David Smith

TL;DR: This study demonstrates how NASP compares with other tools in the analysis of two real bacterial genomics datasets and one simulated dataset and demonstrates differences in results based on the choice of the reference genome and choice of inferring phylogenies from concatenated SNPs or alignments including monomorphic positions.

TL;DR: SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations, and will provide insights into interventions aimed at suppressing minor DR sub Populations before they become clinically significant.

TL;DR: This analysis indicates that all 28 isolates associated with the outbreak had nearly identical genomes of 33.8 Mb, and observed significant genomic variability among strains unrelated to the outbreak, which may suggest the possibility of cryptic speciation in E. rostratum.

TL;DR: This study demonstrates how NASP compares to other tools in the analysis of two real bacterial genomics datasets and one simulated dataset and demonstrates differences in results based on the choice of the reference genome and choice of inferring phylogenies from concatenated SNPs or alignments including monomorphic positions.

TL;DR: In this article, the authors proposed a method of detecting a heteroresistant population of a pathogen in a sample, the method comprising: a) providing a sample comprising a population of the pathogen; b) extracting nucleic acids from the sample; c) amplifying a target locus of the genome of the organism in the extracted nucleic acid; d) consecutively sequencing both overlapping DNA strands from a single DNA molecule on a Next Generation Sequencing (NGS) platform; and f) performing an analysis of the aligned sequencing data to detect the at least one minor