Mechanisms of bacterial defense against conjugative plasmids and their phages

The National Institute of General Medical Sciences awarded Health Research, Inc. Wadsworth Center $386,003 on August 1, 2026, to fund research on mechanisms of bacterial defense against conjugative plasmids and their phages under the Biomedical Research and Research Training program (CFDA 93.859).

The research addresses antibiotic resistance by investigating how bacteria defend against conjugative plasmids—which spread resistance genes across bacterial populations—and plasmid-dependent phages that use plasmid-encoded pili as viral receptors. The project will dissect a newly discovered plasmid defense system called CPDA in Pseudomonas aeruginosa to reveal how it detects and blocks plasmid transfer; determine the molecular basis of plasmid-dependent phage host range through comparative genomics and evolution experiments; and apply unbiased functional metagenomic screening to discover new defense mechanisms, including direct anti-phage systems and regulators of conjugative pili. The work combines genetics, biochemistry, imaging, and metagenomics approaches.

Performance occurs at the Wadsworth Center in Albany, New York, with a period of performance extending from August 1, 2026, through June 30, 2031. The assistance type is Project Grant.

Abstract

Antibiotic resistance is one of the greatest threats to public health. Conjugative plasmids are key drivers of resistance because they spread resistance genes across bacterial populations. These plasmids encode pili that mediate transfer, but the same pili also act as receptors for plasmid-dependent phages (pdps). This creates a unique evolutionary conflict: plasmids enable resistance dissemination yet simultaneously expose their hosts to viral predation. Despite this central role, little is known about how bacteria defend against plasmids or pdps. We recently generated a diverse collection of pdps that revealed dramatic host range variation between closely related phages. We also identified bacterial strains resistant to plasmid acquisition, providing molecular evidence for a specialized plasmid defense system. These findings highlight the unexplored diversity of defenses acting at the plasmid-phage interface. This proposal will define mechanisms of bacterial defense against conjugative plasmids and their phages through three interconnected research focuses. First, we will dissect the newly discovered plasmid defense system cpda in pseudomonas aeruginosa to reveal how IT detects and blocks plasmid transfer. Second, we will determine the molecular basis of PDP host range, using comparative genomics and evolution experiments to understand how phages coordinate pilus recognition with replication in diverse hosts. Third, we will apply unbiased functional metagenomic screening to discover new defenses, including direct anti-PDP systems and regulators of conjugative pili. This work is innovative because IT uses pdps, a neglected class of viruses, as tools to probe plasmid biology and because IT applies unbiased functional screens to uncover defense mechanisms that cannot be predicted from sequence. By combining genetics, biochemistry, imaging, and metagenomics, this research will establish a framework for how bacteria navigate conflicts with plasmids and phages. Exploring PDP biology not only expands our understanding of bacterial immunity but also lays the groundwork for future translational use of pdps to control plasmid-borne antibiotic resistance. Expected outcomes over the next five years include mechanistic definition of a novel plasmid defense system, insights into PDP host range, and the first catalogue of defenses active at the plasmid-phage interface. These discoveries will expand the known repertoire of bacterial immunity, explain how plasmid spread is naturally limited, and suggest new strategies to combat antibiotic resistance.