Project Summary
Staphylococci are ubiquitous bacterial residents of human skin and major causes of antibiotic-resistant
infections. Of the ~40 skin-associated species, S. aureus and S. epidermidis have the greatest pathogenic
potential: S. aureus is the leading cause of skin and soft tissue infections and S. epidermidis is the most common
cause of infections associated with indwelling medical devices. Compounding the problem, S. epidermidis strains
harbor a reservoir of genes that enhance fitness/virulence (e.g. genes that encode toxins and antibiotic
resistance) which can be horizontally transferred to S. aureus. In light of these facts, a thorough understanding
of the mechanisms that regulate horizontal gene transfer between these species would be an invaluable asset
in neutralizing or stemming the flow of these factors at the source. In this context, staphylococcal phages (i.e.
viruses) and the immune systems targeted against them have profound impacts on staphylococcal survival and
pathogenesis. For instance, lysogenic phages can enhance pathogenic potential by transferring pathogenicity
islands from one strain to another and carrying virulence factors that integrate along with the phage genome into
the host. In contrast, strictly lytic phages can kill the bacterial host within minutes and are being used as
alternative therapeutics to combat antibiotic-resistant infections. Bacterial immune systems target lytic and
lysogenic phages alike, and can therefore counter these opposing effects. As it stands, we are only just beginning
to understand these dynamics and identify the specific immune systems that staphylococci employ, and
alarmingly, almost nothing is known about how these systems are horizontally spread. These knowledge gaps
continue to undermine our ability to implement effective therapeutics and improve overall healthcare outcomes.
The long-term objective of this R01 project is to gain a comprehensive understanding of the anti-phage immune
systems in staphylococci and the pathways by which they spread. Towards this goal, this research uses S.
epidermidis and a collection of diverse phages as model organisms to achieve three specific aims: Aim 1 will
identify and characterize new anti-phage defenses in a suite of S. epidermidis clinical isolates using genetics,
biochemical, and bioinformatics approaches. Aim 2 will determine the major genetic and environmental factors
that drive mobilization of these defenses using molecular and genetic approaches. Aim 3 seeks to determine the
global impacts of the molecular machinery that mediate defense mobilization using high-throughput genetics
approaches. By revealing new insights into mechanisms of anti-phage defenses in staphylococci and the
pathways by which they spread, the proposed work will enable the development of more effective approaches
for not only combatting the spread of resistance to antibiotics but also saving the burgeoning phage therapeutics
from a similar fate. This work will also open up exciting new research directions in understanding staphylococci
and other organisms that harbor similar systems.