Farm dust resistomes and bacterial microbiomes in European poultry and pig farms
Background: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a po...
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Elsevier
2020-10-01
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Series: | Environment International |
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Online Access: | http://www.sciencedirect.com/science/article/pii/S0160412020319267 |
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doaj-db18d2c481394b268a0c0fa5e44fd57d |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Roosmarijn E.C. Luiken Liese Van Gompel Alex Bossers Patrick Munk Philip Joosten Rasmus Borup Hansen Berith E. Knudsen Silvia García-Cobos Jeroen Dewulf Frank M. Aarestrup Jaap A. Wagenaar Lidwien A.M. Smit Dik J. Mevius Dick J.J. Heederik Heike Schmitt |
spellingShingle |
Roosmarijn E.C. Luiken Liese Van Gompel Alex Bossers Patrick Munk Philip Joosten Rasmus Borup Hansen Berith E. Knudsen Silvia García-Cobos Jeroen Dewulf Frank M. Aarestrup Jaap A. Wagenaar Lidwien A.M. Smit Dik J. Mevius Dick J.J. Heederik Heike Schmitt Farm dust resistomes and bacterial microbiomes in European poultry and pig farms Environment International Air Metagenomics Resistome Microbiome Farm One health |
author_facet |
Roosmarijn E.C. Luiken Liese Van Gompel Alex Bossers Patrick Munk Philip Joosten Rasmus Borup Hansen Berith E. Knudsen Silvia García-Cobos Jeroen Dewulf Frank M. Aarestrup Jaap A. Wagenaar Lidwien A.M. Smit Dik J. Mevius Dick J.J. Heederik Heike Schmitt |
author_sort |
Roosmarijn E.C. Luiken |
title |
Farm dust resistomes and bacterial microbiomes in European poultry and pig farms |
title_short |
Farm dust resistomes and bacterial microbiomes in European poultry and pig farms |
title_full |
Farm dust resistomes and bacterial microbiomes in European poultry and pig farms |
title_fullStr |
Farm dust resistomes and bacterial microbiomes in European poultry and pig farms |
title_full_unstemmed |
Farm dust resistomes and bacterial microbiomes in European poultry and pig farms |
title_sort |
farm dust resistomes and bacterial microbiomes in european poultry and pig farms |
publisher |
Elsevier |
series |
Environment International |
issn |
0160-4120 |
publishDate |
2020-10-01 |
description |
Background: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust. Objectives: We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers’ stool resistomes was explored. Methods: In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers’ stool. Results: The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers’ resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study. Conclusion: Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome. |
topic |
Air Metagenomics Resistome Microbiome Farm One health |
url |
http://www.sciencedirect.com/science/article/pii/S0160412020319267 |
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doaj-db18d2c481394b268a0c0fa5e44fd57d2020-11-25T03:31:10ZengElsevierEnvironment International0160-41202020-10-01143105971Farm dust resistomes and bacterial microbiomes in European poultry and pig farmsRoosmarijn E.C. Luiken0Liese Van Gompel1Alex Bossers2Patrick Munk3Philip Joosten4Rasmus Borup Hansen5Berith E. Knudsen6Silvia García-Cobos7Jeroen Dewulf8Frank M. Aarestrup9Jaap A. Wagenaar10Lidwien A.M. Smit11Dik J. Mevius12Dick J.J. Heederik13Heike Schmitt14Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Corresponding author.Institute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the NetherlandsInstitute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the NetherlandsSection for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, DenmarkVeterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, BelgiumIntomics A/S, Lottenborgvej 26, 2800 Kongens Lyngby, DenmarkSection for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, DenmarkUniversity of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, PO Box 30.001, 9700 RB Groningen, the NetherlandsVeterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, BelgiumSection for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kemitorvet 204, 2800 Kongens Lyngby, DenmarkWageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands; Dept. Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the NetherlandsInstitute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the NetherlandsWageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, the Netherlands; Dept. Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the NetherlandsInstitute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the NetherlandsInstitute for Risk Assessment Sciences, Utrecht University, Yalelaan 2, 3584 CM Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721MA Bilthoven, the NetherlandsBackground: Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust. Objectives: We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers’ stool resistomes was explored. Methods: In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers’ stool. Results: The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers’ resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study. Conclusion: Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.http://www.sciencedirect.com/science/article/pii/S0160412020319267AirMetagenomicsResistomeMicrobiomeFarmOne health |