Our research focuses on horizontal gene transfer (HGT) in complex microbial communities. We analyze which bacteria, when, and by what mechanism exchange genetic material in their native environments. Increasing levels of antibiotic resistance in human bacterial pathogens represent one of the most pressing medical challenges of our time. HGT plays a critical role in spreading of antibiotic resistance genes in bacteria. Currently no solution exists to reverse the antibiotic resistance or prevent it from further spreading via HGT apart from the conservative approach of antibiotics stewardship, that has so far showed limited success in eliminating the resistant strains. Therefore, we study mechanisms of HGT and its regulation in human pathogenic and commensal bacteria with a far-reaching goal of countering antibiotic resistance spread by modulating DNA exchange.

Clinical urinary pathogens with multidrug resistance genes

One of the projects within this direction is analysis of carbapenem resistance in Eneterobacteriaceae. Carbapenem-resistant infections are on the rise in hospital environments in the U.S. and considered an urgent threat in the most recent report by the Centers for Disease Control and Prevention (CDC). Recent clinical isolates with carbapenem resistance were sequenced to recover their complete genomes. Preliminary search identified predominant bacterial species, carbapenem resistance genes and their association with multiple extrachromosomal elements - plasmids. In silico analysis predicts that carbapenem resistance genes are frequently reside on plasmids capable for transfer among bacteria.

Interaction of uropathogens with commensal bacteria from human bladder

It has recently become evident that human urinary tract contains a diverse set of microorganisms - urinary microbiome. This microbiome appears to correlate with several urological conditions. We analyze urinary microbiome and have collected a library of urinary commensal bacteria to analyze their genotype and phenotype. We are in particular interested in understanding how urinary commensals interact with uropathogens and whether these microbial interaction can be used in diagnostics or treatment of recurrent and multidrug-resistant urinary tract infections.

Regulation of plasmid conjugation in E. coli

Identifying roles of DNA uptake in microbial communities