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3. RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation

Author

Martell, Danya J., Merens, Hope E., Caulier, Alexis, Fiorini, Claudia, Ulirsch, Jacob C., Ietswaart, Robert, Choquet, Karine, Graziadei, Giovanna, Brancaleoni, Valentina, Cappellini, Maria Domenica, Scott, Caroline, Roberts, Nigel, Proven, Melanie, Roy, Noémi B.A., Babbs, Christian, Higgs, Douglas R., Sankaran, Vijay G., and Churchman, L. Stirling

Published
2023
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5. Chikungunya Outbreak in Country with Multiple Vectorborne Diseases, Djibouti, 2019–2020

Author

Emilie Javelle, Franck de Laval, Guillaume André Durand, Aissata Dia, Cécile Ficko, Aurore Bousquet, Deborah Delaune, Sébastien Briolant, Audrey Mérens, Constance Brossier, Hervé Pommier, Florian Gala, Alain Courtiol, Quentin Savreux, Sébastien Sicard, Jean-Philippe Sanchez, Francis Robin, Fabrice Simon, Xavier de Lamballerie, Gilda Grard, Isabelle Leparc-Goffart, and Vincent Pommier de Santi

Subjects
Chikungunya virus, dengue virus, chikungunya, dengue fever, malaria, outbreak, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

During 2019–2020, a chikungunya outbreak occurred in Djibouti City, Djibouti, while dengue virus and malaria parasites were cocirculating. We used blotting paper to detect arbovirus emergence and confirm that it is a robust method for detecting and monitoring arbovirus outbreaks remotely.

Published
2023
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6. Performances, feasibility and acceptability of nasopharyngeal swab, saliva and oral-self sampling swab for the detection of severe acute respiratory syndrome coronavirus 2

Author

Plantamura, Julie, Bousquet, Aurore, Otto, Marie-Pierre, Bigaillon, Christine, Legland, Anne-Margaux, Delacour, Hervé, Vest, Philippe, Astier, Hélène, Valero, Elodie, Bylicki, Olivier, Renard, Christophe, Martin, Solenne, Verret, Catherine, Garnotel, Eric, Foissaud, Vincent, Mérens, Audrey, and Janvier, Frédéric

Published
2021
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7. Cryptosporidiosis outbreaks linked to the public water supply in a military camp, France.

Author

Stéphanie Watier-Grillot, Damien Costa, Cédric Petit, Romy Razakandrainibe, Sébastien Larréché, Christelle Tong, Gwenaëlle Demont, David Billetorte, Damien Mouly, Didier Fontan, Guillaume Velut, Alexandra Le Corre, Jean-Christophe Beauvir, Audrey Mérens, Loïc Favennec, and Vincent Pommier de Santi

Subjects
Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270
Abstract

IntroductionContaminated drinking and recreational waters account for most of the reported Cryptosporidium spp. exposures in high-income countries. In June 2017, two successive cryptosporidiosis outbreaks occurred among service members in a military training camp located in Southwest France. Several other gastroenteritis outbreaks were previously reported in this camp, all among trainees in the days following their arrival, without any causative pathogen identification. Epidemiological, microbiological and environmental investigations were carried out to explain theses outbreaks.Material and methodsSyndromic diagnosis using multiplex PCR was used for stool testing. Water samples (100 L) were collected at 10 points of the drinking water installations and enumeration of Cryptosporidium oocysts performed. The identification of Cryptosporidium species was performed using real-time 18S SSU rRNA PCR and confirmed by GP60 sequencing.ResultsA total of 100 human cases were reported with a global attack rate of 27.8%. Cryptosporidium spp. was identified in 93% of stool samples with syndromic multiplex PCR. The entire drinking water network was contaminated with Cryptosporidium spp. The highest level of contamination was found in groundwater and in the water leaving the treatment plant, with >1,000 oocysts per 100 L. The same Cryptosporidium hominis isolate subtype IbA10G2 was identified in patients' stool and water samples. Several polluting activities were identified within the protection perimeters of the water resource. An additional ultrafiltration module was installed at the outlet of the water treatment plant. After several weeks, no Cryptosporidium oocysts were found in the public water supply.ConclusionsAfter successive and unexplained gastroenteritis outbreaks, this investigation confirmed a waterborne outbreak due to Cryptosporidium hominis subtype IbA10G2. Our study demonstrates the value of syndromic diagnosis for gastroenteritis outbreak investigation. Our results also highlight the importance of better assessing the microbiological risk associated with raw water and the need for sensitive and easy-to-implement tools for parasite detection.

Published
2022
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8. Lessons learned from the investigation of a COVID-19 cluster in Creil, France: effectiveness of targeting symptomatic cases and conducting contact tracing around them

Author

Franck de Laval, Anaïs Grosset-Janin, François Delon, Alexandre Allonneau, Christelle Tong, Flavie Letois, Anne Couderc, Marc-Antoine Sanchez, César Destanque, Fabrice Biot, Françoise Raynaud, Christine Bigaillon, Olivier Ferraris, Etienne Simon-Loriere, Vincent Enouf, Dinaherisoa Andriamanantena, Vincent Pommier de Santi, Emilie Javelle, and Audrey Mérens

