Insights into the circular: the cryptic plasmidome and its derived antibiotic resistome in the urban water systems

Zhuofeng Yu, Wanli He, Franziska Klincke, Jonas Stenløkke Madsen, Witold Kot, Lars Hestbjerg Hansen, Marcos Quintela-Baluja, Sabela Balboa, Arnaud Dechesne, Barth Smets, Joseph Nesme*, Søren Johannes Sørensen*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

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Plasmids have been a concern in the dissemination and evolution of antibiotic resistance in the environment. In this study, we investigated the total pool of plasmids (plasmidome) and its derived antibiotic resistance genes (ARGs) in different compartments of urban water systems (UWSs) in three European countries representing different antibiotic usage regimes. We applied a direct plasmidome approach using wet-lab methods to enrich circular DNA in the samples, followed by shotgun sequencing and in silico contig circularisation. We identified 9,538 novel sequences in a total of 10,942 recovered circular plasmids. Of these, 66 were identified as conjugative, 1,896 mobilisable and 8,970 non-mobilisable plasmids. The UWSs’ plasmidome was dominated by small plasmids (≤10 Kbp) representing a broad diversity of mobility (MOB) types and incompatibility (Inc) groups. A shared collection of plasmids from different countries was detected in all treatment compartments, and plasmids could be source-tracked in the UWSs. More than half of the ARGs-encoding plasmids carried mobility genes for mobilisation/conjugation. The richness and abundance of ARGs-encoding plasmids generally decreased with the flow, while we observed that non-mobilisable ARGs-harbouring plasmids maintained their abundance in the Spanish wastewater treatment plant. Overall, our work unravels that the UWS plasmidome is dominated by cryptic (i.e., non-mobilisable, non-typeable and previously unknown) plasmids. Considering that some of these plasmids carried ARGs, were prevalent across three countries and could persist throughout the UWSs compartments, these results should alarm and call for attention.
Original languageEnglish
Article number108351
JournalEnvironment International
Number of pages12
Publication statusPublished - 2024


  • Wastewater
  • Urban water systems
  • Circular plasmidome
  • Source tracking
  • Antibiotic resistome


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