The #antimicrobial #resistome in relation to antimicrobial use and #biosecurity in #pig #farming, a metagenome-wide association study in nine #European countries (J Antimicrob Chemother., abstract)

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

The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries

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

Journal of Antimicrobial Chemotherapy, dky518, https://doi.org/10.1093/jac/dky518

Published: 14 January 2019

 

Abstract

Objectives

Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.

Methods

A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).

Results

Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.

Conclusions

Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.

Issue Section: ORIGINAL RESEARCH

© 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; Macrolides; Colistin; Tetracyclines; Pigs; European Region.

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Quantitative and qualitative analysis of #antimicrobial usage at #farm and #flock level on 181 #broiler farms in nine #European countries (J Antimicrob Chemother., abstract)

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

Quantitative and qualitative analysis of antimicrobial usage at farm and flock level on 181 broiler farms in nine European countries

Philip Joosten, Steven Sarrazin, Liese Van Gompel, Roosmarijn E C Luiken, Dik J Mevius, Jaap A Wagenaar, Dick J J Heederik, Jeroen Dewulf, EFFORT consortium

Journal of Antimicrobial Chemotherapy, dky498, https://doi.org/10.1093/jac/dky498

Published: 10 January 2019

 

Abstract

Objectives

To control the emerging threat of antimicrobial resistance, international policy appeals for appropriate monitoring of antimicrobial usage (AMU) at supranational, species and farm level. The aim of this study was to quantify AMU in broilers at farm and flock level in nine European countries.

Methods

Antimicrobial treatment data of one flock and purchased antimicrobials over one year were collected at 181 European broiler farms. Afterwards AMU was quantified using treatment incidence (TI) per 100 days based on Defined Daily Dose (DDDvet), Defined Course Dose (DCDvet) or Used Daily Dose (UDDvet) values. Total AMU at flock level was obtained by summing the TIDDDvet of all treatments in the sampled flock (TIDDDvetFl*).

Results

The median TIDDDvetFl* was 9.0 (95% CI 5.5–10.8), meaning that broilers were treated with antimicrobials during 9% of their rearing period. TIDDDvetFl* varied considerably within and between countries. However, in every country at least one untreated flock was present. Average TIDDDvetFl* at country level ranged from 3.3 to 36.7. Polymyxins, extended-spectrum aminopenicillins and fluoroquinolones were the most used antimicrobials, accounting for 26%, 26% and 18% of total AMU, respectively. Twenty-six percent of the farms started a treatment on day 1 of production, and 49% of overall AMU was administered within the first week.

Conclusions

Results show that rearing broilers without AMU is feasible. However, a huge variation in AMU in terms of amount, moment of administration and antimicrobial classes was observed. This shows that there is still ground to be covered when it comes to AMU on broiler farms.

Issue Section: ORIGINAL RESEARCH

© 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; Polymyxins; Penicillin; Fluoroquinolones; European Region.

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#Antimicrobial #resistance monitoring in commensal #enterococci from healthy #cattle, #pigs and #chickens across #Europe during 2004–14 (EASSA Study) (J Antimicrob Chemother., abstract)

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

Antimicrobial resistance monitoring in commensal enterococci from healthy cattle, pigs and chickens across Europe during 2004–14 (EASSA Study)

Anno de Jong, Shabbir Simjee, Markus Rose, Hilde Moyaert, Farid El Garch, Myriam Youala, EASSA Study Group

Journal of Antimicrobial Chemotherapy, dky537, https://doi.org/10.1093/jac/dky537

Published: 08 January 2019

 

Abstract

Objectives

The European Antimicrobial Susceptibility Surveillance in Animals (EASSA) programme collects zoonotic and commensal bacteria from healthy food-producing animals at slaughter and tracks their susceptibility to medically important antibiotics. Results for enterococci, collected over three time periods, are presented.

Methods

Intestinal contents from cattle, pigs and chickens were randomly sampled (five or six countries/host; at least four abattoirs/country; one sample/animal/farm) for isolation of enterococci; antimicrobial susceptibilities were centrally assessed by CLSI agar dilution. Clinical breakpoints (CLSI) and epidemiological cut-off values (EUCAST) were applied for data interpretation.

