Marti E, Variatza E, Balcazar JL (2014) The role of aquatic ecosystems as reservoirs of antibiotic resistance. Trends Microbiol 22: 36–41. doi: 10.1016/j.tim.2013.11.001
[2]
Frost LS, Leplae R, Summers AO, Toussaint A (2005) Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 3: 722–732. doi: 10.1038/nrmicro1235
[3]
Chibani-Chennoufi S, Bruttin A, Dillmann M-L, Brüssow H (2004) Phage-host interaction: an ecological perspective. J Bacteriol 186: 3677–3686. doi: 10.1128/jb.186.12.3677-3686.2004
[4]
Brabban AD, Hite E, Callaway TR (2005) Evolution of foodborne pathogens via temperate bacteriophage-mediated gene transfer. Foodborne Pathog Dis 2: 287–303. doi: 10.1089/fpd.2005.2.287
[5]
Modi SR, Lee HH, Spina CS, Collins JJ (2013) Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499: 219–223. doi: 10.1038/nature12212
Wellington EMH, Boxall ABA, Cross P, Feil EJ, Gaze WH, et al. (2013) The role of the natural environment in the emergence of antibiotic resistance in Gram-negative bacteria. Lancet Infect Dis 13: 155–165. doi: 10.1016/s1473-3099(12)70317-1
[8]
Parsley LC, Consuegra EJ, Kakirde KS, Land AM, Harper WF Jr, et al. (2010) Identification of diverse antimicrobial resistance determinants carried on bacterial, plasmid, or viral metagenomes from an activated sludge microbial assemblage. Appl Environ Microbiol 76: 3753–3757. doi: 10.1128/aem.03080-09
[9]
Colomer-Lluch M, Jofre J, Muniesa M (2011) Antibiotic resistance genes in the bacteriophage DNA fraction of environmental samples. PLoS ONE 6: e17549. doi: 10.1371/journal.pone.0017549
[10]
Marti E, Variatza E, Balcázar JL (2014) Bacteriophages as a reservoir of extended-spectrum β-lactamase and fluoroquinolone resistance genes in the environment. Clin Microbiol Infect E-pub ahead of print. doi:10.1111/1469-0691.12446.
[11]
Colomer-Lluch M, Jofre J, Muniesa M (2014) Quinolone resistance genes (qnrA and qnrS) in bacteriophage particles from wastewater samples and the effect of inducing agents on packaged antibiotic resistance genes. J Antimicrob Chemother 69: 1265–1274. doi: 10.1093/jac/dkt528
[12]
Monier J-M, Demanèche S, Delmont TO, Mathieu A, Vogel TM, et al. (2011) Metagenomic exploration of antibiotic resistance in soil. Curr Opin Microbiol 14: 229–235. doi: 10.1016/j.mib.2011.04.010
[13]
Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386. doi: 10.1186/1471-2105-9-386
[14]
Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40: D115–D122. doi: 10.1093/nar/gkr1044
[15]
Wright GD (2010) Antibiotic resistance in the environment: a link to the clinic? Curr Opin Microbiol 13: 589–594. doi: 10.1016/j.mib.2010.08.005
[16]
Pruden A (2014) Balancing water sustainability and public health goals in the fate of growing concerns about antibiotic resistance. Environ Sci Technol 48: 5–14. doi: 10.1021/es403883p
[17]
Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, et al. (2012) The shared antibiotic resistome of soil bacteria and human pathogens. Science 337: 1107–1111. doi: 10.1126/science.1220761