Mobile genetic elements define the non-random structure of the serovar Typhi pangenome.

Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens.

COPLA, a taxonomic classifier of plasmids.

Background: Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality.

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids.

Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members.

Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets.

Mobile Genetic Elements (MGE) play essential roles in adaptive bacterial evolution, facilitating genetic exchange for extrachromosomal DNA, especially antibiotic resistance genes and virulence factors. For this reason, high-throughput next-generation sequencing of bacteria is of great relevance, especially for clinical pathogenic bacteria. Accurate identification of MGE from whole-genome sequencing (WGS) datasets is one of the major challenges, still hindered by methodological limitations and high sequencing costs.

MOBscan: Automated Annotation of MOB Relaxases.

Relaxase-based plasmid classification has become popular in the past 10 years. Nevertheless, it is not obvious how to assign a query protein to a relaxase MOB family. Automated protein annotation is commonly used to classify them into families, gathering evolutionarily related proteins that likely perform the same function, while circumventing the problem of different naming conventions.

PLACNETw: a web-based tool for plasmid reconstruction from bacterial genomes.

Summary: PLACNET is a graph-based tool for reconstruction of plasmids from next generation sequence pair-end datasets. PLACNET graphs contain two types of nodes (assembled contigs and reference genomes) and two types of edges (scaffold links and homology to references). Manual pruning of the graphs is a necessary requirement in PLACNET, but this is difficult for users without solid bioinformatic background.

Determination of conjugation rates on solid surfaces.

A cytometric method for the estimation of end-point conjugation rates is developed and adapted to surface conjugation. This method improves the through-put of conjugation assays based on replica-plating and results in less noisy experimental data. Although conjugation on solid surfaces deviates from ideal conditions in which cells are continuously mixed, results show that, within the limits of high initial population densities and short mating times, end-point estimates of the conjugation rates are robust measurements.

Numbers on the edges: a simplified and scalable method for quantifying the gene regulation function.

The gene regulation function (GRF) provides an operational description of a promoter behavior as a function of the concentration of one of its transcriptional regulators. Behind this apparently trivial definition lies a central concept in biological control: the GRF provides the input/output relationship of each edge in a transcriptional network, independently from the molecular interactions involved. Here we discuss how existing methods allow direct measurement of the GRF, and how several trade-offs between scalability and accuracy have hindered its application to relatively large networks.

Dynamics of the IncW genetic backbone imply general trends in conjugative plasmid evolution.

Plasmids cannot be understood as mere tools for genetic exchange: they are themselves subject to the forces of evolution. Their genomic and phylogenetic features have been less studied in this respect. Focusing on the IncW incompatibility group, which includes the smallest known conjugative plasmids, we attempt to unveil some common trends in plasmid evolution.