Lab Matters Spring 2023 - Page 26


Building Collaboration in Asia Through PulseNet International

By Kristy Kubota , manager , PulseNet
Antimicrobial resistance ( AR ) accounts for a large proportion of morbidity and mortality worldwide . Global initiatives have been developed to support surveillance and identify emerging drug-resistant strains circulating within regions and globally . Use of genomic tools such as whole genome sequencing ( WGS ) provides opportunities to conduct surveillance of AR bacteria by detecting emerging strains at the population level , which can impact clinical treatment and contribute to the understanding of how resistance spreads throughout the human , animal and environmental ecosystems .
In 2021 , PulseNet International became part of a larger US Centers for Disease Control and Prevention ( CDC ) initiative — the Global Antimicrobial Resistance Laboratory and Response Network — focusing on building laboratory capacity for detecting AR within regions encompassing PulseNet International . APHL is one of 26 organizations that received funding to develop systems to respond to the threats posed by the spread of resistant bacteria . As part of this work , APHL received funding in its first year to support PulseNet Asia Pacific with developing capacity for PulseNet WGS workflows , data analysis and data sharing in the region .
New PulseNet Asia Pacific Coordinators
In 2021 , Professor Ben Howden ’ s team at the Peter Doherty Institute for Infection and Immunity at the University of Melbourne in Australia became the new PulseNet regional coordinators for the Asia Pacific region due to the retirement of Dr . Kai-Man Kam from the Chinese University of Hong Kong . Professor Howden is the Director of the Microbiological Diagnostic Unit Public Health Laboratory ( MDU PHL ) at the Doherty Institute for Applied Microbial Genomics and Head of the Howden Research Group . Their research interests include translational microbial genomics for clinical and public health practice . Additionally , the Centre for Pathogen Genomics at the Doherty Institute was established to support new collaborative opportunities for translational research , genomics-informed infectious disease surveillance and capacity building and training . The Centre ’ s program is focused on four key themes : infectious diseases surveillance and response , antimicrobial resistance , One Health and pandemic preparedness and response . Leveraging the expertise of the applied public health research and surveillance activities at MDU PHL , this new collaboration will provide opportunities to grow PulseNet Asia Pacific activities within the region .
Implementing a New Network
APHL utilized funding through the Global Antimicrobial Resistance Laboratory and Response Network to support PulseNet Asia Pacific laboratories in developing capacity in the region for PulseNet WGS workflows , data analysis and data sharing . APHL launched a feasibility study with public health laboratories within the region to demonstrate PulseNet ’ s surveillance system for both enteric foodborne cluster detection and emerging antimicrobial resistance monitoring . The five public health laboratories selected to participate include :
• Centers for Disease Control , Taiwan
• Research Institute for Tropical Medicine ( RITM ), Philippines
• Institute for Medical Research ( IMR ), Malaysia
• National Institute of Health , Thailand
• Centers for Disease Control and Prevention , Thailand
• Institute of Environmental Science and Research ( IESR ), New Zealand
APHL partnered with Theiagen Genomics to develop a Terra workspace , a web-based application that enables users to access open source bioinformatic workflows through cloud computing
From l to r : MDU PHL Manager Tuyet Hoang , Kristy Kubota , MDU PHL director Professor Ben Howden and MDU PHL Associate Professor Torsten Seemann at the 7th World One Health Congress meeting in Singapore , November 2022
resources . Developed by the Broad Institute at MIT and Harvard University , Terra has been widely implemented by public health laboratories for SARS-CoV-2 sequence analysis . Bioinformatic workflows were developed in Terra for analysis of enteric bacteria and training was conducted during fall 2022 with the study sites . In-person wet-bench training is planned at the University of Melbourne in February 2023 .
Following training , participating laboratories plan to sequence and analyze 100 enteric bacterial isolates as part of this study throughout 2023 . It is hoped that this study will demonstrate the utility of WGS methods and use of bioinformatic tools for the identification of AR resistance genes in enteric bacteria . Through data sharing in Terra , laboratories within the Asia Pacific region will be able to collectively monitor and identify AR pathogens circulating within the region . APHL hopes to expand laboratory capacity to other PulseNet International regions including Africa and elsewhere in future years . g
24 LAB MATTERS Spring 2023
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