Results

In total, 2435 Enterococcus faecium and 1389 Enterococcus faecalis strains were recovered. Seven E. faecium/faecalis strains were linezolid resistant. One E. faecium strain was non-WT (NWT), with a daptomycin MIC of 8 mg/L. Clinical vancomycin resistance was very low or absent; eight strains had decreased susceptibility (MICs of 8 mg/L). Two strains were clinically resistant to tigecycline. Little resistance to ampicillin or gentamicin was observed. Clinical resistance of E. faecium to quinupristin/dalfopristin was slightly higher (2.2%–33.6%) and 38.5%–83.2% of the strains were classified NWT. Very high resistance to tetracycline (67.4%–79.1%) and erythromycin (27.1%–57.0%) was noted for E. faecium and E. faecalis in pigs and chickens. For both of these compounds, similar NWT results were observed for Enterococcus hirae (n = 935), Enterococcus durans (n = 286) and Enterococcus casseliflavus (n = 154) whereas the percentage of NWT for linezolid, tigecycline and vancomycin was generally zero or low.

Conclusions

In this pan-EU survey of commensal enterococci, antibiotic susceptibility varied widely between antibiotics, animal species, countries and enterococcal species. Clinical resistance to antibiotics that are critically important for human medicine was absent or low, except for erythromycin.

Issue Section: ORIGINAL RESEARCH

© 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; Enterococcus spp.; Pigs; Cattle; Poultry; European Region.

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Attributable #deaths and #disability-adjusted life-years caused by #infections with #antibiotic-resistant bacteria in the #EU and the #EEA in 2015: a population-level modelling analysis (Lancet Infect Dis., abstract)

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

Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis

Alessandro Cassini, MD,  Liselotte Diaz Högberg, PhD, Diamantis Plachouras, PhD, Annalisa Quattrocchi, PhD, Ana Hoxha, MSc, Gunnar Skov Simonsen, PhD, Mélanie Colomb-Cotinat, PhD, Mirjam E Kretzschmar, PhD, Brecht Devleesschauwer, PhD, Michele Cecchini, PhD, Driss Ait Ouakrim, PhD, Tiago Cravo Oliveira, PhD, Marc J Struelens, PhD, Carl Suetens, MD, Dominique L Monnet, PhD, theBurden of AMR Collaborative Group †

Open Access / Published: November 05, 2018 / DOI: https://doi.org/10.1016/S1473-3099(18)30605-4

 

Summary

Background

Infections due to antibiotic-resistant bacteria are threatening modern health care. However, estimating their incidence, complications, and attributable mortality is challenging. We aimed to estimate the burden of infections caused by antibiotic-resistant bacteria of public health concern in countries of the EU and European Economic Area (EEA) in 2015, measured in number of cases, attributable deaths, and disability-adjusted life-years (DALYs).

Methods

We estimated the incidence of infections with 16 antibiotic resistance–bacterium combinations from European Antimicrobial Resistance Surveillance Network (EARS-Net) 2015 data that was country-corrected for population coverage. We multiplied the number of bloodstream infections (BSIs) by a conversion factor derived from the European Centre for Disease Prevention and Control point prevalence survey of health-care-associated infections in European acute care hospitals in 2011–12 to estimate the number of non-BSIs. We developed disease outcome models for five types of infection on the basis of systematic reviews of the literature.

Findings

From EARS-Net data collected between Jan 1, 2015, and Dec 31, 2015, we estimated 671 689 (95% uncertainty interval [UI] 583 148–763 966) infections with antibiotic-resistant bacteria, of which 63·5% (426 277 of 671 689) were associated with health care. These infections accounted for an estimated 33 110 (28 480–38 430) attributable deaths and 874 541 (768 837–989 068) DALYs. The burden for the EU and EEA was highest in infants (aged <1 year) and people aged 65 years or older, had increased since 2007, and was highest in Italy and Greece.

Interpretation

Our results present the health burden of five types of infection with antibiotic-resistant bacteria expressed, for the first time, in DALYs. The estimated burden of infections with antibiotic-resistant bacteria in the EU and EEA is substantial compared with that of other infectious diseases, and has increased since 2007. Our burden estimates provide useful information for public health decision-makers prioritising interventions for infectious diseases.

Funding

European Centre for Disease Prevention and Control.

Keywords: Antibiotics; Drugs Resistance; EU; Excess mortality.

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#Comparison of 2016–17 and Previous #Epizootics of Highly Pathogenic #Avian #Influenza #H5 #Guangdong Lineage in #Europe (Emerg Infect Dis., abstract)

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

Volume 24, Number 12—December 2018 / Research

Comparison of 2016–17 and Previous Epizootics of Highly Pathogenic Avian Influenza H5 Guangdong Lineage in Europe

Pablo Alarcon1, Adam Brouwer1, Divya Venkatesh, Daisy Duncan, Chrysostomos I. Dovas, George Georgiades, Isabella Monne, Alice Fusaro, Adam Dan, Krzysztof Śmietanka, Vassilios Ragias, Andrew C. Breed, Taxiarchis Chassalevris, Gabriela Goujgoulova, Charlotte Kristiane Hjulsager, Eoin Ryan, Azucena Sánchez, Eric Niqueux, Niina Tammiranta, Siamak Zohari, David A. Stroud, Vladimir Savić, Nicola S. Lewis, and Ian H. Brown

