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1. Antimicrobial resistance genes aph(3')-III, erm(B), sul2 and tet(W) abundance in animal faeces, meat, production environments and human faeces in Europe

Author

Yang, Dongsheng, Heederik, Dick J.J., Scherpenisse, Peter, Van Gompel, Liese, Luiken, Roosmarijn E.C., Wadepohl, Katharina, Skarżyńska, Magdalena, Van Heijnsbergen, Eri, Wouters, Inge M., Greve, Gerdit D., Jongerius-Gortemaker, Betty G.M., Tersteeg-Zijderveld, Monique, Portengen, Lützen, Juraschek, Katharina, Fischer, Jennie, Zajac, Magdalena, Wasyl, Dariusz, Wagenaar, Jaap A., Mevius, Dik J., Smit, Lidwien A.M., Schmitt, Heike, Graveland, Haitske, Joosten, Philip, Sarrazin, Steven, Dewulf, Jeroen, Van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, David, Julie, Soumet, Christophe, Battisti, Antonio, Caprioli, Andrea, Blaha, Thomas, Brandt, Maximiliane, Aarestrup, Frank, Hald, Tine, Duarte, Ana Sofia Ribeiro, Hoszowski, Andrzej, Pekala-Safinnska, Agnieszka, Pazdzior, Ewa, Daskalov, Hristo, Saatkamp, Helmut W., Stark, Katharina D.C., IRAS OH Epidemiology Microbial Agents, Faculteit Diergeneeskunde, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, Klinische infectiologie en microb. lab., LS IRAS EEPI GRA (Gezh.risico-analyse), One Health Microbieel, IRAS OH Epidemiology Chemical Agents, dIRAS RA-2, and dI&I I&I-4

Subjects
Microbiology (medical), Livestock, Meat, Drivers, Swine, Epidemiology, Bioinformatica & Diermodellen, GTB Gewasgez. Bodem en Water, Bedrijfseconomie, WASS, Escherichia-coli, Feces, Crop health, Anti-Infective Agents, Business Economics, RNA, Ribosomal, 16S, Drug Resistance, Bacterial, Bio-informatics & Animal models, Mechanisms, Animals, Humans, Life Science, Epidemiology, Bio-informatics & Animal models, Pharmacology (medical), Host Pathogen Interaction & Diagnostics, Epidemiologie, Pharmacology, Carriage, Ecology, Bacteriologie, Bacteriology, Bacteriology, Host Pathogen Interaction & Diagnostics, Chicken, Host Pathogen Interactie & Diagnostiek, Anti-Bacterial Agents, Risk-factors, Cross-Sectional Studies, Infectious Diseases, Genes, Bacterial, Epidemiologie, Bioinformatica & Diermodellen, Gewasgezondheid, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Cattle, Pigs, Chickens
Abstract

Background Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains. Objectives We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed. Methods A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3′)-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman’s rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data. Results ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains (‘farm to fork’) was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman’s ρ > 0.7) between qPCR data and metagenomic data of pooled samples. Conclusions qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.

Published
2022

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

Author

Luiken, Roosmarijn, van Gompel, Liese, Munk, Patrick, Sarrazin, Steven, Joosten, Philip, Dorado-García, Alejandro, Borup Hansen, Rasmus, Knudsen, Berith, Bossers, Alex, Wagenaar, Jaap, Aarestrup, Frank, Dewulf, Jeroen, Mevius, Dik, Heederik, Dick, Smit, Lidwien, Schmitt, Heike, Graveland, Haitske, Vanessen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Hald, Tine, Ribeiro Duarte, Ana Sofia, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut, Stärk, Katharina, One Health Microbieel, dI&I I&I-4, Dep IRAS, dIRAS RA-I&I RA, Part of Wageningen UR, Central Veterinary Institute, Obstetrics, Reproduction and Herd Health, Universiteit Gent = Ghent University (UGENT), Environmental and Occupational Health Group, Wageningen University and Research [Wageningen] (WUR), Division of Environmental Epidemiology [Utrecht, The Netherlands], Utrecht University [Utrecht]- Institute of Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Institute for Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Utrecht University [Utrecht], Facultad de Veterinaria, Dpto. de Sanidad Animal - VISAVET, Universidad Complutense de Madrid = Complutense University of Madrid [Madrid] (UCM), Laboratoire de Fougères - ANSES, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Pharmacoepidemiologie et évaluation de l'impact des produits de santé sur les populations, Université Bordeaux Segalen - Bordeaux 2-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Istituto Zooprofilattico Sperimentale del Lazio e della Toscana (IZSLT), Department of Microbiology, National Veterinary Research Institute [Pulawy, Pologne] (NVRI), European Project: 613754,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,EFFORT(2013), Universiteit Gent = Ghent University [Belgium] (UGENT), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Bordeaux Segalen - Bordeaux 2-Université de Rouen Normandie (UNIROUEN), and Normandie Université (NU)-Normandie Université (NU)

