VN-PHAGE: A platform of in silico bacteriophage screening for antimicrobial resistance (VNPHAGE - VietNam Precise Host-strain Assignment & Genomic Evaluation platform)

Antimicrobial resistance (AMR) is a major global health threat. We will need novel alternatives to, or co-therapies for, existing antibiotics. Bacteriophages (“phages”), viruses that infect bacteria, have emerged as a promising candidate. Unlike antibiotics, phages co‑evolve highly specific interactions with unique bacterial surface receptors, leading to narrow host ranges, and so typically infect only a restricted set of bacterial strains. These unique biomarkers are also founded in specific antibiotic resistant bacterial or pathogenic bacterial strains. While this limits side effects of phage resistance like antibiotic resistance, it also presents a bottleneck, relying on labor-intensive and low-throughput in-vitro experiments to identify effective phage-host matches. Furthermore, the ability of phages to kill a host is not the sole determinant of clinical viability; other characteristics must also be considered, such as the absence of virulence factors or antibiotic resistance genes (ARGs) and optimizing selection of lytic dsDNA phages.

In order to address these mechanistic challenges, we have introduced an integrated web-based platform for end-to-end phage screening, which provides three core functionalities. The first module handles genomic data processing and quality checking, including read trimming, assembly, and genome quality checking. The second module performs annotation and phage quality assessment, specifically screening for lifestyle, nucleic acid type, and genetic elements such as lysogeny-related genes, toxins, and ARG biomarkers. The last module leverages machine learning techniques to offer both broad host range estimation against bacterial databases and high resolution, strain-level lytic interaction predictions for specific phage-host pairs. By consolidating these separate workflows, our VNPHAGE platform aims to streamline the discovery of candidates for bacteriophage therapy.

Speaker Bio

Hien T.T. Ngo is a research fellow and laboratory manager with a strong background in Molecular Biology. She obtained her Ph.D. in Biotechnology from Kyung Hee University, South Korea, in 2019, where she continued her postdoctoral research until 2020 before joining Aarhus University Hospital, Denmark. Dr. Ngo has been with the VinUni-Illinois Smart Health Center (VISHC), VinUniversity since 2022, currently serving as a full-time Postdoctoral Research Fellow under the guidance of Prof. Helen Nguyen at University of Illinois at Urbana-Champaign and Prof. Andrew W. Taylor-Robinson at VinUni. Her current research at VISHC focuses on wastewater-based epidemiology, bacteriophages, and the genomic surveillance of antimicrobial resistance and infectious diseases, contributing to the development of advanced molecular tools for public health protection. From 2026 April, Dr. Ngo serves as a Co-Principal Investigator for the Phage-Host Interaction Research Project at VISHC. An accomplished researcher with over 45 peer-reviewed publications, Dr. Ngo also serves as the Managing Editor for the journal Environmental Pollution.