#Hepatitis E virus #infections in #Europe (J Clin Virol., abstract)

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

Journal of Clinical Virology / Available online 8 September 2019 / In Press, Journal Pre-proof

Hepatitis E virus infections in Europe

Jacques Izopet a,b, Pauline Tremeaux d, Olivier Marion a,b, Marion Migueres a,b, Nicolas Capelli a,b, Sabine Chapuy-Regaud a,b, Jean-Michel Mansuy a, Florence Abravanel a,b, Nassim Kamar b,c, Sébastien Lhomme a, b

{a} CHU Toulouse, Hôpital Purpan, Laboratoire de virologie, National Reference Center for Hepatitis E, F-31300, France; {b} INSERM, U1043, Centre de Physiopathologie de Toulouse Purpan, Toulouse, F-31300, France; {c} CHU Toulouse, Hôpital Rangueil, Department of Nephrology, Dialysis and Organ Transplantation, F-31300, France; {d} APHP, Hôpital Cochin, Laboratoire de Virologie, F-75679, France

Received 2 August 2019, Accepted 6 September 2019, Available online 8 September 2019.

DOI: https://doi.org/10.1016/j.jcv.2019.09.004



  • Following the introduction of robust serological and molecular tools, our understanding of the epidemiology and clinical consequences of HEV infection has improved conderably.
  • The increasing number of symptomatic cases reported in Europe is linked to greater clinical awareness and the optimisation of test algorithms.
  • HEV genotype 3, which is zoonotic, is the most prevalent genotype in Europe.
  • The three major clades and subgenotypes of HEV-3 differ geographically and changes in distribution over the time have been observed.
  • Although clinically silent in the vast majority of patients, severe acute HEV-3 hepatitis occur in patients with underlying chronic liver disease and chronic HEV-3 hepatitis occur in immunocompromised patients.
  • Extrahepatic manifestations of HEV infection, including neurological and renal manifestations, are increasingly recognised.



Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide. The systematic use of improved tools for diagnosing and genotyping has completely changed our understanding of the epidemiology and clinical consequences of HEV infection. Most cases of HEV in Europe arise from infected animals such as pigs, wild boar, deer and rabbits. Zoonotic HEV genotypes (HEV genotypes 3-8) are mainly food-borne or transmitted by direct contact, but recent data suggest that infection can also be water-borne or even iatrogenic throught contamined blood products.

HEV-3 is the most prevalent genotype in Europe but the geographic distributions of the 3 major clades and subgenotypes (HEV-3abjkchi, HEV-3efg, and HEV-3ra) differ. Most HEV-3 infections are asymptomatic but they can result in severe acute hepatitis in patients with chronic liver disease, chronic hepatitis in immunocompromised patients, and to extra-hepatic manifestations.

Despite more frequent reports of symptomatic hepatitis E cases across Europe, systems for monitoring HEV infections vary greatly. Severe HEV-associated illnesses, hospitalizations and deaths are probably underestimated. The seroprevalence and incidence of locally acquired hepatitis E varies between and within European countries and over time. The precise origin of these variations is uncertain but may be linked to environmental factors or the degree to which HEV contaminates the human food chain. Collaborative initiatives such as the establishment of the One Health platform for HEV sequences (HEVnet database) will be very useful for a better understanding of the epidemiology of HEV in Europe and the development of effective prevention strategies.

Keywords: Hepatitis E virus – Europe – Zoonosis – Hepatitis E

© 2019 Published by Elsevier B.V.

Keywords: Hepatitis E; European Region.



#Fireworks-like #Surveillance #Approach: The case of HPAI #H5N1 in #WildBirds in #Europe (Transbound Emerg Dis., abstract)

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

Transbound Emerg Dis. 2019 Sep 3. doi: 10.1111/tbed.13342. [Epub ahead of print]

Fireworks-like Surveillance Approach: The case of HPAI H5N1 in Wild Birds in Europe.

Pereira H1,2,3, Artois M1, Bicout DJ1,4.

Author information: 1 VetAgro Sup, Veterinary Campus of Lyon, 69280, Marcy l’Étoile, France. 2 Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges-Pompidou, Unité de Recherche Clinique, Paris, France. 3 INSERM, Centre d’Investigation Clinique 1418 (CIC1418), Paris, France. 4 Biomathematics and Epidemiology, EPSP- Labo TIMC, UMR 5525, CNRS, Grenoble Alpes University and VetAgro Sup, 69280, Marcy l’Étoile, France.