Subjects
SARS-CoV-2, COVID-19, Cluster, RT-PCR, Asymptomatic, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background This study presents the methods and results of the investigation into a SARS-CoV-2 outbreak in a professional community. Due to the limited testing capacity available in France at the time, we elaborated a testing strategy according to pre-test probability. Methods The investigation design combined active case finding and contact tracing around each confirmed case with testing of at-risk contact persons who had any evocative symptoms (n = 88). One month later, we performed serology testing to test and screen symptomatic and asymptomatic cases again (n = 79). Results Twenty-four patients were confirmed (14 with RT-PCR and 10 with serology). The attack rate was 29% (24/83). Median age was 40 (24 to 59), and the sex ratio was 15/12. Only three cases were asymptomatic (= no symptoms at all, 13%, 95% CI, 3–32). Nineteen symptomatic cases (79%, 95% CI, 63–95) presented a respiratory infection, two of which were severe. All the RT-PCR confirmed cases acquired protective antibodies. Median incubation was 4 days (from 1 to 13 days), and the median serial interval was 3 days (0 to 15). We identified pre-symptomatic transmission in 40% of this cluster, but no transmission from asymptomatic to symptomatic cases. Conclusion We report the effective use of targeted testing according to pre-test probability, specifically prioritizing symptomatic COVID-19 diagnosis and contact tracing. The asymptomatic rate raises questions about the real role of asymptomatic infected people in transmission. Conversely, pre-symptomatic contamination occurred frequently in this cluster, highlighting the need to identify, test, and quarantine asymptomatic at-risk contact persons (= contact tracing). The local lockdown imposed helped reduce transmission during the investigation period.

Published
2021
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10. Community-acquired bacterial meningitis in adults: in-hospital prognosis, long-term disability and determinants of outcome in a multicentre prospective cohort

Author

Duval, Xavier, Hoen, Bruno, Mourvillier, Bruno, Ploy, Marie-Cécile, Tubiana, Sarah, Varon, Emmanuelle, Caron, François, Bollaert, Pierre-Edouard, Gaillot, Olivier, Taha, Muhamed-Kheir, Poyart, Claire, Bonacorsi, Stephane, Vandenesch, François, Cambau, Emmanuelle, Lecuit, Marc, Gravet, Alain, Frachet, Bruno, Broucker, Thomas De, Levy Bruhl, Daniel, Raffi, François, Anguel, Nadia, Argaud, Laurent, Arista, Sophie, Armand-Lefevre, Laurence, Balavoine, Stéphanie, Baraduc, Régine, Barnaud, Guilène, Beraud, Guillaume, Bernard, Louis, Bernars, Georges, Bertei, Dominique, Bessede, Emilie, Billard Pomares, Typhaine, Biron, Charlotte, Bland, Stéphane, Boileau, Julien, Boubeau, Patrice, Bourdon, Sandra, Bousquet, Aurore, Boyer, Sophie, Bozorg-Grayeli, Alexis, Bret, Laurent, Bretonniere, Cédric, Bricaire, François, Brocas, Elsa, Brun, Michel, Buret, Jennifer, Burucoa, Christophe, Cabalion, Jean, Cabon, Mathieu, Camuset, Guillaume, Canevet, Christophe, Carricajo, Anne, Castan, Bernard, Caumes, Eric, Cazanave, Charles, Chabrol, Amélie, Challan-Belval, Thibaut, Chanteperdrix-Marillier, Vanessa, Chaplain, Chantal, Charlier-Woerther, Caroline, Chaussade, Hélène, Chirouze, Catherine, Clair, Bernard, Colot, Julien, Conil, Jean-Marie, Cordel, Hugues, Cormier, Philippe, Cousson, Joël, Cronier, Pierrick, Cua, Eric, Dao-Dubremetz, Anne, Dargere, Sylvie, Degand, Nicolas, Dekeyser, Sophie, Delaune, Deborah, Denes, Eric, Dequin, Pierre-Francois, Descamps, Diane, Descloux, Elodie, Desmaretz, Jean-Luc, Diehl, Jean-Luc, Dimet, Jérôme, Dinh, Aurélien, Escaut, Lelia, Fabe, Claude, Faibis, Frédéric, Flateau, Clara, Fonsale, Nathalie, Forestier, Emmanuel, Fortineau, Nicolas, Gagneux-Brunon, Amandine, Garandeau, Garcia, Magali, Garot, Denis, Gaudry, Stéphane, Goehringer, François, Gregoire-Faucher, Valérie, Grosset, Marine, Gubavu, Camélia, Gueit, Isabelle, Guelon, Dominique, Guimard, Thomas, Guinard, Jérôme, Hadou, Tahar, Helene, Jean-Pierre, Henard, Sandrine, Henry, Benoit, Hochart, Anne-Cécile, Illes, Gabriela, Jaffuel, Sylvain, Jarrin, Irène, Jaureguy, Françoise, Joseph, Cédric, Juvin, Marie-Emmanuelle, Kayal, Samer, Lacassin, Flore, Lamaury, Isabelle, Lanotte, Philippe, Laurens, Etienne, Laurichesse, Henri, Le Brun, Cécile, Le Moing, Vincent, Le Turnier, Paul, Lecuyer, Hervé, Ledru, Sylvie, Legrix, Céline, Lemaignen, Adrien, Lemble, Chantal, Lemee, Ludovic, Lesens, Olivier, Levast, Marion, Lhommet, Claire, Males, Silvija, Malpote, Edith, Martin-Blondel, Guillaume, Marx, Matthieu, Masson, Raphael, Matray, Olivier, Mbadi, Aurore, Mechai, Frédéric, Mellon, Guillaume, Merens, Audrey, Meyohas, Marie Caroline, Michon, Adrien, Mootien Yoganaden, Joy, Morquin, David, Mouly, Stéphane, Mrozek, Natacha, Nguyen, Sophie, Nguyen, Yohan, Ogielska, Maja, Oziol, Eric, Page, Bernard, Patrat-Delon, Solène, Patry, Isabelle, Pechinot, André, Picot, Sandrine, Pierrejean, Piroth, Lionel, Plassart, Claire, Plessis, Patrice, Portel, Laurent, Poubeau, Patrice, Poupard, Marie, Prazuck, Thierry, Quaesaet, Luc, Ramanantsoa, Adriatsiferana, Rapp, Christophe, Raskine, Laurent, Raymond, Josette, Revest, Matthieu, Riche, Agnès, Robaday-Voisin, Stéphanie, Robin, Frédéric, Romaszko, Jean-Pierre, Rousseau, Florence, Roux, Anne-Laure, Royer, Cecile, Saada, Matthieu, Salmon, Dominique, Saroufim, Carlo, Schmit, Jean-Luc, Sebire, Manuela, Segonds, Christine, Sivadon-Tardy, Valérie, Soismier, Nathalie, Kerneis, Solen, Son, Olivia, Sunder, Simon, Suy, Florence, Tande, Didier, Tankovic, Jacques, Valin, Nadia, Van Grunderbeeck, Nicolas, Verdon, Renaud, Vergnaud, Michel, Vernet-Garnier, Véronique, Vidal, Magali, Vitrat, Virginie, Vittecoq, Daniel, Vuotto, Fanny, Coordination and statistical analyses, Gorenne, Isabelle, Laouenan, Cédric, Marcault, Estelle, Mentre, France, Pasquet, Blandine, Roy, Carine, Tubiana, S., Varon, E., Biron, C., Ploy, M.-C., Mourvillier, B., Taha, M.-K., Revest, M., Poyart, C., Martin-Blondel, G., Lecuit, M., Cua, E., Pasquet, B., Preau, M., Hoen, B., and Duval, X.

