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Home > Research Teams > Bactéries Pathogènes Opportunistes et Environnement

Bactéries Pathogènes Opportunistes et Environnement

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).

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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



  • Bernardin-Souibgui, C., Barraud, S., Bourgeois, E., Aubin, J. - B., Becouze-Lareure, C., Wiest, L., et al. (2018). Incidence of hydrological, chemical, and physical constraints on bacterial pathogens, <Emphasis Type="Italic">Nocardia</Emphasis> cells, and fecal indicator bacteria trapped in an urban stormwater detention basin in Chassieu, France. Environmental Science And Pollution Research, 1-22. doi:10.1007/s11356-018-1994-2

  • Kosova-Maali, D., Bergeron, E., Maali, Y., Durand, T., Gonzalez, J., Mouniée, D., et al. (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. Biomed Research International. Research article. Retrieved June 6, 2018, from https://www.hindawi.com/journals/bmri/2018/7314054/


  • Lebeaux, D., Bergeron, E., Berthet, J., Djadi-Prat, J., Mouniée, D., Boiron, P., et al. (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. doi:10.1016/j.cmi.2018.06.013


  • Lipeme Kouyi, G., Barraud, S., Becouze-Lareure, C., Blaha, D., Perrodin, Y., Wiest, L., et al. (2018). Caractérisation des sédiments d’un bassin de retenue-décantation des eaux pluviales et éléments pour la gestion. Techniques Sciences Méthodes, (9), 65-75. doi:10.1051/tsm/201809065


  • Radix, S., Jordheim, A. D., Rocheblave, L., N'Digo, S., Prignon, A. - L., Commun, C., et al. (2018). N,N′ -disubstituted cinnamamide derivatives potentiate ciprofloxacin activity against overexpressing NorA efflux pump Staphylococcus aureus 1199B strains. European Journal Of Medicinal Chemistry. doi:10.1016/j.ejmech.2018.03.028


  • 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. doi:10.1007/s00253-018-9380-z


  • 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. doi:10.1016/j.scitotenv.2018.05.094

2017



  • Bernardin Souibgui, C., Zoropogui, A., Voisin, J., Ribun, S., Vasselon, V., Pujic, P., et al. (2017). Virulence test using nematodes to prescreen <i>Nocardia</i> species capable of inducing neurodegeneration and behavioral disorders. Peerj, 5, e3823. doi:10.7717/peerj.3823


  • Bertin, Y., Habouzit, C., Dunière, L., Laurier, M., Durand, A., Duchez, D., et al. (2017). Lactobacillus reuteri suppresses E. coli O157:H7 in bovine ruminal fluid: Toward a pre-slaughter strategy to improve food safety? Plos One, 12(11), e0187229. doi:10.1371/journal.pone.0187229


  • Canouï, E., Blanc, K., Loubinoux, J., Valade, S., Hamard, C., Lefebvre, A., et al. (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. doi:10.1016/j.ijid.2017.09.015


  • Chonova, T., Lecomte, V., Bertrand-Krajewski, J. - L., Bouchez, A., Labanowski, J., Dagot, C., et al. (2017). The SIPIBEL project: treatment of hospital and urban wastewater in a conventional urban wastewater treatment plant. Environmental Science And Pollution Research, 1-10. doi: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. doi: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, 16, Supplement 1, S108. doi:10.1016/S1569-1993(17)30528-3


  • Galia, W., Leriche, F., Cruveiller, S., Garnier, C., Navratil, V., Dubost, A., et al. (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(1), 574. doi: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. doi:10.1016/j.ijfoodmicro.2017.10.018


  • Lebeaux, D., Freund, R., van Delden, C., Guillot, H., Marbus, S. D., Matignon, M., et al. (2017). Outcome and Treatment of Nocardiosis After Solid Organ Transplantation: New Insights From a European Study. Clinical Infectious Diseases, 64(10), 1396-1405. doi:10.1093/cid/cix124


  • Legendre, C., Hannetel, H., Ranc, A. - G., Bezza, W., Pages, L., Vandenesch, F., et al. (2017). Listeria monocytogenes and ocular abscess: an atypical but yet potential association. International Ophthalmology, 1-8. doi: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. doi:10.1016/j.ijfoodmicro.2017.03.009


  • Marti, R., Bécouze-Lareure, C., Ribun, S., Marjolet, L., Bernardin Souibgui, C., Aubin, J. - B., et al. (2017). Bacteriome genetic structures of urban deposits are indicative of their origin and impacted by chemical pollutants. Scientific Reports, 7. doi:10.1038/s41598-017-13594-8