Subjects
Veterinary medicine, antibiotic resistance, Epidemiology, animal diseases, Biosecurity, Drug resistance, veterinary drug, antibiotique, Anti-Infective Agents, Risk Factors, Pharmacology (medical), Veterinary drug, bacteria, Original Research, agriculture, 2. Zero hunger, bactérie, 0303 health sciences, Lincosamides, Microbiota, poultry, Bacteriologie, Bacteriology, Host Pathogen Interaction & Diagnostics, Antimicrobial, usage, médicamentvétérinaire, Europe, Infectious Diseases, farm, Microbiology (medical), Farms, medicine.drug_class, Bioinformatica & Diermodellen, Biology, 03 medical and health sciences, Antibiotic resistance, Drug Resistance, Bacterial, Bio-informatics & Animal models, medicine, Animals, Life Science, Epidemiology, Bio-informatics & Animal models, antimicrobial resistance, microbiologie, 030304 developmental biology, Pharmacology, Host Pathogen Interaction & Diagnostics, Epidemiologie, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, 030306 microbiology, microbiology, Computational Biology, Bacteriology, antimicrobial use, Host Pathogen Interactie & Diagnostiek, Resistome, volaille, Cross-Sectional Studies, feces, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, Flock, Metagenomics, antimicrobien, Chickens
Abstract

Objectives 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. Methods 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. Results 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. Conclusions 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.

Published
2019

3. Erratum to: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries (Nature Microbiology, (2018), 3, 8, (898-908), 10.1038/s41564-018-0192-9)

Author

Munk, Patrick, Knudsen, Berith Elkær, Lukjancenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., dIRAS RA-I&I I&I, One Health Microbieel, dIRAS RA-I&I RA, Dep IRAS, dI&I I&I-4, and LS Klinisch Onderzoek Wagenaar

Subjects
Coronacrisis-Taverne
Abstract

In the version of this Article originally published, the surname of author Oksana Lukjancenko was spelt incorrectly as ‘Lukjacenko’. This has now been corrected.

Published
2018

4. Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Author

Munk, Patrick, Knudsen, Berith Elkær, Lukjacenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., Munk, Patrick, Knudsen, Berith Elkær, Lukjacenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, and Aarestrup, Frank M.

Abstract

Antimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. The use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock and in humans. We quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, sequencing more than 5,000 Gb of DNA using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a second database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than in poultry. We found higher AMR loads in pigs, whereas poultry resistomes were more diverse. We detected several recently described, critical AMR genes, including mcr-1 and optrA, the abundance of which differed both between host species and between countries. We found that the total acquired AMR level was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. However, functionally determined AMR genes were not associated with total drug use.

Published
2018

5. Erratum to: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries (Nature Microbiology, (2018), 3, 8, (898-908), 10.1038/s41564-018-0192-9)

Author

dIRAS RA-I&I I&I, One Health Microbieel, dIRAS RA-I&I RA, Dep IRAS, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Munk, Patrick, Knudsen, Berith Elkær, Lukjancenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., dIRAS RA-I&I I&I, One Health Microbieel, dIRAS RA-I&I RA, Dep IRAS, dI&I I&I-4, LS Klinisch Onderzoek Wagenaar, Munk, Patrick, Knudsen, Berith Elkær, Lukjancenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., and Stärk, Katharina D.C.

Published
2018

6. Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Author

One Health Microbieel, LS Klinisch Onderzoek Wagenaar, Dep IRAS, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, dI&I I&I-4, Munk, Patrick, Knudsen, Berith Elkær, Lukjacenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., One Health Microbieel, LS Klinisch Onderzoek Wagenaar, Dep IRAS, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, dI&I I&I-4, Munk, Patrick, Knudsen, Berith Elkær, Lukjacenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, and Aarestrup, Frank M.

Published
2018

7. Author Correction: Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries

Author

Munk, Patrick, Knudsen, Berith Elkær, Lukjancenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., Munk, Patrick, Knudsen, Berith Elkær, Lukjancenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., and Stärk, Katharina D.C.

Abstract

In the version of this Article originally published, the surname of author Oksana Lukjancenko was spelt incorrectly as ‘Lukjacenko’. This has now been corrected.