Published
2020
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12. Lessons learned from the investigation of a COVID-19 cluster in Creil, France: effectiveness of targeting symptomatic cases and conducting contact tracing around them

Author

de Laval, Franck, Grosset-Janin, Anaïs, Delon, François, Allonneau, Alexandre, Tong, Christelle, Letois, Flavie, Couderc, Anne, Sanchez, Marc-Antoine, Destanque, César, Biot, Fabrice, Raynaud, Françoise, Bigaillon, Christine, Ferraris, Olivier, Simon-Loriere, Etienne, Enouf, Vincent, Andriamanantena, Dinaherisoa, de Santi, Vincent Pommier, Javelle, Emilie, and Mérens, Audrey

Published
2021
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16. Occupational Exposures to Ebola Virus in Ebola Treatment Center, Conakry, Guinea

Author

Hélène Savini, Frédéric Janvier, Ludovic Karkowski, Magali Billhot, Marc Aletti, Julien Bordes, Fassou Koulibaly, Pierre-Yves Cordier, Jean-Marie Cournac, Nancy Maugey, Nicolas Gagnon, Jean Cotte, Audrey Cambon, Christine Mac Nab, Sophie Moroge, Claire Rousseau, Vincent Foissaud, Thierry De Greslan, Hervé Granier, Gilles Cellarier, Eric Valade, Philippe Kraemer, Philippe Alla, Audrey Mérens, Emmanuel Sagui, Thierry Carmoi, and Christophe Rapp

Subjects
Ebola virus, disease, viruses, occupational exposure, healthcare workers, Conakry, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

We report 77 cases of occupational exposures for 57 healthcare workers at the Ebola Treatment Center in Conakry, Guinea, during the Ebola virus disease outbreak in 2014−2015. Despite the high incidence of 3.5 occupational exposures/healthcare worker/year, only 18% of workers were at high risk for transmission, and no infections occurred.

Published
2017
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17. Deployment of the French Military Field Laboratory Dedicated to Ebola Virus Infected Patients in Guinea, January–July 2015

Author

Janvier, Frédéric, Foissaud, Vincent, Delaune, Deborah, Flusin, Olivier, Dubrous, Philippe, Nab, Christine Mac, Gaillard, Tiphaine, Perez, Pascale, Poyot, Thomas, Paucod, Jean-Charles, Richard, Stéphane, Ferraris, Olivier, Delacour, Hervè, Bigaillon, Christine, Leparc-Goffard, Isabelle, Peyrefitte, Christophe, Patrick, Brisou, Renard, Christophe, Garnotel, Eric, Koeck, J.-L., Thibault, François, Valade, Eric, Mérens, Audrey, Brisou, Patrick, and Leparc-Goffart, Isabelle

Published
2016

18. Rhabdomyolysis in Ebola Virus Disease. Results of an Observational Study in a Treatment Center in Guinea

Author

Cournac, Jean Marie, Karkowski, Ludovic, Bordes, Julien, Aletti, Marc, Duron, Sandrine, Janvier, Frédéric, Foissaud, Vincent, Savini, Héléne, de Greslan, Thierry, Rousseau, Claire, Billhot, Magali, Gagnon, Nicolas, Nab, Christine Mac, Dubrous, Philippe, Moroge, Sophie, Broto, Helene, Cotte, Jean, Maugey, Nancy, Cordier, Pierre-Yves, Sagui, Emmanuel, Merens, Audrey, Rapp, Christophe, Quentin, Benoit, Granier, Hervé, Carmoi, Thierry, and Cellarier, Gilles

Published
2016

20. Evaluation of ceftolozane-tazobactam susceptibility on a French nationwide collection of Enterobacterales

Author

Jousset, Agnès B., Bernabeu, Sandrine, Emeraud, Cécile, Bonnin, Rémy A., Lomont, Alexandra, Zahar, Jean Ralph, Merens, Audrey, Isnard, Christophe, Soismier, Nathalie, Farfour, Eric, Fihman, Vincent, Yin, Nicolas, Barraud, Olivier, Jacquier, Hervé, Ranc, Anne-Gaëlle, Laurent, Frédéric, Corvec, Stéphane, d'Epenoux, Louise Ruffier, Bille, Emmanuelle, Degand, Nicolas, Plouzeau, Chloé, Guillard, Thomas, Cattoir, Vincent, Mizrahi, Asaf, Grillon, Antoine, Janvier, Frédéric, Brun, Cécile Le, Amara, Marlène, Bastide, Mathilda, Lemonnier, Alban, and Dortet, Laurent

Published
2023
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24. Ebola Virus RNA Stability in Human Blood and Urine in West Africa’s Environmental Conditions

Author

Frédéric Janvier, Deborah Delaune, Thomas Poyot, Eric Valade, Audrey Mérens, Pierre E. Rollin, and Vincent Foissaud

Subjects
Ebola virus, RNA stability, human samples, rRT-PCR, viruses, West Africa, Medicine, Infectious and parasitic diseases, RC109-216
Abstract

We evaluated RNA stability of Ebola virus in EDTA blood and urine samples collected from infected patients and stored in West Africa’s environmental conditions. In blood, RNA was stable for at least 18 days when initial cycle threshold values were

Published
2016
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25. Prevalence and risk factors of sexually transmitted infections among French service members.

