Consistent typing of plasmids with the mge-cluster pipeline

Arredondo-Alonso, S.; Gladstone, R. A.; Pontinen, A. K.; Gama, J. A.; Schurch, A. C.; Lanza, V. F.; Johnsen, P. J.; Samuelsen, O.; Tonkin-Hill, G.; Corander, J.

doi:10.1101/2022.12.16.520696

bioRxiv · 10.1101/2022.12.16.520696

Consistent typing of plasmids with the mge-cluster pipeline

Arredondo-Alonso, S.·Gladstone, R. A.·Pontinen, A. K.·Gama, J. A.·Schurch, A. C.·Lanza, V. F.·Johnsen, P. J.·Samuelsen, O.·Tonkin-Hill, G.·Corander, J.

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Abstract

Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Our method can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. We provide an intuitive visualization, classification and clustering scheme that users can explore interactively. This provides a framework that can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We illustrate the attractive features of our approach by the analysis of population-wide plasmid data from the opportunistic pathogen Escherichia coli and the distribution of the colistin resistance gene mcr-1.1 in the plasmid population.

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Arredondo-Alonso, S., Gladstone, R. A., Pontinen, A. K., Gama, J. A., Schurch, A. C., Lanza, V. F., Johnsen, P. J., Samuelsen, O., Tonkin-Hill, G., Corander, J.. 2022-12-19. Consistent typing of plasmids with the mge-cluster pipeline. https://doi.org/10.1101/2022.12.16.520696

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