Duy Pham

Participant from the from the Working with Pathogen Genomes course, Vietnam

 

Recently, I was appointed as Joint Head of Molecular Epidemiology Group at Oxford University Clinical Research Unit (OUCRU), in Vietnam. My research focuses on evolution, genomics and epidemiology of antimicrobial resistant bacteria causing enteric diseases, as well as other topical bacterial infectious diseases in Vietnam and other low-and-middle-income countries. Our multidisciplinary research approach integrates genomics and molecular biology techniques with epidemiological and clinical research to understand how antimicrobial resistant organisms evolve and spread in different populations and their impact on clinical outcomes.
Since 2010, OUCRU has been a collaborating host institution for Wellcome Genome Campus Advanced Courses Overseas programme. I was a participant on the Working with Pathogen Genomes course held at the OUCRU in March 2010.
  1. Working with Pathogen Genomes, Vietnam (2010)

This training opportunity introduced me to genomics and bioinformatics for the first time. Not only did I gain new knowledge and skills in a different field, but also expanded my research interests, perspectives and professional network. Although there was no genome sequencing facility at OUCRU, the skills that I acquired from the course contributed greatly to my research projects at that time.

In August 2013, I visited Wellcome Sanger Institute in Cambridge, UK for more advanced hands-on bioinformatics training and genome sequencing techniques, with Nick Thomson’s research team. My previous exposure to bacterial genomics through the advanced course, enabled me to develop new in-depth informatic skills with much greater speed and ease.

After that, I came back and helped to set up and run the very first Illumina Miseq Sequencing platform at OUCRU. Since 2013, my leading expertise in genomics and whole genome sequencing have made substantial contributions to the research activities within my group and at OUCRU.

I have been involved in, and also led a number of genomic epidemiological investigations of Shigella spp, Salmonella spp, Klebsiella pneumoniae, Acinetobacter baumanii, Enterobacter spp, E. coli, from different bacterial infections such as diarrhea, Salmonellosis, typhoid fever, community-onset and hospital-onset bloodstream infections, in different countries including; Vietnam, Laos, Cambodia, Thailand, India, Nepal and sub-Saharan African countries.

These studies have resulted in several significant publications in prestigious international journals (Nat. Microbiol, Nat. Commun, Plos Patho.), providing novel insights into the evolution, transmission patterns and molecular mechanisms of antimicrobial resistance of these bacterial pathogens in different settings. Throughout these projects, I have established a research network with international collaborators in India, Nepal, Cambodia, Laos, Thailand, Indonesia, UK, U.S. and Australia. In 2015, I received a five-year leadership fellowship from the Oak Foundation to further develop my research career and leadership skills.

In 2016 and 2017, I was also a host instructor during the Genomics and Molecular Epidemiology of Bacterial Pathogens, and the Working with Pathogen Genomes courses held at the OUCRU for Asian participants. I have also provided academic teaching and hands-on training in whole genome sequencing and bioinformatics for the postgraduates from a local university since 2018. Having been both a trainee and trainer of these advanced genomics courses was special to me as I could directly transfer the knowledge and skills that I have gained from the training and my work experience. This clearly demonstrates the impact the training courses have had in advancing my career as a research and trainer in genomics, benefiting other researchers in Asia.

  1. Genomics and Epidemiology of Bacterial Pathogens, Vietnam (2016)

The Wellcome Genome Campus Advanced Courses helped to shape my career in bacterial genomics and facilitated establishment of my mentoring relations and research networks. I have also met many extraordinary people from these courses who have directly and indirectly contributed to my success, as I now hold a senior position in my institute.

I hope my story will be inspiring and motivating to those who are keen on learning and developing research in this important field of genomics. The Wellcome Genome Campus Advanced Courses is a great start on your journey.

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