Author

Sandrine Duron, Henri Panjo, Aline Bohet, Christine Bigaillon, Sébastien Sicard, Nathalie Bajos, Jean-Baptiste Meynard, Audrey Mérens, and Caroline Moreau

Subjects
Medicine, Science
Abstract

Sexually Transmitted Infections (STIs) have always represented a public health concern in the military, yet most studies rely on self-reports among non-random samples of military populations. In addition, most of the studies exploring STI rates among the military focus on US service members. This paper assesses the prevalence and correlates of STIs in the French military using biomarkers and compares self-reported versus diagnosed STIs.Data are drawn from the COSEMIL study, a national sexual health survey conducted in the French military in 2014 and 2015. A random sample of 784 men and 141 women aged 18-57 years completed a self-administered questionnaire and provided biological samples for STI testing. We used logistic regression modeling to identify the correlates of STI diagnosis and self-reports.The prevalence of diagnosed STIs was 4.7% [3.8-5.9], mostly due to Chlamydia trachomatis. This rate was four times higher than the 12 months self-reported rate of 1.1% [0.6-2.3]. Reported STI rates were similar among men and women (1.1% versus 1.8%), but diagnosed STI rates were twice as high among females versus males (10.4% versus 4.1%, p = 0.007). There were significant differences in the determinants of reported versus diagnosed STIs. In particular, age and sexual orientation were associated with reported STIs, but not with diagnosed STIs. Conversely, STI counseling and depression were associated with STI diagnosis but not with STI reports.This study underlines the need to use biomarkers in population-based surveys, given the differential and substantial underreporting of STIs. Results also highlight the need for programmatic adaptation to address gender inequalities in STI rates, by developing women's health services in the French military. Addressing such needs not only benefits women but could also serve as a strategy to reduce overall STI rates as most military women have military partners, increasing the risk of internal transmission.

Published
2018
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27. 1702 - EPIDEMIOLOGÍA Y RESULTADOS CLÍNICOS DE LA ENDOCARDITIS INFECCIOSA POR ENTEROCOCCUS FEACALIS

Author

García, Mónica Gutiérrez, Rivo, Ana Belén Sanjurjo, Valerio, Laura Cristina Intanno, Vázquez, Patricia Vidal, Corvo, Luis Chamorro, Suárez, Sara Francisco, Fernández, Emilia Fernández, Vila, Marta Costas, Vázquez, Irene Merens, Ferreiro, José Luis Lamas, Basanta, Aida Lidia Baroja, Otero, Judith Álvarez, Conde, Paula Sánchez, and de la Fuente Aguado, Javier

Published
2024
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31. First cases of Omicron in France are exhibiting mild symptoms, November 2021–January 2022

Author

Andrieu, A., Broustal, O., Chene, S., Chent, S., Fougère, E., Gbaguidi, G., Hamidouche, M., Lamy, A., Mano, Q., Mastrovito, B., Mercier, A., Modenesi, G., Picard, G., Prudhomme, J., Rapilly, F., Riondel, A., Rivière, M., Villegas Ramirez, B., Zhu-Soubise, A., Zurbaran, M., Amzert, A., Andreoletti, L., Bal, A., Beaurepere, R., Behillil, S., Belec, L., Bernard, C., Bocket, L., Bouri, L., Bourlet, T., Bressollette-Bodin, C., Brichler, S., Brugerolles, C., Cado, S., Calvez, V., Capron, N., Castelain, S., Castro-Alvarez, J., Chaix, M.-L., Charpentier, C., Che, D., Chillou, C., Colson, P., Coudene, P., Crinquette, A., De Rougemont, A., Delagrèverie, H., Delamare, C., Denecker-Berardino, T., Descamps, D., Desroches, M., Destras, G., Dos Santos, G., Ducancelle, A., Ducreux, S., Duret, T., Enouf, V., Fafi-Kremer, S., Felici, C., Fourati, S., Fournier, P.-E., Gaudy, C., Germain, H., Giordanengo, V., Gorge, O., Haim-Boukobza, S., Henquell, C., Holstein, A., Houhamdi, L., Izopet, J., Jacomo, V., Jacques, A., Jaffar-Bandjee, M.-C., Jimenez, M., Josset, L., Kemeny, S., Lafon, M.-E., Le Bars, A., Le Corguille, G., Lepiller, Q., Levasseur, A., Leveque, N., Lina, B., Madelaine, C., Malabat, C., Marque-Juillet, S., Martin-Dunavit, T., Mavingui, P., Merens, A., Messak, I., Morand-Joubert, L., Naudot, X., Neybecker, P., Pawlotsky, J.-M., Pilorge, L., Plantier, J.-C., Poggi, C., Pretet, M., Ragot, C., Raoul, H., Rogez, S., Roque-Afonso, A.-M., Roquebert, B., Rousset, D., Rozenberg, F., Sagot, C., Sahnoune, S., Salgado, D., Sand, O., Saudemont, C., Schvoerer, E., Simon-Loriere, E., Stephan, R., Sudour, J., Thibault, V., Tuaillon, E., Vabret, A., Vallee, E., Van Der Werf, S., Van Helden, J., Verdurme, L., Vignola, A., Wilkinson, D., Yazdanpanah, Y., Maisa, A., Spaccaferri, G., Fournier, L., Schaeffer, J., Deniau, J., Rolland, P., and Coignard, B.

