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6. A 16(th) century Escherichia coli draft genome associated with an opportunistic bile infection

Author

Long, GS, Klunk, J, Duggan, AT, Tapson, M, Giuffra, V, Gazze, L, Fornaciari, A, Duchene, S, Fornaciari, G, Clermont, O, Denamur, E, Golding, GB, Poinar, H, Long, GS, Klunk, J, Duggan, AT, Tapson, M, Giuffra, V, Gazze, L, Fornaciari, A, Duchene, S, Fornaciari, G, Clermont, O, Denamur, E, Golding, GB, and Poinar, H

Abstract

Escherichia coli - one of the most characterized bacteria and a major public health concern - remains invisible across the temporal landscape. Here, we present the meticulous reconstruction of the first ancient E. coli genome from a 16th century gallstone from an Italian mummy with chronic cholecystitis. We isolated ancient DNA and reconstructed the ancient E. coli genome. It consisted of one chromosome of 4446 genes and two putative plasmids with 52 genes. The E. coli strain belonged to the phylogroup A and an exceptionally rare sequence type 4995. The type VI secretion system component genes appears to be horizontally acquired from Klebsiella aerogenes, however we could not identify any pathovar specific genes nor any acquired antibiotic resistances. A sepsis mouse assay showed that a closely related contemporary E. coli strain was avirulent. Our reconstruction of this ancient E. coli helps paint a more complete picture of the burden of opportunistic infections of the past.

Published
2022

14. Mortality in Escherichia coli bloodstream infections: antibiotic resistance still does not make it.

Author

Lastours, V de, Laouénan, C, Royer, G, Carbonnelle, E, Lepeule, R, Esposito-Farèse, M, Clermont, O, Duval, X, Fantin, B, Mentré, F, Decousser, J W, Denamur, E, Lefort, A, de Lastours, V, and SEPTICOLI Group

Subjects
ESCHERICHIA coli diseases, DRUG resistance in bacteria, DRUG resistance in microorganisms, SEPTIC shock, MORTALITY, ANTIBIOTICS, BACTEREMIA, ESCHERICHIA coli, RESEARCH, RESEARCH methodology, MEDICAL cooperation, EVALUATION research, SEPSIS, HYDROLASES, HOSPITAL mortality, COMPARATIVE studies, PHARMACODYNAMICS
Abstract

Background: Escherichia coli bloodstream infections (BSIs) account for high mortality rates (5%-30%). Determinants of death are unclear, especially since the emergence of ESBL producers.Objectives: To determine the relative weight of host characteristics, bacterial virulence and antibiotic resistance in the outcome of patients suffering from E. coli BSI.Methods: All consecutive patients suffering from E. coli BSI in seven teaching hospitals around Paris were prospectively included for 10 months. E. coli isolates were sequenced using Illumina NextSeq technology to determine the phylogroup, ST/ST complex (STc), virulence and antimicrobial resistance gene content. Risk factors associated with death at discharge or Day 28 were determined.Results: Overall, 545 patients (mean ± SD age 68.5 ± 16.5 years; 52.5% male) were included. Mean Charlson comorbidity index (CCI) was 5.6 (± 3.1); 19.6% and 12.8% presented with sepsis and septic shock, respectively. Portals of entry were mainly urinary (51.9%), digestive (41.9%) and pulmonary (3.5%); 98/545 isolates (18%) were third-generation cephalosporin resistant (3GC-R), including 86 ESBL producers. In-hospital death (or at Day 28) was 52/545 (9.5%). Factors independently associated with death were a pulmonary portal of entry [adjusted OR (aOR) 6.54, 95% CI 2.23-19.2, P = 0.0006], the iha_17 virulence gene (aOR 4.41, 95% CI 1.23-15.74, P = 0.022), the STc88 (aOR 3.62, 95% CI 1.30-10.09, P = 0.014), healthcare-associated infections (aOR 1.98, 95% CI 1.04-3.76, P = 0.036) and high CCI (aOR 1.14, 95% CI 1.04-1.26, P = 0.006), but not ESBL/3GC-R.Conclusions: Host factors, portal of entry and bacterial characteristics remain major determinants associated with mortality in E. coli BSIs. Despite a high prevalence of ESBL producers, antibiotic resistance did not impact mortality. (ClinicalTrials.gov identifier: NCT02890901.). [ABSTRACT FROM AUTHOR]

Published
2020
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16. Escherichia coli population structure and antibiotic resistance at a buffalo/cattle interface in southern Africa

Author

Mercat, M., Clermont, O., Massot, M., Ruppe, E., De Garine-Wichatitsky, M., Miguel, E, Valls Fox, H., Cornelis, D., Andremont, A., Denamur, E., Caron, A., and International Wildlife Ranching Symposium, Publisher

Abstract

Presented at the 9th international wildlife ranching symposium: wildlife - the key to prosperity for rural communities, held on 12-16 September 2016 at Hotel Safari & the Safari Court, Windhoek, Namibia in conjuction with the IUCN 2nd African Buffalo Symposium., Human/livestock/wildlife interfaces create favorable conditions for microorganisms spill over between hosts. In landscapes where human expansion encroaches into natural ecosystems, the resulting epidemics are a major cause of human/wildlife conflicts that challenge the sustainable coexistence between Mankind and Nature. Escherichia coli is a well-known bacteria, ubiquitous and harboring antibiotic resistance. It provides a good model to understand the diffusion of antibiotic resistance between hosts and the environment. This is also a good candidate to explore the mechanisms of microorganism transmission between hosts and could be used to track pathogen transmission. We used phenotypic and molecular characterization techniques to describe antibiotic resistance and the diversity of E.coli populations found in sympatric African buffalo (Syncerus caffer caffer) and cattle populations at the Hwange National Park interface, Zimbabwe. Although the structure of E. coli populations was similar between cattle and buffalo populations, we found a gradient of antibiotic resistance, highest in cattle, intermediate in buffalo that were in contact with cattle, and lowest in isolated buffalo. The types and molecular characterization of antibiotic resistance further confirm the observed gradient and suggest that antibiotic resistance is spreading from human to animal populations. We demonstrate that there is a risk of antibiotic resistance diffusion between wildlife, livestock and human populations, with unknown consequences on the health of host populations. These results also confirm that E. coli could be used as a tool to identify transmission pathways in multi-host systems, in an attempt to characterize pathogen spread and risks of emergence.

