DR. YOUSIF SHAMOO
There is an urgent need for new antibiotics as well as strategies to combat resistance, particularly in hospital settings where drugs of last resort like daptomycin (DAP) are becoming ineffective. A critical step in the development of such strategies lies in understanding the evolutionary trajectories responsible for resistance and the identification of proteins or biochemical pathways that can be good targets for the design of novel treatment strategies and co-drugs. To this end, the lab uses a combinatorial approach that involves experimental evolution, genomics, biophysical and biochemical techniques to delineate the molecular basis of antimicrobial resistance. This holistic approach enables the deconstruction of complex mechanisms leading to resistance.
One of the focuses in the lab is to understand the basis for daptomycin resistance in enterococci which are a type of ESKAPE pathogen that cause over 66,000 infections per year in the United States. Experimental evolution of Enterococcus faecalis to DAP led to the identification of mutations in the LiaFSR 3-component system and the discovery of a novel downstream target, LiaX whose upregulation was required for resistance. Physico-chemical studies led to the determination of the crystal structure of LiaR that regulates transcription in response to daptomycin mediated membrane stress. Biochemical studies with mutants helped determine the role of specific LiaR mutations in conferring DAP resistance. Both these proteins serve as putative targets for drug discovery.
Other organisms of interest to the lab include E. faecium, Acinetobacter baumannii, Pseudomonas aeruginosa, Nocardia and Francisella.
In addition to determining the molecular mechanisms leading to resistance, the lab is also interested in studying microbial interactions. With the help of microfluidic techniques to create spatially segregated emulsion systems, we wish to understand bacterial interactions and the evolutionary processes that lead to such relations.
Shamoo Lab News
New publication!! Congratulations to Saoirse on her new publication using microfluidics to study the evolutionary trajectories of Pseudomonas aeruginosa in microaerobic environments. Link.
New publication!! Congratulations to Dr. Xinhao Song on his new publication, which introduces a non-optical detection method utilizing methyl halide gases for the quantification of filamentous bacteria in microdroplets! Link.
Congratulations to graduate student Adeline Supandy for successfully defending her PhD thesis!
Congratulations to graduate student Xinhao Song for successfully defending his PhD thesis!
New publication!! Congratulations to Dr. Ramya Ganiga Prabhakar for her paper in establishing parameters for enrichment of rare bacterial subpopulations in microdroplets! Link.
New publication!! Congratulations to Dr. Heer Mehta for her paper in investigating Francisella tularensis subsp. holarctica antibiotic resistance in macrophages! Link.
New publication!! Congratulations to graduate student Yue Zhou for her paper in characterizing Enolpyruvate transferase MurAAA149ELink.
Congratulations to Dr. Heer Mehta to her new position at Cemvita!
IBB Best Poster Award Congratulations to Lauren LeDay for winning Best Poster at the IBB summer research event! Link.
New publication!! Congratulations to graduate student Adeline Supandy for her paper identifying the mechanisms of resistance in Enterococcus faecium to daptomycin and fosfomycin Link.
New publication in collaboration with Craig Miller and Chris Marx from UIdaho! Mutational Switch-Backs Can Accelerate Evolution of Francisella to a Combination of Ciprofloxacin and Doxycycline. Link
New publication!! Congratulations to Post-doc Seokju Seo and the entire microfluidics team for the new Star Protocols paper.
New paper out! Congratulations to everyone involved in establishing the microfluidics platform for conducting experimental evolution in our lab. Check out the first of many papers on this topic here.
Congratulations to Ramya for a successful thesis defense!
New publication in collaboration with Chris Marx at University of Idaho! EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde
Dr. Yousif Shamoo in his own words https://magazine.rice.edu/2021/05/the-experimentalist/
Post-doc position open in Shamoo Lab https://jobs.rice.edu/postings/25590
New publication: Daptomycin resistance in Enterococcus faecium can be delayed by disruption of the LiaFSR stress response pathway. DOI: 10.1128/AAC.01317-20
Check out Dr. Shamoo's podcast on "Hold These Truths with Dan Crenshaw" about Innovating the Future: The Next Frontiers In Clean Energy, Vaccines and Agriculture!!
Check out our latest PLoS Pathogens review article on pathogenic Nocardia - https://doi.org/10.1371/journal.ppat.1008280
Shamoo Lab on EurekAlert!
New publication: Environment Shapes the Accessible Daptomycin Resistance Mechanisms in Enterococcus faecium. DOI: 10.1128/AAC.00790-19
Congratulations to graduate student Amy Prater for successfully defending her PhD thesis!
Congratulations to postdoc Zaigao Tan for getting a faculty position at Shanghai Jiao Tong University