Published
2018

8. Abundance and diversity of the fecal resistome in slaughter pigs and broilers in nine European countries

Author

Munk, Patrick, Knudsen, Berith Elkær, Lukjacenko, Oksana, Duarte, Ana Sofia Ribeiro, Van Gompel, Liese, Luiken, Roosmarijn E.C., Smit, Lidwien A.M., Schmitt, Heike, Garcia, Alejandro Dorado, Hansen, Rasmus Borup, Petersen, Thomas Nordahl, Bossers, Alex, Ruppé, Etienne, Graveland, Haitske, van Essen, Alieda, Gonzalez-Zorn, Bruno, Moyano, Gabriel, Sanders, Pascal, Chauvin, Claire, David, Julie, Battisti, Antonio, Caprioli, Andrea, Dewulf, Jeroen, Blaha, Thomas, Wadepohl, Katharina, Brandt, Maximiliane, Wasyl, Dariusz, Skarzyńska, Magdalena, Zajac, Magdalena, Daskalov, Hristo, Saatkamp, Helmut W., Stärk, Katharina D.C., Lund, Ole, Hald, Tine, Pamp, Sünje Johanna, Vigre, Håkan, Heederik, Dick, Wagenaar, Jaap A., Mevius, Dik, Aarestrup, Frank M., One Health Microbieel, LS Klinisch Onderzoek Wagenaar, Dep IRAS, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, dI&I I&I-4, Institute for Risk Assessment Sciences [Utrecht, The Netherlands] (IRAS), Utrecht University [Utrecht], Part of Wageningen UR, Central Veterinary Institute, Genomic Research Laboratory [Geneva, Switzerland], Geneva University Hospital (HUG), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Ploufragan - Plouzané, Center for Biological Sequence Analysis, Technical University of Denmark [Lyngby] (DTU), Division of Occupational and Environmental Health, Institute for Risk Assessment (IRAS), EFFORT Group, One Health Microbieel, LS Klinisch Onderzoek Wagenaar, Dep IRAS, dIRAS RA-I&I RA, dIRAS RA-I&I I&I, and dI&I I&I-4

Subjects
0301 basic medicine, pig, Veterinary medicine, antibiotic resistance, Epidemiology, Swine, WASS, Applied Microbiology and Biotechnology, Feces, Environmental DNA, animal, proc, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, bactérie, 0303 health sciences, poultry, Bacteriologie, Bacteriology, Host Pathogen Interaction & Diagnostics, Biodiversity, Poultry farming, Human morbidity, Europe, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Livestock, Gene pool, Microbiology (medical), Bioinformatica & Diermodellen, Immunology, Bedrijfseconomie, Coronacrisis-Taverne, Biology, 03 medical and health sciences, Antibiotic resistance, SDG 3 - Good Health and Well-being, Bacterial Proteins, Species Specificity, Business Economics, Bio-informatics & Animal models, Drug Resistance, Bacterial, Genetics, Life Science, Animals, Epidemiology, Bio-informatics & Animal models, microbiologie, 030304 developmental biology, Host Pathogen Interaction & Diagnostics, Epidemiologie, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Bacteria, 030306 microbiology, business.industry, résistane aux antibiotiques, Gene Expression Profiling, microbiology, Bacteriology, Cell Biology, Sequence Analysis, DNA, Host Pathogen Interactie & Diagnostiek, Biotechnology, Resistome, volaille, 030104 developmental biology, Metagenomics, Epidemiologie, Bioinformatica & Diermodellen, Bacteriologie, Host Pathogen Interactie & Diagnostiek, business, Chickens
Abstract

EFFORT groupHaitske Graveland, Alieda van Essen, Bruno Gonzalez-Zorn, Gabriel Moyano, Pascal Sanders, Claire Chauvin, Julie David, Antonio Battisti, Andrea Caprioli, Jeroen Dewulf, Thomas Blaha, Katharina Wadepohl, Maximiliane Brandt, Dariusz Wasyl, Magdalena Skarzyñska, Magdalena Zajac, Hristo Daskalov, Helmut W Saatkamp, Katharina D.C. Stärk.AbstractAntimicrobial resistance (AMR) in bacteria and associated human morbidity and mortality is increasing. Use of antimicrobials in livestock selects for AMR that can subsequently be transferred to humans. This flow of AMR between reservoirs demands surveillance in livestock as well as in humans. As part of the EFFORT project (www.effort-against-amr.eu), we have quantified and characterized the acquired resistance gene pools (resistomes) of 181 pig and 178 poultry farms from nine European countries, generating more than 5,000 gigabases of DNA sequence, using shotgun metagenomics. We quantified acquired AMR using the ResFinder database and a database constructed for this study, consisting of AMR genes identified through screening environmental DNA. The pig and poultry resistomes were very different in abundance and composition. There was a significant country effect on the resistomes, more so in pigs than poultry. We found higher AMR loads in pigs, while poultry resistomes were more diverse. We detected several recently described, critical AMR genes, includingmcr-1andoptrA, the abundance of which differed both between host species and countries. We found that the total acquired AMR level, was associated with the overall country-specific antimicrobial usage in livestock and that countries with comparable usage patterns had similar resistomes. Novel, functionally-determined AMR genes were, however, not associated with total drug use.

Published
2017
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