Browsing by Author "Fong, Yang (Richard)"

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    A comparison of next-generation sequencing protocols for microbial profiling : a thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Genetics, Massey University, Palmerston North, New Zealand
    (Massey University, 2016) Fong, Yang (Richard)
    The introduction of massive parallel sequencing has revolutionized analyses of microbial communities. Illumina and other Whole Genome Shotgun Sequencing (WGS) sequencing protocols have promised improved opportunities for investigation of microbial communities. In the present work, we compared and contrasted the findings from different NGS library preparation protocols (Illumina Nextera, Nextera-XT, NEXTFlex PCR-free and Ion-Xpress-400bp) and two sequencing platforms (MiSeq and Ion-Torrent). Short reads were analysed using the rapid database matching software PAUDA and visualization software MEGAN5, which provides a conservative approach for taxonomic identification and functional analyses. In analyses of a Tamaki River water sample, biological inferences were made and compared across platforms and protocols. For even a relatively small number of reads generated on the MiSeq sequencing platform important pathogens were identified in the water sample. Far greater phylogenetic resolution was obtained with WGS sequencing protocols than has been reported in similar studies that have used 16S rDNA Illumina sequencing protocols. TruSeq and Nextera-XT sequencing protocols produced similar results. The latter protocol offered cheaper, and faster results from less DNA starting material. Proteobacteria (alpha, beta and gamma), Actinobacteria and Bacteroidetes were identified as major microbial elements in the Tamaki River sample. Our findings support the emerging view that short read sequence data and enzymatic library prep protocols provide a cost effective tool for evaluating, cataloguing and monitoring microbial species and communities. This is an approach that complements, and provides additional insight to microbial culture “water testing” protocols routinely used for analysing aquatic environments.
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    The dynamics of drug resistance evolution and diagnosis in Mycobacterium tuberculosis : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Genetics/Genomics, Massey University, Manawatu, New Zealand
    (Massey University, 2024-07-30) Fong, Yang (Richard)
    Tuberculosis (TB) remains a critical global health challenge with over 10.4 million new cases annually, complicated by rising antimicrobial resistance (AMR) threatening to surpass cancer mortality by 2050. This PhD thesis establishes a systematic diagnostic framework addressing AMR challenges through progressive research from fundamental microbiome characterization to innovative diagnostic applications in resource-limited settings like Myanmar. The "Microbiome Dataset from the Upper Respiratory Tract of Patients Living with HIV, HIV/TB and TB from Myanmar" establishes the foundational understanding of microbial community structures in complex clinical presentations (n=309 isolates). This microbiome characterization reveals critical signatures that directly inform direct sequencing strategies for enhanced MTBC detection in polymicrobial environments, addressing a fundamental challenge in AMR detection. Next, the "Genomic Profiling of Mycobacterium tuberculosis Strains, Myanmar" validates and expands these microbiome-informed approaches through comprehensive whole genome sequencing surveillance, establishing genotype-phenotype correlations that achieve 97.8% concordance with phenotypic testing. This genomic profiling directly addresses AMR surveillance gaps by enabling rapid resistance prediction. Subsequently by "Unveiling Hr-TB in Myanmar: Comprehensive Genotypic and Phenotypic Insights for Improved TB Management" demonstrates targeted application of microbiome-informed diagnostic approaches to isoniazid mono-resistant TB, a clinically critical AMR variant frequently missed by conventional methods. The integrated microbiome-genomic approach enhances MTBC detection accuracy by 23% compared to standard methods, reducing diagnostic time from weeks to under one week. Future perspectives translate these discoveries into field-deployable MDA primer systems for point-of-care AMR detection using portable MinION sequencing technology. This systematic progression from microbiome foundation to diagnostic innovation establishes a replicable technological blueprint for next-generation TB AMR diagnostics, supporting Myanmar's National TB Control Program while providing a framework for global TB elimination efforts Keywords: Mycobacterium tuberculosis (MTB), Tuberculosis (TB), Antimicrobial Resistance (AMR), Isoniazid Mono-Resistant (Hr-TB), Drug-Resistant Tuberculosis (DR-TB), Whole-genome sequencing (WGS), Resistance associated Mutations, Epidemiology, Surveillance, Rapid Diagnosis, Microbiome, Yangon, Myanmar.