Published
2016
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17. French Intensive Care Society, International congress - Réanimation 2016

Author

Jaillette, E, Girault, C, Brunin, G, Zerimech, F, Chiche, A, Broucqsault Dedrie, C, Fayolle, C, Minacori, F, Alves, I, Barrailler, S, Robriquet, L, Delaporte, E, Thellier, D, Delcourte, C, Duhamel, A, Nseir, S, Valette, X, Desmeulles, I, Savary, B, Masson, R, Seguin, A, Daubin, C, Sauneuf, B, Verrier, P, Pottier, V, Orabona, M, Samba, D, Viquesnel, G, Lermuzeaux, M, Hazera, P, Hanouz, J, Parienti, J, Du Cheyron, D, Demoule, A, Clavel, M, Rolland Debord, C, Perbet, S, Terzi, N, Kouatchet, A, Wallet, F, Roze, H, Vargas, F, Guérin, C, Dellamonica, J, Jaber, S, Similowski, T, Quenot, J, Binquet, C, Vinsonneau, C, Barbar, S, Vinault, S, Deckert, V, Lemaire, S, Hssain, A, Bruyère, R, Souweine, B, Lagrost, L, Adrie, C, Jung, B, Daurat, A, De Jong, A, Chanques, G, Mahul, M, Monnin, M, Molinari, N, Lheureux, O, Trepo, E, Hites, M, Cotton, F, Wolff, F, Surin, R, Créteur, J, Vincent, J, Gustot, T, Jacobs, F, Taccone, F, Neuville, M, Timsit, J, El Helali, N, Le Monnier, A, Magalhaes, E, Radjou, A, Smonig, R, Soubirou, J, Voiriot, G, Sonneville, R, Bouadma, L, Mourvillier, B, Gélisse, E, Brasseur, A, Roisin, S, De Backer, D, Van Ruychevelt, V, Carlier, E, Piagnerelli, M, Vanhaeverbeek, M, Danguy, C, Biston, P, Au, S, Begot, E, Dalmay, F, Repessé, X, Prat, G, Bouferrache, K, Slama, M, Vieillard Baron, A, Monnet, X, Marik, P, Teboul, J, Jozwiak, M, Richard, C, Chauvet, J, El Dash, S, Delastre, O, Bouffandeau, B, Jusserand, D, Michot, J, Bauer, F, Brazier, F, Mercado, P, Kontar, L, Titeca, D, De Cagny, B, Bacari Risal, G, Riviere, A, Maizel, J, Guillot, C, Le Reun, C, Lampin, M, Sadik, A, Botte, A, Leteurtre, S, Collins, A, Kempeneers, C, Cajgfinger, N, Ohlmann, C, Pouyau, R, Subtil, F, Baudin, F, Massenavette, B, Javouhey, E, Milesi, C, Essouri, S, Liet, J, Afanetti, M, Durand, S, Durand, P, Roze, J, Dupont, D, Cambonie, G, Soyer, B, Rusca, M, Lukaszewicz, A, Crassard, I, Guichard, J, Bresson, D, de la Garanderie, D, Cantier, M, Sabben, C, Louedec, L, Delbosc, S, Journé, C, Ou, P, Klein, I, Chau, F, Lefort, A, Desilles, J, Michel, J, Mazighi, M, Salem, O, Demeret, S, Bolgert, F, Sharshar, T, Grabli, D, Arib, S, Crippa, I, Soummer, A, Engrand, N, Guedin, P, Aldea, S, Cerf, C, Desailly, V, Pasquier, P, Brun, P, Roux, D, Latournerie, G, Kasprzyk, L, Grosjean, V, Latreche, A, Habert, P, Huot, S, Jobin, T, Tesnière, A, Dreyfuss, D, Ricard, J, Mignon, A, Gaudry, S, Laithier, F, Kimmoun, A, Chouihed, T, Albizzati, S, Camenzind, E, Vanhuyse, F, Levy, B, Cour, M, Venet, F, Hernu, R, Demaret, J, Monneret, G, Argaud, L, Dumas, F, Lamhaut, L, Rosencher, J, Pène, F, Varenne, O, Carli, P, Jouven, X, Spaulding, C, Cariou, A, Geri, G, Bonnetain, F, Marijon, E, Empana, J, Mirouse, A, Resche Rigon, M, Mayaux, J, Rabbat, A, Meert, A, Benoit, D, Bruneel, F, Azoulay, E, Dupuis, C, Schwebel, C, Ruckly, S, Goldgran Toledano, D, Marcotte, G, Lafarge, A, Pichereau, C, Theodose, I, Scotto, M, Kemlin, D, Ghrenassia, E, Schlemmer, B, Vimpere, D, Galicier, L, Contou, D, Guérot, E, Grimaldi, D, Ricome, S, Maury, E, Plantefève, G, Dessap, A, Brun Buisson, C, de Prost, N, Dubé, B, Delemazure, J, Dres, M, Rousseau, L, Drouot, X, Diaz, V, Rebollar, Y, Frat, J, Thille, A, Aissa, D, Coquet, P, Ruiz, J, Ferre, F, Hoarau, L, Riu Poulenc, B, Bataille, B, Silva, S, Baudel, J, Bigé, N, Tahiri, J, Dubée, V, Guidet, B, Ait Oufella, H, Jinglun, L, Shen, F, Bailly, S, Leroy, O, Montravers, P, Constantin, J, Dupont, H, Guillemot, D, Lortholary, O, Perrigault, P, Gangneux, J, Razazi, K, Mekontso Dessap, A, Jansen, C, Lecronier, M, Sandrine, V, Mira, J, Blein, S, Marin, N, Rousseau, C, Charpentier, J, Pachot, A, Hraiech, S, Bordes, J, De, L, Mège, J, Forel, J, Guervilly, C, Adda, M, Raoult, D, Papazian, L, Kentish Barnes, N, Cohen Solal, Z, Souppart, V, Kerhuel, L, Haubertin, C, Exbrayat, I, Rozières, E, Argain, A, Suc, A, Vignes, M, Cougot, P, Fourcade, O, Brunel, E, Messika, J, Tubach, F, Dubief, E, Pasquet, B, Guillo, S, Pierron, C, Grimaud, M, Farnoux, C, Maillard, A, Decavèle, M, Prodanovic, H, Idbaih, A, Alentorn, A, Delattre, J, De Montmollin, E, Brule, N, Conrad, M, Dailler, F, Navellou, J, Alves, M, Tonnelier, J, Picard, G, Rogemond, V, Honnorat, J, Marzorati, C, Lebert, C, Perez, P, Citerio, G, Legriel, S, Tripon, S, Mallet, M, Rudler, M, Imbert