V. S. Cooper

Harnessing the diversity of Burkholderia spp. prophages for therapeutic potential

The paper identifies prophages in Burkholderia spp. genomes that show lytic activity against conspecific and heterospecific isolates, suggesting their potential for phage therapy.

Evolution of genotypic and phenotypic diversity in multispecies biofilms

This study shows how interspecies interactions in biofilms drive phenotypic diversity in Bacillus thuringiensis, with mutations in spo0A affecting matrix production and coexistence with Pseudomonas species.

Inoviridae prophage and host dynamics during diversification, succession and Atlantic invasion of Pacific-native Vibrio parahaemolyticus.

This study investigates how Inoviridae prophages and host dynamics contributed to the diversification, succession, and Atlantic invasion of Vibrio parahaemolyticus lineage ST36.

Adaptation to overflow metabolism by mutations that impair tRNA modification in experimentally evolved bacteria

The paper shows that mutations in tilS, which impair tRNA modification, enhance bacterial growth under oxidative overflow metabolism by reducing lag phase duration.

Novel Requirement for Staphylococcal Cell Wall-Anchored Protein SasD in Pulmonary Infection

This study identifies SasD, a cell wall-anchored protein in S. aureus, as a novel virulence factor that influences inflammatory signaling and outcomes in pulmonary infections, particularly in the context of super-infection with influenza.

Genomic diversity of hospital-acquired infections revealed through prospective whole genome sequencing-based surveillance

This study uses whole-genome sequencing to analyze 3,004 bacterial isolates from hospitalized patients, revealing genomic diversity and evolutionary rates across 97 species and informing outbreak detection.

Carbapenem-Resistant Acinetobacter baumannii in US hospitals: diversification of circulating lineages and antimicrobial resistance

This study analyzes CRAb isolates from US hospitals using WGS, identifying new sub-lineages and resistance patterns, highlighting shifts in CRAb population structure and clinical impact.

The nutritional environment is sufficient to select coexisting biofilm and quorum-sensing mutants of Pseudomonas aeruginosa

This study shows that nutrient conditions and biofilm selection alone can drive the evolution of Pseudomonas aeruginosa mutants with clinical phenotypes like increased biofilm and altered quorum sensing.

Excess dietary sugar impairs colonic epithelial regeneration in response to damage.

This study shows that high sugar diets impair colonic epithelial regeneration by altering metabolic pathways in intestinal stem cells.

Evolutionary divergence of the Wsp signal transduction system in β- and γ-proteobacteria

This study shows the Wsp system is conserved across β- and γ-proteobacteria, with functional differences in Burkholderia cenocepacia compared to Pseudomonas species.

Immunosuppression broadens evolutionary pathways to treatment failure during Acinetobacter baumannii pneumonia

This study shows that immunosuppression promotes antibiotic resistance evolution in Acinetobacter baumannii pneumonia by enabling persistence mutations that cause treatment failure without clinical resistance.

Rampant prophage movement among transient competitors drives rapid adaptation during infection

The paper shows prophage-mediated active lysogeny drives rapid, parallel adaptations in bacterial infections by disrupting global regulator genes, increasing cyclic-di-GMP and biofilm production.

Polygenic adaptation, clonal interference, and the evolution of mutators in experimental Pseudomonas aeruginosa populations

This paper shows that Pseudomonas aeruginosa populations evolve extensive genetic diversity and clonal interference in biofilm-promoting environments, with mutator genotypes contributing to persistent variation.

Experimental evolution to identify undescribed mechanisms of resistance to a novel cationic peptide antibiotic

This study uses experimental evolution and whole genome sequencing to identify genetic mechanisms of resistance to the cationic peptide antibiotic WLBU2 in Pseudomonas aeruginosa.

Evolution and adaptation of Pseudomonas aeruginosa in the paranasal sinuses of people with cystic fibrosis

This study identifies three evolutionary genetic routes of Pseudomonas aeruginosa adaptation in the sinuses of people with cystic fibrosis, suggesting sinuses may be an early site of pathoadaptation before lung infections.

One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity

This study identifies parallel mutations in the rpfR gene of Burkholderia cenocepacia that enable distinct ecological strategies by regulating signaling networks and biofilm formation.

Genomic and chemical diversity of Bacillus subtilis secondary metabolites against plant pathogenic fungi

This study examines the genomic and chemical diversity of secondary metabolites in Bacillus subtilis strains to understand their biocontrol properties against plant pathogenic fungi.

The roles of history, chance, and natural selection in the evolution of antibiotic resistance

This study quantifies how history, chance, and selection influence the evolution of antibiotic resistance in Acinetobacter baumannii through controlled experiments.

Quorum sensing provides a molecular mechanism for evolution to tune and maintain investment in cooperation

The paper shows that quorum sensing (QS) in Vibrio harveyi maintains cooperation by preventing defectors from outcompeting cooperators over evolutionary timescales.

Quantitative mapping of mRNA 3' ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3' end formation in response to azithromycin

This study uses 3pMap to analyze mRNA 3' ends in Pseudomonas aeruginosa under azithromycin treatment, revealing premature 3' end formation as a key response mechanism.

Genotypic diversity between surgical and nasal Staphylococcus aureus isolates

The paper compares genotypic diversity between nasal and surgical Staphylococcus aureus isolates, finding greater diversity in PJI isolates and associations with immune status and virulence.

SARS-CoV-2 genome evolution exposes early human adaptations

This study analyzes SARS-CoV-2 genome evolution during the pandemic to identify adaptive mutations and purifying selection patterns.

Host adaptations in the fixLJ pathway of the Burkholderia cepacia complex increase virulence

This study shows that evolved variants of the fixLJ pathway in BCC species enhance virulence in host models but reduce survival in soil.

Comprehensive analysis of horizontal gene transfer among multidrug-resistant bacterial pathogens in a single hospital

This study tracks horizontal gene transfer of mobile genetic elements in a hospital setting using genomic analysis of 2,173 bacterial isolates.

Experimental Evolution in vivo to Identify Selective Pressures During Pneumococcal Colonization

This study uses experimental evolution in mice to identify genetic adaptations of Streptococcus pneumoniae during nasal colonization and reveals fitness trade-offs in different host niches.

Parallel evolution of tobramycin resistance across species and environments

This study identifies parallel mutations in fusA1 and ptsP across two bacterial species under tobramycin selection, showing predictable resistance mechanisms despite environmental and genetic differences.

Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

This study shows that negative frequency-dependent selection maintains coexisting genotypes in fluctuating environments by balancing mutations in biofilm and planktonic growth regulators.

Altered Nucleoprotein Binding to Influenza Virus RNA Impacts Packaging Efficiency and Replication

This study shows that changes in one influenza virus RNA segment's nucleotide sequence can alter NP binding across the entire genome, impacting replication efficiency.

Mutations that improve the efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome

The paper shows that mutations improving a weak-link enzyme's efficiency are rare compared to other adaptive mutations in the genome during bacterial evolution.

Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

This study shows that biofilm lifestyle in Acinetobacter baumannii leads to different genetic pathways and fitness trade-offs in antibiotic resistance evolution compared to planktonic growth.