08 Mar 2024
Boosting pathogen genomics capacity for enteric surveillance in the Asia-Pacific region
In late 2022, Professor Ben Howden and Tuyet Hoang, Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL), were appointed as the new co-coordinators of PulseNet Asia Pacific, the regional arm of PulseNet International - a network of national and regional laboratories dedicated to tracking foodborne infections world-wide. Since then, MDU PHL and the Centre for Pathogen Genomics (the Centre) have hosted two cohorts of trainees from nine countries.
This year's training, held from 31 January to 8 February at the Doherty Institute in Melbourne, was not intended as solely an educational exercise. It is an important step towards the “PulseNet Feasibility Study”, aiming to build genomic sequencing capacity specifically for AMR surveillance of enteric pathogens through the Global Antimicrobial Resistance Laboratory and Response Network program, in addition to serving as an excellent networking opportunity for PNAP members across the region.
Twelve scientists from public health and medical research laboratories in Bangladesh, Sri Lanka, Vietnam and Japan were hosted to undertake training in whole genome sequencing approaches for public health action. This entailed wet lab training in DNA extractions for sequencing, Illumina library preparation, and sequencing on the Illumina MiSeq instrument, followed by dry lab training in bioinformatics and genomic epidemiology.
The Centre and MDU PHL’s partnership with various experts and trainers brings an enriching diversity of knowledge and experience to the program, with the blend of internal and external expertise underscoring the collaborative strength of the initiative.
Hasini Walpola, one of the key facilitators of the training program, spoke on the relevance of these activities to the region.
Trainees during the wet-lab portion of the training program
“Training such as this contributes to upskilling future leaders in pathogen genomics, but also serves to foster networking and collaboration in the region” said Ms Walpola, Genomics Training Specialist for Centre for Pathogen Genomics
“This training promotes the harmonisation of whole genome sequencing protocols in the region and also aims to build a pool of pathogen genomics trainers who will then disseminate the training in their own countries.”
“Our aim is to empower and equip laboratories in the region with the necessary skills to respond to public health threats with the support of the network.”
Tuyet Hoang, Pathogen Genomics Lead and PNAP Co-Coordinator, MDU PHL, remarked on the significance of this training.
"By providing these teaching and training opportunities to the laboratories in our region, we're not just building capacity but also fostering a community of practice across the Asia Pacific to strengthen enteric pathogen diseases response and surveillance," she said.
Transitioning to the bioinformatics aspect with the guidance of trainers
Angela Poates, Lead Specialist in NGS & Bioinformatics, APHL, shared insights into the program's impact.
"This initiative not only builds skills but also encourages a culture of continuous learning and collaboration in the face of evolving pathogens," Ms Poates observed.
Peera (P) Hemarajata, Southeast Asia Laboratory Technical Advisor, APHL, also reflected on the program's broader goals.
"Our aim is to create a robust network of skilled professionals within the Asia-Pacific region who can lead the way in establishing and strengthening pathogen genomic surveillance efforts in their respective countries."
The initiative reflects a concerted effort by multiple organisations dedicated to improving public health outcomes through the implementation of WGS. The collaborative nature of this training underscores the global commitment to managing enteric diseases and enhancing health security across the Asia Pacific.
Organisations involved in training:
Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL) at the Doherty Institute, Melbourne, Australia
Centre for Pathogen Genomics at the Doherty Institute, Melbourne, Australia
Theiagen Genomics, Colorado, USA
Association of Public Health Laboratories (APHL), Maryland, USA
Centers for Disease Control and Prevention (CDC), Atlanta, USA
Medical Research Institute, Colombo, Sri Lanka
National Institute of Infectious Diseases, Tokyo, Japan
Institut Pasteur, Ho Chi Minh City, Vietnam
National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
International Centre for Diarrheal Disease Research, Dhaka, Bangladesh