Towards Genomic AMR surveillance in Southeast Asia

We propose whole genome sequencing AMR surveillance in farmed animals and currently untapped environmental samples e.g., wastewater and abattoir effluents to yield new knowledge of AMR extent and understand transmission dynamics between humans, animals, and the environment as a model for capacity building of genomic AMR surveillance in Southeast Asia.

Prof Rungtip Chuanchuen, Director of Thailand FAO Reference Centre for AMR, Primary Investigator

Southeast Asia is a global hotspot for the emergence and spread of AMR. Comprehending the extent of AMR is a basis for driving action and critical to measuring the impact of initiatives and progress made in addressing this problem. Currently, AMR data generation in this region relies on conventional methods with the dearth of high-quality data. Local AMR surveillance is limited to humans and terrestrial food animals and that of environment is very limited. Data of antimicrobial residues in farm and abattoir environment that could be linked to antimicrobials used is scarce. This impairs ways towards Integrated One Health AMR surveillance.

Using WGS to support AMR surveillance has been proved by identifying resistance mechanisms, uncovering transmission patterns, and pinpointing the sources and transmission pathways of AMR. However, genomic AMR surveillance is rare in Southeast Asia. We, Thailand FAO Reference Centre for AMR, have progressively built local capacity towards a sustainable AMR surveillance system in the food and agriculture sectors in the region since 2013 and will continue the momentum on AMR surveillance by building capacity for local AMR data generation using WGS analysis. This will expand to water waste-based surveillance of AMR and antimicrobial residues.

The proposed solution “Whole genome sequencing AMR surveillance in farmed animals and their environment” is the continuing momentum of the current efforts on the local capacity towards a sustainable AMR surveillance system in the food and agriculture sectors in Southeast Asia. Our current venture, the Thailand FAO Reference Centre for AMR has brought about substantial transformation on AMR laboratory capacities in the region, particularly through harmonization of laboratory methods. The technical support and initiatives required to improve national AMR surveillance for each country have been defined by assessing national AMR surveillance and laboratory capacity using the FAO Assessment Tool for Laboratories and Antimicrobial resistance Surveillance Systems (ATLASS). The assessment findings suggested that the whole genome sequencing of sentinel species is a required component of a Southeast Asian surveillance programme to comprehend AMR in the region. The knowledge and technology obtained will be transferred to laboratory staff who are tasked with AMR testing as part of national AMR surveillance in Southeast Asian countries through regional training workshops. The solution will benefit national AMR surveillance in the region. It will be introduced to improve quality of AMR surveillance and answer specific questions that cannot be answered by phenotype-based AMR surveillance.

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The outputs of the proposed solution include 1) whole genome sequence of AMR data of target bacteria from farmed animals and related environment in Thailand deposited to genomic sequence databases that publicly open, 2) a model or framework for establishing whole genome sequence AMR surveillance, 3) laboratory network on whole genome sequencing AMR surveillance, 4) laboratory staff tasked with AMR testing and surveillance having skilled for whole genome sequencing analysis, 5) a free-to-use dashboard containing all the data will provide access to the data to stake-holders, end-users and policy makers.6) peer-review publication and 7) presentation of findings in conferences. 

AMR surveillance is a cornerstone for AMR management in Southeast Asia. In each country, the AMR surveillance in human health is usually more advanced than that in animal and environmental health. Several international organizations have provided technological and financial support to the countries for capacity building on AMR testing and surveillance. To date, almost all countries have national AMR surveillance programs in different sectors and at different development levels. While they are moving forward Integrated One Health surveillance, it is essential to advance phenotypic-based AMR surveillance to genomic AMR surveillance.

The solution will provide a paradigm and framework for genomic AMR surveillance in farmed animals and their environment that will a significant impact on the improvement of national AMR surveillance in Thailand and other countries Southeast Asia by accelerating the progress. These will strengthen the key objectives of FAO Action plan 2021-2025 including strengthening surveillance and research and promoting responsible use of antimicrobials. The solution indisputably reinforces our task and responsibilities as Thailand FAO reference for AMR.

