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Aims: To evaluate the role of manure treatment lagoons of swine operations in the fate of faeces- and feed-borne tetracycline-resistant genes (TRG)., Methods and Results: Samples of feed, faeces, lagoon liquid and lagoon sediment in farm's vicinity were collected at three swine operations varied on their operational practices and analysed on the presence and frequencies of incidence of sixteen TRG in upstream sources (feed, faeces) and downstream receptacles (lagoon liquid and sediments). The highest frequency of TRG incidence was observed in a farm with extensive antibiotic usage and the lowest in the antibiotic-free farm. The study revealed a decrease in TRG richness and diversity in the downstream habitats of each farm. The observed TRG diverged into two groups, the persistent genes that were detected both upstream and downstream, and the transient genes that were detected in the upstream habitats but became nondetectable in the lagoons. Quantitative PCR analysis revealed that upstream concentrations and abundances (determined as TRG/16S rRNA gene ratios) of transient and persistent TRG were similar; however, the former were attenuated in the lagoons to the levels below the detection limit, whereas the latter were ∼ 100-1000 fold amplified in their (mostly) liquid phases and were also detected in farms' vicinities., Conclusion: Manure lagoons of swine operations imposed both positive and negative selection towards faeces- and feed-borne TRG that, respectively, caused either their proliferation or attenuation in those environments., Significance and Impact of the Study: The study reveals that discharge of antibiotic resistance genes from swine farms to the environment is linked to their positive selection (defined as an impact leading to proliferation of those genes) in manure lagoons., (© 2012 The Authors. Journal of Applied Microbiology © 2012 The Society for Applied Microbiology.)