Highly pathogenic avian influenza (HPAI) risk management requires efficient surveillance of the infection in wild birds for early warning purposes. In this study, our aim was to describe the spread of continent-wide infection cases using a fireworks model and thereby improve current surveillance systems. The fireworks model is a metaphor illustrating the spread of HPAI as a point source epizootic. The approach is based on early detection of the outbreak seeds (sparks from the fireworks) and uses a predictive model of the probability of the occurrence of new cases following a seed introduction; this then determines the spatiotemporal perimeter for intense surveillance investigations. For a case study, we used surveillance data on HPAI H5N1 in wild birds across Europe between 2005 and 2010 to describe the outbreaks and determine the success of the case detection used to inform management of the disease. The fireworks description assumes simultaneous introductions of “seeds” of cases, which then “explode” in local foci but do not merge into a progressive disease wave. This model fit the data well. Using this predictive approach for HPAI cases in EU countries, we found that the investigation radius needed to achieve a detection level of 90% of new cases after an outbreak ranged from 10 km to more than 300 km, depending on the outbreak pattern. Based on these findings, the fireworks approach can be a valuable method for identifying the perimeters and risk areas to be targeted for enhanced surveillance. The rationale of the fireworks approach is quite generic and can easily be adapted to different situations and contexts.

This article is protected by copyright. All rights reserved. © 2019 Blackwell Verlag GmbH.

KEYWORDS: H5N1; Highly pathogenic avian influenza; fireworks-based surveillance; mathematical modelling; wild birds

PMID: 31482660 DOI: 10.1111/tbed.13342

Keywords: Avian Influenza; H5N1; Wild Birds; European Region.


#European #Pandemic #Influenza #Preparedness #Planning: A Review of National Plans, July 2016 (Disaster Med Public Health Prep., abstract)

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

Disaster Med Public Health Prep. 2019 Jun;13(3):582-592. doi: 10.1017/dmp.2018.60.

European Pandemic Influenza Preparedness Planning: A Review of National Plans, July 2016.

Droogers M1, Ciotti M2, Kreidl P3, Melidou A2, Penttinen P2, Sellwood C4, Tsolova S2, Snacken R2.

Author information: 1 European Public Health Association,Utrecht,Netherlands. 2 European Centre for Disease Prevention and Control,Stockholm,Sweden. 3 Department of Hygiene,Medical Microbiology and Public Health,Medical University Innsbruck,Austria. 4 National Health Service England,London,United Kingdom.



Pandemic influenza A (H1N1) commenced in April 2009. Robust planning and preparedness are needed to minimize the impact of a pandemic. This study aims to review if key elements of pandemic preparedness are included in national plans of European countries. Key elements were identified before and during the evaluations of the 2009 pandemic and are defined in this study by 42 items. These items are used to score a total of 28 publicly available national pandemic influenza plans. We found that plans published before the 2009 influenza pandemic score lower than plans published after the pandemic. Plans from countries with a small population size score significantly lower compared to national plans from countries with a big population (P <.05). We stress that the review of written plans does not reflect the actual preparedness level, as the level of preparedness entails much more than the existence of a plan. However, we do identify areas of improvement for the written plans, such as including aspects on the recovery and transition phase and several opportunities to improve coordination and communication, including a description of the handover of leadership from health to wider sector management and communication activities during the pre-pandemic phase. (Disaster Med Public Health Preparedness. 2019;13:582-592).

KEYWORDS: national preparedness plans; pandemic influenza; preparedness planning; public health preparedness

PMID: 31328711 DOI: 10.1017/dmp.2018.60

Keywords: Pandemic Influenza; Pandemic Preparedness; European Region.


Pervasive #Arctic #lead #pollution suggests substantial #growth in #medieval #silver production modulated by #plague, #climate, and #conflict (Proc Natl Acad Sci USA, abstract)

[Source: Proceedings of the National Academy of Sciences of the United States of America, full page: (LINK). Abstract, edited.]

