#Clinical #management of respiratory syndrome in #patients hospitalized for suspected #MERS #coronavirus #infection in the #Paris area from 2013 to 2016 (BMC Infect Dis., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

BMC Infect Dis. 2018 Jul 16;18(1):331. doi: 10.1186/s12879-018-3223-5.

Clinical management of respiratory syndrome in patients hospitalized for suspected Middle East respiratory syndrome coronavirus infection in the Paris area from 2013 to 2016.

Bleibtreu A1,2,3,4, Jaureguiberry S5, Houhou N6, Boutolleau D7, Guillot H5, Vallois D8, Lucet JC9,10,11, Robert J12,13, Mourvillier B10,11,14, Delemazure J15, Jaspard M5, Lescure FX8,10,11, Rioux C8, Caumes E5, Yazdanapanah Y8,10,11.

Author information: 1 APHP, Hôpital Bichat Claude Bernard, Service des Maladies Infectieuses et Tropicales, Paris Diderot University, Paris, France. alexandre.bleibtreu@aphp.fr. 2 APHP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service des Maladies Infectieuses et Tropicales, Paris, France. alexandre.bleibtreu@aphp.fr. 3 INSERM, IAME, UMR 1137, Paris, France. alexandre.bleibtreu@aphp.fr. 4 Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France. alexandre.bleibtreu@aphp.fr. 5 APHP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service des Maladies Infectieuses et Tropicales, Paris, France. 6 Virology Department, APHP-Bichat-Claude Bernard Hospital, Paris, France. 7 AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Service de Virologie, et Sorbonne Universités, UPMC Univ Paris 06, CR7, CIMI, INSERM U1135, Paris, France. 8 APHP, Hôpital Bichat Claude Bernard, Service des Maladies Infectieuses et Tropicales, Paris Diderot University, Paris, France. 9 APHP, Infection control unit, Bichat Claude Bernard hospital, Paris Diderot University, Paris, France. 10 INSERM, IAME, UMR 1137, Paris, France. 11 Univ Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France. 12 AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Bactériologie-Hygiène Hospitalière, Paris, France. 13 Faculté de Médecine P. & M. Curie Paris-6 – Site Pitié, Centre d’Immunologie et des Maladies Infectieuses (CIMI) – E13, Paris, France. 14 APHP- Hôpital Bichat Claude Bernard, Service de Réanimation médicale et Infectieuse, Paris, France. 15 Service de pneumologie et réanimation Département R3S, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, unité de Soin de Réadaptation Post Réanimation (SRPR), Paris, France.




Patients with suspected Middle East respiratory syndrome coronavirus (MERS-CoV) infection should be hospitalized in isolation wards to avoid transmission. This suspicion can also lead to medical confusion and inappropriate management of acute respiratory syndrome due to causes other than MERS-CoV.


We studied the characteristics and outcome of patients hospitalized for suspected MERS-CoV infection in the isolation wards of two referral infectious disease departments in the Paris area between January 2013 and December 2016.


Of 93 adult patients (49 male (52.6%), median age 63.4 years) hospitalized, 82 out of 93 adult patients had returned from Saudi Arabia, and 74 of them were pilgrims (Hajj). Chest X-ray findings were abnormal in 72 (77%) patients. The 93 patients were negative for MERS-CoV RT-PCR, and 70 (75.2%) patients had documented infection, 47 (50.5%) viral, 22 (23.6%) bacterial and one Plasmodium falciparum malaria. Microbiological analysis identified Rhinovirus (27.9%), Influenza virus (26.8%), Legionella pneumophila (7.5%), Streptococcus pneumoniae (7.5%), and non-MERS-coronavirus (6.4%). Antibiotics were initiated in 81 (87%) cases, with two antibiotics in 63 patients (67.7%). The median duration of hospitalization and isolation was 3 days (1-33) and 24 h (8-92), respectively. Time of isolation decreased over time (P < 0.01). Two patients (2%) died.


The management of patients with possible MERS-CoV infection requires medical facilities with trained personnel, and rapid access to virological results. Empirical treatment with neuraminidase inhibitors and an association of antibiotics effective against S. pneumoniae and L. pneumophila are the cornerstones of the management of patients hospitalized for suspected MERS-CoV infection.

KEYWORDS: Isolation ward; Legionella; Middle East respiratory syndrome coronavirus (MERS-CoV); Pilgrims; Respiratory tract infection; Saudi Arabia

PMID: 30012113 PMCID: PMC6048819 DOI: 10.1186/s12879-018-3223-5 [Indexed for MEDLINE]  Free PMC Article

Keywords: MERS-CoV; France.



