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Anupong S, Chadsuthi S, Hongsing P, Hurst C, Phattharapornjaroen P, Rad S.M. AH, Fernandez S, Huang AT, Vatanaprasan P, Saethang T, Luk-in S, Storer RJ, Ounjai P, Devanga Ragupathi NK, Kanthawee P, Ngamwongsatit N, Badavath VN, Thuptimdang W, Leelahavanichkul A, Kanjanabuch T, Miyanaga K, Cui L, Nanbo A, Shibuya K, Kupwiwat R, Sano D, Furukawa T, Sei K, Higgins PG, Kicic A, Singer AC, Chatsuwan T, Trowsdale S, Abe S, Ishikawa H, Amarasiri M, Modchang C, Wannigama DL. Exploring indoor and outdoor dust as a potential tool for detection and monitoring of COVID-19 transmission. iScience 2024; 27:109043. [PMID: 38375225 PMCID: PMC10875567 DOI: 10.1016/j.isci.2024.109043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/09/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
This study investigated the potential of using SARS-CoV-2 viral concentrations in dust as an additional surveillance tool for early detection and monitoring of COVID-19 transmission. Dust samples were collected from 8 public locations in 16 districts of Bangkok, Thailand, from June to August 2021. SARS-CoV-2 RNA concentrations in dust were quantified, and their correlation with community case incidence was assessed. Our findings revealed a positive correlation between viral concentrations detected in dust and the relative risk of COVID-19. The highest risk was observed with no delay (0-day lag), and this risk gradually decreased as the lag time increased. We observed an overall decline in viral concentrations in public places during lockdown, closely associated with reduced human mobility. The effective reproduction number for COVID-19 transmission remained above one throughout the study period, suggesting that transmission may persist in locations beyond public areas even after the lockdown measures were in place.
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Affiliation(s)
- Suparinthon Anupong
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Chiang Rai, Thailand
- School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Cameron Hurst
- Molly Wardaguga Research Centre, Charles Darwin University, Brisbane, QLD, Australia
- Statistics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Phatthranit Phattharapornjaroen
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - Ali Hosseini Rad S.M.
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago 9010, New Zealand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Stefan Fernandez
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Angkana T. Huang
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sirirat Luk-in
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Naveen Kumar Devanga Ragupathi
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Division of Microbial Interactions, Department of Research and Development, Bioberrys Healthcare and Research Centre, Vellore 632009, India
| | - Phitsanuruk Kanthawee
- Public Health Major, School of Health Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Natharin Ngamwongsatit
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Vishnu Nayak Badavath
- School of Pharmacy & Technology Management, SVKM’s Narsee Monjee Institute of Management Studies (NMIMS), Hyderabad 509301, India
| | - Wanwara Thuptimdang
- Institute of Biomedical Engineering, Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Talerngsak Kanjanabuch
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Kazuhiko Miyanaga
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Asuka Nanbo
- The National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Kenji Shibuya
- Tokyo Foundation for Policy Research, Minato-ku, Tokyo, Japan
| | - Rosalyn Kupwiwat
- Department of Dermatology. Faculty of Medicine Siriraj Hospital. Mahidol University, Bangkok, Thailand
| | - Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Takashi Furukawa
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Minato City, Tokyo 108-8641, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Minato City, Tokyo 108-8641, Japan
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands WA 6009, Australia
- School of Population Health, Curtin University, Bentley WA 6102, Australia
| | | | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sam Trowsdale
- Department of Environmental Science, University of Auckland, Auckland 1010, New Zealand
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Hitoshi Ishikawa
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Minato City, Tokyo 108-8641, Japan
| | - Charin Modchang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Centre of Excellence in Mathematics, MHESI, Bangkok 10400, Thailand
- Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok 10400, Thailand
| | - Dhammika Leshan Wannigama
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Pathogen Hunter’s Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
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2
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Wannigama DL, Amarasiri M, Phattharapornjaroen P, Hurst C, Modchang C, Chadsuthi S, Anupong S, Miyanaga K, Cui L, Werawatte WKCP, Ali Hosseini Rad SM, Fernandez S, Huang AT, Vatanaprasan P, Saethang T, Luk-In S, Storer RJ, Ounjai P, Tacharoenmuang R, Ragupathi NKD, Kanthawee P, Cynthia B, Besa JJV, Leelahavanichkul A, Kanjanabuch T, Higgins PG, Nanbo A, Kicic A, Singer AC, Chatsuwan T, Trowsdale S, Furukawa T, Sei K, Sano D, Ishikawa H, Shibuya K, Khatib A, Abe S, Hongsing P. Wastewater-based epidemiological surveillance of SARS-CoV-2 new variants BA.2.86 and offspring JN.1 in south and Southeast Asia. J Travel Med 2024:taae040. [PMID: 38438141 DOI: 10.1093/jtm/taae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Discover the shifting landscape of SARS-CoV-2 variants from October to December 2023, with JN.1 dominating South and Southeast Asia wastewater samples, increasing from < 10% to over 90%. Experience the dynamic evolution of viral strains in this period.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, United Kingdom
- Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences/Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan
| | - Phatthranit Phattharapornjaroen
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - Cameron Hurst
- Molly Wardaguga Research Centre, Charles Darwin University, Queensland, Australia
- Statistics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Charin Modchang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Centre of Excellence in Mathematics, MHESI, Bangkok 10400, Thailand
- Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok 10400, Thailand
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Suparinthon Anupong
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Kazuhiko Miyanaga
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - W K C P Werawatte
- Faculty of Medicine, Wayamba University of Sri Lanka, and Teaching Hospital Kuliyapitiya, Kuliyapitiya, Sri Lanka
| | - S M Ali Hosseini Rad
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Stefan Fernandez
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Angkana T Huang
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Porames Vatanaprasan
- Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Naveen Kumar Devanga Ragupathi
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
- Division of Microbial Interactions, Department of Research and Development, Bioberrys Healthcare and Research Centre, Vellore-632009, India
| | | | - Bernadina Cynthia
- Department of General Medicine, St. Carolus Hospital, Jakarta, Indonesia
| | - John Jefferson V Besa
- College of Medicine, University of the Philippines and Philippine General Hospital, Medicine, Manila, Philippines
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Talerngsak Kanjanabuch
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Asuka Nanbo
- The National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, 6009, Western Australia, Australia
- Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, 6009, Western Australia, Australia
- Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands, 6009, Western Australia, Australia
- School of Population Health, Curtin University, Bentley, 6102, Western Australia, Australia
| | - Andrew C Singer
- UK Centre for Ecology & Hydrology, Wallingford OX10 8BB, United Kingdom
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sam Trowsdale
- School of Environment, University of Auckland, Auckland 1010, New Zealand
| | - Takashi Furukawa
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences/Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences/Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa, 252-0373, Japan
| | - Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Hitoshi Ishikawa
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
| | - Kenji Shibuya
- Tokyo Foundation for Policy Research, Minato-ku, Tokyo, Japan
| | - Aisha Khatib
- Department of Family & Community Medicine, University of Toronto, Toronto, ON, Canada
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Chiang Rai, Thailand
- School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
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3
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Wannigama DL, Amarasiri M, Phattharapornjaroen P, Hurst C, Modchang C, Chadsuthi S, Anupong S, Miyanaga K, Cui L, Thuptimdang W, Ali Hosseini Rad SM, Fernandez S, Huang AT, Vatanaprasan P, Jay DJ, Saethang T, Luk-In S, Storer RJ, Ounjai P, Ragupathi NKD, Kanthawee P, Sano D, Furukawa T, Sei K, Leelahavanichkul A, Kanjanabuch T, Higgins PG, Nanbo A, Kicic A, Singer AC, Chatsuwan T, Trowsdale S, Siow R, Shibuya K, Abe S, Ishikawa H, Hongsing P. Tracing the transmission of mpox through wastewater surveillance in Southeast Asia. J Travel Med 2023; 30:taad096. [PMID: 37462504 DOI: 10.1093/jtm/taad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/03/2023] [Accepted: 07/14/2023] [Indexed: 09/07/2023]
Abstract
High population density and tourism in Southeast Asia increase the risk of mpox due to frequent interpersonal contacts. Our wastewater surveillance in six Southeast Asian countries revealed positive signals for Monkeypox virus (MPXV) DNA, indicating local transmission. This alerts clinicians and helps allocate resources like testing, vaccines and therapeutics in resource-limited countries.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Aoyagi, Yamagata, Japan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Pathum Wan, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, South Yorkshire, UK
- Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Aoyagi, Yamagata, Japan
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences/Graduate School of Medical Sciences, Kitasato University, Sagamihara-Minami, Kanagawa, Japan
| | - Phatthranit Phattharapornjaroen
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Ratchathewi, Bangkok, Thailand
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, Universitetsplatsen 1, 405 30 Gothenburg, Sweden
| | - Cameron Hurst
- Molly Wardaguga Research Centre, Charles Darwin University, Brisbane, Queensland, Australia
- Statistics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Charin Modchang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
- Centre of Excellence in Mathematics, MHESI, Ratchathewi, Bangkok, Thailand
- Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, Ratchathewi, Bangkok, Thailand
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Mueang Phitsanulok District, Phitsanulok, Thailand
| | - Suparinthon Anupong
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kazuhiko Miyanaga
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Longzhu Cui
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Wanwara Thuptimdang
