R. D. Kouyos

Assessing the role of bacterial innate and adaptive immunity as barriers to conjugative plasmids

This study models how bacterial innate and adaptive immunity affect plasmid spread, finding that immunity suppresses costly plasmids but not beneficial ones.

Mycobacterium tuberculosis infection associated immune perturbations correlate with antiretroviral immunity

The paper shows MTB infection in HIV-positive individuals correlates with immune system shifts and reduced HIV-1 viral load.

Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization

This paper evaluates probiotic and antibiotic treatments for nasal Staphylococcus aureus decolonization using computational modeling and in vitro experiments, finding probiotics outperform antibiotics in decolonization and recolonization robustness.

Quantification of within patient Staphylococcus aureus phenotypic heterogeneity as a proxy for presence of persisters across clinical presentations

This study quantifies phenotypic heterogeneity in Staphylococcus aureus from patient samples to assess persisters, finding that rifampicin treatment correlates with increased growth delays.

Genomic surveillance of vancomycin-resistant Enterococcus faecium reveals spread of a linear plasmid conferring a nutrient utilization advantage

This study identifies a linear plasmid in vancomycin-resistant Enterococcus faecium that confers a nutrient utilization advantage, contributing to its spread in a hospital setting.

Quantifying variation in bacterial reproductive fitness with and without antimicrobial resistance: a high-throughput method

This paper introduces baQFA, a low-cost high-throughput method to quantify bacterial reproductive fitness with and without antimicrobial resistance using time-lapse imaging and Gompertz modeling.

Development of a high-throughput bead based assay system to measure HIV-1 specific immune signatures in clinical samples

This paper develops a high-throughput bead-based assay to measure HIV-1 specific immune signatures in clinical samples, demonstrating improved antigen reactivity and reproducibility.