Bismut, F, Thabut, D, Canet, E, Faguer, S, Moreau, A, Barbier, F, Merceron, S, Guitton, C, Labadie, F, Lemiale, V, Faucher, E, Klouche, K, Chevret, S, Ragot, S, Coudroy, R, Boulain, T, Jamet, A, Mercat, A, Brochard, L, Roux, A, Franchineau, G, Brechot, N, Lebreton, G, Hekimian, G, Nieszkowska, A, Leprince, P, Trouillet, J, Combes, A, Schmidt, M, Barrot, L, Piton, G, Bailey, M, Panwar, R, Belin, N, Belon, F, Patry, C, Grandperrin, M, Chaignat, C, Labro, G, Vivet, B, Capellier, G, Daix, T, Guérin, E, Tavernier, E, Mercier, E, Gissot, V, Vallejo, C, François, B, Ravry, C, Pichon, N, Chapellas, C, Fedou, A, Galy, A, Ploy, M, Barraud, O, Vignon, P, Thooft, A, Conotte, R, Colet, J, Le Dorze, M, Tarazona, V, Brumpt, C, Moins Teisserenc, H, Uhel, F, Azzaoui, I, Gregoire, M, Pangault, C, Dulong, J, Cynober, L, Roussel, M, Le Tulzo, Y, Tarte, K, Demiselle, J, Auchabie, J, Dequin, P, Chudeau, N, Fourrier, F, Grange, S, Piquilloud, L, Lautrette, A, Boyer, S, Letheulle, J, Lerolle, N, Truche, A, Clec'H, C, Zaoui, P, Laurent, V, Toledano, D, Ragey, S, Gros, A, Dumenil, A, Jamali, S, Darmon, M, Chouraqui, M, Dewitte, A, Chastel, B, Carles, P, Fleureau, C, Joannes Boyau, O, Ouattara, A, Joseph, A, Garrouste Orgeas, M, Max, A, Lerin, T, Grégoire, C, Kloeckner, M, Bruel, C, Brochon, S, Philippart, F, Pichot, E, Simons, C, Flint, A, Aubron, C, Bellomo, R, Pilcher, D, Cheng, A, Hegarty, C, Martinelli, A, Howden, B, Reade, M, Mcquilten, Z, Bretonnière, C, Villers, D, Soares, M, Gonzalez, F, Vincent, F, Fauché, C, Gay, S, Skowron, O, Levrat, A, Dorez, D, Foucrier, A, Pease, S, Gauss, T, Paugam, C, Gorham, J, Ameye, L, Paesmans, M, Berghmans, T, Sculier, J, Deras, P, Martinez, O, Latry, P, Capdevila, X, Charbit, J, Jaubert, J, Etiennar, C, Ginoux, L, Sebbah, J, Haouache, H, Dhonneur, G, Cheikh, C, Moussaid, I, Ghazaoui, O, Belkadi, K, El Youssoufi, S, Salmi, S, Pajot, L, Zuber, B, Bedos, J, Dupont, B, Eugène, A, Galateau Sallé, F, Michard, B, Lebas, B, Boivin, A, Guillot, M, Harlay, M, Janssen Langenstein, R, Schenck, M, Ellero, B, Woehl Jaegle, M, Besch, C, Castelain, V, Bachellier, P, Schneider, F, Camus, C, Saliba, F, Goubaux, B, Bonadona, A, Lavayssiere, L, Quinart, A, Barbot, O, Dharancy, S, Delafosse, B, Barraud, H, Galbois, A, Veber, B, Cayot, S, Souche, B, Locher, C, Roux, O, Figorilli, F, Putignano, A, Houssel, P, Francoz, C, Weiss, E, Agarwal, B, Jalan, R, Durand, F, Ghezala, H, Daoudi, R, Kaddour, M, Ghadhoune, H, Rachedi, E, Guissouma, J, Ben Slimene, A, Azzeza, W, Brahmi, H, Elghord, H, Kada, A, Chikh, R, Slimani, R, A. Bouyoucef, K, Regaieg, K, Kamilia, C, Baccouche, N, Turki, O, Chaari, A, Ben, H, Bouaziz, M, Medhioub, F, Zekri, M, Rgieg, K, Bhimada, C, Mounir, B, Lang, E, Welschbillig, S, Perrin, M, Devys, J, Benbernou, S, Mokhtari Djebli, H, Ilies, S, Bouyacoub, K, Azza, A, Zogheib, E, Nader, J, Villeret, L, Guilbart, M, Besserve, P, Caus, T, Mastroianni, C, Santi, F, Hékimian, G, Pascal, L, Chastre, J, Perrier, V, Deniau, B, Klasen, F, Ponthus, J, Ngasseu, P, Amilien, V, Barsam, E, Lehericey, P, Tchir, M, Georger, J, Puech, B, Vandroux, D, Roussiaux, A, Belcour, D, Ferdynus, C, Martinet, O, Jabot, J, Fresco, M, Demeilliers Pfister, G, Merle, V, Brunel, V, Dureuil, B, Leydier, S, Clerc Urmes, I, Lemarie, J, Maigrat, C, Cravoisy Popovic, A, Barraud, D, Nace, L, Gibot, S, Agrinier, N, Bollaert, P, Daban, J, Boutonnet, M, Dumas, G, Falzone, E, Jault, P, Lenoir, B, Makunza, J, Mejeni, N, Mazaud, A, Béague, S, Rousselle, A, Durocher, A, Grinea, A, Bedoui, N, Stoian, A, Baboi, L, Gobert, F, Yonis, H, Tapponier, R, Bruyneel, A, Bonus, T, Cuvelier, G, Machayeckhi, S, Olieuz, S, Legrand, A, Feki, F, Jamoussi, A, Merhebene, T, Braham, E, Ghariani, A, Mezni, F, Slim, L, Khelil, J, Besbes, M, Marchalot, A, Beduneau, G, Carpentier, D, Besnier, E, Gastaldi, G, Abily, J, Beuzelin, M, Nay, M, Mankikian, J, Hervé, V, Soulie, M, Cronier, P, Kantor, E, Federici, L, Gilbert, M, Mezhari, I, Choukroun, G, Marque, S, Coppere, Z, Fulgencio, J, Blayau, C, Pham, T, Djibre, M, Reffienna, M, Lefort, S, Debue, A, Daviaud, F, Cabon, S, Addou, Z, Douah, A, Moussati, M, Belhabiche, K, Aouffen, N, Soulier, S, Mauriat, P, Tafer, N, Mortamet, G, Amaddeo, A, Khirani, S, Fauroux, B, Khanes, G, Liutko, O, Bidnenko, S, Doye, E, Voirin, N, Maucort Boulch, D, Kolev Descamp, K, Aouane, I, Essid, A, Hammami, W, Haegy, I, Bataille, J, Bergounioux, J, Morin, L, Ray, S, Maclaren, G, Nadel, S, Kneyber, M, Peters, M, Jansen, K, De Luca, D, Wilson, C, Schlapbach, L, Tissières, P, Girard, A, Savajols, E, Burguet, A, Semama, D, Litzler