- Institute of Biomedical Engineering, Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - S M Ali Hosseini Rad
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago, New Zealand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Pathum Wan Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Ratchathewi, Bangkok, Thailand
| | - Angkana T Huang
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Ratchathewi, Bangkok, Thailand
| | - Porames Vatanaprasan
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Dylan John Jay
- Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Aoyagi, Yamagata, Japan
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Phutthamonthon District, Nakhon Pathom, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Ratchathewi, Bangkok, Thailand
| | - Naveen Kumar Devanga Ragupathi
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, South Yorkshire, UK
| | - Phitsanuruk Kanthawee
- Public Health major, School of Health Science, Mae Fah Luang University, Mueang Chiang Rai District, Chiang Rai, Thailand
| | - Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Takashi Furukawa
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences/Graduate School of Medical Sciences, Kitasato University, Sagamihara-Minami, Kanagawa, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences/Graduate School of Medical Sciences, Kitasato University, Sagamihara-Minami, Kanagawa, Japan
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Pathum Wan, Bangkok, Thailand
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Talerngsak Kanjanabuch
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
- Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
- Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Pathum Wan, Bangkok, Thailand
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Albertus-Magnus-Platz, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Albertus-Magnus-Platz, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Albertus-Magnus-Platz, Cologne, Germany
| | - Asuka Nanbo
- The National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Bunkyo-machi, Nagasaki, Japan
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, Western Australia, Australia
- Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, Western Australia, Australia
- Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands, Western Australia, Australia
- School of Population Health, Curtin University, Bentley, Bentley, 6102, Western Australia, Australia
| | - Andrew C Singer
- UK Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, UK
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Pathum Wan, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, Thailand
| | - Sam Trowsdale
- School of Environmental Science, University of Auckland, Auckland CBD, Auckland, New Zealand
| | - Richard Siow
- King's British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King's College London, Denmark Hill Campus, The James Black Centre, 125 Coldharbour Lane, London, UK
- Vascular Biology and Inflammation Section, School of Cardiovascular Medicine and Sciences, King's College London, Denmark Hill Campus, The James Black Centre, 125 Coldharbour Lane, London, UK
- Department of Physiology, Anatomy & Genetics, University of Oxford, Broad St, Oxford, UK
| | | | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Aoyagi, Yamagata, Japan
| | - Hitoshi Ishikawa
- Yamagata Prefectural University of Health Sciences, Aoyagi, Yamagata, Japan
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Mueang Chiang Rai,Chiang Rai, Thailand
- School of Integrative Medicine, Mae Fah Luang University, Mueang Chiang Rai,Chiang Rai, Thailand
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Wannigama DL, Sithu Shein AM, Hurst C, Monk PN, Hongsing P, Phattharapornjaroen P, Fox Ditcham WG, Ounjai P, Saethang T, Chantaravisoot N, Wapeesittipan P, Luk-in S, Sae-Joo S, Nilgate S, Rirerm U, Tanasatitchai C, Kueakulpattana N, Laowansiri M, Liao T, Kupwiwat R, Rojanathanes R, Ngamwongsatit N, Tungsanga S, Leelahavanichkul A, Devanga Ragupathi NK, Badavath VN, Hosseini Rad SA, Kanjanabuch T, Hirankarn N, Storer RJ, Cui L, Amarasiri M, Ishikawa H, Higgins PG, Stick SM, Kicic A, Chatsuwan T, Abe S. Ca-EDTA restores the activity of ceftazidime-avibactam or aztreonam against carbapenemase-producing Klebsiellapneumoniae infections. iScience 2023; 26:107215. [PMID: 37496674 PMCID: PMC10366478 DOI: 10.1016/j.isci.2023.107215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 07/28/2023] Open
Abstract
Developing an effective therapy to overcome carbapenemase-positive Klebsiella pneumoniae (CPKp) is an important therapeutic challenge that must be addressed urgently. Here, we explored a Ca-EDTA combination with aztreonam or ceftazidime-avibactam in vitro and in vivo against diverse CPKp clinical isolates. The synergy testing of this study demonstrated that novel aztreonam-Ca-EDTA or ceftazidime-avibactam-Ca-EDTA combination was significantly effective in eliminating planktonic and mature biofilms in vitro, as well as eradicating CPKp infections in vivo. Both combinations revealed significant therapeutic efficacies in reducing bacterial load in internal organs and protecting treated mice from mortality. Conclusively, this is the first in vitro and in vivo study to demonstrate that novel aztreonam-Ca-EDTA or ceftazidime-avibactam-Ca-EDTA combinations provide favorable efficacy and safety for successful eradication of carbapenemase-producing Klebsiella pneumoniae planktonic and biofilm infections.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Pathogen Hunter’s Research Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Aye Mya Sithu Shein
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Cameron Hurst
- Molly Wardaguga Research Centre, Charles Darwin University, Brisbane, QLD, Australia
| | - Peter N. Monk
