D., 2017. Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat. BMC Genomics 18, 574. https://doi.org/10.1186/s12864-017-3957-2


  • Kerangart, S., Cournoyer, B., Loukiadis, E., 2017. C-source metabolic profilings of foodborne Shiga-toxin producing E. coli match serogroup differentiations and highlight functional adaptations. International Journal of Food Microbiology. https://doi.org/10.1016/j.ijfoodmicro.2017.10.018


  • Lebeaux, D., Freund, R., van Delden, C., Guillot, H., Marbus, S.D., Matignon, M., Van Wijngaerden, E., Douvry, B., De Greef, J., Vuotto, F., Tricot, L., Fernández-Ruiz, M., Dantal, J., Hirzel, C., Jais, J.-P., Rodriguez-Nava, V., Jacobs, F., Lortholary, O., Coussement, J., Anstey, J.R., Antoine, M., Ausselet, N., Belhaj, A., Boelens, J., de Beenhouwer, H., Denis, C., Ho, E., Ieven, M., Jonckheere, S., Knoop, C., le Moine, A., Rodriguez-Villalobos, H., Racapé, J., Roisin, S., Vandercam, B., Vander Zwalmen, M.-L., Vanfraechem, G., Van Laecke, S., Verhaegen, J., Barrou, B., Battistella, P., Bergeron, E., Bouvier, N., Caillard, S., Caumes, E., Chaussade, H., Chauvet, C., Crochette, R., Epailly, E., Essig, M., Gallien, S., Guillemain, R., Herel, C., Hoen, B., Kamar, N., le Gall, T., Levi, C., Lionet, A., Longuet, H., Melica, G., Miel, A., Morel, H., Ammar, S.O., Pattier, S., Peraldi, M.-N., Sayegh, J., Scemla, A., Senechal, A., Tourret, J., Boggian, K., Egli, A., Garzoni, C., Hoffman, M., Hirsch, H.H., Khanna, N., Manuel, O., Meylan, P., Mueller, N.J., Posfay-Barbe, K.M., Vu, D.-L., Weisser, M., Vollaard, A.M., Wunderink, H.F., 2017. Outcome and Treatment of Nocardiosis After Solid Organ Transplantation: New Insights From a European Study. Clinical Infectious Diseases 64, 1396-1405. https://doi.org/10.1093/cid/cix124


  • Legendre, C., Hannetel, H., Ranc, A.-G., Bezza, W., Pages, L., Vandenesch, F., Tristan, A., Doleans-Jordheim, A., 2017. Listeria monocytogenes and ocular abscess: an atypical but yet potential association. International Ophthalmology 1-8. https://doi.org/10.1007/s10792-017-0723-z


  • Loukiadis, E., Bièche-Terrier, C., Malayrat, C., Ferré, F., Cartier, P., Augustin, J.-C., 2017. Distribution of Escherichia coli O157:H7 in ground beef: Assessing the clustering intensity for an industrial-scale grinder and a low and localized initial contamination. International Journal of Food Microbiology 250, 75-81. https://doi.org/10.1016/j.ijfoodmicro.2017.03.009


  • Marti, R., Bécouze-Lareure, C., Ribun, S., Marjolet, L., Bernardin Souibgui, C., Aubin, J.-B., Lipeme Kouyi, G., Wiest, L., Blaha, D., Cournoyer, B., 2017. Bacteriome genetic structures of urban deposits are indicative of their origin and impacted by chemical pollutants. Scientific Reports 7. https://doi.org/10.1038/s41598-017-13594-8


  • Marti, R., Ribun, S., Aubin, J.-B., Colinon, C., Petit, S., Marjolet, L., Gourmelon, M., Schmitt, L., Breil, P., Cottet, M., Cournoyer, B., 2017. Human-Driven Microbiological Contamination of Benthic and Hyporheic Sediments of an Intermittent Peri-Urban River Assessed from MST and 16S rRNA Genetic Structure Analyses. Frontiers in Microbiology 8. https://doi.org/10.3389/fmicb.2017.00019