Author affiliations: Royal Veterinary College, London, UK (P. Alarcon); Animal and Plant Health Agency, Addlestone, UK (P. Alarcon, A. Brouwer, D. Duncan, A.C. Breed, N.S. Lewis, I.H. Brown); University of Cambridge, Cambridge, U K (D. Venkatesh); Aristotle University of Thessaloniki, Thessaloniki, Greece (C.I. Dovas, T. Chassalevris); Ministry of Rural Development and Food, Thessaloniki (G. Georgiades, V. Ragias); Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy (I. Monne, A. Fusaro); Veterinary Diagnostic Institute, Budapest, Hungary (A. Dan); National Veterinary Research Institute, Pulawy, Poland (K. Śmietanka); Department of Agriculture and Water Resources, Canberra, Australian Capital Territory, Australia (A.C. Breed); University of Queensland, Brisbane, Queensland, Australia (A.C. Breed); NDRVMI, Sofia, Bulgaria (G. Goujgoulova); Technical University of Denmark, Lyngby, Denmark (C.K. Hjulsager); Central Veterinary Research Laboratory, Celbridge, Ireland (E. Ryan); Central Veterinary Laboratory, Madrid, Spain (A. Sánchez); French Agency for Food, Environmental and Occupational Health & Safety, Ploufragan, France (E. Niqueux); Finnish Food Safety Authority Evira, Helsinki, Finland (N. Tammiranta); National Veterinary Institute and World Organisation for Animal Health Collaborating Center, Uppsala, Sweden (S. Zohari); Joint Nature Conservation Committee, Peterborough, UK (D. Stroud); Croatian Veterinary Institute, Zagreb, Croatia (V. Savić)

 

Abstract

We analyzed the highly pathogenic avian influenza (HPAI) H5 epizootic of 2016–17 in Europe by epidemiologic and genetic characteristics and compared it with 2 previous epizootics caused by the same H5 Guangdong lineage. The 2016–17 epizootic was the largest in Europe by number of countries and farms affected and greatest diversity of wild birds infected. We observed significant differences among the 3 epizootics regarding region affected, epidemic curve, seasonality, and outbreak duration, making it difficult to predict future HPAI epizootics. However, we know that in 2005–06 and 2016–17 the initial peak of wild bird detections preceded the peak of poultry outbreaks within Europe. Phylogenetic analysis of 2016–17 viruses indicates 2 main pathways into Europe. Our findings highlight the need for global surveillance of viral changes to inform disease preparedness, detection, and control.

Keywords: Avian Influenza; H5; Poultry; Wild Birds; European Region.

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#Upsurge in #echovirus 30 detections in five #EU/EEA countries, April to September, 2018 (Euro Surveill., abstract)

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

Upsurge in echovirus 30 detections in five EU/EEA countries, April to September, 2018

Eeva K Broberg1, Benedetto Simone1, Josep Jansa1, the EU/EEA Member State contributors1

Affiliations: 1 European Centre for Disease Prevention and Control, Stockholm, Sweden

Citation style for this article: Broberg Eeva K, Simone Benedetto, Jansa Josep, the EU/EEA Member State contributors. Upsurge in echovirus 30 detections in five EU/EEA countries, April to September, 2018. Euro Surveill. 2018;23(44):pii=1800537. https://doi.org/10.2807/1560-7917.ES.2018.23.44.1800537

Received: 02 Oct 2018;   Accepted: 30 Oct 2018

 

Abstract

An upsurge in Echovirus 30 (E30) infections, associated with meningitis/meningoencephalitis, has been observed in Denmark, Germany, the Netherlands, Norway and Sweden in the period April to September 2018, compared with 2015–2017. In total, 658 E30 infections among 4,537 enterovirus infections were detected in 15 countries between January and September 2018 and affected mainly newborns and 26–45 year-olds. National public health institutes are reminded to remain vigilant and inform clinicians of the ongoing epidemic.

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

Keywords: Echovirus 30; Enterovirus; Viral meningitis; Encephalitis; European Region.

