Research Thrust 2

Research Team: Misty Thomas (NCAT, lead), Joseph Graves, Jr. (NCAT), Joe Brown (UNCCH), Megan Lott (UNCCH), Mark Weisner (DUKE), A-Andrew Jones (DUKE), Kayla Fericy (Duke), Kobi Talma (DUKE), Will Stiffler (DUKE), Georgie Sawyer (DUKE), Karl Linden (EXT), Carla Calderon (EXT), Sergio Gutiérrez Cortez (EXT), Megan Hill (DUKE), Lindsay Saber (UNCCH), Caroline Butler (UNCCH).

Description: This project advances PreMiEr’s mission by developing evolution-informed, physico-chemical interventions to reduce the persistence of ESKAPEE pathogens in the built environment. Through a convergent research approach spanning materials science, microbiology, engineering, and ecology, we are designing passive, scalable tools for microbial control that emphasize durability, environmental safety, and resistance avoidance. Key efforts include the development of antimicrobial surfaces using shape-controlled silver nanoparticles, a bioinspired p-trap for biofilm disruption, computational tools for modeling microbial transport in plumbing, and ecological inoculants for post-cleaning pathogen suppression. These innovations target deployment in PreMiEr testbeds and clinical settings, aligning with strategic goals for translational engineering solutions that proactively shape healthy microbiomes in hospitals and the built environment.

Research Team: Ophelia Venturelli (DUKE, lead), Claudia Gunsch (DUKE), Lingchong You (DUKE), Conrad Moss (DUKE), Aaron Yip (DUKE), Job Grant (DUKE), Will Stiffler (DUKE), Neil Gottel (DUKE), David Singleton (DUKE), John Zhou (DUKE).

Description: Hospital plumbing systems are persistent reservoirs for antibiotic-resistant pathogens, including Pseudomonas aeruginosa and bacteria carrying plasmid-borne antimicrobial resistance (AMR) genes. We propose an integrated experimental–computational approach to develop microbiome-based interventions that competitively exclude pathogens, disrupt biofilms, and reduce AMR persistence. In Aim 1, we will use robotic high-throughput screening, active learning, and mechanistic–machine learning models to design probiotic consortia and nutrient supplements that inhibit P. aeruginosa growth and biofilm formation in physiologically relevant “p-trap” media. Aim 2 will combine high-throughput conjugation assays, multi-omic trait analysis, and a data-driven computational models to predict and minimize plasmid persistence using targeted biological and chemical interventions. Aim 3 will extend these strategies to engineer colonizable surfaces and natural microbial communities that exclude ESKAPEE bacteria and SPACES fungi using natural communities. Our project will deliver probiotic inoculants, predictive computational modeling frameworks for community functions and plasmid persistence, precision interventions to inhibit target pathogens and antimicrobial resistance genes and engineered biocontrol surfaces, providing sustainable alternatives to chemical disinfection in healthcare infrastructure.

Research Team: Nathan Crook (NCSU, lead), John Rawls (DUKE), Robert Newman (NCAT), Jessica McCann (DUKE), Akinwunmi Afuape (NCAT), Qiaochu Li (NCSU).

Description: Healthcare-associated infections (HAIs) are a persistent challenge in clinical settings, with hospital sinks serving as reservoirs for multidrug-resistant pathogens. To address this issue, we are pursuing several innovative strategies. First, we are using transposon insertion sequencing (Tn-Seq) to identify the genetic factors that allow a model bacterium, Phocaeicola vulgatus, to thrive on different built environment surfaces. In parallel, we are developing a rapid, cell-free workflow for creating synthetic bacteriophages from scratch that can specifically target and eliminate sink pathogens. Additionally, we are designing a genetically engineered probiotic strain that will colonize sink plumbing and suppress pathogen growth, featuring a kill-switch triggered by hydrogen sulfide. Finally, we are engineering an AI-driven platform to discover and validate synergistic drug combinations against multidrug-resistant pathogens. Collectively, this work generates novel genetically engineered microbes that can remove AMR pathogens from the P-trap environment.

Research Team: Jeseth Delgado Vela (DUKE, lead), Nicole Rockey (DUKE), Robert Newman (NCAT), Kevin Garcia (NCSU), Crissy Massimino (DUKE), Zachariah Broemell (DUKE), Madison Pinckney (NCAT), Gavin Duffy (DUKE), Brianna Jamison (NCSU), Akinwunmi Afuape (NCAT).

Description: This research focuses on modulating the microbiome of the built environment (BE) using viruses that infect bacteria and fungi. Our team brings together expertise in virology, synthetic biology, bioinformatics, and mycology to develop two novel virus-host systems. To modulate the microbiome of the home environment, we will leverage fungal viruses, termed mycoviruses, that infect BE fungal strains we have isolated from the PreMiEr test home, among other indoor spaces. To this end, we will apply genetic engineering approaches to generate virus-infected isogenic strains of target fungal populations and evaluate the effect of viral infection on growth and virulence (Aim 1). In parallel, we will evaluate delivery systems of synthetic and engineered phage designed to reduce ESKAPEE pathogen load and modulate sink biofilms (Aim 2). The team will continue to support interdisciplinary workforce development by exchanging students in different laboratories.

Status: Currently part of PreMiEr core project “Microbiome Engineering: Probiotic Inoculants” effective September 1, 2024

Faculty: Claudia Gunsch (Duke), Deverick Anderson (Duke), Sandra Clinton (CHAR), Lawrence David (Duke), Liesl Jeffers-Francis (NCAT), Joshua Granek (Duke), A-Andrew Jones (Duke), Lingchong You (Duke)

Description: Traditionally, waterborne disease outbreaks have been prevented through centralized water treatment in utility water treatment plants. However, several CDC studies have shown that a significant number of waterborne disease outbreaks result from opportunistic pathogens that reside in premise plumbing environments as opposed to those associated with either water treatment plants or water supplies. This project will identify and characterize opportunistic pathogens in hospital and home premise plumbing systems. The project also considers how the environment as well as an individual’s oral and skin microbiome may contribute to the development of premise plumbing biofilms and investigates potential exposure pathways.

Status: Some aspects currently part of PreMiEr core project “Microbiome Engineering: Physico-Chemical Treatments” effective September 1, 2024

Faculty: Sandra Clinton (CHAR), Claudia Gunsch (Duke), Jacelyn Rice-Boayue (NCSU), Mark Wiesner (Duke)

Description: Premise plumbing comprises the complete hot and cold water systems in a building and includes everything from the hot water heater and HVAC to the showers, faucets, sinks, and toilets. These systems are composed of a variety of materials (e.g. copper, PVC, PEX) that result in an environment that varies both temporally and spatially in its physical and chemical properties. This project collects fine scale data on the materials commonly used in premise plumbing and uses it to create a set of known substrates of varying properties that can be used to grow and characterize biofilms under varying environmental conditions.

Status: Currently part of PreMiEr core project “Microbiome Engineering: Synthetic Biology” effective September 1, 2024

Faculty: John Rawls (Duke), Joe Brown (UNCCH), Nathan Crook (NCSU), Glenn Morrison (UNCCH), Barbara Turpin (UNCCH), Lingchong You (Duke)

Description: A fundamental challenge in microbiome science is to understand the mechanisms that determine fitness of individual community members in a given habitat. The objective of this project is to establish multiple complementary approaches to defining genes and traits that confer fitness to members of built environment microbiomes. Planned methods include transposon insertion, heterologous expression, and high-throughput sequencing.