Renault, S, Fredj, H, Hassouna, M, Hechmi, Y, Cherif, M, Zouheir, J, Dernane, A, Bouakkaz, F, Taleb, L, Zeddine Mouhsen, A, Lyazidi, A, Richard, J, Mouhsen, A, Harmouchi, M, Rattal, M, Huck, M, Leclerc, T, Donat, N, Cirodde, A, Schaal, J, Masson, Y, Hoffmann, C, Cerland, L, Valentino, R, Chabartier, C, Villain Coquet, L, Ferge, J, Brouste, Y, Mehdaoui, H, Louriz, M, Madani, N, Amlaiky, F, Dendane, T, Abidi, K, Zekraoui, A, Zeggwagh, A, Abouqal, R, Brahim, A, Ferhi, F, Bouslama, M, Benjazia, K, Zeineb, A, Mahassen, D, Cadiet, J, Ferron, M, Prat, V, Erraud, A, Aillerie, V, Mevel, M, Grabherr, A, Chatham, J, Gauthier, C, Lauzier, B, Rozec, B, Joffre, J, Loyer, X, Lavillegrand, J, Zeboudj, L, Laurans, L, Esposito, B, Tedgui, A, Mallat, Z, Wei, C, Kattani, N, Louis, H, Orlowski, S, Tharaux, P, Burban, M, Meyer, G, Olland, A, Yver, B, Toti, F, Schini Kerth, V, Monnier, A, Leborgne, P, Meziani, F, Clavier, T, Paulus, M, Castel, H, Richard, V, Pons, S, Skurnik, D, Six, S, Jaffal, K, Vigneron, C, Large, A, Bador, J, Aho, S, Prin, S, Touil, Y, Ayed, S, Ali, H, Tilouch, N, Mateur, H, Talik, I, Gharbi, R, Hassen, M, Elatrous, S, Patry, I, Bertrand, X, Zahar, J, Essaied, W, Wolkewitz, M, Soued, M, Cook, F, Lobo, D, Mounier, R, Emirian, A, Decousser, J, Slaoui, M, Benslama, A, Valance, D, Allou, N, Allyn, J, Jean Bart, E, Bel, F, Morey, F, Sedillot, N, Biard, L, Galliot, R, Zunarelli, R, Gauzere, B, Cartier, J, Jouve, T, Hilleret, M, Hamidfar Roy, R, Ara Somohano, C, Minet, C, Pourcelet, A, Hougardy, J, Defrance, P, De Laforcade, L, Boyer, A, Gruson, D, Clouzeau, B, Hajjam, N, Nasri, H, Doghri, H, Mongardon, N, Levesque, E, Bastide, M, Richecoeur, J, Frenoy, E, Lemaire, C, Schortgen, F, Preau, S, Ehooman, F, Montlahuc, C, Bardon, J, Postel Vinay, N, Lafi, M, Prat, D, Le Meur, M, Moneger, G, Demars, N, Trouiller, P, Tencé, N, Zaien, I, Wolf, M, Allardet Servent, J, Lebsir, M, Dubroca, C, Portugal, M, Castanier, M, Signouret, T, Soundaravelou, R, Lepidi, A, Halfon, P, Seghboyan, J, Gamblin, C, Benturquia, N, Roussel, O, Chevillard, L, Risede, P, Callebert, J, Khelfa, M, Blel, Y, Thabet, H, Brahmi, N, Amamou, M, Le Louët, A, Baud, F, Le Beller, C, Vivien, B, Soufir, L, Le Louët, H, Essafi, F, Foudhaili, N, Slimen, A, Jabla, R, Hammed, H, Marzouk, M, Boujelbene, N, Dachraoui, F, Hachani, A, Abdallah, S, Lakhal, H, Ghribi, C, Ali, I, Abdellaoui, I, Ouanes Besbes, L, Abroug, F, Demiri, S, Lorut, C, Van Lang, D, Lefebvre, A, Alifano, M, Reignard, J, Samama, M, Dusser, D, Roche, N, Réminiac, F, Landel, C, Gensburger, S, Bocar, T, Mordier, L, Philippe, M, Le Pennec, D, Vecellio, L, Ehrmann, S, Poiroux, L, Thevoz, D, Simons, J, Roeseler, J, Loiez, A, Gérard, S, Dousse, N, L'Hotellier, S, Baumgarten, E, Borschneck, S, Kharcha, F, Ghander, C, Tresallet, C, Puymirat, E, Fagon, J, Aegerter, P, Diehl, J, Hauw Berlemont, C, Chatellier, G, Danchin, N, Aissaoui, N, Aissat, N, Bernard, R, Amour, J, Bouglé, A, Vidal, C, Nima, D, Shaida, V, Dorget, A, Bréchot, N, Toufiki, R, Mouaffak, Y, Adib, A, Amine, M, Moumine, S, Jonard, M, Ducloy Bouthors, A, Bouju, P, Barbarot, N, Gacouin, A, Fillatre, P, Grillet, G, Goepp, A, Clairet, A, Limat, S, Cornette, C, Fatnassi, A, Romdhani, C, Sammoud, W, Labbene, I, Ferjani, M, Taibi, H, Elatiqi, I, Iraqui, A, Cherkab, R, Haddad, W, Elkettani, C, Barrou, L, Cave, F, Doutrellot, P, Vaysse, B, Inan, M, Khelfoun, K, Nasserallah, M, Legrand Monteil, C, Tasseel Ponche, S, Kowalski, B, Guaguere, A, Boulle Geronimi, C, Masse, J, Vanbaelinghem, C, Herbecq, P, Mokline, A, Draief, S, Gharsallah, L, Rahmani, I, Gasri, B, Tlaili, S, Hammouda, R, Messadi, A, Michel, P, Gelée, B, Fadel, F, Thuong, M, Ait Aoudia, S, Laddi, S, Sahraoui, M, Muller, M, Faucher, A, Hermann, B, Berlemont, C, Arnaout, M, Busson, J, Dhumeaux, J, Ericher, N, Lucas, P, Dumas, M, Chapelle, C, Philippon Jouve, B, Morel, J, Beuret, P, Bureau, C, Poitou, T, Petua, P, Prades, A, Basty, M, Monet, C, Mounet, B, Futier, E, Leroux, A, Oudinot, X, Laurent, M, 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Gisbert Mora, C, Bonnardel, E, Biais, M, Hilbert, G, Joannon, T, Marincamp, A, Chiche, J, Ferre, A, Lichtenstein, D, Meziere, G, Gonzalez, C, Hamzaoui, O, Geffriaud, T, Leleu, F, Boissier, F, Cuquemelle, E, Lim, P, Amara, R, Léger, J, Jacob, C, Bouferache, K, Ragot, C, Corradi, L, Maurice, L, Julliand, S, Deho, A, Le