  • Pages-Monteiro, L., Marti, R., Commun, C., Alliot, N., Bardel, C., Meugnier, H., Perouse-de-Montclos, M., Reix, P., Durieu, I., Durupt, S., Vandenesch, F., Freney, J., Cournoyer, B., Doleans-Jordheim, A., 2017. Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa. PLOS ONE 12, e0173022. https://doi.org/10.1371/journal.pone.0173022


  • Sánchez-Herrera, K., Sandoval, H., Mouniee, D., Ramírez-Durán, N., Bergeron, E., Boiron, P., Sánchez-Saucedo, N., Rodríguez-Nava, V., 2017. Molecular identification of Nocardia species using the sod A gene. New Microbes and New Infections 19, 96-116. https://doi.org/10.1016/j.nmni.2017.03.008

2016



  • Bonanno, L., Petit, M.-A., Loukiadis, E., Michel, V., Auvray, F., 2016. Heterogeneity in Induction Level, Infection Ability, and Morphology of Shiga Toxin-Encoding Phages (Stx Phages) from Dairy and Human Shiga Toxin-Producing Escherichia coli O26:H11 Isolates. Applied and Environmental Microbiology 82, 2177-2186. https://doi.org/10.1128/AEM.03463-15


  • Boukerb, A.M., Decor, A., Ribun, S., Tabaroni, R., Rousset, A., Commin, L., Buff, S., Doléans-Jordheim, A., Vidal, S., Varrot, A., Imberty, A., Cournoyer, B., 2016. Genomic Rearrangements and Functional Diversification of lecA and lecB Lectin-Coding Regions Impacting the Efficacy of Glycomimetics Directed against Pseudomonas aeruginosa. Antimicrobials, Resistance and Chemotherapy 811. https://doi.org/10.3389/fmicb.2016.00811


  • Coussement, J., Lebeaux, D., van Delden, C., Guillot, H., Freund, R., Marbus, S., Melica, G., Van Wijngaerden, E., Douvry, B., Van Laecke, S., Vuotto, F., Tricot, L., Fernández-Ruiz, M., Dantal, J., Hirzel, C., Jais, J.-P., Rodriguez-Nava, V., Lortholary, O., Jacobs, F., European Study Group for Nocardia in Solid Organ Transplantation, 2016. Nocardia infection in solid organ transplant recipients: a multicenter European case-control study. Clinical Infectious Diseases ciw241. https://doi.org/10.1093/cid/ciw241


  • Douëllou, T., Delannoy, S., Ganet, S., Mariani-Kurkdjian, P., Fach, P., Loukiadis, E., Montel, M., Thevenot-Sergentet, D., 2016. Shiga toxin-producing Escherichia coli strains isolated from dairy products — Genetic diversity and virulence gene profiles. International Journal of Food Microbiology 232, 52-62. https://doi.org/10.1016/j.ijfoodmicro.2016.04.032


  • Galia, W., Jameh, N., Perrin, C., Genay, M., Dary-Mourot, A., 2016. Acquisition of PrtS in Streptococcus thermophilus is not enough in certain strains to achieve rapid milk acidification. Dairy Science & Technology 1-14. https://doi.org/10.1007/s13594-016-0292-3


  • Jameh, N., Galia, W., Awussi, A.A., Roux, E., Genay, M., Perrin, C., Dary-Mourot, A., 2016. Characterization of a new peptide transport system in Streptococcus thermophilus. Food Research International 86, 34-45. https://doi.org/10.1016/j.foodres.2016.04.039


  • Kerangart, S., Douëllou, T., Delannoy, S., Fach, P., Beutin, L., Sergentet-Thévenot, D., Cournoyer, B., Loukiadis, E., 2016. Variable tellurite resistance profiles of clinically-relevant Shiga toxin-producing Escherichia coli (STEC) influence their recovery from foodstuffs. Food Microbiology 59, 32-42. https://doi.org/10.1016/j.fm.2016.05.005


