Eva Top, Ph.D.

Summary: The rapid spread of antibiotic resistance into bacterial pathogens is a severe problem in human health care because it restricts our ability to effectively treat life-threatening infections. The transfer of multiple antibiotic resistance genes in a single step by means of plasmids is one of the major causes of this antibiotic resistance crisis. We urgently need novel therapies that limit the spread of new resistance genes by plasmids. Unfortunately, little is known about how well plasmids persist in different bacterial strains in the absence of any antibiotics, and how that plasmid persistence can change over time due to plasmid-host coevolution. Experimental studies on plasmid-host coevolution can provide insights into the specific genetic interactions between plasmids and their bacteria that result in improved retention of antibiotic resistance plasmids in human pathogens. The aim of one project is to determine the molecular mechanisms by which the bacteria adapt to novel plasmids and thereby better retain antibiotic resistance. In a second project we study the spread of multi-drug resistance (MDR) plasmids from manure to soil bacteria. MDR pathogens emerge in part by acquiring resistance genes on plasmids from bacteria in farm or feedlot animals. However, we still poorly understand the trajectories of resistance plasmids from farms to human pathogens. Fertilization with manure is thought to spread antimicrobial resistance in soil, but evidence is limited. Our long-term goal is to determine if spreading manure on agricultural soils promotes the establishment of resistance plasmids in the soil microbiome.

Minimum Classes: A basic biology or microbiology class (like BIOL 115 or BIOL 154 or BIOL 250)

Projects:

In project 1 we will test how often bacterial adaptation to one MDR plasmid leads to improved retention of other MDR plasmids, and determine the molecular mechanisms of adaptation. This will be done by experimentally evolving a set of bacteria/plasmid pairs in the presence of antibiotic selection for one plasmid. These will include critical pathogens as recently defined by the World Health Organization. We will test if adaptation to one plasmid pre-adapts bacteria, allowing for improved persistence of other plasmids. We will also identify the mutations resulting in increased plasmid persistence by whole genome sequencing of evolved clones, and reconstruct some of these mutations in the ancestor to confirm their role.

In project 2 we will first determine and improve the limits of a modified version of the molecular DNA sequence-based method ‘Hi-C’ to detect horizontal transfer of antibiotic resistance plasmids in agricultural soils. Hi-C physically links plasmid DNA with the chromosomal DNA of its bacterial host. Thus without any cultivation methods, this technique will help us determine if an introduced MDR plasmid has spread to soil bacteria, to what extent, and to which range of bacteria. We will then also determine the effect of manure treatment on the spread of that plasmid in the rhizosphere, using this novel method. There is grant funding for both of these projects.