Se Eun Park
Participant from the from the Working with Pathogen Genomes course, Vietnam
I am an Associate Research Scientist at the International Vaccine Institute, and a Adjunct Professor at the Yonsei University Graduate School of Public Health, in Seoul, South Korea. My research focus has been on vaccine preventable diseases and infectious diseases in resource limited settings. Studies cover various epidemiological investigations and observational studies on enteric and diarrheal diseases such as typhoid fever, invasive nontyphoidal Salmonella disease, nontyphoidal Salmonella, cholera, and other common diarrheal diseases.
These multi-country studies were conducted in collaboration with many distinguished institutes across African countries and academia. Selected publications include: Park SE et al., The Severe Typhoid Fever in Africa Program: Study Design and Methodology to Assess Disease Severity, Host Immunity, and Carriage Associated with Invasive Salmonellosis; Park SE et al., The Relationship Between Invasive Nontyphoidal Salmonella Disease, Other Bacterial Bloodstream Infections, and Malaria in sub-Saharan Africa; von Kalckreuth et al., The Typhoid Fever Surveillance in Africa Program (TSAP): Clinical, Diagnostic, and Epidemiological Methodologies.
In 2017, I attended the ‘Working with Pathogen Genomes’ Advanced Course at the Oxford University Clinical Research Unit (OUCRU), Ho Chi Minh City, Vietnam, organized by the Wellcome Genome Campus Advanced Courses and Scientific Conferences (ACSC).
The course provided comprehensive training on genomic analyses. Several modules included topical lectures and hands-on work using various genome analysis software tools to run phylogenetics. These covered mapping Illumina sequence data, SNP calling, genome assembly and annotation, and also running antimicrobial resistance gene analysis. The training was essential for my research particularly on phylogenetics and molecular epidemiological analysis of bacterial pathogens detected in the multi-country typhoid fever surveillance. In collaboration with Prof. Gordon Dougan’s group at the Wellcome Sanger Institute, these bacterial isolates were whole genome sequenced.
This Advanced Course, as well as on-the-job bioinformatics training at OUCRU-HCMC, supported by Prof. Stephen Baker and Dr. Duy Thanh Pham, provided me with a great opportunity to learn and perform analyses of the Salmonella genomes yielded through this research project.
Publications and articles that resulted from this work includes: Park SE et al., The Phylogeography and Incidence of Multi-drug Resistant Typhoid Fever in sub-Saharan Africa; Coalition against Typhoid (CAT) blog piece Today’s reality: a battle against multi-drug resistant typhoid in sub-Saharan Africa
Another paper on The Genomic Epidemiology of Multi-drug Resistant Nontyphoidal Salmonella Causing Invasive Disease in sub-Saharan Africa has been submitted to a journal and is currently under review.
The ACSC Advanced Course on pathogen genomes helped expand my knowledge and understanding on the multitude of complex genomic epidemiological analyses. As a result, I am currently leading projects on other enteric diseases, focusing on cholera and diarrheal diseases (funding awarded from the government of the Republic of Korea/Korea International Cooperation Agency and the Korea Support Committee of the International Vaccine Institute). I have ambition to further explore this area of research, utilizing the knowledge and skillset obtained on the course to conduct genomic analysis of surveillance data as the ongoing projects unfold. These projects aim to conduct various epidemiological investigations on cholera and diarrheal diseases in the study target areas in low and middle income countries (LMICs), including phylogenetics of V. cholerae and other bacterial pathogens that may be detected. Studies on post-licensure (post-registration) vaccine effectiveness and impact of oral cholera vaccine (OCV), and site-specific risk factors and healthcare seeking behaviour associated with cholera in the target populations are also planned.