Bourgeois, F, Jacquot, A, Valla, F, Letois, F, Salvadori, A, Ottonello, G, Blanot, S, Montmayeur, J, Orliaguet, G, Tarmiz, K, Habas, F, Baleine, J, Lebouhellec, J, Combes, C, Chomton, M, Jouvet, P, Ranchin, B, Macher, M, Gaillot, T, Moine, M, Ageron, F, Jannel, C, Debillon, T, Wroblewski, I, Duprey, M, Jarlier, V, Luyt, C, Longval, T, Schnell, D, Padoin, C, Cohen, Y, Gaies, E, Triki, S, Klouz, A, Moussa, M, Desrumaux, F, May, F, Nguyen, J, Tiercelet, K, Fournier, J, Cherin, M, Kitzis, M, Misset, B, Mathien, C, Poidevin, A, Donatti, L, Mootien, J, Pinto, L, Egard, M, Bodur, G, Barberet, G, Ionescu, C, Ganster, F, Guiot, P, Kuteifan, K, Mpela, A, Chelly, J, Guérin, L, Persichini, R, Hullin, T, Deye, N, Aubertein, P, Paul, M, Bougouin, W, Sandroni, C, Passouant, O, Llitjos, J, Chenevier Gobeaux, C, Batteux, F, Drouet, L, Voicu, S, Henry, P, Dillinger, J, Resiere, D, Dessoy, A, Faivre, V, Damoisel, C, Stiel, L, Galoisy, A, Mauvieux, L, Zobairi, F, Angles Cano, E, Piau, C, Jeannet, R, Feuillard, J, Jolly, L, Boufenzer, A, Carrasco, K, Derive, M, Merdji, H, Belaidouni, N, Toubiana, J, L'Hermitte, Y, Woimant, F, Oppenheim, C, Couvreur, C, Dolveck, F, Devriese, M, Dupeyrat, S, Ray, P, Lefevre, G, Fartoukh, M, Roothaer, N, Carpentier, A, Vaniet, F, Maisonneuve, A, Wiel, E, Canu, S, Hammad, E, Antonini, F, Poirier, M, Vigne, C, Haddam, M, Alingrin, J, Dangers, L, Mangiapan, G, Huet, I, Dhalluin, X, Bautin, N, Quiot, J, De Vecchi, C, Chenivesse, C, Smaoui, M, El Alami, E, Weiss, N, Mochel, F, Galanaud, D, Puybasset, L, Lodey, M, Guiller, E, Vuillaume, C, De Pasquale, F, Demonet, J, Sinnah, F, Dalloz, M, D'Ortho, M, Rouvel Tallec, A, Couret, D, Catan, A, Nativel, B, Planesse, C, Diotel, N, Meilhac, O, Roy Gash, F, Lebard, C, Larbi, A, Gaudin, V, Bonnin, F, Sultan, O, Hoc, C, Mathieu, E, Lapergue, B, Bourdain, F, Caron, M, Parrot, A, Labbe, V, Hafiani, E, Quesnel, C, Genay, S, Décaudin, B, Ethgen, S, Odou, P, Lebuffe, G, Mcquilte, Z, Allaouchiche, B, Verdière, B, Nyunga, M, Banaias, N, Colling, D, Kauv, M, Blondeau, E, Auclin, E, Haw Berlemont, C, Taieb, J, Oudard, S, Morissette, G, Kechaou, W, Litalien, C, Merouani, A, Phan, V, Bouchard, J, Starck, J, Briand, N, Sachs, P, Angoulvant, F, Sommet, J, Holvoet, L, Benkerrou, M, Dreyfus, L, Bordet, F, Touzet, S, Denis, A, Le Coz, J, Chéron, G, Nabbout, R, Patteau, G, Heilbronner, C, Hubert, P, Oualha, M, Crulli, B, Toledano, B, Poirier, N, Vobecky, S, Khouadja, H, Vinet, M, Vinclair, C, Beloncle, F, Radermacher, P, Asfar, P, Coupez, E, Bohé, J, Shinotsuka, C, Caironi, P, Villois, P, Fontana, V, Creteur, J, Pourcine, F, Vong, L, Weyer, C, Akando, B, Abdallah, R, Wetzstein, M, Antier, N, Serroukh, Y, Boudjeltia, K, Joosten, A, Rousseau, A, Delabranche, X, Grunebaum, L, Mootien, Y, Gaci, R, Garric, J, Delbove, A, Darreau, C, Dargent, A, Soudry Faure, A, De Chambrun, M, Demondion, P, Blanchard, J, Chocron, S, Meneveau, N, Corsi, F, Meynieu, P, Repusseau, B, Germain, A, Baudry, G, Hierle, L, Besch, G, Thomas, G, Cassir, N, Dizier, S, Roch, A, Trebbia, G, Govindaradjou, K, Devaquet, J, Picard, C, Parquin, F, Leguen, M, Felten, M, Sage, E, Chapelier, A, Duruisseaux, M, Fleury, J, Antoine, M, Carette, M, Wislez, M, Givel, C, De Margerie Mellon, C, De Kerviler, E, Tandjaoui Lambiotte, Y, Freynet, O, Baux, E, Das, V, Talec, P, Anguel, N, Louis, G, Girerd, N, Tallon, P, Hadchouel Duvergé, A, Salvi, N, Cairet, P, Delacourt, C, Blandine, B, Beraud, L, Lamaziere, A, Lionnet, F, Lehingue, S, D'Journo, X, Jean Marie, F, Thibault, R, Makhlouf, A, Mulliez, A, Dadet, S, Kekstas, G, Preiser, J, Rotovnik, K, Rozalen, I, Kupczyk, K, Krznaric, Z, Cano, N, Pichard, C, Le Roux, B, Jotterand, C, Rooze, S, Moullet, C, Henin, A, Ettori, F, Zemmour, C, Boher, J, Feltry, A, Ben, S, Audibert, J, Conia, A, Gontier, O, Hamrouni, M, Lherm, T, Ouchenir, A, Rétif, J, Proudhom, A, Lagardere, C, Tissot, S, Kalfon, P, Sacre, L, Villa, A, Khadija, A, Garnier, R, Vasset, B, Heinzelman, A, Jouffroy, R, Durand, E, Compagnon, P, Jebri, A, Legout, C, Castot Villepelet, A, Valade, S, Lesieur, O, Delmas, B, Visseaux, B, Cohen, J, Nguyen, L, Morbieu, C, Burdet, C, Lescure, F, Armand Lefevre, L, Yazdanpanah, Y, Houhou Fidouh, N, Cazaux, M, Goff Jérôme, L, Meignin, V, Boutboul, D, Rispail, P, Besnard, N, Ceballos, P, Stoclin, A, Rotolo, F, Wartelle, M, Hicheri, Y, Maillet, S, Chachaty, E, Pignon, J, Bialais, E, Julie, D, Paoloni, L, Wittebolle, X, Hickmann, C, Castanares Zapatero, D, Tordeur, A, Colmant, L, Wittebole, X, Tirone, G, Laterre, P, Ducroux, L, Kemlin, C, Moulton, E, Rosso, C, Le Neindre, A, Mongodi, S, Bouhemad, B, Rodrigues, J, Botteau, C, Waroquier, F, Christiaens, K, Vantrimpont, F, Elkhawand, C, Vermeesh, F, Vermeesh, F., and CITERIO, GIUSEPPE