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Effect of childhood #pneumococcal conjugate #vaccination on invasive disease in older #adults of 10 #European countries: implications for adult vaccination (Thorax, abstract)

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

Effect of childhood pneumococcal conjugate vaccination on invasive disease in older adults of 10 European countries: implications for adult vaccination

Germaine Hanquet1,2, Pavla Krizova3, Palle Valentiner-Branth4, Shamez N Ladhani5, J Pekka Nuorti6,7, Agnes Lepoutre8, Jolita Mereckiene9, Mirjam Knol10, Brita A Winje11, Pilar Ciruela12,13, Maria Ordobas14, Marcela Guevara13,15, Eisin McDonald16, Eva Morfeldt17, Jana Kozakova3, Hans-Christian Slotved4, Norman K Fry5, Hanna Rinta-Kokko6, Emmanuelle Varon18, Mary Corcoran19, Arie van der Ende20, Didrik F Vestrheim11, Carmen Munoz-Almagro13,21, Pello Latasa14, Jesus Castilla13,15, Andrew Smith22, Birgitta Henriques-Normark17,23,24, Robert Whittaker25, Lucia Pastore Celentano25, Camelia Savulescu1 on behalf of The SpIDnet/I-MOVE+ Pneumo Group

Author affiliations: 1 EpiConcept, Paris, France; 2 Antwerp University, Antwerp, Belgium; 3 National Institute of Public Health, Prague, Czech Republic; 4 Statens Serum Institut, Copenhagen, Denmark; 5 Public Health England, London, UK; 6 National Institute for Health and Welfare, Helsinki, Finland; 7 University of Tampere, Tampere, Finland; 8 Santé publique France, Saint-Maurice, France; 9 Health Protection Surveillance Centre, Dublin, Ireland; 10 National Institute for Public Health and the Environment, Bilthoven, The Netherlands; 11 Norwegian Institute of Public Health, Oslo, Norway; 12 Public Health Agency of Catalunya, Barcelona, Spain; 13 CIBER Epidemiología y Salud Pública, Madrid, Spain; 14 General Directorate of Public Health, Madrid, Spain; 15 Instituto de Salud Pública de Navarra – IdiSNA, Pamplona, Spain; 16 Health Protection Scotland, National Services Scotland, Glasgow, UK; 17 Public Health Agency of Sweden, Solna, Sweden; 18 National Centre for Pneumococci, European Hospital George Pompidou, Paris, France; 19 Irish Pneumococcal Reference Laboratory, Temple Street Children’s University Hospital, Dublin, Ireland; 20 Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Centre, Amsterdam, The Netherlands; 21 Instituto de Recerca Pediátrica, Hospital Sant Joan de Deu, Universitat Internacional de Catalunya, Barcelona, Spain; 22 Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference Laboratory, Glasgow, UK; 23 Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; 24 Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; 25 European Centre for Disease Prevention and Control, Stockholm, Sweden

Correspondence to Dr Germaine Hanquet, Epidemiology Department, EpiConcept, Paris 75012, France; ghanquet@skynet.be

 

Abstract

Background 

Pneumococcal conjugate vaccines (PCVs) have the potential to prevent pneumococcal disease through direct and indirect protection. This multicentre European study estimated the indirect effects of 5-year childhood PCV10 and/or PCV13 programmes on invasive pneumococcal disease (IPD) in older adults across 13 sites in 10 European countries, to support decision-making on pneumococcal vaccination policies.

Methods 

For each site we calculated IPD incidence rate ratios (IRR) in people aged ≥65 years by serotype for each PCV10/13 year (2011–2015) compared with 2009 (pre-PCV10/13). We calculated pooled IRR and 95% CI using random-effects meta-analysis and PCV10/13 effect as (1 − IRR)*100.

Results 

After five PCV10/13 years, the incidence of IPD caused by all types, PCV7 and additional PCV13 serotypes declined 9% (95% CI −4% to 19%), 77% (95% CI 67% to 84%) and 38% (95% CI 19% to 53%), respectively, while the incidence of non-PCV13 serotypes increased 63% (95% CI 39% to 91%). The incidence of serotypes included in PCV13 and not in PCV10 decreased 37% (95% CI 22% to 50%) in six PCV13 sites and increased by 50% (95% CI −8% to 146%) in the four sites using PCV10 (alone or with PCV13). In 2015, PCV13 serotypes represented 20–29% and 32–53% of IPD cases in PCV13 and PCV10 sites, respectively.

Conclusion 

Overall IPD incidence in older adults decreased moderately after five childhood PCV10/13 years in 13 European sites. Large declines in PCV10/13 serotype IPD, due to the indirect effect of childhood vaccination, were countered by increases in non-PCV13 IPD, but these declines varied according to the childhood vaccine used. Decision-making on pneumococcal vaccination for older adults must consider the indirect effects of childhood PCV programmes. Sustained monitoring of IPD epidemiology is imperative.

This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/.

DOI: http://dx.doi.org/10.1136/thoraxjnl-2018-211767

Keywords: S. Pneumoniae; Vaccines; European Region; Invasive Pneumococcal Disease.

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