Mechanisms and applications of bacterial viruses (phages) and the immune systems targeted against them

Research in the Hatoum-Aslan lab seeks to gain a mechanistic understanding of the perpetual microscopic war that has been raging for billions of years between bacteria and the viruses that infect them. Bacterial viruses, also known as phages, attach to a specific host, inject their DNA, and replicate exponentially in a process that typically kills the host. In response, bacteria have evolved a myriad of complex immune systems to fend off invading phages. Our research uses the tools of molecular biology, genetic engineering, and biochemistry to probe and understand the defensive and offensive molecular mechanisms that bacteria and phages use against each other. A second research focus seeks to leverage the antimicrobial properties of phages and genetically engineer them for use in novel therapeutics that will help addresses the global health care crisis incited by the rise in antibiotic-resistant infections. We are also interested in exploring novel genome editing technologies and other potential applications for bacterial immune systems such as CRISPR-Cas.

Investigating mechanisms of CRISPR-Cas immunity in staphylococci

CRISPR-Cas systems are a class of prokaryotic immune systems that use small CRISPR RNAs (crRNAs) and CRISPR-associated (Cas) proteins to detect and destroy mobile genetic elements such as plasmids and invading phages. CRISPR-Cas systems are remarkably diverse, with two broad classes and six distinct Types currently described. Type III systems are among the most widespread in nature, and likely the most complex. We study a model Type III CRISPR-Cas system found in Staphylococcus species, also known as CRISPR-Cas10. Several ongoing projects in the lab carry out pioneering research on CRISPR-Cas10 to understand the complex ways in which it is regulated in the cell, and the extent to which it interacts with and impacts cellular processes previously considered unrelated to immunity (Walker et al, 2017; Chou-Zheng and Hatoum-Aslan, 2019).

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Engineering phage-based diagnostics and antimicrobials

The spread of antibiotic resistance in pathogenic bacteria, coupled with the sharp decline in the discovery of new antibiotics, are together responsible for inciting a global public health crisis. Drug-resistant staphylococci are leading causes of healthcare-associated infections, and virulent phages, which kill staphylococci within minutes of infection, represent viable alternatives or supplements to conventional antibiotics. However, phage genomes are replete with genes of undetermined functions which can cause harmful downstream side-effects. Our work aims to help stem regulatory and safety concerns over the routine use of phages in humans. To achieve this, we developed a platform for the genetic engineering of virulent phages using CRISPR-Cas10 (Bari et al, 2017). Ongoing work seeks to engineer phages with well-defined components that can potentially be used as diagnostic tools and alternatives to antibiotics for the treatment of drug-resistant infections.

Discovering and characterizing new phages and anti-phage immune systems

Phages are considered the most abundant entities on the planet, with an estimated 10³¹ particles in the biosphere; However, a detailed understanding of their diversity and lifestyles remains in its infancy. Ongoing projects in the lab and in Dr. Hatoum-Aslan’s Research Experience in Microbiology course seek to discover and characterize new phages that infect pathogenic Staphylococcus and Streptococcus species. Dozens of phages have already been discovered (see Cater et al, 2017, for an example), and the continual expansion of our phage collection is paramount to understanding not only phage diversity, but also the diverse immune systems targeted against them. As an example, using our unique collection of S. epidermidis phages, we have uncovered a new immune system unlike any other described to date (Bari et al, 2022). Ongoing work continues to discover and characterize new phages and new defense systems, particularly in bacterial pathogens.

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Stimulating interest in science through education and outreach

Our group has also been engaged in synergistic educational activities that provide research experiences and active learning opportunities for undergraduates and underrepresented groups in STEM disciplines, with a goal to inspire the next generation of scientists to enter into STEM careers. Such activities include developing and implementing a semester-long research-based lab course for undergraduates called MCB 493-REM Research Experience in Microbiology, and a five-day educational module/kit titled Exploring the CRISPR-Cas defense system for high school students. Thus far, MCB 493-REM and its predecessor offered at the University of Alabama (called Phage Discovery) has provided 95 undergraduates with authentic research experiences while discovering dozens of new phages, many of which have formed the basis for ongoing research projects in the lab. In addition, the educational kit has been piloted in five high schools in diverse communities in Alabama and is currently being offered nationwide through Carolina Biological Supply Company (https://tinyurl.com/4nr7vdnu).