Pathogen genomic surveillance status among lower resource settings in Asia
Issued Date
2024-01-01
Resource Type
eISSN
20585276
Scopus ID
2-s2.0-85204786027
Journal Title
Nature Microbiology
Rights Holder(s)
SCOPUS
Bibliographic Citation
Nature Microbiology (2024)
Suggested Citation
Getchell M., Wulandari S., de Alwis R., Agoramurthy S., Khoo Y.K., Mak T.M., Moe L., Stona A.C., Pang J., Momin M.H.F.H.A., Amir A., Andalucia L.R., Azzam G., Chin S., Chookajorn T., Arunkumar G., Hung D.T., Ikram A., Jha R., Karlsson E.A., Le Thi M.Q., Mahasirimongkol S., Malavige G.N., Manning J.E., Munira S.L., Trung N.V., Nisar I., Qadri F., Qamar F.N., Robinson M.T., Saloma C.P., Setk S., Shirin T., Tan L.V., Dizon T.J.R., Thayan R., Thu H.M., Tissera H., Xangsayarath P., Zaini Z., Lim J.C.W., Maurer-Stroh S., Smith G.J.D., Wang L.F., Pronyk P. Pathogen genomic surveillance status among lower resource settings in Asia. Nature Microbiology (2024). doi:10.1038/s41564-024-01809-4 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/101437
Title
Pathogen genomic surveillance status among lower resource settings in Asia
Author(s)
Getchell M.
Wulandari S.
de Alwis R.
Agoramurthy S.
Khoo Y.K.
Mak T.M.
Moe L.
Stona A.C.
Pang J.
Momin M.H.F.H.A.
Amir A.
Andalucia L.R.
Azzam G.
Chin S.
Chookajorn T.
Arunkumar G.
Hung D.T.
Ikram A.
Jha R.
Karlsson E.A.
Le Thi M.Q.
Mahasirimongkol S.
Malavige G.N.
Manning J.E.
Munira S.L.
Trung N.V.
Nisar I.
Qadri F.
Qamar F.N.
Robinson M.T.
Saloma C.P.
Setk S.
Shirin T.
Tan L.V.
Dizon T.J.R.
Thayan R.
Thu H.M.
Tissera H.
Xangsayarath P.
Zaini Z.
Lim J.C.W.
Maurer-Stroh S.
Smith G.J.D.
Wang L.F.
Pronyk P.
Wulandari S.
de Alwis R.
Agoramurthy S.
Khoo Y.K.
Mak T.M.
Moe L.
Stona A.C.
Pang J.
Momin M.H.F.H.A.
Amir A.
Andalucia L.R.
Azzam G.
Chin S.
Chookajorn T.
Arunkumar G.
Hung D.T.
Ikram A.
Jha R.
Karlsson E.A.
Le Thi M.Q.
Mahasirimongkol S.
Malavige G.N.
Manning J.E.
Munira S.L.
Trung N.V.
Nisar I.
Qadri F.
Qamar F.N.
Robinson M.T.
Saloma C.P.
Setk S.
Shirin T.
Tan L.V.
Dizon T.J.R.
Thayan R.
Thu H.M.
Tissera H.
Xangsayarath P.
Zaini Z.
Lim J.C.W.
Maurer-Stroh S.
Smith G.J.D.
Wang L.F.
Pronyk P.
Author's Affiliation
Malaysia Genome and Vaccine Institute
Oxford University Clinical Research Unit
Pasteur Institute in Ho Chi Minh City
University of Sri Jayewardenepura
Duke-NUS Medical School
Singapore Health Services
Ministry of Health Myanmar
Ministry of Health Brunei
National Institute of Public Health Cambodia
Institut Pasteur du Cambodge
University of the Philippines
Nha Trang Pasteur Institute
Ministry of Health Colombo
Kementerian Kesehatan Republik Indonesia
National Institute of Health Pakistan
The Aga Khan University
Umeå Universitet
Institute for Medical Research
NUS Yong Loo Lin School of Medicine
Agency for Science, Technology and Research, Singapore
A-Star, Bioinformatics Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Mahosot Hospital, Lao
Mahidol University
International Centre for Diarrhoeal Disease Research Bangladesh
Nuffield Department of Medicine
Universiti Sains Malaysia
National Institute of Hygien and Epidemiology (NIHE)
Research Institute of Medical Science
Disease Control and Research (IEDCR)
Nepal Country Office
National Center for Laboratory and Epidemiology
Research Institute for Tropical Medicine (RITM)
National Public Health Laboratory
Oxford University Clinical Research Unit
Pasteur Institute in Ho Chi Minh City
University of Sri Jayewardenepura
Duke-NUS Medical School
Singapore Health Services
Ministry of Health Myanmar
Ministry of Health Brunei
National Institute of Public Health Cambodia
Institut Pasteur du Cambodge
University of the Philippines
Nha Trang Pasteur Institute
Ministry of Health Colombo
Kementerian Kesehatan Republik Indonesia
National Institute of Health Pakistan
The Aga Khan University
Umeå Universitet
Institute for Medical Research
NUS Yong Loo Lin School of Medicine
Agency for Science, Technology and Research, Singapore
A-Star, Bioinformatics Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Mahosot Hospital, Lao
Mahidol University
International Centre for Diarrhoeal Disease Research Bangladesh
Nuffield Department of Medicine
Universiti Sains Malaysia
National Institute of Hygien and Epidemiology (NIHE)
Research Institute of Medical Science
Disease Control and Research (IEDCR)
Nepal Country Office
National Center for Laboratory and Epidemiology
Research Institute for Tropical Medicine (RITM)
National Public Health Laboratory
Corresponding Author(s)
Other Contributor(s)
Abstract
Asia remains vulnerable to new and emerging infectious diseases. Understanding how to improve next generation sequencing (NGS) use in pathogen surveillance is an urgent priority for regional health security. Here we developed a pathogen genomic surveillance assessment framework to assess capacity in low-resource settings in South and Southeast Asia. Data collected between June 2022 and March 2023 from 42 institutions in 13 countries showed pathogen genomics capacity exists, but use is limited and under-resourced. All countries had NGS capacity and seven countries had strategic plans integrating pathogen genomics into wider surveillance efforts. Several pathogens were prioritized for human surveillance, but NGS application to environmental and human–animal interface surveillance was limited. Barriers to NGS implementation include reliance on external funding, supply chain challenges, trained personnel shortages and limited quality assurance mechanisms. Coordinated efforts are required to support national planning, address capacity gaps, enhance quality assurance and facilitate data sharing for decision making.