{"id":{"repo_id":"nus","oai_identifier":"oai:scholarbank.nus.edu.sg:10635/318381"},"canonical_url":"https://search.dev.ndltd.org/etd/nus/oai:scholarbank.nus.edu.sg:10635/318381","repository":{"repo_id":"nus","name":"National University of Singapore","base_url":"https://scholarbank.nus.edu.sg/oai/request"},"display":{"title":"GENOMIC SURVEILLANCE AND RISK-BASED ASSESSMENT OF ANTIBIOTIC RESISTANCE TRANSMISSION ACROSS TROPICAL AQUATIC ENVIRONMENTS","abstract":"Antimicrobial resistance (AMR) transmitted through aquatic environments poses a growing public health threat, yet the genomic mechanisms governing resistance gene flow across interconnected water systems remain poorly understood. This thesis investigates β-lactam resistance transmission across Singapore's tropical aquatic continuum—from hospital sewage and community wastewater to freshwater, aquaculture, and coastal environments—using integrated metagenomic and whole-genome sequencing approaches within a One Health framework. A genome-informed risk-profiling framework was developed to classify antibiotic resistance genes (ARGs) by clinical significance, genetic mobility, and host pathogenicity. Analysis of 557 Escherichia coli and 189 Klebsiella pneumoniae isolates, alongside metagenome-assembled genomes, revealed three distinct ARG transmission trajectories defined by the integrity of the ARG–mobile genetic element–pathogen linkage. High-risk clones (ST131, ST147) carrying clinically significant resistance genes (CTX-M-15, NDM-19) were shared between clinical and sewage sources, while downstream environments showed progressive linkage disruption. These findings establish a scalable surveillance framework identifying priority intervention points for environmental AMR mitigation.","abstract_html":"Antimicrobial resistance (AMR) transmitted through aquatic environments poses a growing public health threat, yet the genomic mechanisms governing resistance gene flow across interconnected water systems remain poorly understood. This thesis investigates β-lactam resistance transmission across Singapore's tropical aquatic continuum—from hospital sewage and community wastewater to freshwater, aquaculture, and coastal environments—using integrated metagenomic and whole-genome sequencing approaches within a One Health framework. A genome-informed risk-profiling framework was developed to classify antibiotic resistance genes (ARGs) by clinical significance, genetic mobility, and host pathogenicity. Analysis of 557 Escherichia coli and 189 Klebsiella pneumoniae isolates, alongside metagenome-assembled genomes, revealed three distinct ARG transmission trajectories defined by the integrity of the ARG–mobile genetic element–pathogen linkage. High-risk clones (ST131, ST147) carrying clinically significant resistance genes (CTX-M-15, NDM-19) were shared between clinical and sewage sources, while downstream environments showed progressive linkage disruption. These findings establish a scalable surveillance framework identifying priority intervention points for environmental AMR mitigation.","abstract_has_math":false,"creators":["YUAN QIYI"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-07-30","date_published":"2025-07-30","updated_at":"2026-07-24T03:32:56Z","subjects":["One Health","whole-genome sequencing","aquatic environments","β-lactam resistance","metagenomics","antimicrobial resistance"],"languages":[],"rights":[],"rights_urls":["https://scholarbank.nus.edu.sg/bitstreams/d7f1cb49-b994-4175-af25-a89a50c729ba/download"],"identifier_entries":[]},"links":{"outbound_url":null,"outbound_label":null,"outbound_source":null},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:creator","label":"Author","values":["YUAN QIYI"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2025-07-30"]},{"key":"dc:relation.isreferencedby","label":"Dc Relation Isreferencedby","values":["https://scholarbank.nus.edu.sg/handle/10635/318381"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["One Health","whole-genome sequencing","aquatic environments","β-lactam resistance","metagenomics","antimicrobial resistance"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:rights","label":"Dc Rights","values":["https://scholarbank.nus.edu.sg/bitstreams/d7f1cb49-b994-4175-af25-a89a50c729ba/download"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://scholarbank.nus.edu.sg/bitstreams/f439961a-fbf3-4b19-bec8-336e8570dd43/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Antimicrobial resistance (AMR) transmitted through aquatic environments poses a growing public health threat, yet the genomic mechanisms governing resistance gene flow across interconnected water systems remain poorly understood. 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This thesis investigates β-lactam resistance transmission across Singapore's tropical aquatic continuum—from hospital sewage and community wastewater to freshwater, aquaculture, and coastal environments—using integrated metagenomic and whole-genome sequencing approaches within a One Health framework. A genome-informed risk-profiling framework was developed to classify antibiotic resistance genes (ARGs) by clinical significance, genetic mobility, and host pathogenicity. Analysis of 557 Escherichia coli and 189 Klebsiella pneumoniae isolates, alongside metagenome-assembled genomes, revealed three distinct ARG transmission trajectories defined by the integrity of the ARG–mobile genetic element–pathogen linkage. High-risk clones (ST131, ST147) carrying clinically significant resistance genes (CTX-M-15, NDM-19) were shared between clinical and sewage sources, while downstream environments showed progressive linkage disruption. 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