Antimicrobial Resistance Global Report on Surveillance 2014 (WHO, 2014).
Aarestrup, F. M. The livestock reservoir for antimicrobial resistance: a personal view on changing patterns of risks, effects of interventions and the way forward. Phil. Trans. R. Soc. B 370, 20140085 (2015).
Chantziaras, I., Boyen, F., Callens, B. & Dewulf, J. Correlation between veterinary antimicrobial use and antimicrobial resistance in food-producing animals: a report on seven countries. J. Antimicrob. Chemother. 69, 827–834 (2014).
Dunlop, R. H. et al. Associations among antimicrobial drug treatments and antimicrobial resistance of fecal Escherichia coli of swine on 34 farrow-to-finish farms in Ontario, Canada. Prev. Vet. Med. 34, 283–305 (1998).
Aarestrup, F. M., Seyfarth, A. M., Emborg, H., Pedersen, K. & Bager, F. Effect of abolishment of the use of antimicrobial agents for growth promotion on occurrence of antimicrobial resistance in fecal enterococci from food animals in Denmark. Antimicrob. Agents Chemother. 45, 2054–2059 (2001).
Agersø, Y. & Aarestrup, F. M. Voluntary ban on cephalosporin use in Danish pig production has effectively reduced extended-spectrum cephalosporinase-producing Escherichia coli in slaughter pigs. J. Antimicrob. Chemother. 68, 569–572 (2013).
Dutil, L. et al. Ceftiofur resistance in Salmonella enterica serovar Heidelberg from chicken meat and humans, Canada. Emerg. Infect. Dis. 16, 48–54 (2010).
Dorado-García, A. et al. Quantitative assessment of antimicrobial resistance in livestock during the course of a nationwide antimicrobial use reduction in the Netherlands. J. Antimicrob. Chemother. 71, 3607–3619 (2016).
Aarestrup, F. M. et al. Resistance to antimicrobial agents used for animal therapy in pathogenic-, zoonotic- and indicator bacteria isolated from different food animals in Denmark: a baseline study for the Danish Integrated Antimicrobial Resistance Monitoring Programme (DANMAP). APMIS 106, 745–770 (1998).
European Food Safety Authority Harmonised monitoring of antimicrobial resistance in Salmonella and Campylobacter isolates from food animals in the European Union. Clin. Microbiol. Infect. 14, 522–533 (2008).
McEwan, S. A., Aarestrup, F. M. & Jordan, D. in Antimicrobial Resistance in Bacteria of Animal Origin (ed. Aarestrup, F. M.) 397–413 (ASM Press, Washington DC, 2006).
Veterinary Medicines Division European Medicines Agency, European Surveillance of Veterinary Antimicrobial Consumption, 2016 (EMA, 2016).
European Centre for Disease Prevention and Control, European Food Safety Authority & European Medicines Agency ECDC/EFSA/EMA first joint report on the integrated analysis of the consumption of antimicrobial agents and occurrence of antimicrobial resistance in bacteria from humans and food-producing animals. EFSA J. 13, 4006 (2015).
European Food Safety Authority Technical specifications on the harmonised monitoring and reporting of antimicrobial resistance in Salmonella, Campylobacter and indicator Escherichia coli and Enterococcus spp. bacteria transmitted through food. EFSA J. 10, 64 (2012).
Nordahl Petersen, T. et al. Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance. Sci. Rep. 5, 11444 (2015).
Xiao, L. et al. A reference gene catalogue of the pig gut microbiome. Nat. Microbiol. 1, 16161 (2016).
Munk, P. et al. A sampling and metagenomic sequencing-based methodology for monitoring antimicrobial resistance in swine herds. J. Antimicrob. Chemother. 72, 385–392 (2016).
Hasman, H. et al. Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Suveill. 20, 30085 (2015).
Wang, Y. et al. A novel gene, optrA, that confers transferable resistance to oxazolidinones and phenicols and its presence in Enterococcus faecalis and Enterococcus faecium of human and animal origin. J. Antimicrob. Chemother. 70, 2182–2190 (2015).
Forsberg, K. J. et al. Bacterial phylogeny structures soil resistomes across habitats. Nature 509, 612–616 (2014).
Pehrsson, E. C. et al. Interconnected microbiomes and resistomes in low-income human habitats. Nature 533, 212–216 (2016).
Martínez, J. L., Coque, T. M. & Baquero, F. What is a resistance gene? Ranking risk in resistomes. Nat. Rev. Microbiol. 13, 116–123 (2014).
Knudsen, B. E. et al. Impact of sample type and DNA isolation procedure on genomic inference of microbiome composition. mSystems 1, e00095-16 (2016).
Bowers, R. M. et al. Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community. BMC Genomics 16, 856 (2015).
Hammerum, A. M. et al. Characterization of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli obtained from Danish pigs, pig farmers and their families from farms with high or no consumption of third- or fourth-generation cephalosporins. J. Antimicrob. Chemother. 69, 2650–2657 (2014).
Nielsen, H. B. et al. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat. Biotechnol. 32, 822–828 (2014).
Anantharaman, K. et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat. Commun. 7, 13219 (2016).
Ma, L. et al. Metagenomic assembly reveals hosts of antibiotic resistance genes and the shared resistome in pig, chicken, and human feces. Environ. Sci. Technol. 50, 420–427 (2016).
BBduk v39.92 (Bushnell, B., 2018); https://sourceforge.net/projects/bbmap/
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Zankari, E. et al. Identification of acquired antimicrobial resistance genes. J. Antimicrob. Chemother. 67, 2640–2644 (2012).
Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
Pehrsson, E. C., Forsberg, K. J., Gibson, M. K., Ahmadi, S. & Dantas, G. Novel resistance functions uncovered using functional metagenomic investigations of resistance reservoirs. Front. Microbiol. 4, 145 (2013).
Moore, A. M. et al. Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PLoS ONE 8, e78822 (2013).
Sommer, M. O. A., Dantas, G. & Church, G. M. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325, 1128–1131 (2009).
Legendre, P. & Gallagher, E. D. Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271–280 (2001).
Timmerman, T. et al. Quantification and evaluation of antimicrobial drug use in group treatments for fattening pigs in Belgium. Prev. Vet. Med. 74, 251–263 (2006).
Oksanen, J. et al. vegan: Community Ecology Package v2.4-1 (CRAN, 2016); https://CRAN.R-project.org/package=vegan
Pielou, E. C. The measurement of diversity in different types of biological collections. J. Theor. Biol. 13, 131–144 (1966).
Paradis, E., Claude, J. & Strimmer, K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 (2004).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, New York, NY, 2009).
Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw. 67, 1–48 (2015).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
McMurdie, P. J. & Holmes, S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput. Biol. 10, e1003531 (2014).
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 57, 289–300 (1995).