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A Peek into the Plasmidome of Global Sewage

Philipp Kirstahler, Frederik Teudt, Saria Otani, Frank M. Aarestrup, View ORCID ProfileSünje Johanna Pamp
doi: https://doi.org/10.1101/2021.03.08.434362
Philipp Kirstahler
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
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Frederik Teudt
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
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Saria Otani
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
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Frank M. Aarestrup
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
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Sünje Johanna Pamp
1Research Group for Genomic Epidemiology, Technical University of Denmark, Kgs. Lyngby, Denmark
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  • ORCID record for Sünje Johanna Pamp
  • For correspondence: sjpa@dtu.dk
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Abstract

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions. Plasmid-encoded traits, such as antimicrobial resistance (AMR) or virulence, impact on the ecology and evolution of bacteria and can significantly influence the burden of infectious diseases. Insight about the identity and functions encoded on plasmids on the global scale are largely lacking. Here we investigate the plasmidome of 24 samples (22 countries, 5 continents) from the global sewage surveillance project. We obtained 105 Gbp Oxford Nanopore and 167 Gbp Illumina DNA sequences from plasmid DNA preparations and assembled 165,302 contigs (159,322 circular). Of these, 58,429 encoded for genes with plasmid-related and 11,222 with virus/phage-related proteins. About 90% of the circular DNA elements did not have any similarity to known plasmids. Those that exhibited similarity, had similarity to plasmids whose hosts were previously detected in these sewage samples (e.g. Acinetobacter, Escherichia, Moraxella, Enterobacter, Bacteroides, and Klebsiella). Some AMR classes were detected at a higher abundance in plasmidomes (e.g. macrolide-lincosamide-streptogramin B, macrolide, and quinolone), as compared to the respective complex sewage samples. In addition to AMR genes, a range of functions were encoded on the candidate plasmids, including plasmid replication and maintenance, mobilization, and conjugation. In summary, we describe a laboratory and bioinformatics workflow for the recovery of plasmids and other potential extrachromosomal DNA elements from complex microbiomes. Moreover, the obtained data could provide further valuable insight into the ecology and evolution of microbiomes, knowledge about AMR transmission, and the discovery of novel functions.

Importance This is, to the best of our knowledge, the first study to investigate plasmidomes at a global scale using long read sequencing from complex untreated domestic sewage. Previous metagenomic surveys have detected AMR genes in a variety of environments, including sewage. However, it is unknown whether the AMR genes were encoded on the microbial chromosome or are located on extrachromosomal elements, such as plasmids. Using our approach, we recovered a large number of plasmids, of which most appear novel. We identified distinct AMR genes that were preferentially located on plasmids, potentially contributing to their transmissibility. Overall, plasmids are of great importance for the biology of microorganisms in their natural environments (free-living and host-associated), as well as molecular biology, and biotechnology. Plasmidome collections may therefore be valuable resources for the discovery of fundamental biological mechanisms and novel functions useful in a variety of contexts.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://figshare.com/projects/A_Peek_into_the_Plasmidome_of_Global_Sewage/94448

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 28, 2021.
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A Peek into the Plasmidome of Global Sewage
Philipp Kirstahler, Frederik Teudt, Saria Otani, Frank M. Aarestrup, Sünje Johanna Pamp
bioRxiv 2021.03.08.434362; doi: https://doi.org/10.1101/2021.03.08.434362
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A Peek into the Plasmidome of Global Sewage
Philipp Kirstahler, Frederik Teudt, Saria Otani, Frank M. Aarestrup, Sünje Johanna Pamp
bioRxiv 2021.03.08.434362; doi: https://doi.org/10.1101/2021.03.08.434362

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