Abstract

Determinants of outcome in critically ill patients with hematological malignancy and central neurological failure: data from the TRIAL OH study

Published
2016

18. Escherichia coli bacteraemia in pregnant women is life-threatening for foetuses

Author

Surgers, Laure, Bleibtreu, A, Burdet, C, Clermont, O., Laouénan, C, Lefort, A., Mentré, F, Carbonne, B, Bingen, E, Meynard, J-L., Denamur, E., Mereghetti, Laurent, Quentin, Roland, COLIBAFI Group, ., Hôpital Antoine Béclère, Assistance Publique - Hôpitaux de Paris (AP-HP), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC), Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Biostatistiques, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-AP-HP - Hôpital Bichat - Claude Bernard [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université Paris Diderot - Paris 7 (UPD7), Hôpital Beaujon [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Pierre et Marie Curie - Paris 6 (UPMC), AP-HP Hôpital universitaire Robert-Debré [Paris], CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours, 'Bourse Medico-Scientifique' de la 'Fondation pour la Recherche Medicale', Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), and Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
Microbiology (medical), Adult, Adolescent, Genotype, medicine.drug_class, Virulence Factors, Urinary system, Antibiotics, Virulence, Bacteremia, Biology, medicine.disease_cause, Chorioamnionitis, Virulence factor, Microbiology, 03 medical and health sciences, Young Adult, phylogenetic group, medicine, Escherichia coli, Humans, Sex organ, Pregnancy Complications, Infectious, Fetal Death, Escherichia coli Infections, 030304 developmental biology, Retrospective Studies, 0303 health sciences, Pregnancy, 030306 microbiology, General Medicine, Middle Aged, medicine.disease, bacterial infections and mycoses, Survival Analysis, chorioamnionitis, 3. Good health, Community-Acquired Infections, virulence, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, foetal mortality, Bacteraemia, Female, pregnancy, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience; In order to improve knowledge on Escherichia coli bacteraemia during pregnancy, we studied clinical data and performed molecular characterization of strains for 29 E. coli bacteraemia occurring in pregnant women. Bacteraemia mostly occurred in the third trimester of pregnancy (45%) and was community-acquired (79%). Portals of entry were urinary (55%) and genital (45%). E. coli strains belonged mainly to phylogroups B2 (72%) and D (17%). Four clonal lineages (i.e. sequence type complex (STc) 73, STc95, STc12 and STc69) represented 65% of the strains. The strains exhibited a high number of virulence factor coding genes (10 (3-16)). Six foetuses died (27%), five of them due to bacteraemia of genital origin (83%). Foetal deaths occurred despite adequate antibiotic regimens. Strains associated with foetal mortality had fewer virulence factors (8 (6-10)) than strains involved in no foetal mortality (11 (4-12)) (p 0.02). When comparing E. coli strains involved in bacteraemia with a urinary portal of entry in non-immunocompromised pregnant vs. non-immunocompromised non-pregnant women from the COLIBAFI study, there was no significant difference of phylogroups and virulence factor coding genes. These results show that E. coli bacteraemia in pregnant women involve few highly virulent clones but that severity, represented by foetal death, is mainly related to bacteraemia of genital origin.

Published
2014

19. Two levels of specialization in bacteraemic Escherichia coli strains revealed by their comparison with commensal strains.

Author

CLERMONT, O., COUFFIGNAL, C., BLANCO, J., MENTRÉ, F., PICARD, B., DENAMUR, E., Mentré, F, and COLIVILLE and COLIBAFI groups

Abstract

Bacteraemia caused by Escherichia coli are particularly frequent and severe, contrasting with the commensal character of the strains found in the digestive tract. A better understanding of the relationships between strains of both origins is needed to unravel the pathogenesis of this disease. Two hundred and forty-three commensal strains were compared to 243 bacteraemic strains isolated from adult hosts matched in terms of gender and age, and from similar location and epoch. Phylogenetic grouping, O-type determination, virulence factor content and antibiotic resistance were compared. Compared to commensal strains, the bacteraemic strains were characterized by a higher proportion of B2, C and D phylogroups, and a lower proportion of A, E and F phylogroups. They also had a lower proportion of the B2 subgroup IV (STc141), a higher proportion of virulence factors, and a higher frequency of antibiotic resistance. These differences were more marked for the bacteraemic strains of urinary tract origin with the presence of specific clones, whereas the bacteraemic strains of digestive origin remained non-significantly different from the commensal strains, except for their antibiotic resistance. Thus, two levels of specialization from commensal strains were demonstrated in the bacteraemic strains: resistance to antibiotics in all cases, and virulence for those of urinary tract origin. [ABSTRACT FROM PUBLISHER]

Published
2017
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23. Use of Genetic and Physical Mapping to Locate the Spinal Muscular Atrophy Locus between Two New Highly Polymorphic DNA Markers

Author

Clermont, O., Burlet, P., Burglen, L., Lefebvre, S., Pascal, F., John McPherson, Wasmuth, J. J., Cohen, D., Le Paslier, D., Weissenbach, J., Lathrop, M., Munnich, A., and Melki, J.

Subjects
Genetic Markers, Male, Muscular Atrophy, Spinal, Polymorphism, Genetic, Genetic Linkage, Homozygote, Chromosome Mapping, Chromosomes, Human, Pair 5, Humans, Female, Original Articles, Child, Chromosomes, Artificial, Yeast
Abstract

The gene for autosomal recessive forms of spinal muscular atrophy (SMA) has recently been mapped to chromosome 5q13, within a 4-cM region between the blocks D5S465/D5S125 and MAP-1B/D5S112. We identified two new highly polymorphic microsatellite DNA markers--namely, AFM265wf5 (D5S629) and AFM281yh9 (D5S637)--which are the closest markers to the SMA locus. Multilocus analysis by the location-score method was used to establish the best estimate of the SMA gene location. Our data suggest that the most likely location for SMA is between locus D5S629 and the block D5S637/D5S351/MAP-1B/D5S112/D5S357. Genetic analysis of inbred SMA families, based on homozygosity by descent and physical mapping using mega-YACs, gave additional information for the loci order as follows: cen-D5S6-D5S125/D5S465-D5S435-D5S629-SMA-+ ++D5S637-D5S351-MAP-1B/D5S112-D5S357- D5S39-tel. These data give the direction for bidirectional walking in order to clone this interval and isolate the SMA gene.

Published
1994

24. [Physical study of big fragments and search strategy of genes. Application to locus of infant spinal muscular atrophies]

Author

Melki, J, Lefebvre, S, Burglen, L, Burlet, P, Clermont, O, Millasseau, P, Reboulet, S, Benichou, B, Zeviani, M, and Le Paslier, D

Subjects
Male, Nucleic Acid, Chromosome Mapping, Spinal Muscular Atrophies of Childhood, Chromosomes, Repetitive Sequences, Chromosomes, Human, Pair 5, Female, Gene Deletion, Humans, Repetitive Sequences, Nucleic Acid, Pair 5, Human
Abstract

Spinal muscular atrophies (SMA) represent the second most common fatal autosomal recessive disorder after cystic fibrosis. Childhood SMAs are divided into severe (type I) and mild forms (types II and III). By a combination of genetic and physical mapping, a YAC contig of the 5q13 region spanning the disease locus was constructed that showed the presence of low copy-repeats in this region. Allele segregation was analyzed at the closest genetic loci detected by markers C212 and C272 in 201 SMA families. Inherited and de novo deletions were observed in 10 SMA patients. Moreover, deletions were strongly suggested in at least 18% of SMA type I patients by the observation of marked heterozygosity deficiency for the loci studied. These results indicate that deletion events are statistically associated with the severe form of SMA.

Published
1994

28. Rapid detection of the O25b-ST131 clone of Escherichia coli encompassing the CTX-M-15-producing strains

Author

Clermont, O., primary, Dhanji, H., additional, Upton, M., additional, Gibreel, T., additional, Fox, A., additional, Boyd, D., additional, Mulvey, M. R., additional, Nordmann, P., additional, Ruppe, E., additional, Sarthou, J. L., additional, Frank, T., additional, Vimont, S., additional, Arlet, G., additional, Branger, C., additional, Woodford, N., additional, and Denamur, E., additional

Published
2009
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31. Escherichia coli bacteraemia in adults: age-related differences in clinical and bacteriological characteristics, and outcome.

Author

ROUBAUD BAUDRON, C., PANHARD, X., CLERMONT, O., MENTRÉ, F., FANTIN, B., DENAMUR, E., and LEFORT, A.

