New Manuscript: Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing
Congratulations to collaborators on the publication of "Rapid inference of antibiotic resistance and susceptibility by genomic neighbor typing" in Nature Microbiology! Here we present a new method for identifying resistant bacteria within minutes (<10 min), using real-time Nanopore sequencing and phenotypic inference from near phylogenetic neighbors. One step closer to point of care resistance diagnostics which will enable tailored therapies for individual patients! Check it out here: https://doi.org/10.1038/s41564-019-0656-6.
The lab is finally coming together, and I am so excited to get started with my incoming students this semester. I can not wait to see the paths we will take towards discovery, the unexpected challenges and creative solutions used to overcome these obstacles, and the team that we will build. Here's to the future, watch out gonococcus!
The ecological pressures that bacteria face can be hard to determine, however selection leaves clear signatures within the genome. In our recent preprint, spearheaded by Dr. Brian Arnold, we look at patterns of linkage to nominate the selective pressures faced by the recombining bacterial pathogen Neisseria gonorrhoeae. Clear signatures emerge, suggestive of a large role of adaptive interspecies admixture and/or balancing selection (perhaps due to the existence of distinct ecological niches or colonization sites) in shaping population level diversity in this species. Congratulations to all involved!
See our preprint here: https://www.biorxiv.org/content/10.1101/634147v1
Our study, lead by Dr. Genevieve M. Kozak, was recently published as a preprint on bioRxiv. Congratulations to all involved! This work highlights that the genetic basis of complex traits like seasonal timing and resultant ecological speciation, can be controlled by a relatively simple genetic basis. Here, we find that two genes involved in the circadian clock pathway underlie this trait in the European Corn Borer moth, a major agricultural pest of corn in North America and Europe. Ultimately, describing the genetic basis of seasonality may help us better predict the extinction or survival outcomes due to climate change for particular species, and also gain a better understanding of range expansions in insect systems.
See our preprint here: https://www.biorxiv.org/content/10.1101/633362v1
Our new preprint is now available on bioRxiv! This study highlights the promise of rapid phenotypic RNA-based tests for antimicrobial resistance, however also emphasizes the importance of controlling for population structure. Check it out here!
The making of a bad bug! Finally, after 5 days of selection and nursing these little guys along I am seeing a HUGE increase in resistance in my gonococcal cell lines (causal agent of gonorrhea). Though is may seem like a bad idea to evolve bacterial resistance to antibiotics in the lab, we are trying to understand how these bacteria gain resistance mutations. For example, can they gain resistance mutations alone and be totally fine and happy or do they need other mutations that are enabling or compensatory first. Ultimately, this may help us target new pathways for antibiotic development or in discovering bacterial populations that are more likely to evolve resistance to certain drugs than others which may impact prescription practices in certain areas.
I am very grateful to have been invited to RIT to talk about my work on antimicrobial resistance within the Neisseria! I was able to spend a few days learning about the School of Life Sciences, and the exciting research conducted by faculty and students in the department. Their innovative approaches to experiential hands-on learning in the classroom were awesome to learn about, and something that I would like to model in my own future teaching!