PulseNet Asia Pacific Delivers First Nanopore Sequencing Training in Bangkok

Building on the success of previous PulseNet Asia Pacific (PNAP) training programs held in Melbourne (2023 Illumina Training, 2024 Illumina Training), the Centre for Pathogen Genomics (The Centre) co-hosted an ONT training program from the 24th – 28th of June in Bangkok, Thailand. This training was conducted in partnership with the Association of Public Health Laboratories (APHL), the U.S. Centers for Disease Control and Prevention (U.S. CDC) and The Training Center for Excellence in Medical Sciences (TEMs DMSc) to further bolster enteric disease and antimicrobial resistance surveillance capabilities across the Asia Pacific region.

PNAP, a regional arm of PulseNet International, is co-coordinated by Professor Benjamin Howden and Tuyet Hoang (Centre for Pathogen Genomics and MDU PHL, University of Melbourne). It is a network of national and regional laboratories dedicated to tracking foodborne infections and facilitating timely public health interventions using molecular methods, harmonised protocols and data sharing.

In the last two years, PNAP has focused on the implementation of whole genome sequencing (WGS) in favour of other molecular typing methods, to contribute to the equitable access to new technologies within the Asia-Pacific region. A feasibility study to demonstrate the utility of WGS for surveillance, currently in its second year, is underway with funding from the Global Antimicrobial Resistance Laboratory and Response Network. To date, 12 laboratories across eleven countries are participating in the study, with over 450 sequences generated within the region.

Initial training and implementation that was conducted as part of the feasibility study focused on the use of Illumina platforms, but this limited participation from laboratories that only had access to Oxford Nanopore Technology (ONT) platforms, and so the breadth of training was expanded to include ONT training.

“This groundbreaking...training on Oxford Nanopore Technologies is just the beginning of bringing accessible Next-Generation Sequencing Technology for surveillance of enteric bacterial diseases to the global stage. We are excited to see the impact of this training on the PulseNet Asia-Pacific network” notes Peyton Smith, WGS Technical Lead for PulseNet International at the US CDC.

The training program was one of the largest ONT training programs held in the Asia Pacific and was the first ONT training program delivered through PNAP. It included wet lab training for ONT sequencing and bioinformatics training for analysing data on the Terra.bio platform. The program is also an opportunity to network with other member labs.

The training attracted 31 participants from across the region, with representation from Bangladesh, Fiji, Japan, Malaysia, New Zealand, Philippines, Sri Lanka, Taiwan, Thailand, Timor Leste and Vietnam.

Dr. Louise Judd, Senior Scientist at The Centre commented on the success of the wet lab training, “Given this was the first iteration of this training program and the program was delivered to a large cohort with diverse experience in genomics we were delighted that the trainees were able to consistently generate very high-quality sequencing data that could be used for outbreak detection and disease surveillance.”

Scientists working in the laboratory

Participants included both Illumina Feasibility Study Cohort 1 and 2 participants, and welcomed additional scientists from the Pacific, Fiji and Timor Leste. Trainers from the Lugar Centre in Georgia were also invited to participate in the training to share learnings, approaches and methods for training in preparation for PulseNet Eastern Europe and Central Asia training.

Dr. Peera Hemarajata, Southeast Asia Laboratory Technical Advisor for APHL, remarked on the suitability of TEMs DMSc for large group training. “...with its dedicated lab space for training and high-throughput ONT sequencing capabilities. The facility also included 40 high-performance workstations, enabling comprehensive bioinformatics analysis training. This setup allowed trainees to experience an end-to-end NGS workflow, from sequencing to data analysis, ensuring a robust and immersive learning experience.”

The collaborative effort among the partners in developing and delivering this training in the region contributes to sustainability, accessibility, harmonisation and data sharing, strengthening aims for pathogen genomics in the Asia Pacific region being led by the Centre for Pathogen Genomics, University of Melbourne.

We thank all our partners for the collaborative effort in delivering capacity building activities in pathogen genomics in the region:

  • Association of Public Health Laboratories
  • Centers for Disease Control, Taiwan
  • Centers for Disease Control and Prevention, Thailand
  • Fiji Centre for Communicable Disease Control, Mataika House, Fiji
  • International Centre for Diarrheal Disease Research, Bangladesh
  • Institute for Medical Research, Malaysia
  • The Institute of Environmental Science and Research, New Zealand
  • Laboratorio Nacional de Saude, Timor Leste
  • Medical Research Institute, Sri Lanka
  • National Institute of Health, Thailand
  • National Institute of Hygiene and Epidemiology, Vietnam
  • National Institute of Infectious Diseases, Japan
  • Pasteur Institute, Vietnam
  • Research Institute for Tropical Medicine, Philippines
  • The Training Center for Excellence in Medical Sciences, Thailand
  • U.S. Centers for Disease Control and Prevention

If you would like to get in touch to hear more, please feel free to contact the Centre for Pathogen Genomics at Centre-PathoGen@unimelb.edu.au.