Pervasive Arctic lead pollution suggests substantial growth in medieval silver production modulated by plague, climate, and conflict

Joseph R. McConnell, Nathan J. Chellman, Andrew I. Wilson, Andreas Stohl, Monica M. Arienzo, Sabine Eckhardt, Diedrich Fritzsche, Sepp Kipfstuhl, Thomas Opel, Philip F. Place, and Jørgen Peder Steffensen

PNAS first published July 8, 2019 / DOI: https://doi.org/10.1073/pnas.1904515116

Edited by Eric W. Wolff, University of Cambridge, Cambridge, United Kingdom, and accepted by Editorial Board Member A. R. Ravishankara June 13, 2019 (received for review March 15, 2019)



Detailed lead pollution measurements in an array of 13 ice cores spanning nearly half the Arctic showed surprisingly similar temporal variability during the past 2 millennia until the Industrial Revolution. Lead pollution increased by 250- to 300-fold from the Early Middle Ages to the 1970s industrial peak, reflecting large-scale emissions changes from ancient European silver production, recent fossil fuel burning, and other industrial activities. Pronounced decadal-scale increases coincided with exploitation of new mining districts, technology development, and periods of economic prosperity, while decreases coincided with climate disruptions, famines, major wars, and plagues. Despite midlatitude pollution abatement policies that reduced Arctic lead pollution by >80% since the 1970s, recent levels remain 60-fold higher than at the start of the Middle Ages.



Lead pollution in Arctic ice reflects large-scale historical changes in midlatitude industrial activities such as ancient lead/silver production and recent fossil fuel burning. Here we used measurements in a broad array of 13 accurately dated ice cores from Greenland and Severnaya Zemlya to document spatial and temporal changes in Arctic lead pollution from 200 BCE to 2010 CE, with interpretation focused on 500 to 2010 CE. Atmospheric transport modeling indicates that Arctic lead pollution was primarily from European emissions before the 19th-century Industrial Revolution. Temporal variability was surprisingly similar across the large swath of the Arctic represented by the array, with 250- to 300-fold increases in lead pollution observed from the Early Middle Ages to the 1970s industrial peak. Superimposed on these exponential changes were pronounced, multiannual to multidecadal variations, marked by increases coincident with exploitation of new mining regions, improved technologies, and periods of economic prosperity; and decreases coincident with climate disruptions, famines, major wars, and plagues. Results suggest substantial overall growth in lead/silver mining and smelting emissions—and so silver production—from the Early through High Middle Ages, particularly in northern Europe, with lower growth during the Late Middle Ages into the Early Modern Period. Near the end of the second plague pandemic (1348 to ∼1700 CE), lead pollution increased sharply through the Industrial Revolution. North American and European pollution abatement policies have reduced Arctic lead pollution by >80% since the 1970s, but recent levels remain ∼60-fold higher than at the start of the Middle Ages.

ice core – lead pollution – Arctic  – plague – Middle Ages



1 To whom correspondence may be addressed. Email: Joe.McConnell@dri.edu.

Author contributions: J.R.M. designed research; J.R.M., N.J.C., A.S., M.M.A., S.E., D.F., S.K., T.O., P.F.P., and J.P.S. performed research; J.R.M., N.J.C., A.I.W., and A.S. analyzed data; and J.R.M., N.J.C., A.I.W., and A.S. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission. E.W.W. is a guest editor invited by the Editorial Board.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1904515116/-/DCSupplemental.

Published under the PNAS license.

Keywords: Arctic; Environmental Pollution; Middle Age; Plague; Wars.


Circulation of a #novel strain of #dolphin #morbillivirus (DMV) in stranded #cetaceans in the #Mediterranean Sea (Sci Rep., abstract)

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

Article | OPEN | Published: 05 July 2019

Circulation of a novel strain of dolphin morbillivirus (DMV) in stranded cetaceans in the Mediterranean Sea

Francesco Mira, Consuelo Rubio-Guerri, Giuseppa Purpari, Roberto Puleio, Giulia Caracappa, Francesca Gucciardi, Laura Russotto, Guido Ruggero Loria & Annalisa Guercio

Scientific Reports, volume 9, Article number: 9792 (2019)