Published
2022
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34. Incidence rates of carbapenemase-producing Enterobacteriaceae clinical isolates in France: a prospective nationwide study in 2011–12

Author

Robert, Jérôme, Pantel, Alix, Mérens, Audrey, Lavigne, Jean-Philippe, Nicolas-Chanoine, Marie-Hélène, Brieu, N., Vrain, A., Scanvic, A., Porcheret, H., Garnier, P., Bertrand, X., Descamps, D., Hombrouck, C., Soullié, B., Heym, B., de Montclos, H., Garrec, H., Levast, M., Mendes-Martins, L., Decousser, J. W., Huet, C., Bert, F., Herzig, V., Klein, J. P., Nebbad, B., Hendricx, S., Verhaeghe, A., Lafaurie, C., Lanselle, C., Elsayed, F., Carrer, A., Drieux-Rouzet, L., Evreux, F., Varache, C., Wallet, F., Martin, C., Le-Bris, J. M., Moulhade, M. C., Deville, E., Menouni, O., Jean-Pierre, H., Pierrot, P., Delarbre, J. M., Coude, B., Foca, M., Degand, N., Prots, L., Pantel, A., Adam, M. N., Laurens, E., Raskine, L., Laouira, S., Arlet, G., Sanchez, R., Peuchant, O., Grau, V., Laurent, C., De-Champs, C., Vachée, A., Harriau, P., Mérens, A., Belmonte, O., Michel, G., Henry, C., Picot, S., Glatz, I., Gueudet, T., Honderlick, P., Cavalié, L., Galinier, J. L., Patoz, P., van-der-Mee-Marquet, N., Haguenoer, E., Canis, F., Kassis-Chikhany, N., and Le-Garrec, Y.

Published
2014
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37. Chikungunya Outbreak in Country with Multiple Vectorborne Diseases, Djibouti, 2019-2020.

Author

Javelle, Emilie, de Laval, Franck, Durand, Guillaume André, Dia, Aissata, Ficko, Cécile, Bousquet, Aurore, Delaune, Deborah, Briolant, Sébastien, Mérens, Audrey, Brossier, Constance, Pommier, Hervé, Gala, Florian, Courtiol, Alain, Savreux, Quentin, Sicard, Sébastien, Sanchez, Jean-Philippe, Robin, Francis, Simon, Fabrice, de Lamballerie, Xavier, and Grard, Gilda

Subjects
CHIKUNGUNYA, DENGUE viruses, PLASMODIUM, DENGUE hemorrhagic fever
Abstract

During 2019-2020, a chikungunya outbreak occurred in Djibouti City, Djibouti, while dengue virus and malaria parasites were cocirculating. We used blotting paper to detect arbovirus emergence and confirm that it is a robust method for detecting and monitoring arbovirus outbreaks remotely. [ABSTRACT FROM AUTHOR]

Published
2023
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38. Performances, feasibility and acceptability of nasopharyngeal swab, saliva and oral-self sampling swab for the detection of severe acute respiratory syndrome coronavirus 2

Author

Audrey Mérens, Christophe Renard, Anne Margaux Legland, Julie Plantamura, Olivier Bylicki, Marie Pierre Otto, Eric Garnotel, Aurore Bousquet, Frédéric Janvier, Hervé Delacour, Elodie Valero, Christine Bigaillon, Vincent Foissaud, P. Vest, Catherine Verret, Solenne Martin, Hélène Astier, Laboratoire de Microbiologie [Hôpital d'Instruction des Armées Bégin, Saint-Mandé] (Service de Santé des Armées), Hôpital d'Instruction des Armées Bégin [Saint-Mandé, France], Hopital d'instruction des armées Sainte-Anne [Toulon] (HIA), Service de Santé des Armées, École du Val de Grâce (EVDG), French Military Health Service Academy, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Hôpital d'Instruction des Armées Laveran, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de biologie médicale, and Service de Santé des Armées-Hôpital d'instruction des Armées Percy

Subjects
0301 basic medicine, Microbiology (medical), medicine.medical_specialty, 2019-20 coronavirus outbreak, Saliva, Coronavirus disease 2019 (COVID-19), Hospitalized patients, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Internal medicine, Medicine, Sampling (medicine), [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Infectious Diseases, Multicenter study, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, business, Self sampling
Abstract

Molecular diagnosis on nasopharyngeal swabs (NPS) is the current standard for COVID-19 diagnosis, but saliva may be an alternative specimen to facilitate access to diagnosis. We compared analytic performances, feasibility and acceptability of NPS, saliva, and oral-self sampling swab for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A prospective, multicenter study was conducted in military hospitals in France among adult outpatients attending COVID-19 diagnosis centers or hospitalized patients. For each patient, all samples were obtained and analyzed simultaneously with RT-PCR or transcription-mediated amplification method. Clinical signs, feasibility, and acceptability for each type of sample were collected. A total of 1220 patients were included, corresponding to 1205 NPS and saliva and 771 OS. Compared to NPS, the sensitivity, specificity, and kappa coefficient for tests performed on saliva were 87.8% (95% CI 83.3-92.3), 97.1% (95% CI 96.1-98.1), and 0.84 (95% CI 0.80-0.88). Analytical performances were better in symptomatic patients. Ct values were significantly lower in NPS than saliva. For OS, sensitivity was estimated to be 61.1% (95% CI 52.7-69.4) and Kappa coefficient to be 0.69 (95% CI 0.62-0.76). OS was the technique preferred by the patients (44.3%) before saliva (42.4%) and NPS (13.4%). Instructions were perceived as simple by patients (> 90%) for saliva and OS. Finally, the painful nature was estimated to be 0.9 for OS, on a scale from 0 to 10, and to be 5.3 for NPS. Performances of OS are not sufficient. Saliva is an acceptable alternative to NPS for symptomatic patient but the process required additional steps to fluidize the sample.

