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

@article{Munk2018AbundanceAD,
  title={Abundance and diversity of the faecal resistome in slaughter pigs and broilers in nine European countries},
  author={P. Munk and B. E. Knudsen and O. Lukjancenko and A. S. Duarte and L. Van Gompel and R. Luiken and L. Smit and H. Schmitt and A. D. Garcia and R. B. Hansen and T. N. Petersen and A. Bossers and E. Rupp{\'e} and O. Lund and T. Hald and S. J. Pamp and H. Vigre and D. Heederik and J. Wagenaar and D. Mevius and F. Aarestrup},
  journal={Nature Microbiology},
  year={2018},
  volume={3},
  pages={898-908}
}
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… Expand
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References

SHOWING 1-10 OF 52 REFERENCES
A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds
TLDR
Metagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption and should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs. Expand
The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward
  • F. Aarestrup
  • Biology, Medicine
  • Philosophical Transactions of the Royal Society B: Biological Sciences
  • 2015
TLDR
There is a need for global harmonized integrated and continuous surveillance of antimicrobial usage and antimicrobial resistance, preferably associated with data on production and animal diseases to determine the positive and negative impact of reducing antimicrobial use in livestock. Expand
Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken, and Human Feces.
TLDR
A pipeline for annotating antibiotic resistance genes (ARGs) based on metagenomic assembly is established to investigate ARGs and their co-occurrence with associated genetic elements and successfully establishes the relationship between ARGs, hosts, and environments. Expand
Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora
TLDR
To understand the process by which antibiotic resistance genes are acquired by human pathogens, functionally characterized the resistance reservoir in the microbial flora of healthy individuals and identified most of the resistance genes, which have not been previously identified and are evolutionarily distant from known resistance genes. Expand
Quantitative assessment of antimicrobial resistance in livestock during the course of a nationwide antimicrobial use reduction in the Netherlands.
TLDR
Data suggest that recent Dutch policies aimed at reducing total use of antimicrobials have decreased E. coli resistance in the pig and veal calf production sectors while the impact on the dairy cattle and poultry sectors is less clear. Expand
Correlation between veterinary antimicrobial use and antimicrobial resistance in food-producing animals: a report on seven countries.
OBJECTIVES To evaluate correlations between antimicrobial use and the prevalence of resistance in commensal Escherichia coli isolates from pigs, poultry and cattle, using data from publicly availableExpand
Quantification and evaluation of antimicrobial drug use in group treatments for fattening pigs in Belgium.
TLDR
Proportionally, the most often applied oral antimicrobial drugs were: doxycycline, amoxicillin, combination trimethoprim-sulphonamides and polymyxin E. Expand
Voluntary ban on cephalosporin use in Danish pig production has effectively reduced extended-spectrum cephalosporinase-producing Escherichia coli in slaughter pigs.
TLDR
The discontinuation of an already low use of cephalosporins in pig production has significantly reduced the occurrence of ESC-producing E. coli in pigs and pork. Expand
Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
TLDR
This study performs shotgun sequencing of toilet waste from 18 international airplanes arriving in Copenhagen, Denmark, to find significantly higher abundance and diversity of genes encoding antimicrobial resistance, including critical important resistance carried on airplanes from South Asia compared to North America. Expand
Pediatric Fecal Microbiota Harbor Diverse and Novel Antibiotic Resistance Genes
TLDR
This functional metagenomic survey of gut-associated resistomes, the largest of its kind to date, demonstrates that fecal resistomes of healthy children are far more diverse than previously suspected, that clinically relevant resistance genes are present even without recent selective antibiotic pressure in the human host, and that cryptic gut microbes are an important resistance reservoir. Expand
...
1
2
3
4
5
...