Plasmids are independently replicating DNA fragments within a bacterial cell. Over the past decade, my team has focused on the development of tools and methods to decode bacterial plasmids using sequencing data. We created tools like mlplasmids, gplas, PlasmidEC, and gplasCC, and co-created mge-cluster, which use machine-learning, graph-based algorithms, and network analysis to reconstruct and classify plasmids, even withouth long-read data, enabling species-wide epidemiology. Our research has advanced the understanding of plasmid-driven adaptation in pathogens such as Enterococcus faecium, Enterococcus faecalis and Escherichia coli and also provided the global community with open-access resources to combat the spread of multidrug-resistant infections.

Selected 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) (2017)

Plasmids shaped the recent emergence of the major nosocomial pathogen Enterococcus faecium. S Arredondo-Alonso, J Top, A McNally, S Puranen, M Pesonen, J Pensar et al. mBio 11 (2020)

gplas: a comprehensive tool for plasmid analysis using short-read graphs S Arredondo-Alonso, M Bootsma, Y Hein, MRC Rogers, J Corander, et al. Bioinformatics 36 (12), 3874-3876 (2020)

Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals S Arredondo-Alonso, J Top, J Corander, RJL Willems, AC Schürch Genome Medicine 13 (1), 9 (2021)

Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era AK Pöntinen, J Top, S Arredondo-Alonso, G Tonkin-Hill, AR Freitas, et al. Nature Communications 12 (1), 1523 (2021)

gplasCC: classification and reconstruction of plasmids from short-read sequencing data for any bacterial species JA Paganini, JJ Kerkvliet, G Teunis, O Jordan, NL Plantinga, R Meneses, et al. bioRxiv, 2024.11. 28.625923 (2024)