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield Medical School, UK
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Chiang Rai, Thailand
- School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Phatthranit Phattharapornjaroen
- Department of Emergency Medicine, Center of Excellence, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - William Graham Fox Ditcham
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Naphat Chantaravisoot
- Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Sirirat Luk-in
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Sasipen Sae-Joo
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sumanee Nilgate
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ubolrat Rirerm
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chanikan Tanasatitchai
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naris Kueakulpattana
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Matchima Laowansiri
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tingting Liao
- Department of Physiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Microcirculation, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rosalyn Kupwiwat
- Pathogen Hunter’s Research Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Department of Dermatology. Faculty of Medicine Siriraj Hospital. Mahidol University, Bangkok, Thailand
| | - Rojrit Rojanathanes
- Center of Excellence in Materials and Bio-Interfaces, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Natharin Ngamwongsatit
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Somkanya Tungsanga
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Division of General Internal Medicine-Nephrology Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Naveen Kumar Devanga Ragupathi
- Pathogen Hunter’s Research Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Vishnu Nayak Badavath
- School of Pharmacy & Technology Management, SVKM’s Narsee Monjee Institute of Management Studies (NMIMS), Hyderabad 509301, India
| | - S.M. Ali Hosseini Rad
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago 9010, New Zealand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Talerngsak Kanjanabuch
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Nattiya Hirankarn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Longzhu Cui
- Division of Bacteriology, School of Medicine, Jichi Medical University, Tochigi, Japan
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Hitoshi Ishikawa
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
| | - Stephen M. Stick
- Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands, WA 6009, Australia
| | - Anthony Kicic
- Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands, WA 6009, Australia
- School of Public Health, Curtin University, Bentley, WA 6102, Australia
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship Research, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shuichi Abe
- Biofilms and Antimicrobial Resistance Consortium of ODA Receiving Countries, The University of Sheffield, Sheffield, UK
- Pathogen Hunter’s Research Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
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Wannigama DL, Amarasiri M, Hongsing P, Hurst C, Modchang C, Chadsuthi S, Anupong S, Phattharapornjaroen P, Rad S. M. AH, Fernandez S, Huang AT, Vatanaprasan P, Jay DJ, Saethang T, Luk-in S, Storer RJ, Ounjai P, Devanga Ragupathi NK, Kanthawee P, Sano D, Furukawa T, Sei K, Leelahavanichkul A, Kanjanabuch T, Hirankarn N, Higgins PG, Kicic A, Singer AC, Chatsuwan T, Trowsdale S, Abe S, McLellan AD, Ishikawa H. COVID-19 monitoring with sparse sampling of sewered and non-sewered wastewater in urban and rural communities. iScience 2023; 26:107019. [PMID: 37351501 PMCID: PMC10250052 DOI: 10.1016/j.isci.2023.107019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/31/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Equitable SARS-CoV-2 surveillance in low-resource communities lacking centralized sewers is critical as wastewater-based epidemiology (WBE) progresses. However, large-scale studies on SARS-CoV-2 detection in wastewater from low-and middle-income countries is limited because of economic and technical reasons. In this study, wastewater samples were collected twice a month from 186 urban and rural subdistricts in nine provinces of Thailand mostly having decentralized and non-sewered sanitation infrastructure and analyzed for SARS-CoV-2 RNA variants using allele-specific RT-qPCR. Wastewater SARS-CoV-2 RNA concentration was used to estimate the real-time incidence and time-varying effective reproduction number (Re). Results showed an increase in SARS-CoV-2 RNA concentrations in wastewater from urban and rural areas 14-20 days earlier than infected individuals were officially reported. It also showed that community/food markets were "hot spots" for infected people. This approach offers an opportunity for early detection of transmission surges, allowing preparedness and potentially mitigating significant outbreaks at both spatial and temporal scales.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, UK
- Pathogen Hunter’s Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Chiang Rai, Thailand
- School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Cameron Hurst
- Molly Wardaguga Research Centre, Charles Darwin University, Brisbane, QLD, Australia
- Statistics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Charin Modchang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Centre of Excellence in Mathematics, MHESI, Bangkok 10400, Thailand
- Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok 10400, Thailand
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Suparinthon Anupong
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Phatthranit Phattharapornjaroen
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - Ali Hosseini Rad S. M.