Published
2021
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39. Global phylogeography and evolutionary history of Shigella dysenteriae type 1

Author

Njamkepo, Elisabeth, Fawal, Nizar, Tran-Dien, Alicia, Hawkey, Jane, Strockbine, Nancy, Jenkins, Claire, Talukder, Kaisar A., Bercion, Raymond, Kuleshov, Konstantin, Kolínská, Renáta, Russell, Julie E., Kaftyreva, Lidia, Accou-Demartin, Marie, Karas, Andreas, Vandenberg, Olivier, Mather, Alison E., Mason, Carl J., Page, Andrew J., Ramamurthy, Thandavarayan, Bizet, Chantal, Gamian, Andrzej, Carle, Isabelle, Sow, Amy Gassama, Bouchier, Christiane, Wester, Astrid Louise, Lejay-Collin, Monique, Fonkoua, Marie-Christine, Le Hello, Simon, Blaser, Martin J., Jernberg, Cecilia, Ruckly, Corinne, Mérens, Audrey, Page, Anne-Laure, Aslett, Martin, Roggentin, Peter, Fruth, Angelika, Denamur, Erick, Venkatesan, Malabi, Bercovier, Hervé, Bodhidatta, Ladaporn, Chiou, Chien-Shun, Clermont, Dominique, Colonna, Bianca, Egorova, Svetlana, Pazhani, Gururaja P., Ezernitchi, Analia V., Guigon, Ghislaine, Harris, Simon R., Izumiya, Hidemasa, Korzeniowska-Kowal, Agnieszka, Lutyńska, Anna, Gouali, Malika, Grimont, Francine, Langendorf, Céline, Marejková, Monika, Peterson, Lorea A.M., Perez-Perez, Guillermo, Ngandjio, Antoinette, Podkolzin, Alexander, Souche, Erika, Makarova, Mariia, Shipulin, German A., Ye, Changyun, Žemličková, Helena, Herpay, Mária, Grimont, Patrick A. D., Parkhill, Julian, Sansonetti, Philippe, Holt, Kathryn E., Brisse, Sylvain, Thomson, Nicholas R., and Weill, François-Xavier

Published
2016
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40. Temocillin susceptibility among Enterobacterales strains recovered from blood culture in France

Author

Philippe Lesprit, Emmanuelle Bille, Paul-Louis Woerther, Typhaine Billard-Pomares, Cécile Le Brun, Christophe Isnard, Nicolas Yin, Audrey Mérens, Nicolas Degand, Eric Farfour, J. Lourtet, Antoine Grillon, S. Corvec, Emilie Flevin, Damien Fournier, Thomas Guillard, Vincent Cattoir, Anne-Gaëlle Si Larbi, Alban Le Monnier, Chloé Plouzeau, Hôpital Foch [Suresnes], CHU Pontchaillou [Rennes], ARN régulateurs bactériens et médecine (BRM), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Centre hospitalier universitaire de Nantes (CHU Nantes), Pathologies Pulmonaires et Plasticité Cellulaire - UMR-S 1250 (P3CELL), Université de Reims Champagne-Ardenne (URCA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Reims (CHU Reims), Les Hôpitaux Universitaires de Strasbourg (HUS), CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Centre Hospitalier Universitaire de Nice (CHU Nice), Hôpital Avicenne [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Centre Hospitalier Régional Universitaire de Besançon (CHRU Besançon), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Hôpital Bretonneau, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Centre hospitalier universitaire de Poitiers (CHU Poitiers), Centre hospitalier de Dieppe, Institut Gustave Roussy (IGR), Génétique (Biologie pathologie), Département de biologie et pathologie médicales [Gustave Roussy], Institut Gustave Roussy (IGR)-Institut Gustave Roussy (IGR), CHU Henri Mondor, Centre hospitalier Saint-Joseph [Paris], None, Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), and CHU Henri Mondor [Créteil]

Subjects
0301 basic medicine, Microbiology (medical), Extended-spectrum beta-lactamases (ESBL), medicine.drug_class, Antibiotic resistance, [SDV]Life Sciences [q-bio], 030106 microbiology, Cephalosporin, Microbial Sensitivity Tests, Penicillins, Third-generation cephalosporin (3GC), Microbiology, 03 medical and health sciences, 0302 clinical medicine, Enterobacteriaceae, Enterobacterales, Drug Resistance, Bacterial, medicine, Humans, Blood culture, Temocillin, 030212 general & internal medicine, Cephalosporinase-overproducing strain (COPE), medicine.diagnostic_test, Dose-Response Relationship, Drug, business.industry, Enterobacteriaceae Infections, General Medicine, 3. Good health, Anti-Bacterial Agents, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, France, business, medicine.drug
Abstract

International audience; Temocillin is used for several years in some European countries but, only since 2015 in France. We assessed the susceptibility of Enterobacterales strains isolated from blood culture 1 year before (2014) and 2 years after (2017) its use in France. 1,387 strains were included by 17 clinical laboratories located throughout France: 363 in 2014 and 1,024 in 2017. The rate of resistance to temocillin was 4.6% and 26.7% in 3rd generation cephalosporin (3GC) susceptible and resistant strains respectively. Cephalosporinase-overproducer (COPE) strains were significantly more resistant to temocillin (37.7%) than ESBL-producer (ESBL-PE) (23.5%) (P < 0.01). The rate of temocillin resistance was correlated to the number of inactive beta-lactams. The rate of resistance to temocillin trend to increase from 13.9% in 2014 to 23.9% in 2017 (P < 0.01). Temocillin remains highly active against Enterobacterales but the trend in resistance should be assessed over time.

