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:


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: 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,

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:

This article is published and distributed under the terms of the Oxford University Press, Standard Journals 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.


#Pathogenesis, host innate immune response and #aerosol transmission of #Influenza D virus in #cattle (J Virol., abstract)

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

Pathogenesis, host innate immune response and aerosol transmission of Influenza D virus in cattle

Elias Salem, Sara Hägglund, Hervé Cassard, Tifenn Corre, Katarina Näslund, Charlotte Foret, David Gauthier, Anne Pinard, Maxence Delverdier, Siamak Zohari, Jean-François Valarcher,Mariette Ducatez, Gilles Meyer

DOI: 10.1128/JVI.01853-18



The recently discovered influenza D virus (IDV) of the Orthomyxoviridae family has been detected in swine and ruminants with a worldwide distribution. Cattle are considered to be the primary host and reservoir and previous studies suggested a tropism of IDV for the upper respiratory tract and a putative role in the Bovine Respiratory Disease complex. This study aimed to characterize the pathogenicity of IDV in naive calves, as well as the ability of this virus to transmit by air. Eight naive calves were infected by aerosol with a recent French isolate, D/bovine/France/5920/2014. Results show that IDV replicates not only in the upper but also the lower respiratory tracts (LRT), inducing moderate bronchopneumonia with restricted lesions of interstitial pneumonia. Inoculation was followed by IDV-specific IgG1 production as early as 10 days post challenge, and likely both Th1 and Th2 responses. Study of the innate immune response in the LRT of IDV infected calves indicated the overexpression of pathogen recognition receptors and of chemokines CCL2, CCL3 and CCL4, but without overexpression of genes involved in the type I interferon pathway. Finally, virological examination of three aerosol-sentinel animals, housed 3 meters apart from inoculated calves, and IDV detection in air samples collected in different areas showed that IDV can be airborne transmitted and infect naïve contact calves on short distances. This study suggests that IDV is a respiratory virus with moderate pathogenicity and probably a high level of transmission. It consequently can be considered as predisposing or co-factor of respiratory disease.



Influenza D virus (IDV), a new Genus of the Orthomyxoviridae family, has a broad geographical distribution and can infect several animal species. Cattle are so far considered as the primary host for IDV, but the pathogenicity and the prevalence of this virus is still unclear. We demonstrated that under experimental conditions (in a controlled environment and in the absence of co-infecting pathogens), IDV is able to cause mild to moderate disease and targets both the upper and lower respiratory tracts. The virus can transmit by direct as well as aerosol contacts. While this study evidenced overexpression of pathogen recognition receptors and chemokines in the lower respiratory tract, IDV-specific IgG1 production as early as 10 days post challenge, and likely both Th1 and Th2 responses, further studies are warranted to better understand the immune responses triggered by IDV and its role as part of the Bovine Respiratory Disease complex.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Influenza D; Cattle; Bovine respiratory disease complex.


Emergence of #EVD68 clade D1, #France, August to November 2018 (Euro Surveill., abstract)

[Source: Eurosurveillance, full page: (LINK). Abstract, edited.]

Emergence of enterovirus D68 clade D1, France, August to November 2018

Antonin Bal1,2,3,4, Marina Sabatier1,2,3, Thierry Wirth5,6, Marianne Coste-Burel7, Mouna Lazrek8, Karl Stefic9,10, Karen Brengel-Pesce4, Florence Morfin2,3, Bruno Lina1,2,3, Isabelle Schuffenecker1,2, Laurence Josset1,2,3

Affiliations: 1 Centre National de Référence des Enterovirus et Parechovirus, Hospices Civils de Lyon, Lyon, France; 2 Laboratoire de Virologie, Institut des Agents Infectieux, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon, France; 3 Université Lyon 1, Faculté de Médecine Lyon Est, CIRI, Inserm U1111, CNRS UMR5308, Virpath, Lyon, France; 4 Laboratoire Commun de Recherche Hospices Civils de Lyon-bioMerieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France; 5 Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, EPHE, PSL Université, Paris, France; 6 Institut Systématique, Evolution, Biodiversité (ISYEB), EPHE, MNHN, CNRS, Sorbonne Université, Paris, France; 7 Laboratoire de Virologie, UIC9 CIC infectieux, Centre Hospitalier Universitaire de Nantes, Nantes, France; 8 Laboratoire de Virologie, EA3610, Centre Hospitalier Universitaire de Lille, Université de Lille, Lille, France; 9 INSERM U1259, Université de Tours, Tours, France; 10 Laboratoire de Virologie and CNR VIH-Laboratoire Associé, Centre Hospitalier Régional Universitaire de Tours, Tours, France

Correspondence: Laurence

Citation style for this article: Bal Antonin, Sabatier Marina, Wirth Thierry, Coste-Burel Marianne, Lazrek Mouna, Stefic Karl, Brengel-Pesce Karen, Morfin Florence, Lina Bruno, Schuffenecker Isabelle, Josset Laurence. Emergence of enterovirus D68 clade D1, France, August to November 2018. Euro Surveill. 2019;24(3):pii=1800699.

Received: 26 Dec 2018;   Accepted: 16 Jan 2019



We report a seasonal increase of enterovirus D68 (EV-D68) cases in France, with 54 cases detected between 19 August and 14 November 2018. Molecular typing revealed that 20 of 32 of the isolates belonged to clade D1, only sporadically detected before in France. Median age of D1-cases was 42 years, 10 developed severe respiratory signs and one had neurological complications. The 2018-D1 viruses showed a genetic divergence of 3.34 % with D1 viruses identified previously.

©  This work is licensed under a Creative Commons Attribution 4.0 International License.

Keywords: Enterovirus; EV-D68; France.