Abstract

To explore the specificities of Escherichia coli bacteraemia in the elderly, the demographic, clinical and bacteriological characteristics and in-hospital mortality rate of ‘young’ (18–64 years, n = 395), ‘old’ (65–79 years, n = 372) and ‘very old’ (⩾80 years, n = 284) adult patients of the multicentre COLIBAFI cohort study were compared. Clinical and bacteriological risk factors for death were jointly identified by logistic regression and multivariate analysis within each group. ‘Young’ and ‘old’ patients had more comorbidities than ‘very old’ patients (comorbidity score: 1·5 ± 1·3 and 1·6 ± 1·2 vs. 1·2 ± 1·2, respectively; P < 0·001), and were more frequently nosocomially infected (22·3% and 23·8% vs. 8·8%, respectively; P < 0·001). ‘Old’ patients had the poorest prognosis (death rate: 16·4% vs.10·4% for ‘young’ and 12·0% for ‘very old’ patients, respectively; P = 0·039). Risk factors for death were age group-specific, suggesting a host–pathogen relationship evolving with age. [ABSTRACT FROM PUBLISHER]

Published
2014
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32. Frameshift mutation in the survival motor neuron gene in a severe case of SMA type I

Author

Brahe, Cristina Beate, Clermont, O, Zappata, S, Tiziano, Francesco Danilo, Melki, J, Neri, Giovanni, Tiziano, Francesco Danilo (ORCID:0000-0002-5545-6158), Brahe, Cristina Beate, Clermont, O, Zappata, S, Tiziano, Francesco Danilo, Melki, J, Neri, Giovanni, and Tiziano, Francesco Danilo (ORCID:0000-0002-5545-6158)

Abstract

Recently, a spinal muscular atrophy (SMA) determining gene, termed survival motor neuron (SMN) gene, has been isolated from the 5q13 region and found deleted in most patients. A highly homologous copy of this gene has also been isolated and located in a centromeric position. We have analyzed 158 patients (SMA types I-IV) and found deletions of SMN exon 7 in 96.8%. Mutations other than gross deletions seem to be extremely rare. In one of the undeleted SMA type I patients, a newborn who survived for only 42 days, we detected a maternally inherited 5 bp microdeletion in exon 3, resulting in a premature stop codon. By RT-PCR and long range PCR amplification we were able to show that the deletion belongs to the SMN gene, rather than to the centromeric copy, and that the proposita had no paternal SMN gene. Analysis of the neuronal apoptosis inhibitor protein (NAIP) gene, which maps close to SMN and has been proposed as a SMA modifying gene, suggests the presence of at least one full-length copy. Haplotype analysis of closely linked polymorphic markers suggests that the proposita also lacks the maternally derived copy of the centromeric homologue of SMN supporting the hypothesis that the severity of the phenotype might depend on the reduced number of centromeric genes in addition to the frameshift mutation.

Published
1996

40. Dernière heure : identification et caractérisation d'un gène déterminant dans les amyotrophies spinales

Author

Bürglen, L, primary, Lefebvre, S, additional, Reboullet, S, additional, Clermont, O, additional, Burlet, P, additional, Viollet, L, additional, Bénichou, B, additional, Cruaud, C, additional, Millasseau, P, additional, Zeviani, M, additional, Le Paslier, D, additional, Frézal, J, additional, Cohen, D, additional, Weissenbach, J, additional, Munnich, A, additional, and Melki, J, additional

Published
1995
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42. Experimental mouse lethality of Escherichia coli isolates, in relation to accessory traits, phylogenetic group, and ecological source.

Author

Johnson JR, Clermont O, Menard M, Kuskowski MA, Picard B, Denamur E, Johnson, James R, Clermont, Olivier, Menard, Megan, Kuskowski, Michael A, Picard, Bertrand, and Denamur, Erick

Abstract

Background: Whether accessory traits, phylogenetic background, or ecological source best predicts extraintestinal virulence within Escherichia coli is undefined.Methods: A total of 90 E. coli strains (18 fecal isolates and 72 extraintestinal-infection isolates) were characterized for 55 accessory traits and phylogenetic group (A, B1, B2, or D). Bacterial traits and ecological source were compared with experimental mouse lethality.Results: Of the 90 strains, 41% were "killers" (i.e., killed > or =90% of mice). By univariate analysis, multiple group B2-associated traits (including malX [pathogenicity-island marker], pap [P fimbriae] elements, usp [uropathogenic-specific protein], and fyuA [yersiniabactin system]) were most closely associated with killer status, followed by group B2 (or non-group A) status and then by nonfecal origin. Stepwise multivariate analysis identified pap, malX, usp, fyuA, and B2 (all of which were positive predictors) and ireA (which was a negative predictor) as significant predictors of killer status. Killer strains segregated significantly from nonkiller strains, according to accessory-trait profiles. Factorial analysis of correspondence placed group B2 among the traits most closely associated with killer status, but not as the closest.Conclusions: Specific group B2-associated accessory traits are more potent predictors of experimental virulence among E. coli isolates than is either phylogenetic background or ecological source. Molecular typing can estimate an E. coli isolate's extraintestinal virulence potential, regardless of source. [ABSTRACT FROM AUTHOR]

Published
2006

43. Identification par hybridation soustractive de régions chromosomiques spécifiques des souches de Escherichia coliresponsables de méningites néonatales

Author

Bonacorsi, S.P.P., Clermont, O., Tinsley, C., Le Gall, I., Beaudoin, J.C., Elion, J., Nassif, X., and Bingen, E.

Abstract

Le polysaccharide capsulaire K1, l'aérobactine, l'adhésine S et la protéine Ibe 10 sont des facteurs de virulence spécifiques de E. coliresponsables de méningites néonatales. Des souches de ECNM dépourvues de ces facteurs ont été décrites et suggèrent l'existence d'autres facteurs de virulence. Afin d'identifier de nouvelles régions génomiques impliquées dans la virulence de ces souches, nous avons utilisé la technique de Representational Difference Analysis.

Published
2000
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44. Identification of regions of the Escherichia coli chromosome specific for neonatal meningitis-associated strains.

Author

Bonacorsi, S P, Clermont, O, Tinsley, C, Le Gall, I, Beaudoin, J C, Elion, J, Nassif, X, and Bingen, E

Abstract

Specific virulence factors associated with the pathogenesis of Escherichia coli strains causing neonatal meningitis (ECNM), such as the K1 capsular polysaccharide, the S fimbriae, and the Ibe10 protein, have been previously identified. However, some other yet unidentified factors are likely to be involved in the pathogenesis of ECNM. To identify specialized unique DNA regions associated with ECNM virulence, we used the representational difference analysis technique. The genomes of two strains belonging to nonpathogenic phylogenetic group A of the ECOR reference collection were subtracted from E. coli strain C5, isolated from a case of neonatal meningitis. Strain C5 belongs to the phylogenetic group B2 as do the majority of ECNM. We have isolated and mapped 64 DNA fragments which are specific for strain C5 and not found in nonpathogenic strains. Of these clones, 44 were clustered in six distinct regions on the chromosome. The sfa and ibe10 genes were located in regions 2 and 6, respectively. A group of genes (cnf1, hra, hly, and prs) known to be present in a pathogenicity island of the uropathogenic strain E. coli J96 colocalized with region 6. The occurrence of these DNA regions was tested in a set of meningitis-associated strains and in a control group composed of non-meningitis-associated strains belonging to the same B2 group. Regions 1, 3, and 4 were present in 91, 82, and 81%, respectively, of the meningitis strains and in 40, 13, and 47% of the control strains. Together, these data suggest that regions 1, 3, and 4 code for factors associated with the ability of E. coli to invade the meninges of neonates.