  • Marti, R., Ribun, S., Aubin, J. - B., Colinon, C., Petit, S., Marjolet, L., et al. (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. doi:10.3389/fmicb.2017.00019


  • Pages-Monteiro, L., Marti, R., Commun, C., Alliot, N., Bardel, C., Meugnier, H., et al. (2017). Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa. Plos One, 12(3), e0173022. doi:10.1371/journal.pone.0173022


  • Sánchez-Herrera, K., Sandoval, H., Mouniee, D., Ramírez-Durán, N., Bergeron, E., Boiron, P., et al. (2017). Molecular identification of Nocardia species using the sod A gene. New Microbes And New Infections, 19, 96-116. doi: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. (E. G. Dudley, Eds.)Applied And Environmental Microbiology, 82(7), 2177-2186. doi:10.1128/AEM.03463-15


  • Boukerb, A. M., Decor, A., Ribun, S., Tabaroni, R., Rousset, A., Commin, L., et al. (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. doi:10.3389/fmicb.2016.00811


  • Coussement, J., Lebeaux, D., van Delden, C., Guillot, H., Freund, R., Marbus, S., et al. (2016). Nocardia infection in solid organ transplant recipients: a multicenter European case-control study. Clinical Infectious Diseases, ciw241. doi:10.1093/cid/ciw241


  • Douëllou, T., Delannoy, S., Ganet, S., Mariani-Kurkdjian, P., Fach, P., Loukiadis, E., et al. (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. doi: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. doi: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. doi:10.1016/j.foodres.2016.04.039


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


  • Labanowski, J., Laurent, E., Chonova, T., Bouchez, A., Cournoyer, B., Marjolet, L., et al. (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, (6), 22-30. doi:10.1051/tsm/201606022


  • Roussel, C., Cordonnier, C., Galia, W., Olivier, L. G., Thévenot, J., Chalancon, S., et al. (2016). Increased EHEC survival and virulence gene expression indicate an enhanced pathogenicity upon simulated pediatric gastrointestinal conditions. Pediatric Research. doi:10.1038/pr.2016.144

  • Schmitt, L., Grosprêtre, L., Breil, P., Namour, P., Lafont, M., Delile, H., et al. (2016). Pour l’étude interdisciplinaire des petits hydrosystèmes périurbains (bassin de l’Yzeron, France). Bsglg. Retrieved from http://popups.ulg.ac.be/0770-7576/index.php?id=4420
  • Vautrin, F., Le Floch, A., Gutbraut, E., Bergeron, E., Marjolet, L., Gleizal, A., et al. (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. doi: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(4), 315-320. doi: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. Retrieved from http://www.theses.fr/2015LYO10356


  • Boukerb, A. M., Marti, R., & Cournoyer, B. (2015). Genome Sequences of Three Strains of the Pseudomonas aeruginosa PA7 Clade. Genome Announcements, 3(6), e01366-15. doi: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(4). doi:10.1099/jmmcr.0.000046


  • Galia, W., Mariani-Kurkdjian, P., Loukiadis, E., Blanquet-Diot, S., Leriche, F., Brugère, H., et al. (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(1), e01568-14. doi:10.1128/genomeA.01568-14


  • Heraud, S., Freydiere, A. - M., Doleans-Jordheim, A., Bes, M., Tristan, A., Vandenesch, F., et al. (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(4), 454. doi:10.3343/alm.2015.35.4.454


  • Lebaron, P., Cournoyer, B., Lemarchand, K., Nazaret, S., & Servais, P. (2015). Environmental and Human Pathogenic Microorganisms. In J. - C. Bertrand, P. Caumette, P. Lebaron, R. Matheron, P. Normand, & T. Sime-Ngando (Eds.), Environmental Microbiology: Fundamentals And Applications (p. 619-658). Springer Netherlands. Retrieved from http://link.springer.com/chapter/10.1007/978-94-017-9118-2_15


  • Piau, C., Kerjouan, M., Le Mouel, M., Patrat-Delon, S., Henaux, P. - L., Brun, V., et al. (2015). First case of disseminated human infection with Nocardia cerradoensis. Journal Of Clinical Microbiology, JCM.02979-14. doi: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, (4), 52-57. doi: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(1), 196-202. doi:10.4315/0362-028X.JFP-14-263