  • Labanowski, J., Laurent, E., Chonova, T., Bouchez, A., Cournoyer, B., Marjolet, L., Marti, R., Mondamert, L., 2016. Rejets d’effluents hospitaliers : évaluation de la persistance environnementale des médicaments et des bactéries pathogènes: La démarche du projet Persist-Env. Techniques Sciences Méthodes 22-30. https://doi.org/10.1051/tsm/201606022


  • Roussel, C., Cordonnier, C., Galia, W., Olivier, L.G., Thévenot, J., Chalancon, S., Alric, M., Thevenot-Sergentet, D., Leriche, F., Van de Wiele, T., Livrelli, V., Blanquet-Diot, S., 2016. Increased EHEC survival and virulence gene expression indicate an enhanced pathogenicity upon simulated pediatric gastrointestinal conditions. Pediatric Research. https://doi.org/10.1038/pr.2016.144

  • Schmitt, L., Grosprêtre, L., Breil, P., Namour, P., Lafont, M., Delile, H., Eschbach, D., Jacob-Rousseau, N., Cournoyer, B., 2016. Pour l’étude interdisciplinaire des petits hydrosystèmes périurbains (bassin de l’Yzeron, France). BSGLg.
  • Vautrin, F., Le Floch, A., Gutbraut, E., Bergeron, E., Marjolet, L., Gleizal, A., Gervaix, J., Cournoyer, B., Winiarski, T., Rodriguez-Nava, V., 2016. Nocardia, un pathogène au fil de l’eau.


  • Voisin, J., Cournoyer, B., Mermillod-Blondin, F., 2016. Assessment of artificial substrates for evaluating groundwater microbial quality. Ecological Indicators 71, 577-586. https://doi.org/10.1016/j.ecolind.2016.07.035

2015



  • Balière, C., Rincé, A., Thevenot-Sergentet, D., Gourmelon, M., 2015. Successful detection of pathogenic Shiga-toxin-producing Escherichia coli in shellfish, environmental waters and sediment using the ISO/TS-13136 method. Letters in Applied Microbiology 60, 315-320. https://doi.org/10.1111/lam.12386

  • Boukerb, A.M., 2015. Sources, diversité et propriétés d’adhérence des Pseudomonas aeruginosa introduits en rivière péri-urbaine par temps de pluie. Lyon 1.


  • Boukerb, A.M., Marti, R., Cournoyer, B., 2015. Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade. Genome Announcements 3, e01366-15. https://doi.org/10.1128/genomeA.01366-15


  • Branco, L., Rodriguez-Nava, V., Boiron, P., Pinheiro, D., 2015. Disseminated nocardiosis: report of five cases. JMM Case Reports 2. https://doi.org/10.1099/jmmcr.0.000046


  • Galia, W., Mariani-Kurkdjian, P., Loukiadis, E., Blanquet-Diot, S., Leriche, F., Brugère, H., Shima, A., Oswald, E., Cournoyer, B., Thevenot-Sergentet, D., 2015. Genome Sequence and Annotation of a Human Infection Isolate of Escherichia coli O26:H11 Involved in a Raw Milk Cheese Outbreak. Genome Announcements 3, e01568-14. https://doi.org/10.1128/genomeA.01568-14


  • Heraud, S., Freydiere, A.-M., Doleans-Jordheim, A., Bes, M., Tristan, A., Vandenesch, F., Laurent, F., Dauwalder, O., 2015. Direct Identification of <i>Staphylococcus aureus</i> and Determination of Methicillin Susceptibility From Positive Blood-Culture Bottles in a Bact/ALERT System Using Binax Now <i>S. aureus</i> and PBP2a Tests. Annals of Laboratory Medicine 35, 454. https://doi.org/10.3343/alm.2015.35.4.454


  • Lebaron, P., Cournoyer, B., Lemarchand, K., Nazaret, S., Servais, P., 2015. Environmental and Human Pathogenic Microorganisms, dans: Bertrand, J.-C., Caumette, P., Lebaron, P., Matheron, R., Normand, P., Sime-Ngando, T. (Éd.), Environmental Microbiology: Fundamentals And Applications. Springer Netherlands, p. 619-658.