First year of #PrEP implementation in #France with daily or on-demand #tenofovir disoproxil fumarate/emtricitabine (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

First year of pre-exposure prophylaxis implementation in France with daily or on-demand tenofovir disoproxil fumarate/emtricitabine

M Siguier, R Mera, G Pialoux, M Ohayon, L Cotte, N Valin, J Ghosn, E Cua, C Pintado, J Chas, G Barriere, F Durand, J M Molina

Journal of Antimicrobial Chemotherapy, dkz220, https://doi.org/10.1093/jac/dkz220

Published: 20 June 2019




In January 2016, the French Medicine Agency initiated a Temporary Recommendation for Use (TRU) to allow the use of oral intake of tenofovir disoproxil fumarate and emtricitabine for pre-exposure prophylaxis (PrEP) in adults at high risk of HIV. We report the results of the first year of PrEP implementation in France.


Data were collected by physicians using a secured web subject-monitoring interface, with two forms: an initiation form, with patients’ baseline characteristics, and an HIV seroconversion form. Univariate and adjusted multivariate analysis using a logistic regression model were performed to identify baseline factors associated with on-demand PrEP regimen prescription.


From 4 January 2016 to 28 February 2017, 3405 subjects were enrolled, with 2774 initiation forms completed; 98.1% were male and 96.9% were MSM. An on-demand regimen was prescribed to 57% of subjects. Older age (OR for participants older than 50 years = 1.76, 95% CI 1.35–2.3, P < 0.001) and site of prescription (OR of former IPERGAY sites = 2.28, 95% CI 1.84–2.83, P < 0.001) were associated with on-demand prescription. Those reporting sexually transmitted infection (STI) and condomless anal sex with at least two different partners were less likely to receive on-demand PrEP (OR = 0.68, 95% CI 0.57–0.82 and 0.75, 95% CI 0.57–0.98, respectively; P < 0.05 for all). Four breakthrough HIV infections were reported during the study, in the context of PrEP interruption or acute infection at the time of PrEP initiation.


In a real-life setting in France, PrEP was used, either daily or on-demand, mostly by MSM, with breakthrough infections being rare.


Keywords: HIV/AIDS; PrEP; Antivirals.


Multi- #recombinant #Enterovirus A71 Subgenogroup C1 Isolates Associated with #Neurologic Disease, #France, 2016–2017 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 6—June 2019 / Dispatch

Multirecombinant Enterovirus A71 Subgenogroup C1 Isolates Associated with Neurologic Disease, France, 2016–2017

Stéphanie Tomba Ngangas, Alexander Lukashev, Gwendoline Jugie, Olga Ivanova, Jean-Michel Mansuy, Catherine Mengelle, Jacques Izopet, Anne-Sophie L’honneur, Flore Rozenberg, David Leyssene, Denise Hecquet, Stéphanie Marque-Juillet, David Boutolleau, Sonia Burrel, Hélène Peigue-Lafeuille, Christine Archimbaud, Kimberley Benschop, Cécile Henquell, Audrey Mirand, and Jean-Luc Bailly

Author affiliations: Université Clermont Auvergne, Clermont-Ferrand, France (S. Tomba Ngangas, G. Jugie, H. Peigue-Lafeuille, C. Archimbaud, C. Henquell, A. Mirand, J.-L. Bailly); Sechenov University, Moscow, Russia (A. Lukashev); Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow (O. Ivanova); Centre Hospitalier Universitaire de Toulouse, Toulouse, France (J.-M. Mansuy, C. Mengelle, J. Izopet); Assistance Publique-Hôspitaux de Paris Cochin, Paris, France (A.-S. L’honneur, F. Rozenberg); Centre Hospitalier de la Côte Basque, Bayonne, France (D. Leyssene); Centre Hospitalier Universitaire Amiens, Amiens, France (D. Hecquet); Centre Hospitalier de Versailles, Le Chesnay, France (S. Marque-Juillet); Assistance Publique-Hôspitaux de Paris Pitié-Salpêtrière-Charles Foix, Paris (D. Boutolleau, S. Burrel); CHU Clermont-Ferrand, Clermont-Ferrand (H. Peigue-Lafeuille, C. Archimbaud, C. Henquell, A. Mirand, J.-L. Bailly); National Institute for Public Health and the Environment, Bilthoven, the Netherlands (K. Benschop)



In 2016, an upsurge of neurologic disease associated with infection with multirecombinant enterovirus A71 subgenogroup C1 lineage viruses was reported in France. These viruses emerged in the 2000s; 1 recombinant is widespread. This virus lineage has the potential to be associated with a long-term risk for severe disease among children.

Keywords: EV-A71; Encephalitis; Neurology; Pediatrics; France.


