Plasmid Diversity and Adaptation Analyzed by Massive Sequencing of Escherichia coli Plasmids

Abstract

Whole-genome sequencing is revolutionizing the analysis of bacterial genomes. It leads to a massive increase in the amount of available data to be analyzed. Bacterial genomes are usually composed of one main chromosome and a number of accessory chromosomes, called plasmids. A recently developed methodology called PLACNET (for plasmid constellation networks) allows the reconstruction of the plasmids of a given genome. Thus, it opens an avenue for plasmidome analysis on a global scale. This work reviews our knowledge of the genetic determinants for plasmid propagation (conjugation and related functions), their diversity, and their prevalence in the variety of plasmids found by whole-genome sequencing. It focuses on the results obtained from a collection of 255 Escherichia coli plasmids reconstructed by PLACNET. The plasmids found in E. coli represent a nonaleatory subset of the plasmids found in proteobacteria. Potential reasons for the prevalence of some specific plasmid groups will be discussed and, more importantly, additional questions will be posed.

Plasmid Detection, Characterization, and Ecology

“…To date the initial plasmid typing is done by PCR with primers targeting either plasmid replication [10,13,55] or transfer regions [56]. More details on the relaxase-based typing are given in the chapter by de Toro et al [57] (this book). Plasmid multilocus sequencing typing is used for few plasmid families within the Enterobacteriaceae , e.g.…”

“…As described in the chapter by de Toro et al [57] in this book, more and more plasmids are discovered and assembled from whole genome sequences of isolates. The assembly of plasmid replicons is particularly challenging due to the short read length of Illumina sequences and the high abundance of IS, IS CR , transposons, and truncated sequences due to multiple insertion processes.…”

“…Publically available web-based tools are indeed urgently needed to manage the enormous plasmid-related sequence data sets. A few recently mentioned tools in addition to PLACNET introduced in the chapter by de Torro et al [57] (this book) are Seqfindr and plasmid barcodes which were recently used for rapid plasmid profiling and comparison of plasmids encoding CTX-M-15 beta-lactamase genes from globally disseminated E. coli ST131 strains.…”

Bacterial evolution: Resistance is a numbers game

“…This opens up the question of what conditions favour the maintena Along with other drivers of rapid phenotypic change, such as contingency loci and increased mutation rate, it is possible that multicopy plasmids form part of a toolkit employed by bacteria to deal with rapidly changing environmental challenges 7 . Importantly, these results may also explain the rapid evolution and dissemination of antibiotic resistance in bacterial populations, as ColE1 plasmids of the type used in this study are widespread and often carry relevant phenotypic traits such as antibiotic resistance 8 , and bla TEM-1 is highly adaptable with >170 known variants and many different antibiotic resistance phenotypes 9 . Plasmids can appear deceptively simple, consisting sometimes of just a few kilobases and carrying only a handful of genes.…”

<i>Escherichia coli</i> as a Model Organism and Its Application in Biotechnology

“…Recently, novel tools for plasmid mining have been developed and uncover from Next Generation Sequencing data that plasmids can be uncovered and analyzed for further characterization [53,54].…”