Published
2000

45. In vivo selection of a target/efflux double mutant of Pseudomonas aeruginosa by ciprofloxacin therapy

Author

Thomas, I. Le, Couetdic, G., Clermont, O., Brahimi, N., Plésiat, P., and Bingen, E.

Abstract

We report the emergence after 4 days of ciprofloxacin monotherapy of a double mutant of Pseudomonas aeruginosa overexpressing the multidrug efflux system MexAB-OprM and harbouring a mutation in the gyrB gene. Compared with its initial susceptible counterpart, this mutant exhibited a significant increase in resistance to most of the β-lactam antibiotics tested (16 × MIC of ticarcillin) and to ciprofloxacin (128 × MIC). Combined ceftazidime and amikacin therapy finally eradicated the resistant isolate and cured the patient of his infection. This case illustrates how strains of P. aeruginosa may develop high levels of fluoroquinolone resistance by combining efflux mechanisms and target alterations.

Published
2001

48. Influence of hydrological conditions on the Escherichia coli population structure in the water of a creek on a rural watershed

Author

Ratajczak Mehdy, Laroche Emilie, Berthe Thierry, Clermont Olivier, Pawlak Barbara, Denamur Erick, and Petit Fabienne

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Escherichia coli is a commensal bacterium of the gastro-intestinal tract of human and vertebrate animals, although the aquatic environment could be a secondary habitat. The aim of this study was to investigate the effect of hydrological conditions on the structure of the E. coli population in the water of a creek on a small rural watershed in France composed of pasture and with human occupation. Results It became apparent, after studying the distribution in the four main E. coli phylo-groups (A, B1, B2, D), the presence of the hly (hemolysin) gene and the antibiotic resistance pattern, that the E. coli population structure was modified not only by the hydrological conditions (dry versus wet periods, rainfall events), but also by how the watershed was used (presence or absence of cattle). Isolates of the B1 phylo-group devoid of hly and sensitive to antibiotics were particularly abundant during the dry period. During the wet period and the rainfall events, contamination from human sources was predominantly characterized by strains of the A phylo-group, whereas contamination by cattle mainly involved B1 phylo-group strains resistant to antibiotics and exhibiting hly. As E. coli B1 was the main phylo-group isolated in water, the diversity of 112 E. coli B1 isolates was further investigated by studying uidA alleles (beta-D-glucuronidase), the presence of hly, the O-type, and antibiotic resistance. Among the forty epidemiolgical types (ETs) identified, five E. coli B1 ETs were more abundant in slightly contaminated water. Conclusions The structure of an E. coli population in water is not stable, but depends on the hydrological conditions and on current use of the land on the watershed. In our study it was the ratio of A to B1 phylo-groups that changed. However, a set of B1 phylo-group isolates seems to be persistent in water, strengthening the hypothesis that they may correspond to specifically adapted strains.

Published
2010
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49. aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species

Author

Tuffery Pierre, Darlu Pierre, Garry Louis, Clermont Olivier, Hoede Claire, Lescat Mathilde, Denamur Erick, and Picard Bertrand

Subjects
Microbiology, QR1-502
Abstract

Abstract Background Previous studies have established a correlation between electrophoretic polymorphism of esterase B, and virulence and phylogeny of Escherichia coli. Strains belonging to the phylogenetic group B2 are more frequently implicated in extraintestinal infections and include esterase B2 variants, whereas phylogenetic groups A, B1 and D contain less virulent strains and include esterase B1 variants. We investigated esterase B as a marker of phylogeny and/or virulence, in a thorough analysis of the esterase B-encoding gene. Results We identified the gene encoding esterase B as the acetyl-esterase gene (aes) using gene disruption. The analysis of aes nucleotide sequences in a panel of 78 reference strains, including the E. coli reference (ECOR) strains, demonstrated that the gene is under purifying selection. The phylogenetic tree reconstructed from aes sequences showed a strong correlation with the species phylogenetic history, based on multi-locus sequence typing using six housekeeping genes. The unambiguous distinction between variants B1 and B2 by electrophoresis was consistent with Aes amino-acid sequence analysis and protein modelling, which showed that substituted amino acids in the two esterase B variants occurred mostly at different sites on the protein surface. Studies in an experimental mouse model of septicaemia using mutant strains did not reveal a direct link between aes and extraintestinal virulence. Moreover, we did not find any genes in the chromosomal region of aes to be associated with virulence. Conclusion Our findings suggest that aes does not play a direct role in the virulence of E. coli extraintestinal infection. However, this gene acts as a powerful marker of phylogeny, illustrating the extensive divergence of B2 phylogenetic group strains from the rest of the species.

Published
2009
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50. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

Author

Clermont Olivier, Lortholary Olivier, Carbonnelle Etienne, Guigon Ghislaine, Frapy Eric, Diancourt Laure, Passet Virginie, Landraud Luce, Jaureguy Françoise, Denamur Erick, Picard Bertrand, Nassif Xavier, and Brisse Sylvain

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Extraintestinal pathogenic Escherichia coli (ExPEC) strains represent a huge public health burden. Knowledge of their clonal diversity and of the association of clones with genomic content and clinical features is a prerequisite to recognize strains with a high invasive potential. In order to provide an unbiased view of the diversity of E. coli strains responsible for bacteremia, we studied 161 consecutive isolates from patients with positive blood culture obtained during one year in two French university hospitals. We collected precise clinical information, multilocus sequence typing (MLST) data and virulence gene content for all isolates. A subset representative of the clonal diversity was subjected to comparative genomic hybridization (CGH) using 2,324 amplicons from the flexible gene pool of E. coli. Results Recombination-insensitive phylogenetic analysis of MLST data in combination with the ECOR collection revealed that bacteremic E. coli isolates were highly diverse and distributed into five major lineages, corresponding to the classical E. coli phylogroups (A+B1, B2, D and E) and group F, which comprises strains previously assigned to D. Compared to other strains of phylogenetic group B2, strains belonging to MLST-derived clonal complexes (CCs) CC1 and CC4 were associated (P < 0.05) with a urinary origin. In contrast, no CC appeared associated with severe sepsis or unfavorable outcome of the bacteremia. CGH analysis revealed genomic characteristics of the distinct CCs and identified genomic regions associated with CC1 and/or CC4. Conclusion Our results demonstrate that human bacteremia strains distribute over the entire span of E. coli phylogenetic diversity and that CCs represent important phylogenetic units for pathogenesis and comparative genomics.

Published
2008
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