Dolphin morbillivirus (DMV) has been responsible for several outbreaks of systemic infection and has resulted in cetacean strandings in the Mediterranean. In August-October 2016, seven striped dolphins (Stenella coeruleoalba) stranded on the Sicilian coastline (Italy) tested positive for DMV. Tissue samples from brain, lung, pulmonary lymph nodes, heart, spleen, liver, stomach, intestine, kidneys and urinary bladder, as well as blowhole swabs, were collected during necropsy for molecular diagnostics and pathology studies. Extracted tissue RNA was screened for DMV by real-time reverse transcription polymerase chain reaction (PCR). Some tissues exhibited microscopic lesions that were consistent with DMV infection on histopathological and immunohistochemical grounds. Conventional reverse transcription PCR to target partial nucleoprotein and phosphoprotein genes yielded sequences used to genetically characterize the associated DMV strain. DMV RNA was detected by both PCR assays in all tested tissues of the seven dolphins, which suggests systemic infections, but was absent from another dolphin stranded on the Sicilian coastline during the same period. The partial phosphoprotein and nucleoprotein gene sequences from the positive dolphins were 99.7% and 99.5% identical, respectively, to the DMV sequences recently observed in cetaceans stranded on the Spanish Mediterranean. Our study suggests that this DMV strain is circulating in the Mediterranean.

Keywords: Morbillivirus; Dolphins; Wildlife; European Region.


#Trends and prediction of #antimicrobial susceptibility in #urinary #bacteria isolated in #European emergency departments: the #EuroUTI 2010-2016 Study (J Antimicrob Chemother., abstract)

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

Trends and prediction of antimicrobial susceptibility in urinary bacteria isolated in European emergency departments: the EuroUTI 2010-2016 Study

Alice Quaegebeur, Loïc Brunard, François Javaudin, Marie-Anne Vibet, Pascale Bemer, Quentin Le Bastard, Eric Batard, Emmanuel Montassier, EuroUTI 2010-2016 Study Group

Journal of Antimicrobial Chemotherapy, dkz274, https://doi.org/10.1093/jac/dkz274

Published: 30 June 2019




To assess recent trends in susceptibility to antibiotics among urinary isolates isolated in European emergency departments (EDs) and to identify isolates with a high (90% or more) predicted probability of susceptibility to fluoroquinolones or third-generation cephalosporins (3GCs).


In this cross-sectional study, we included urine cultures obtained from adult patients between 2010 and 2016 in 24 European EDs. Temporal trends were assessed using time-series analysis and multivariate logistic models. Multivariate logistic models were also used to predict susceptibility to fluoroquinolones or 3GCs from patient age and sex, year, month and ED.


We included 88 242 isolates. Time-series analysis found a significant increase in susceptibility to fluoroquinolones and no significant trend for susceptibility to 3GCs. Adjusting for patient age and sex, ED and organism, multivariate models showed that susceptibility to 3GCs decreased from 2014 to 2016, while susceptibility to fluoroquinolones increased in 2015 and 2016. Among isolates from 2016, multivariate models predicted high probability of susceptibility to fluoroquinolones in 11% of isolates (positive predictive value 91%) and a high probability of susceptibility to 3GCs in 35% of isolates (positive predictive value 94%).


Susceptibility of ED urinary isolates to fluoroquinolones increased from 2014, while susceptibility to 3GCs decreased from 2015. Predictive models identified isolates with a high probability of susceptibility to fluoroquinolones or 3GCs. The ability of such models to guide the empirical treatment of pyelonephritis in the ED remains to be determined.

Topic: antibiotics – cephalosporins – adult – emergency service, hospital – fluoroquinolones – pyelonephritis – urinary tract – bacteria – urine culture – antimicrobial susceptibility


© 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; Fluoroquinolones; Cephalosporins; UTI; European Region.


Associations between #antimicrobial use and the #faecal #resistome on #broiler #farms from nine #European countries (J Antimicrob Chemother., abstract)

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

Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries

Roosmarijn E C Luiken, Liese Van Gompel, Patrick Munk, Steven Sarrazin, Philip Joosten, Alejandro Dorado-García, Rasmus Borup, Hansen Berith E Knudsen, Alex Bossers, Jaap A Wagenaar, Frank M Aarestrup, Jeroen Dewulf, Dik J Mevius, Dick J J Heederik, Lidwien A M Smit, Heike Schmitt, EFFORT consortium

Journal of Antimicrobial Chemotherapy, dkz235, https://doi.org/10.1093/jac/dkz235

Published: 14 June 2019




To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms.


In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored.


Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity.


The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes.

Topic: feces – genes – lactams – trimethoprim – macrolides – tetracycline – aminoglycosides – antimicrobials – gene clusters  – farming environment


© 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; Poultry; European Region.