| Author: | Lam, Alison Yee Ting |
| Title: | Metagenomics-enabled investigation of multidrug resistant organisms and antimicrobial resistance genes in urban built environments |
| Advisors: | Siu, Gilman (HTI) |
| Degree: | Ph.D. |
| Year: | 2026 |
| Department: | Department of Health Technology and Informatics |
| Pages: | 294 pages : color illustrations |
| Language: | English |
| Abstract: | Background: The urban built environments (BE) contain a diverse set of microorganisms. However, their health impacts remain poorly understood. In this thesis, large-scale, city-wide surveillance for multidrug-resistant organisms (MDROs) and antimicrobial resistance genes (ARGs) was conducted in two urban BE, the Hong Kong subway system and public washrooms. Methods: Surface samples were collected from high-touch surfaces from both environments, which were subjected to both culture-dependent and culture-independent methods. Chromogenic agars were used to isolate MDROs from direct surface samples, followed by whole-genome sequencing (WGS) to obtain the full genome for molecular typing and comprehensive ARG profiles. For culture-independent approach, unbiased shotgun metagenomics was performed, followed by taxonomic classification and resistome profiling. For a subset of samples, target enrichment by oligonucleotide probe was performed on metagenomic libraries to enhance the detection of low-abundance and clinically important taxa and ARGs. Results: Using culture-dependent methods, MDROs were detected in 4.11% of subway samples and 7.33% of washroom samples, with methicillin-resistant Staphylococcus aureus (MRSA) being the most detected MDRO in both environments. Whole genome sequencing (WGS) identified clinically significant sequence types (STs), highlighting the presence of high-risk strains in both environments. Metagenomic profiling revealed the ubiquitous existence of high-risk opportunistic pathogens, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and S. aureus in high-contact surfaces. Furthermore, clinically relevant ARGs were identified, with mecA, the hallmark of MRSA resistance, dominating both environments. Comparative analysis demonstrated that target probe capture enrichment significantly improved the detection for rare taxa and ARGs by several folds compared to conventional shotgun metagenomics, highlighting its efficacy in detecting low-abundance targets. Conclusions: These findings contextualize urban BE as reservoirs for MDROs and ARGs, particularly MRSA and the mecA gene, posing potential health risks to their occupants. Furthermore, this study demonstrates the utility of metagenomics and target probe capture enrichment in public health surveillance by enabling a sensitive detection of rare but high-risk resistance determinants in low-biomass environmental samples. This study offers a comprehensive and nuanced assessment of the microbial and resistome landscape of urban BE, offering a revolutionary approach for future environmental surveillance. |
| Rights: | All rights reserved |
| Access: | open access |
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