PlaScope: a targeted approach to assess the plasmidome of Escherichia coli strains [article]

Guilhem Royer, Jean-Winoc Decousser, Catherine Branger, Claudine Medigue, Erick Denamur, David Vallenet
2018 bioRxiv   pre-print
Plasmid prediction may be of great interest when studying bacteria such as Enterobacteriaceae. Indeed many resistance and virulence genes are located on such replicons and can have major impact in terms of pathogenicity and spreading capacities. Beyond strains outbreak, plasmids outbreaks have been reported especially for some extended-spectrum beta-lactamase or carbapenemase producing Enterobacteriaceae. Several tools are now available to explore the "plasmidome" from whole-genome sequence
more » ... , with many interesting and various approaches. However recent benchmarks have highlighted that none of them succeed to combine high sensitivity and specificity. With this in mind we developed PlaScope, a targeted approach to recover plasmidic sequences in Escherichia coli. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, it performs a classification of contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, Plasflow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes containing plasmids. Finally we tested our method on a dataset of E. coli strains exhibiting an elevated rate of extended-spectrum beta-lactamase coding gene chromosomal integration, and we were able to identify 20/21 of these events. Moreover virulence genes and operons predicted locations were also in agreement with the literature. Similar approaches could also be developed for other well-characterized bacteria such as Klebsiella pneumoniae.
doi:10.1101/334805 fatcat:z3ahq4pxjfhmppqing574ewsvy