CEE Seminars and Conferences

A Multiscale Investigation of Pathogen and Resistome: Transmission, Characterization, and Evolution

Advisor: Professor Thanh H. Nguyen

Abstract

Driven by intensive human mobility, global trade, and rapid urbanization, the emergence and dissemination of pathogens and antimicrobial resistance (AMR) pose significant public health challenges. In this context, environmental surveillance is being established as a key tool for the early warning of these risks. However, its effectiveness is limited by several knowledge gaps. First, the environmental reservoirs and transmission routes of outbreak-causing pathogens remain poorly understood. Second, despite the thousands of antibiotic resistance gene (ARG) records in public databases, a comprehensive yet cost-effective pipeline for systematic AMR surveillance is still lacking. Furthermore, the prediction of multidrug resistance remains at an early stage, due to a fundamental lack of understanding of multidrug-resistant (MDR) plasmid evolution. By integrating pathogen transmission, ARG characterization, and MDR plasmid evolution, this work provides a multiscale perspective that informs the development of next-generation environmental surveillance.

I investigated the transmission of Salmonella enterica in water bodies in an agricultural production area after a flood caused by Hurricane Florence. The flooded water bodies harbored significantly higher abundance of S. enterica than unflooded water bodies. The S. enterica emerged after the flood originated from the environment instead of upstream swine farms. This study suggests that the natural environment can serve as a significant pathogen reservoir. These findings highlight the need to incorporate environmental baseline monitoring into risk assessment frameworks, especially for agricultural areas prone to extreme weather events.

I developed a CRISPR-Cas9-based target-enrichment next-generation sequencing (NGS) method for comprehensive characterization of ARGs in municipal wastewater. This method enabled the detection of up to 1189 more ARGs than regular NGS, with approximately 10-fold higher read depths. Complementing this method, I developed MSEDAP (Metagenomic Sequencing Data to ARG Primers), a tool that translates metagenomic data into practical qPCR-based assays. Together, these tools provide a cost-effective, high-throughput scheme that bridges the gap between comprehensive ARG detection and routine wastewater AMR surveillance.

I analyzed a comprehensive set of sequences from environmental samples and public databases to investigate the evolution of MDR plasmids. ARGs and transposon-related genes were found widely shared across plasmid lineages with diverse backbone sequences. The synergistic interaction of integrons, IS26, and ISCR elements were found to drive the stepwise evolution of MDR plasmids. In the presence of integrons and ISCR elements, the plasmid ARG load was strongly and positively correlated with IS26 copies. The integron-IS26-ISCR (3I) framework established in this study identifies these three mobile genetic elements as key genomic predictors for multidrug resistance, offering a robust metric for the surveillance and risk assessment of evolving MDR plasmids.