We will employ a multifaceted approach centered on scientific innovation, collaboration, and strategic partnerships to scale the impact of the solution as follows:  

Research collaborative networks expansion: Building on the current AMR network, we will expand the collaborations to AMR researchers in universities and research institutes, industry partners and governmental laboratories at national and regional levels to share data, resources, and expertise.

Capacity building: We will technically support capacity building initiatives in AMR surveillance for countries with required resources. The findings will be communicated to the committee of Thailand One health AMR surveillance for further improvement of the program.

Technology transfer: In addition to the regional training workshop as planned, we will explore opportunities for follow up technology transfer to ensure that innovative solutions reach those who need them most.

Public awareness and education: The findings will be communicated to public to raise awareness on AMR e.g., annual conference, seminar, webinar. This will include highlighting the importance of antibiotic stewardship and the role of research in combating AMR.

Impact goal 1: Establish the capacity for genomic surveillance in Thailand.

Measure of success:

• Assessment of competencies for genomic surveillance infrastructure in Thailand, including necessary equipment, protocols, and trained personnel.
• Evidence of the generation of genomic AMR data in Thailand, contributing to global AMR databases and research efforts.
• Integration of genomic surveillance data into national AMR monitoring and control programs.

Impact goal 2: Enhance regional capacity for AMR surveillance and control through training workshops and knowledge dissemination.

Measure of success:

• Successful organization of regional training workshops on AMR surveillance.
• Evaluation of workshop participants demonstrating increased knowledge and skills.
• Subsequent training of participants in their respective countries, leading to improved AMR surveillance practices.
• Observation of a ripple effect, with trained participants influencing others and contributing to broader social impact.

Impact goal 3: Establish wastewater-based AMR and antimicrobial residues monitoring.

Measure of success:

• Evidence of the generation of AMR and antimicrobial residue data in farm and abattoir environment.
• Successful integration of wastewater-based AMR and antimicrobial residues monitoring into the existing AMR surveillance network.

Impact goal 4: Develop dashboard containing genomic AMR data and antimicrobial residues

Measure of success:

• A free-to-use dashboard containing all the data opens for stake-holders, end-users and policy makers

1. Financial limitations: Whole genome sequencing analysis and regional training workshop is costly. This may hinder our research intervention and expansion. To address this, we should diversify funding sources and seek support from government grants and the private sector. Virtual training is a choice if it is necessary to lower the cost.
2. Technical challenges. These include complexity of big data, quality assurance, and specialized expertise requirements in genomics and bioinformatics. Standardizing protocols, managing data, and integrating whole genome sequence with clinical data are crucial. Collaborations with experts can help overcome these challenges.
3. Policy barriers. These may occur during sampling plan and sample collection. This could be overcome by requiring collaboration with local authorities, farm owners and stakeholders.

The main reasons that we are applying to the Trinity Challenge is derived from our major task and responsibility in capacity building for national AMR surveillance in animals and agriculture in Southeast Asia as Thailand FAO Reference Centre for AMR, we have been involved. Currently, AMR data generation in this region relies on conventional methods and is limited to humans and terrestrial food animals and that of environment is very limited. This results in limited use of AMR data and impairs ways towards Integrated One Health AMR surveillance. Therefore, we have progressively built local capacity towards local AMR data generation using whole genome sequencing analysis. However, genomic surveillance is rare in the region. We believe this challenge fits well with The Trinity Challenge’s objective. This work conducted in Thailand will be the basis for whole genome sequencing AMR surveillance in other countries in the region. Therefore, the solution will benefit not only Thailand but also other countries in the region. As AMR is a global issue, the solution will benefit the global prevention and control strategies of AMR.

• Chulalongkorn University
• University of South Australia
• University of Adelaide
• CSIRO
  
• Queensland Alliance for Environmental Health Sciences - The University of Queensland
• Department of livestock development, Thailand
• FAO Regional Office for Asia and the Pacific (FAO RAP)