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago 9010, New Zealand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Stefan Fernandez
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Angkana T. Huang
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Dylan John Jay
- Pathogen Hunter’s Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sirirat Luk-in
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Naveen Kumar Devanga Ragupathi
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
- Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | - Phitsanuruk Kanthawee
- Public Health major, School of Health Science, Mae Fah Luang University, Chiang Rai, Thailand
| | - Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Takashi Furukawa
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Asada Leelahavanichkul
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
- Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Talerngsak Kanjanabuch
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Nattiya Hirankarn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, University of Western Australia, Nedlands, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital, Nedlands, WA 6009, Australia
- School of Population Health, Curtin University, Bentley, WA 6102, Australia
| | | | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sam Trowsdale
- Department of Environmental Science, University of Auckland, Auckland 1010, New Zealand
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Alexander D. McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin, Otago 9010, New Zealand
| | - Hitoshi Ishikawa
- Yamagata Prefectural University of Health Sciences, Kamiyanagi, Yamagata 990-2212, Japan
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Na S, Wannigama DL, Saethang T. Antimicrobial peptides recognition using weighted physicochemical property encoding. J Bioinform Comput Biol 2023; 21:2350006. [PMID: 37120707 DOI: 10.1142/s0219720023500063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Antimicrobial resistance is a major public health concern. Antimicrobial peptides (AMPs) are one of the host defense mechanisms responding efficiently against multidrug-resistant microbes. Since the process of screening AMPs from a large number of peptides is still high-priced and time-consuming, the development of a precise and rapid computer-aided tool is essential for preliminary AMPs selection ahead of laboratory experiments. In this study, we proposed AMPs recognition models using a new peptide encoding method called amino acid index weight (AAIW). Four AMPs recognition models including antimicrobial, antibacterial, antiviral, and antifungal were trained based on datasets combined from the DRAMP and other published databases. These models achieved high performance compared to the preceding AMPs recognition models when evaluated on two independent test sets. All four models yielded over 93% in accuracy and 0.87 in Matthew's correlation coefficient (MCC). An online AMPs recognition server is accessible at https://amppred-aaiw.com.