#Purulent #bronchitis in 1917 and #pandemic #influenza in 1918 (Lancet Infect Dis., summary)

[Source: The Lancet Infectious Diseases, full page: (LINK). Summary, edited.]

Purulent bronchitis in 1917 and pandemic influenza in 1918

Jim Cox, Douglas Gill, Fiona Cox, Michael Worobey

Published: April, 2019 / DOI: https://doi.org/10.1016/S1473-3099(19)30114-8


A remarkable Lancet paper, which is probably the first description of the so-called 1918 Spanish influenza outbreak,1 is omitted from the journal’s Pandemic influenza: 100 years microsite. We wish to draw attention to this work, both to augment the excellent timeline of landmark events in influenza history in the microsite and to describe this early paper’s relevance to understanding the origin of the 1918 influenza pandemic.


We declare no competing interests.

Keywords: Pandemic Influenza; Spanish Flu; France; Pneumonia.


Emergence and multiple #reassortments of #French 2015-2016 highly pathogenic #H5 #avian #influenza viruses (Infect Genet Evol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Infect Genet Evol. 2018 Jul;61:208-214. doi: 10.1016/j.meegid.2018.04.007. Epub 2018 Apr 9.

Emergence and multiple reassortments of French 2015-2016 highly pathogenic H5 avian influenza viruses.

Briand FX1, Niqueux E2, Schmitz A2, Hirchaud E2, Quenault H2, Allée C2, Le Prioux A2, Guillou-Cloarec C2, Ogor K2, Le Bras MO2, Gares H3, Daniel P4, Fediaevsky A5, Martenot C2, Massin P2, Le Bouquin S2, Blanchard Y2, Eterradossi N2.

Author information: 1 Anses, Université Bretagne-Loire, Ploufragan, France. Electronic address: francois-xavier.briand@anses.fr. 2 Anses, Université Bretagne-Loire, Ploufragan, France. 3 Laboratoire Départemental d’Analyses et de Recherche, Coulounieix Chamiers, France. 4 Laboratoire des Pyrénées et des Landes, Mont-de-Marsan, France. 5 Ministère de l’Agriculture, Paris, France.



From November 2015 to August 2016, 81 outbreaks of highly pathogenic (HP) H5 avian influenza virus were detected in poultry farms from South-Western France. These viruses were mainly detected in farms raising waterfowl, but also in chicken or guinea fowl flocks, and did not induce severe signs in waterfowl although they did meet the HP criteria. Three different types of neuraminidases (N1, N2 and N9) were associated with the HP H5 gene. Full genomes sequences of 24 H5HP and 6 LP viruses that circulated in the same period were obtained by next generation sequencing, from direct field samples or after virus isolation in SPF embryonated eggs. Phylogenetic analyses of the eight viral segments confirmed that they were all related to the avian Eurasian lineage. In addition, analyses of the “Time of the Most Recent Common Ancestor” showed that the common ancestor of the H5HP sequences from South-Western France could date back to early 2014 (±1 year). This pre-dated the first detection of H5 HP in poultry farms and was consistent with a silent circulation of these viruses for several months. Finally, the phylogenetic study of the different segments showed that several phylogenetic groups could be established. Twelve genotypes of H5HP were detected implying that at least eleven reassortment events did occur after the H5HP cleavage site emerged. This indicates that a large number of co-infections with both highly pathogenic H5 and other avian influenza viruses must have occurred, a finding that lends further support to prolonged silent circulation.

Copyright © 2018. Published by Elsevier B.V.

KEYWORDS: Avian influenza; Emerging; Hemagglutinin; Reassortment; Viruses

PMID: 29649578 DOI: 10.1016/j.meegid.2018.04.007 [Indexed for MEDLINE]

Keywords: Avian Influenza; H5; Poultry; France; Reassortant strain.


#Colistin #resistance in #Parisian inpatient faecal #Escherichia coli as the result of two distinct evolutionary pathways (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

Colistin resistance in Parisian inpatient faecal Escherichia coli as the result of two distinct evolutionary pathways

Anne Sophie Bourrel, Laurent Poirel, Guilhem Royer, Mélanie Darty, Xavier Vuillemin, Nicolas Kieffer, Olivier Clermont, Erick Denamur, Patrice Nordmann, Jean-Winoc Decousser

Journal of Antimicrobial Chemotherapy, dkz090, https://doi.org/10.1093/jac/dkz090

Published: 12 March 2019




Beyond plasmid-encoded resistance (mcr genes) prevalence in strain collections, large epidemiological studies to estimate the human burden of colistin-resistant Escherichia coli gut carriage are lacking.


