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Bactéries Pathogènes Opportunistes et Environnement

Team Leaders : COURNOYER Benoit & SERGENTET Delphine


Permanent Members

BLAHA Didier Lecturer (MCF), UCB
COURNOYER Benoit Research Director (DR), CNRS
GALIA Wessam Lecturer (MCF), VetAgroSup
RODRIGUEZ-NAVA Véronica Lecturer (MCF), UCB
THEVENOT SERGENTET Delphine Professor 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

MAUFOUX Lolita Engineer (IE)
RIBUN Sébastien Engineer (IE)
AIGLE Axel Post-doctoral researcher
DENET Elodie Post-doctoral researcher
DOUELLOU Thomas Post-doctoral researcher
MEYNIER POZZI Adrien Post-doctoral researcher
BAGEL Arthur PhD Student (2019-2022)
BOUCHALI Ryan PhD Student (2018-2021)
VAUTRIN Florian PhD Student (2015-2019)
GARDETTE Marion PhD Student (2016-2019)

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).

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 :


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  • Moyne, O., Castelli, F., Bicout, D.J., Boccard, J., Camara, B., Cournoyer, B., Faudry, E., Terrier, S., Hannani, D., Huot-Marchand, S., Léger, C., Maurin, M., Ngo, T.-D., Plazy, C., Quinn, R.A., Attree, I., Fenaille, F., Toussaint, B., Le Gouëllec, A., 2021. Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance, Virulence and Clinical Outcome in Cystic Fibrosis Chronic Infections. Metabolites 11, 63.

  • Vautrin, F., Pujic, P., Paquet, C., Bergeron, E., Mouniée, D., Marchal, T., Salord, H., Bonnet, J.-M., Cournoyer, B., Winiarski, T., Louzier, V., Rodriguez-Nava, V., 2021. Microbial risk assessment of Nocardia cyriacigeorgica in polluted environments, case of urban rainfall water. Computational and Structural Biotechnology Journal 19, 384-400.


  • Akanny, E., Bonhommé, A., Commun, C., Doleans‐Jordheim, A., Farre, C., Bessueille, F., Bourgeois, S., Bordes, C., 2020. Surface‐enhanced Raman spectroscopy using uncoated gold nanoparticles for bacteria discrimination. Journal of Raman Spectroscopy jrs.5827.

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  • Camus, L., Briaud, P., Bastien, S., Elsen, S., Doléans-Jordheim, A., Vandenesch, F., Moreau, K., 2020. Trophic cooperation promotes bacterial survival of Staphylococcus aureus and Pseudomonas aeruginosa. The ISME Journal 14, 3093-3105.

  • Colin, Y., Bouchali, R., Marjolet, L., Marti, R., Vautrin, F., Voisin, J., Bourgeois, E., Rodriguez-Nava, V., Blaha, D., Winiarski, T., Mermillod-Blondin, F., Cournoyer, B., 2020. Coalescence of bacterial groups originating from urban runoffs and artificial infiltration systems among aquifer microbiomes. Hydrology and Earth System Sciences 24, 4257-4273.

  • Denet, E., Espina-Benitez, M.B., Pitault, I., Pollet, T., Blaha, D., Bolzinger, M.-A., Rodriguez-Nava, V., Briançon, S., 2020. Metal oxide nanoparticles for the decontamination of toxic chemical and biological compounds. International Journal of Pharmaceutics 583, 119373.

  • Gueneau, R., Blanchet, D., Rodriguez-Nava, V., Bergeron, E., Soulier, M., Bestandji, N., Demar, M., Couppie, P., Blaizot, R., 2020. Actinomycetoma caused by Gordonia westfalica: first reported case of human infection. New Microbes and New Infections 100658.

  • Lafont, E., Conan, P.-L., Rodriguez-Nava, V., Lebeaux, D., 2020. Invasive Nocardiosis: Disease Presentation, Diagnosis and Treatment – Old Questions, New Answers? Infection and Drug Resistance Volume 13, 4601-4613.

  • Lafont, E., Marciano, B.E., Mahlaoui, N., Neven, B., Bustamante, J., Rodriguez-Nava, V., Rawat, A., Unzaga, M.J., Fischer, A., Blanche, S., Lortholary, O., Holland, S.M., Lebeaux, D., 2020. Nocardiosis Associated with Primary Immunodeficiencies (Nocar-DIP): an International Retrospective Study and Literature Review. Journal of Clinical Immunology.

  • Lotte, R., Chevalier, A., Dantas, S., Degand, N., Gaudart, A., Rörhlich, P.-S., Boyer, L., Rodriguez-Nava, V., Del Giudice, P., Ruimy, R., 2020. Nocardia takedensis: a newly recognized pathogen responsible for skin and soft tissue infections. Annals of Clinical Microbiology and Antimicrobials 19, 38.

  • Massip, C., Coullaud-Gamel, M., Gaudru, C., Amoureux, L., Doleans-Jordheim, A., Hery-Arnaud, G., Marchandin, H., Oswald, E., Segonds, C., Guet-Revillet, H., 2020. In vitro activity of 20 antibiotics against Cupriavidus clinical strains. Journal of Antimicrobial Chemotherapy 75, 1654-1658.

