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Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology. Expand
Evolutionary Dynamics of Vibrio cholerae O1 following a Single-Source Introduction to Haiti
Intensive mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT), and no evidence that environmental strains have played a role in the evolution of the outbreak strain. Expand
Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation.
Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data. Expand
Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids
A novel genome sequencing strategy is presented, useful when evolutionary diversity is the question of interest, and the unique structure of Lake Malawi cichlid genomes should facilitate conceptually new experiments, employing SNPs to identity genotype-phenotype association, using the entire species flock as a mapping panel. Expand
A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens
Lyve-SET, a high-quality SNP pipeline, which was developed and evaluated by retrospectively investigating 12 outbreak data sets along with four other SNP pipelines that have been used in outbreak investigation or similar scenarios and demonstrated the concordance between Lyve- SET SNP typing and wgMLST. Expand
Mashtree: a rapid comparison of whole genome sequence files
Comparing the multitudes of genomes for phylogenetic relatedness is computationally expensive and laborious and there are many strategies to reduce the complexity of the data for downstream analysis, especially using nucleotide stretches of length k (kmers). Expand
Novel Epidemic Clones of Listeria monocytogenes, United States, 2011
We identified a novel serotype 1/2a outbreak strain and 2 novel epidemic clones of Listeria monocytogenes while investigating a foodborne outbreak of listeriosis associated with consumption ofExpand
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
SNVPhyl can detect SNVs with high sensitivity and specificity, and identify and remove regions of high SNV density (indicative of recombination) and is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds or in the presence of contamination. Expand
Haemophilus haemolyticus Isolates Causing Clinical Disease
This study suggests that a testing scheme that includes reliable PCR assays and standard microbiological methods should be used in order to improve H. haemolyticus identification. Expand
Genome Sequences for Five Strains of the Emerging Pathogen Haemophilus haemolyticus
Preliminary analyses indicate that these genome sequences encode markers that distinguish H. haemolyticus from its closest Haemophilus relatives and provide clues to the identity of its virulence factors. Expand