Published
2021
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42. Early assessment of diffusion and possible expansion of SARS-CoV-2 Lineage 20I/501Y.V1 (B.1.1.7, variant of concern 202012/01) in France, January to March 2021

Author

Gaymard, Alexandre, Bosetti, Paolo, Feri, Adeline, Destras, Gregory, Enouf, Vincent, Andronico, Alessio, Burrel, Sonia, Behillil, Sylvie, Sauvage, Claire, Bal, Antonin, Morfin, Florence, Van Der Werf, Sylvie, Josset, Laurence, Blanquart, François, Coignard, Bruno, Cauchemez, Simon, Lina, Bruno, Gault, Elyanne, Moreau, Frédérique, Brichler, Ségolène, Delagrèverie, Héloïse, Descamps, Diane, Charpentier, Charlotte, Rozenberg, Flore, L'Honneur, Anne-Sophie, Veyer, David, Bélec, Laurent, Fourati, Slim, Rodriguez, Christophe, Pawlotsky, Jean-Michel, Fourgeaud, Jacques, Abid, Hanène, Roque-Afonso, Anne-Marie, Fenaux, Honorine, Jary, Aude, Marot, Stéphane, Salmona, Maud, Chaix, Marie-Laure, Morand-Joubert, Laurence, Schnuriger, Aurélie, Juillet, Stéphanie Marque, Bargain, Pauline, Poggi, Cécile, Chollet, Lionel, Guillaume, Clémence, Guinard, Jérôme, Vallet, Sophie, Pilorgé, Léa, Schvoerer, Evelyne, Hartard, Cédric, Castelain, Sandrine, François, Catherine, Ducancelle, Alexandra, Lefeuvre, Caroline, Lepiller, Quentin, Marty-Quinternet, Solène, Bellecave, Pantxika, Tumiotto, Camille, Dina, Julia, Le Gouil, Meriadeg, Henquell, Cécile, Mirand, Audrey, Césaire, Raymond, de Rougemont, Alexis, Auvray, Christelle, Larrat, Sylvie, Némoz, Benjamin, Tinez, Claire, Guigon, Aurélie, Hantz, Sébastien, Rogez, Sylvie, Dos Santos, Georges, Perez, Pascale, Jost, Christelle, Montes, Brigitte, Foulongne, Vincent, Imbert, Berthe-Marie, Bressollette, Céline, Giordanengo, Valérie, Gonfrier, Géraldine, Garcia, Magali, Lévêque, Nicolas, Brodard, Véronique, Moret, Hélène, Thibault, Vincent, Maillard, Anne, Jaffar-Bandjee, Marie-Christine, Gueudin, Marie, Plantier, Jean-Christophe, Pozzetto, Bruno, Pillet, Sylvie, Fafi-Kremer, Samira, Solis, Morgane, Izopet, Jacques, Trémeaux, Pauline, Stefic, Karl, Handala, Lynda, Billaud, Geneviève, Frobert, Emilie, Mérens, Audrey, Bigaillon, Christine, Desroches, Marine, Thepenier, Cédric, Janvier, Frédéric, Otto, Marie-Pierre, Roquebert, Bénédicte, Haïm-Boukobza, Stéphanie, Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Hospices Civils de Lyon (HCL), Virpath-Grippe, de l'émergence au contrôle -- Virpath-Influenza, from emergence to control (Virpath), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Direction des maladies infectieuses - Infectious Diseases Division [Saint-Maurice], Santé publique France - French National Public Health Agency [Saint-Maurice, France], Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, Agents infectieux, résistance et chimiothérapie - UR UPJV 4294 (AGIR ), Université de Picardie Jules Verne (UPJV)-CHU Amiens-Picardie, Laboratoire de Virologie [CHU Amiens], CHU Amiens-Picardie, ANRS - Maladies infectieuses émergentes (ANRS - MIE), Institut National de la Santé et de la Recherche Médicale (INSERM), We acknowledge financial support from Santé publique France (the French national public health agency), the French Ministry of health (Grant COVIDseq), the Consortium for the surveillance and research on emerging pathogens via microbial genomics (EMERGEN) coordinated by Santé publique France and ANRS Maladies Infectieuses Emergentes, the Investissement d’Avenir programme, the Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases programme (grant ANR-10-LABX-62-IBEID), the European Union’s Horizon 2020 research and in-novation programme under grants 101003589 (RECOVER). This work has been supported by the laboratories belonging to the ColVHB network*., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)-Université Sorbonne Paris Nord, Gestionnaire, Hal Sorbonne Université, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris)

Subjects
Author's Correction, Paris, medicine.medical_specialty, 2019-20 coronavirus outbreak, Lineage (genetic), Coronavirus disease 2019 (COVID-19), Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viral infections, [SDV]Life Sciences [q-bio], Context (language use), Biology, 03 medical and health sciences, 0302 clinical medicine, Virology, medicine, Humans, MESH: COVID-19, MESH: SARS-CoV-2, 030212 general & internal medicine, 030304 developmental biology, COVID, [SDV.MHEP.ME] Life Sciences [q-bio]/Human health and pathology/Emerging diseases, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, 0303 health sciences, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, MESH: Humans, SARS-CoV-2, MESH: Paris, Public Health, Environmental and Occupational Health, COVID-19, [SDV] Life Sciences [q-bio], MESH: France, 20I/501Y.V1, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, surveillance, France, mutation, Rapid Communication, Demography
Abstract

International audience; The emergence of SARS-CoV-2 variant 20I/501Y.V1 (VOC-202012/1 or GR/501Y.V1) is concerning given its increased transmissibility. We reanalysed 11,916 PCR-positive tests (41% of all positive tests) performed on 7-8 January 2021 in France. The prevalence of 20I/501Y.V1 was 3.3% among positive tests nationwide and 6.9% in the Paris region. Analysing the recent rise in the prevalence of 20I/501Y.V1, we estimate that, in the French context, 20I/501Y.V1 is 52-69% more transmissible than the previously circulating lineages, depending on modelling assumptions.

