Cross-resistance and collateral sensitivity between human-targeted drugs and antibiotics in gut microbes

We are currently living in an era of an antibiotic crisis, where very few novel classes of antibiotics (Abx) are being developed. On top of that, the rate of antibiotic resistance evolution is alarmingly faster than the discovery of the novel Abx, which is estimated to lead to 10 million deaths per year by 2050. In addition, cross-resistance (CR), the evolution of resistance to one drug that gives resistance to another, between drugs makes it even more challenging to treat patients. Interestingly, the evolution of resistance to one drug can also increase sensitivity to another drug, which is termed collateral sensitivity (CS). Therefore, I strive to uncover the mechanisms underlying the interactions between CR & CS between drugs, which may hold the key to mitigating the current antibiotic crisis. My PhD project has three main aims, namely (1) to investigate CR&CS interactions between drugs in human gut microbes by doing resistance evolution in the lab, (2) to develop a fast and large-scale CR&CS interaction measurement method, and (3) to screen more bacterial libraries and drugs that can be used by aim 2. Aim 1. Usage of Abx themselves are not the only factor leading to the emergence of resistant pathogens. A study by the Typas lab showed that non-antibiotic, i.e., human-targeted drugs (HTDs), which are consumed more often and for longer periods by patients, have strong antimicrobial effects on human gut microbes. The main goal of my project is to use experimental evolution of single gut microbiota species to assess the effect of resistance developed against HTDs on ABR. In collaboration with Camille Goemans, a PostDoc in the lab, we have evolved five abundant and commensal species of the human gut microbiome in the presence of ten widely used HTDs. Using changes in resistance of evolved lineages versus wild types towards 12 diverse Abx, we have built the first CR&CS interaction network between HTDs and Abx. Next, we aim to perform HTD resistance evolution in microbial communities to investigate changes in the community upon treatment with Abx, uncover mechanisms of these interactions and search for antidotes to mitigate the effect of HTDs. Aim 2. Traditionally, CR&CS interactions are identified by performing resistance evolution experiments, which are time-consuming, limited to few drugs due to poor scalability and do not hint at possible resistance elements without sequencing. To overcome the limitations of this method, I aim to develop a fast, high-throughput, and gene-based computational method that measures CR&CS interactions between drugs using chemical genetics. Chemical genetics is genetic profiling of how mutants (with one gene deleted or over-expressed) behave under stresses (Abx or HTDs). Thus, contribution of each gene to resistance/sensitivity to given chemical can be tested, which could provide a hint at the possible mechanisms. Aim 3. Using high-throughput screening techniques and libraries of other bacteria being developed/available in the lab, I aim to perform chemical genetics screens and to predict CR&CS interactions between/within HTDs and Abx in multiple species. This will result in a large-scale network of CR&CS interactions between drugs in species of the human gut microbiome. To sum up, I am employing an interdisciplinary approach consisting of high-throughput laboratory screens, evolution experiments, and computational methods that can significantly speed up understanding of CR&CS interactions and potentially point us in the right direction to resolving the antibiotic crisis.