Identification and annotation of plasmids in Next Generation Sequencing microbial genomic data

Abstract

Plasmids are autoreplicative mobile elementsconstituted by asingle DNA molecule, which can be linear or circular. They are partof the genetic background of a microbial community and have thepotential to be transferred between different members. This isparticularly important in hospital settingswhere this mobility may contribute todissemination of antibiotic resistance encoded in the plasmids. Indifferent niches, plasmids could be a source of resistance to otherenvironmental factors.Withthe development of NGS techniques, plasmids have become less relevantamong the flood of data. Only recently algorithms have beendeveloped, allowing prediction of sequences belonging to plasmidsfrom short sequence NGS datasets. Public databases present aconstantly increasing number of such datasets. Thus, we aim to applycurrent plasmids detection methodologies to public data and build aplasmid database based on full well characterized plasmids but alsoincluding predictions.This would provide relevant data about the abilityto transfer genetic material of different strains, about geneticdeterminants of resistance (either to antibiotic or environmentalstress) encoded in mobile elements, and on the possibility of usingsome of these plasmids as new genetic tools for different microbialgenera, particularly in those where tools are not available.