To evaluate the prevalence of colistin-resistant E. coli carriage in inpatients and decipher the molecular support of resistance and the genetic background of the strains.


During a 3 month period in 2017, we prospectively screened patients in six Parisian hospitals for rectal carriage of colistin-resistant E. coli using a selective medium, a biochemical confirmatory test and MIC determination. WGS of the resistant strains and their corresponding plasmids was performed.


Among the 1217 screened patients, 153 colistin-resistant E. coli strains were isolated from 152 patients (12.5%). The mcr-1 gene was identified in only seven isolates (4.6%) on different plasmid scaffolds. The genetic background of these MCR-1 producers argued for an animal origin. Conversely, the remaining 146 colistin-resistant E. coli exhibited a phylogenetic distribution corresponding to human gut commensal/clinical population structure (B2 and D phylogroup predominance); 72.6% of those isolates harboured convergent mutations in the PmrA and PmrB proteins, constituting a two-component system shown to be associated with colistin resistance.


We showed that the occurrence at a high rate of colistin resistance in human faecal E. coli is the result of two distinct evolutionary pathways, i.e. the occurrence of chromosomal mutations in an endogenous E. coli population and the rare acquisition of exogenous mcr-1-bearing strains probably of animal origin. The involved selective pressures need to be identified in order to develop preventative strategies.


© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; E. Coli; Plasmids; Colistin; France.


#Pneumonia-Specific #Escherichia coli with Distinct #Phylogenetic and #Virulence Profiles, #France, 2012–2014 (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 25, Number 4—April 2019 / Research

Pneumonia-Specific Escherichia coli with Distinct Phylogenetic and Virulence Profiles, France, 2012–2014

Béatrice La Combe, Olivier Clermont, Jonathan Messika, Matthieu Eveillard, Achille Kouatchet, Sigismond Lasocki, Stéphane Corvec, Karim Lakhal, Typhaine Billard-Pomares, Romain Fernandes, Laurence Armand-Lefevre, Sandra Bourdon, Jean Reignier, Vincent Fihman, Nicolas de Prost, Julien Bador, Julien Goret, Frederic Wallet, Erick Denamur, Jean-Damien Ricard  , and on behalf of the COLOCOLI group

Author affiliations: Infection, Antimicrobiens, Modélisation, Évolution, Paris, France (B. La Combe, O. Clermont, J. Messika, T. Billard-Pomares, R. Fernandes, L. Armand-Lefevre, E. Denamur, J.-D. Ricard); Université Paris Diderot, Paris (B. La Combe, O. Clermont, J. Messika, T. Billard-Pomares, R. Fernandes, L. Armand-Lefevre, E. Denamur, J.-D. Ricard); Hôpital Louis Mourier, Colombes, France (B. La Combe, J. Messika, T. Billard-Pomares, R. Fernandes, J.-D. Ricard); Centre Hospitalier Universitaire, Angers, France (M. Eveillard, A. Kouatchet, S. Lasocki); Centre Hospitalier Universitaire, Nantes, France (S. Corvec, J. Reignier); Hôpital Laënnec, Nantes (K. Lakhal); Hôpital Bichat, AP-HP, Paris (L. Armand-Lefevre, E. Denamur); Centre Hospitalier Départemental Vendée, La Roche-sur-Yon, France (S. Bourdon); Hôpital Henri Mondor, AP-HP, Créteil, France (V. Fihman, N. de Prost); Centre Hospitalier Universitaire Bocage Central, Dijon, France (J. Bador); Centre Hospitalier Universitaire Pellegrin, Bordeaux, France (J. Goret); Centre Hospitalier Régional Universitaire, Lille, France (F. Wallet)



In a prospective, nationwide study in France of Escherichia coli responsible for pneumonia in patients receiving mechanical ventilation, we determined E. coli antimicrobial susceptibility, phylotype, O-type, and virulence factor gene content. We compared 260 isolates with those of 2 published collections containing commensal and bacteremia isolates. The preponderant phylogenetic group was B2 (59.6%), and the predominant sequence type complex (STc) was STc73. STc127 and STc141 were overrepresented and STc95 underrepresented in pneumonia isolates compared with bacteremia isolates. Pneumonia isolates carried higher proportions of virulence genes sfa/foc, papGIII, hlyC, cnf1, and iroN compared with bacteremia isolates. Virulence factor gene content and antimicrobial drug resistance were higher in pneumonia than in commensal isolates. Genomic and phylogenetic characteristics of E. coli pneumonia isolates from critically ill patients indicate that they belong to the extraintestinal pathogenic E. coli pathovar but have distinguishable lung-specific traits.

Keywords: Pneumonia; E. Coli; France.