Published
2021
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46. The French Military influenza surveillance system (MISS): overview of epidemiological and virological results during four influenza seasons – 2008–2012

Author

Sandrine Duron, Aurélie Mayet, Françoise Lienhard, Rachel Haus-Cheymol, Catherine Verret, Serge Védy, Patrick Le Guen, Laurence Berbineau, Patrick Brisou, Philippe Dubrous, Eric Garnotel, Jean-Baptiste Meynard, Xavier Deparis, Audrey Mérens, Christine Bigaillon, and René Migliani

Subjects
armed forces, influenza, surveillance, Medicine
Published
2013
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47. Cryptosporidiosis outbreaks linked to the public water supply in a military camp, France.

Author

Watier-Grillot, Stéphanie, Costa, Damien, Petit, Cédric, Razakandrainibe, Romy, Larréché, Sébastien, Tong, Christelle, Demont, Gwenaëlle, Billetorte, David, Mouly, Damien, Fontan, Didier, Velut, Guillaume, Le Corre, Alexandra, Beauvir, Jean-Christophe, Mérens, Audrey, Favennec, Loïc, and Pommier de Santi, Vincent

Subjects
CRYPTOSPORIDIUM, MILITARY camps, WATER supply, MILITARY supplies, MILITARY training camps, CRYPTOSPORIDIOSIS
Abstract

Introduction: Contaminated drinking and recreational waters account for most of the reported Cryptosporidium spp. exposures in high-income countries. In June 2017, two successive cryptosporidiosis outbreaks occurred among service members in a military training camp located in Southwest France. Several other gastroenteritis outbreaks were previously reported in this camp, all among trainees in the days following their arrival, without any causative pathogen identification. Epidemiological, microbiological and environmental investigations were carried out to explain theses outbreaks. Material and methods: Syndromic diagnosis using multiplex PCR was used for stool testing. Water samples (100 L) were collected at 10 points of the drinking water installations and enumeration of Cryptosporidium oocysts performed. The identification of Cryptosporidium species was performed using real-time 18S SSU rRNA PCR and confirmed by GP60 sequencing. Results: A total of 100 human cases were reported with a global attack rate of 27.8%. Cryptosporidium spp. was identified in 93% of stool samples with syndromic multiplex PCR. The entire drinking water network was contaminated with Cryptosporidium spp. The highest level of contamination was found in groundwater and in the water leaving the treatment plant, with >1,000 oocysts per 100 L. The same Cryptosporidium hominis isolate subtype IbA10G2 was identified in patients' stool and water samples. Several polluting activities were identified within the protection perimeters of the water resource. An additional ultrafiltration module was installed at the outlet of the water treatment plant. After several weeks, no Cryptosporidium oocysts were found in the public water supply. Conclusions: After successive and unexplained gastroenteritis outbreaks, this investigation confirmed a waterborne outbreak due to Cryptosporidium hominis subtype IbA10G2. Our study demonstrates the value of syndromic diagnosis for gastroenteritis outbreak investigation. Our results also highlight the importance of better assessing the microbiological risk associated with raw water and the need for sensitive and easy-to-implement tools for parasite detection. Author summary: Cryptosporidiosis remains a neglected infectious disease, even in high-income countries. Most of the reported cases and outbreaks are related to drinking water and recreational water contaminated with Cryptosporidium spp. In Europe, the search for Cryptosporidium spp. and other parasites in stool or water samples is not routinely performed by laboratories, especially in the absence of dedicated national guidance on testing. In France, cryptosporidiosis is not a notifiable disease. In order to better assess the pathogens involved in foodborne and waterborne disease outbreaks a new outbreak investigation strategy was implemented in the French Armed Forces including: systematic stool sampling, routine syndromic multiplex PCR diagnoses, and pathogens genotyping. After several unexplained gastroenteritis outbreaks in a military camp in France, we identified the same C. hominis IbA10G2 isolate in the stools of patients and in the entire water distribution network. The highest levels of contamination were found in groundwater and in the water leaving the treatment plant. Our study demonstrates the value of syndromic diagnosis for gastroenteritis outbreaks investigation and highlights the importance of better assessing the microbiological risks associated with raw water. [ABSTRACT FROM AUTHOR]

Published
2022
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48. Diversity of Acinetobacter baumannii in four French military hospitals, as assessed by multiple locus variable number of tandem repeats analysis.

Author

Yolande Hauck, Charles Soler, Patrick Jault, Audrey Mérens, Patrick Gérome, Christine Mac Nab, François Trueba, Laurent Bargues, Hoang Vu Thien, Gilles Vergnaud, and Christine Pourcel

Subjects
Medicine, Science
Abstract

BackgroundInfections by A. calcoaceticus-A. baumannii (ACB) complex isolates represent a serious threat for wounded and burn patients. Three international multidrug-resistant (MDR) clones (EU clone I-III) are responsible for a large proportion of nosocomial infections with A. baumannii but other emerging strains with high epidemic potential also occur.Methodology/principal findingsWe automatized a Multiple locus variable number of tandem repeats (VNTR) analysis (MLVA) protocol and used it to investigate the genetic diversity of 136 ACB isolates from four military hospitals and one childrens hospital. Acinetobacter sp other than baumannii isolates represented 22.6% (31/137) with a majority being A. pittii. The genotyping protocol designed for A.baumannii was also efficient to cluster A. pittii isolates. Fifty-five percent of A. baumannii isolates belonged to the two international clones I and II, and we identified new clones which members were found in the different hospitals. Analysis of two CRISPR-cas systems helped define two clonal complexes and provided phylogenetic information to help trace back their emergence.Conclusions/significanceThe increasing occurrence of A. baumannii infections in the hospital calls for measures to rapidly characterize the isolates and identify emerging clones. The automatized MLVA protocol can be the instrument for such surveys. In addition, the investigation of CRISPR/cas systems may give important keys to understand the evolution of some highly successful clonal complexes.

Published
2012
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