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  • Akanny, E., Bonhommé, A., Commun, C., Doleans-Jordheim, A., Bessueille, F., Bourgeois, S., Bordes, C., 2019. Development of uncoated near-spherical gold nanoparticles for the label-free quantification of Lactobacillus rhamnosus GG by surface-enhanced Raman spectroscopy. Analytical and Bioanalytical Chemistry 411, 5563-5576.

  • Bethencourt, L., Vautrin, F., Taib, N., Dubost, A., Castro-Garcia, L., Imbaud, O., Abrouk, D., Fournier, P., Briolay, J., Nguyen, A., Normand, P., Fernandez, M.P., Brochier-Armanet, C., Herrera-Belaroussi, A., 2019. Draft genome sequences for three unisolated <i>Alnus</i> -infective <i>Frankia</i> Sp+ strains, AgTrS, AiOr and AvVan, the first sequenced <i>Frankia</i> strains able to sporulate <i>in-planta</i>. Journal of Genomics 7, 50-55.

  • Canouï, E., Ingen-Housz-Oro, S., Ortonne, N., Lebeaux, D., Rodriguez-Nava, V., Godeau, B., Mahévas, M., 2019. Syndrome d’activation macrophagique associé à une granulomatose et une infiltration lymphocytaire T CD4 diffuse révélant une nocardiose disséminée et une infection pulmonaire à Streptomyces spp. La Revue de Médecine Interne.

  • Durand, T., Vautrin, F., Bergeron, E., Girard, V., Polsinelli, S., Monnin, V., Durand, G., Dauwalder, O., Dumitrescu, O., Laurent, F., Rodríguez-Nava, V., 2019. Assessment of VITEK® MS IVD database V3.0 for identification of Nocardia spp. using two culture media and comparing direct smear and protein extraction procedures. European Journal of Clinical Microbiology & Infectious Diseases.

  • Eymery, M., Morfin, F., Doleans-Jordheim, A., Perceval, M., Ohlmann, C., Mainguy, C., Reix, P., 2019. Viral respiratory tract infections in young children with cystic fibrosis: a prospective full-year seasonal study. Virology Journal 16, 111.
  • Mazuy-Cruchaudet, C., Granjon, A., Félix, S., Donguy, M.-P., Lattard, G., Itié-Hafez, S., Loukiadis, E., Sergentet-Thevenot, D., 2019. Surveillance des E. coli producteurs de shigatoxines (STEC) dans les viandes hachées de bœuf réfrigérées et surgelées mises sur le marché en France en 2016. RIAL 21.


  • Bernardin-Souibgui, C., Barraud, S., Bourgeois, E., Aubin, J.-B., Becouze-Lareure, C., Wiest, L., Marjolet, L., Colinon, C., Lipeme Kouyi, G., Cournoyer, B., Blaha, D., 2018. Incidence of hydrological, chemical, and physical constraints on bacterial pathogens, Nocardia cells, and fecal indicator bacteria trapped in an urban stormwater detention basin in Chassieu, France. Environmental Science and Pollution Research 25, 24860-24881.

  • Chonova, T., Labanowski, J., Cournoyer, B., Chardon, C., Keck, F., Laurent, É., Mondamert, L., Vasselon, V., Wiest, L., Bouchez, A., 2018. River biofilm community changes related to pharmaceutical loads emitted by a wastewater treatment plant. Environmental Science and Pollution Research 25, 9254-9264.

  • 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., 2018. The SIPIBEL project: treatment of hospital and urban wastewater in a conventional urban wastewater treatment plant. Environmental Science and Pollution Research 25, 9197-9206.

  • Kerangart, S., Cournoyer, B., Loukiadis, E., 2018. C-source metabolic profilings of foodborne Shiga-toxin producing E . coli match serogroup differentiations and highlight functional adaptations. International Journal of Food Microbiology 266, 324-336.

  • 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 (accessed 6.6.2018).

  • Lebeaux, D., Bergeron, E., Berthet, J., Djadi-Prat, J., Mouniée, D., Boiron, P., Lortholary, O., Rodriguez-Nava, V., 2018. Antibiotic susceptibility testing and species identification of Nocardia isolates: a retrospective analysis of data from a French expert laboratory, 2010-2015. Clinical Microbiology and Infection.

  • Lipeme Kouyi, G., Barraud, S., Becouze-Lareure, C., Blaha, D., Perrodin, Y., Wiest, L., Aubin, J.-B., Toussaint, J.-Y., Vareilles, S., Mandon, C., Bernardin-Souibgui, C., Marti, R., Bourgeois, É., Marjolet, L., Cournoyer, B., 2018. Caractérisation des sédiments d’un bassin de retenue-décantation des eaux pluviales et éléments pour la gestion. Techniques Sciences Méthodes 65-75.

  • 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.

  • Roussel, C., Galia, W., Leriche, F., Chalancon, S., Denis, S., Van de Wiele, T., Blanquet-Diot, S., 2018. Comparison of conventional plating, PMA-qPCR, and flow cytometry for the determination of viable enterotoxigenic Escherichia coli along a gastrointestinal in vitro model. Applied Microbiology and Biotechnology.

  • 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.


  • 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.

  • 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.

  • 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.

  • 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.

  • Douëllou, T., Montel, M.C., Thevenot Sergentet, D., 2017. Invited review: Anti-adhesive properties of bovine oligosaccharides and bovine milk fat globule membrane-associated glycoconjugates against bacterial food enteropathogens. Journal of Dairy Science 100, 3348-3359.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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, 13219.

  • 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.

  • 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.

  • 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.