$462K NIH Grant to Study Antibiotic Resistance in Bacteria

Robert Smith, Ph.D. is an Associate Professor in the Halmos College of Arts & Sciences (HCAS) at NSU, where he leads the Microbial Cooperation Lab. He was recently funded by the National Institutes of Health (NIH) with a $462K grant to investigate a mechanism by which bacteria resist antibiotics. Specifically, he will investigate the question “Does growth efficiency determine the inoculum effect?”, the title of his funded project.

  

Tell me about your recent grant-funded project.

There’s a mechanism by which bacteria resist antibiotics called the “inoculum effect,” which is just one of the many ways antibiotic resistance occurs. This effect has been observed for just about every antibiotic and bacterial species, and we have known about the general effect since the 1950s/1960s. However, we have never been able to describe the mechanism that accounts for it across all antibiotics.

A couple years ago a group of students and myself came up with a hypothesis about this mechanism. We found that interactions between bacterial growth rate and bacterial metabolism can account for the inoculum effect across different classes of antibiotics.

This preliminary work formed the basis for this R15 grant from NIH, in which I aim to explore the inoculum effect in opportunistic pathogens. These are pathogens that infect individuals who are immunocompromised or who have primary infections. I will investigate and seek to provide a mechanistic explanation at the molecular level for how growth rate and metabolism interact to produce this antibiotic resistance effect.

This type of antibiotic resistance diverges from classic ways that bacteria resist drugs, which typically occurs when bacteria change some aspect of their genetics to counteract the antibiotic’s effect. However, in the case of the inoculum effect, no change in the genetics of the bacteria is needed; the group of bacteria cooperate as a group to resist the antibiotic.

In the long term, I seek to design adjuvants to administer alongside antibiotics that would minimize or eliminate the inoculum effect. These might be small molecules that we have to develop, or small molecules that can be repurposed, which in either case would manipulate the metabolism or growth rate of the bacteria so they cannot resist the antibiotic through cooperation (i.e., the inoculum effect).

 

Who is working with you on this project?

Students have done a lot of work on this project and are critical to the process of my research. This large project, in particular, has been spearheaded by two students: Gabriela Diaz Tang and Estefania Marin (below). These students started in my lab as undergraduate students, and now have joined as graduate students pursuing a Master’s of Biological Sciences. Gabriela is going to be looking at interactions between growth efficiency and metabolism in the opportunistic pathogen Pseudomonas aeruginosa, and Estefania will investigate this same interaction in another pathogen, Staphylococcus aureus. As a result of their work, we will be able to see if the same principle applies in both pathogens.

 

 

Dr. Allison Lopatkin at Barnard College of Columbia University is a collaborator and subaward on this grant. She will be helping me with the computational parts to complement the experimental parts I am conducting.

 

How did you form this beneficial partnership?

Dr. Lopatkin was a PhD student in the lab where I did my postdoc, at Duke University. She picked up one line of research that I started as a postdoc but left behind when I joined NSU.

I realized after working with her that we had similar values and work pace. We wrote three R15s together and tried to get funding from the US Department of Defense, but this is the first project we have been externally-funded to work on together, which is exciting for our collaboration.

 

How does this project connect with your other work at NSU?

The grand scheme of my lab is to understand bacterial cooperation. Another project I am working on, which is funded by the US Army, aims to disrupt cooperation by changing the spatial positioning of cells in an environment. This project is based on the fact that bacteria like to communicate with each other using small molecules. Their location in the environment determines how much of that small molecule they sense. So, if we alter the location of bacteria, we can break up their communication and reduce how infective they are.

This Army-funded project made us realize that changing the spatial positioning of bacteria influenced their metabolism, which inspired the newly-funded NIH project’s focus on metabolism.

 

What advice do you have for other grant seekers at NSU?

You have to put your head down, do the work, and not give up. I have been rejected many more times than I have been accepted and, in fact, this funded R15 was a resubmission. When you get rejected, go through the reviewer comments and find ways to learn and improve. After my original submission and rejection of this grant, I went through the reviewer comments and tried to interpret where those comments came from. I always try to figure out if any part of the grant is unclear, which may diminish reviewer excitement and care while reading my proposal, leading to out-of-scope suggestions, disagreements, or misunderstandings.

Another part of my process is how I generate grant proposal ideas. Typically, I come up with several project ideas, write them up on a whiteboard in my office, and sit on them. I wait for a good grant opportunity to come up, monitoring funder listserv emails and “Funding Alert” emails from Grant Lab, and if an interesting opportunity comes up I see how I can fit or reframe my generated ideas for the call.

Finally, building relationships with Program Officers is important. After a recent rejected proposal I contacted the Program Officer and she helped me understand what the discussion of my proposal was like during the panel review. Also, I recently pitched several ideas to a Program Officer, and she picked them apart, telling me which Aims she thought were too ambitious. This has helped me retool how and what I plan to pitch.

 

What is the next grant proposal or project on your agenda?

In the new R15 grant we are avoiding bacteria that have developed other ways to resist antibiotics, such as through genetic changes, selecting just for those that do not have resistance markers. For an upcoming NIH diversity supplement proposal, I plan to submit a project to explore growth metabolism for bacteria that already have another antibiotic resistance mechanism.

If this NIH project works out, my next step is to test this in mouse models and down the line in the clinic, with the overarching goal to save people’s lives.