Ahmed M. Moustafa

Multi-lineage emergence of USA300 MRSA in in Chile and a potential role for environmental copper resistance

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: A tool for evidence-based, phylogeny-corrected SNP thresholds for whole genome molecular epidemiology

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

Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma

This study identifies microbiome-derived protein biomarkers for predicting immunotherapy response and toxicity in melanoma without relying on taxonomic classification.

Carbohydrate consumption drives adaptive mutations in Escherichia coli associated with increased risk for systemic infection

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

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

Pre-epidemic evolution of the USA300 clade and a molecular key for classification

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.

Efficient Pangenome Construction through Alignment-Free Residue Pangenome Analysis (ARPA)

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

Emerging SARS-CoV-2 diversity revealed by rapid whole genome sequence typing.

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.

Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania

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.

Rapid whole genome sequence typing reveals multiple waves of SARS-CoV-2 spread

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.