Plasmids are independently replicating fragments within a bacterial cell. They often contain genetic information that is beneficial for their host cells, such as features that confer antimicrobial resistance or virulence factors. Plasmids are a major driving force for the spread of resistance and bacterial adaptation. However, to date, the full range and consequence of the spread of beneficial traits on plasmids still needs to be disclosed. This is due to the challenges associated with the reconstruction of plasmids from short read sequencing data which often results in incomplete or merged sequences. We reconstruct plasmids with a combination of long read, hybrid assembly and machine learning techniques and use this prediction to explore plasmidomes.

References

On the (im) possibility of reconstructing plasmids from whole-genome short-read sequencing data Sergio Arredondo-Alonso, Rob J Willems, Willem van Schaik, Anita C Schürch Microbial genomics 3 (10)

mlplasmids: a user-friendly tool to predict plasmid-and chromosome-derived sequences for single species Sergio Arredondo-Alonso, Malbert RC Rogers, Johanna C Braat, Tess D Verschuuren, Janetta Top, Jukka Corander, Rob JL Willems, Anita C Schürch… Microbial genomics 4 (11)

Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome Sergio Arredondo-Alonso, Janetta Top, Anita C Schürch, Alan McNally, Santeri Puranen, Maiju Pesonen, Johan Pensar, Pekka Marttinen, Johanna C Braat, Malbert RC Rogers, Willem van Schaik, Samuel Kaski, Jukka Corander, Rob JL Willems bioRxiv, 530725

[Recovering Escherichia coli Plasmids in the Absence of Long-Read Sequencing Data] (https://www.mdpi.com/2076-2607/9/8/1613) Julina A. Paganini, Nienke L. Plantinga, Sergio Arredondo-Alonso, Rob J.L. Willems, and Anita C. Schürch. 2021. Microorganisms