  • Piau, C., Kerjouan, M., Le Mouel, M., Patrat-Delon, S., Henaux, P.-L., Brun, V., Morin, M.-P., Gautier, P., Rodriguez-Nava, V., Kayal, S., 2015. First case of disseminated human infection with Nocardia cerradoensis. Journal of Clinical Microbiology JCM.02979-14. https://doi.org/10.1128/JCM.02979-14


  • Voisin, J., Cournoyer, B., Mermillod-Blondin, F., 2015. Utilisation de billes de verre comme substrats artificiels pour la caractérisation des communautés microbiennes dans les nappes phréatiques : mise au point méthodologique. La Houille Blanche 52-57. https://doi.org/10.1051/lhb/20150046

  • Wheeler, S.R., Heard, P., Dufour, C., Thevenot-Sergentet, D., Loukiadis, E., Flowers, R.S., McMahon, W., 2015. Detection of Non-O157 Shiga Toxin–Producing Escherichia coli in 375 Grams of Beef Trim Enrichments across Multiple Commercial PCR Detection Platforms. Journal of Food Protection 78, 196-202. https://doi.org/10.4315/0362-028X.JFP-14-263

2014



  • Bibbal, D., Kérourédan, M., Loukiadis, E., Scheutz, F., Oswald, E., Brugère, H., 2014. Slaughterhouse effluent discharges into rivers not responsible for environmental occurrence of enteroaggregative Escherichia coli. Veterinary Microbiology 168, 451-454. https://doi.org/10.1016/j.vetmic.2013.11.042

  • Bibbal, D., Loukiadis, E., Kérourédan, M., Ferré, F., Dilasser, F., Peytavin de Garam, C., Cartier, P., Oswald, E., Gay, E., Auvray, F., Brugère, H., 2014. Prevalence of carriers of Shiga toxin-producing Escherichia coli serotypes O157:H7, O26:H11, O103:H2, O111:H8 and O145:H28 in French slaughtered adult cattle. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.03315-14


  • Deredjian, A., Colinon, C., Hien, E., Brothier, E., Youenou, B., Cournoyer, B., Dequiedt, S., Hartmann, A., Jolivet, C., Houot, S., Ranjard, L., Saby, N.P.A., Nazaret, S., 2014. Low occurrence of Pseudomonas aeruginosa in agricultural soils with and without organic amendment. Frontiers in Cellular and Infection Microbiology 4. https://doi.org/10.3389/fcimb.2014.00053


  • Kouyi, G.L., Cren-Olivé, C., Cournoyer, B., 2014. Chemical, microbiological, and spatial characteristics and impacts of contaminants from urban catchments: CABRRES project. Environmental Science and Pollution Research 21, 5263-5266. https://doi.org/10.1007/s11356-014-2612-6


  • Lavenir, R., Petit, S.M.-C., Alliot, N., Ribun, S., Loiseau, L., Marjolet, L., Briolay, J., Nazaret, S., Cournoyer, B., 2014. Structure and fate of a Pseudomonas aeruginosa population originating from a combined sewer and colonizing a wastewater treatment lagoon. Environmental Science and Pollution Research 21, 5402-5418. https://doi.org/10.1007/s11356-013-2454-7


  • Miszczycha, S.D., Thévenot, J., Denis, S., Callon, C., Livrelli, V., Alric, M., Montel, M.-C., Blanquet-Diot, S., Thevenot-Sergentet, D., 2014. Survival of Escherichia coli O26:H11 exceeds that of Escherichia coli O157:H7 as assessed by simulated human digestion of contaminated raw milk cheeses. International Journal of Food Microbiology 172, 40-48. https://doi.org/10.1016/j.ijfoodmicro.2013.11.029


  • Mungkalasiri, J., Bedel, L., Emieux, F., Vettese-Di Cara, A., Freney, J., Maury, F., Renaud, F.N.R., 2014. Antibacterial properties of TiO2–Cu composite thin films grown by a one step DLICVD process. Surface and Coatings Technology 242, 187-194. https://doi.org/10.1016/j.surfcoat.2013.08.039