Paul Joseph Planet

The paper reports an increase in USA300-SAE MRSA in Chile, links its spread to environmental copper resistance, and suggests copper exposure may enhance its fitness.

THRESHER calculates data-driven SNP thresholds for bacterial genomes to improve strain classification compared to fixed cutoffs.

This study shows that microbial succession during weaning is driven by the ability of microbes to metabolize host glycans, using a mouse model and genomic analysis.

This study identifies a novel subspecies of Enterococcus faecalis, subspecies B, through CRISPR2 screening, revealing its ecological and genomic distinctiveness from the more prevalent subspecies A.

This study shows that fumarate, regulated by host and pathogen, limits S. aureus growth by blocking metabolic pathways, while FumC enables adaptation through fumarate degradation and utilization.

This study investigates the prevalence and role of Staphylococcus aureus superantigens in CF lung disease, showing their ability to induce inflammatory responses in mouse models.

This study shows lactulose consumption selects for E. coli mutations that enhance its metabolic fitness and colonization, increasing infection risk in cirrhosis patients.

The paper compares gnotobiotic microbiomes to identify unique amino acid metabolism in the pre-weaning microbiome.

A defined consortium of early-life microbes shapes immune development and prevents type 1 diabetes.

The paper reconstructs the pre-epidemic evolution of the USA300 MRSA lineage using genomic data and identifies a third major clade and molecular markers for classification.

ARPA uses residue counts to perform fast, alignment-free pangenome analysis, identifying homologous gene clusters more efficiently than standard methods.

The paper develops GNUVID, a tool for SARS-CoV-2 genotype classification, and uses it to analyze viral diversity and transmission patterns across 16 US states.

The paper reports and compares B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania, identifying 7 clonal complexes and 3 distinct clades in the US.

This paper introduces GNUVID, a rapid whole genome sequence typing method for SARS-CoV-2 that identifies clonal groups and tracks spread waves across geographical locations.