Investigator(s)
| Submitter |
Tshering Dorji Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan Tshering Dorji 
|
| Principal Investigator |
Tshering Dorji Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan Tshering Dorji
|
| Co-Investigator(s) |
Sonam Gyeltshen Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan Sonam Gyeltshen
|
| Co-Investigator(s) |
Sangay Zangmo Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan Sangay Zangmo
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| Co-Investigator(s) |
Kinley Gyem Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan Kinley Gyem
|
| Co-Investigator(s) |
Kinley Penjor Royal Centre for Disease Control, Ministry of Health, Royal Government of Bhutan Kinley Penjor
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| Co-Investigator(s) |
Takashi Matsumoto Department of Environmental Preventive Medicine, Faculty of Medicine, Oita University. 1-1 Hasama, Yufu, Oita 879-5593, Japan Takashi Matsumoto
|
Title(s) and abstract
| Scientific title | Genomic Insights and Antimicrobial Resistance Profiling of Diarrheagenic E. coli in Bhutan: A Retrospective Whole Genome Sequencing Study |
| Public title | Genomic Insights and Antimicrobial Resistance Profiling of Diarrheagenic E. coli in Bhutan: A Retrospective Whole Genome Sequencing Study |
| Background | Diarrheal diseases cause significant morbidity and mortality in children under five in developing countries, with 500,000 deaths annually. In Bhutan, diarrhoea remains a major health issue, with 11,793 cases reported in 2022. It is the second most frequently notified disease, heavily impacting the healthcare system, especially among young children. Diarrheagenic Escherichia coli (DEC) is a common cause of diarrhoea worldwide. E. coli is a gram-negative bacterium typically harmless in the gut, but some strains acquire virulence factors (VFs) that make them pathogenic. These VFs, often on mobile genetic elements, result in three clinical syndromes: diarrheal disease, urinary tract infections (UTIs), and sepsis/meningitis. DEC causes symptoms like watery diarrhoea, nausea, vomiting, and cramps. It is classified into six pathotypes: enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli (EAEC), and diffusely adherent E. coli (DAEC). Differentiating DEC from non-pathogenic E. coli requires polymerase chain reaction (PCR) assays targeting specific virulence genes. DEC infections are usually self-limiting and managed with oral rehydration therapy (ORT) to prevent dehydration. Antibiotics are generally avoided for EHEC due to the risk of Shiga toxin release, which can cause haemolytic uremic syndrome (HUS). For other DEC types, antibiotics may be used in severe cases. However, increasing antibiotic resistance, particularly to fluoroquinolones and extended-spectrum β-lactamases (ESBL) or carbapenemases, poses a significant global health challenge. |
| Objectives | This study aims to address the research gap by analyzing the genomic diversity of diarrheagenic E. coli strains in Bhutan, identifying virulence factors, and assessing antimicrobial resistance profiles using Next-Generation Sequencing (NGS). Specifically, it will: 1. Characterize Genomic Diversity: Analyze genomic variations and phylogenetic relationships among strains. 2. Identify Virulence Factors: Detect and identify virulence genes to determine pathogenic potential. 3. Assess Antimicrobial Resistance: Evaluate resistance patterns and identify genetic determinants. 4. Identify Novel Mutations: Find mutations or SNPs linked to antimicrobial resistance and compare WGS data with traditional testing. 5. Investigate ESBL-PE: Study the occurrence of ESBL-producing strains and identify related gene mutations. 6. Establish a Reference Genome: Create a reference genome for pathogenic E. coli in Bhutan. |
| Study Methods | There is a retrospective study, and we will utilize the 30 Diarrheagenic E. coli isolates (DEC), and its corresponding data collected in 2023 for the National Diarrheal Disease Surveillance conducted by the Royal Centre for Disease Control (RCDC). The national diarrheal disease surveillance is an on-going activity, being implemented as a part of public health intervention, covering 12 designated sentinel hospitals. As part of routine surveillance, RCDC collects stool samples and its associated information’s from patients meeting the defined diarrheal case definition at these designated surveillance sites primarily to understand and estimate the burden and magnitude of diarrheal disease, identify high-risk areas and high-risk groups, to monitor seasonal trends and antimicrobial susceptibility patterns of isolated pathogens, and to detect outbreaks. In 2023, a total of 347 stool samples were collected from which 30 were characterized as DEC by standard microbiological testing and stored in the biorepository. We will use these isolates for detail AMR and genetic profiling using high throughput Next-Generation Sequencing (NGS). |
| Expected outcomes and use of results | The anticipated outcomes of our study include enhanced understanding of diarrheagenic E. coli in Bhutan, identification of novel genetic markers associated with virulence and antimicrobial resistance and informing evidence-based public health policies and interventions tailored to the local context. This may also help to deepen our understanding of the relationship between AMR phenotype and genotype, and the resistance profile of AMR E. coli provides a comparative evaluation of this alternative method to traditional AMR detection. We also aim to establish a reference genome for E. coli strains from Bhutan, enhancing the framework for future research and public health strategies. |
| Keywords | AMR, Diarrheagenic E. coli, NGS, WGS |
Research Details
| Student research | No |
| Start Date | 01-Jun-2024 |
| End Date | 01-Jul-2025 |
| Key Implementing Institution | Royal Centre for Disease Control |
| Multi-country research | No |
| Nationwide research | Yes, with randomly selected geographical areas |
| Bhutan, Bhutan, Bhutan, Bhutan, Bhutan, Bhutan, Bhutan, Bhutan, Bhutan, Bhutan, Bhutan, Bhutan | |
| Research Domain(s) | Communicable Disease Research |
| Research field(s) | Infectious Disease |
| Involves human subjects | Yes |
| Other (Retrospective laboratory-based study, Genomic) | |
| Data Collection | Secondary data |
| Proposal reviewed by other Committee | No |