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Affiliation(s)
- Standa Na
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Center of Artificial Intelligence Innovation for Healthtech Research Unit (AIIH), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata 990-2292, Japan
- Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Center of Artificial Intelligence Innovation for Healthtech Research Unit (AIIH), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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7
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Wannigama DL, Amarasiri M, Hongsing P, Hurst C, Modchang C, Chadsuthi S, Anupong S, Phattharapornjaroen P, S M AHR, Fernandez S, Huang AT, Kueakulpattana N, Tanasatitchai C, Vatanaprasan P, Saethang T, Luk-In S, Storer RJ, Ounjai P, Ragupathi NKD, Kanthawee P, Sano D, Furukawa T, Sei K, Leelahavanichkul A, Kanjanabuch T, Hirankarn N, Higgins PG, Kicic A, Chatsuwan T, McLellan AD, Abe S. Multiple traces of monkeypox detected in non-sewered wastewater with sparse sampling from a densely populated metropolitan area in Asia. Sci Total Environ 2023; 858:159816. [PMID: 36461562 PMCID: PMC9620434 DOI: 10.1016/j.scitotenv.2022.159816] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 06/10/2023]
Abstract
The monkeypox virus is excreted in the feces of infected individuals. Therefore, there is an interest in using viral load detection in wastewater for sentinel early surveillance at a community level and as a complementary approach to syndromic surveillance. We collected wastewater from 63 sewered and non-sewered locations in Bangkok city center between May and August 2022. Monkeypox viral DNA copy numbers were quantified using real-time polymerase chain reaction (PCR) and confirmed positive by Sanger sequencing. Monkeypox viral DNA was first detected in wastewater from the second week of June 2022, with a mean copy number of 16.4 copies/ml (n = 3). From the first week of July, the number of viral DNA copies increased to a mean copy number of 45.92 copies/ml. Positive samples were Sanger sequenced and confirmed the presence of the monkeypox virus. Our study is the first to detect monkeypox viral DNA in wastewater from various locations within Thailand. Results suggest that this could be a complementary source for detecting viral DNA and predicting upcoming outbreaks.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan; Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Biofilms and Antimicrobial Resistance Consortium of ODA receiving countries, The University of Sheffield, Sheffield, United Kingdom; Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan.
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Chiang Rai, Thailand; School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Cameron Hurst
- Molly Wardaguga Research Centre, Charles Darwin University, Queensland, Australia; Statistics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Charin Modchang
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Centre of Excellence in Mathematics, MHESI, Bangkok 10400, Thailand; Thailand Center of Excellence in Physics, Ministry of Higher Education, Science, Research and Innovation, 328 Si Ayutthaya Road, Bangkok 10400, Thailand
| | - Sudarat Chadsuthi
- Department of Physics, Faculty of Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Suparinthon Anupong
- Biophysics Group, Department of Physics, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Phatthranit Phattharapornjaroen
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - Ali Hosseini Rad S M
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand; Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Stefan Fernandez
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Angkana T Huang
- Department of Virology, U.S. Army Medical Directorate, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Naris Kueakulpattana
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chanikan Tanasatitchai
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Naveen Kumar Devanga Ragupathi
- School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, United Kingdom; Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | - Daisuke Sano
- Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi, Japan; Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Takashi Furukawa
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Kazunari Sei
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa 252-0373, Japan
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Talerngsak Kanjanabuch
- Division of Nephrology, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Center of Excellence in Kidney Metabolic Disorders, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Dialysis Policy and Practice Program (DiP3), School of Global Health, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Peritoneal Dialysis Excellence Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Nattiya Hirankarn
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan; Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
| | - Anthony Kicic
- Telethon Kids Institute, University of Western Australia, Nedlands, 6009, Western Australia, Australia; School of Population Health, Curtin University, Bentley 6102, Western Australia, Australia; Centre for Cell Therapy and Regenerative Medicine, Medical School, The University of Western Australia, Nedlands 6009, Western Australia, Australia; Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Nedlands 6009, Western Australia, Australia
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Center of Excellence in Antimicrobial Resistance and Stewardship, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Alexander D McLellan
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan; Pathogen Hunter's Research Collaborative Team, Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
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8
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Wannigama DL, Kueakulpattana N, Luk-In S, Hongsing P, Hurst C, Badavath VN, Jenjaroenpun P, Wongsurawat T, Teeratakulpisan N, Kerr SJ, Abe S, Pearson L, Saethang T, Chantaravisoot N, Higgins PG, Chatsuwan T. 1355. Cluster of Multi-drug Resistance Neisseria gonorrhoeae Isolates with Reduce Ceftriaxone Susceptibility, First Report in Thailand. Open Forum Infect Dis 2021. [DOI: 10.1093/ofid/ofab466.1547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Rapid emergence of global azithromycin resistance, with ceftriaxone reduce susceptibility/resistant strains, threatens the current recommends dual therapy with ceftriaxone and azithromycin for gonorrhea to ensure effective treatment. Thailand is a major risk area for gonorrhea because it as a key destination for sex tourism industry, where antibiotic resistance gonorrhea can spread easily and quickly across the region. Here, we identified a first cluster of Neisseria gonorrhoeae isolates with decreased ceftriaxone susceptibility in Thailand.
Methods
A 134 N. gonorrhoeae isolates collected from Thai Red Cross Anonymous Clinic, Bangkok, during 2016–2018 were studied. Broth micro-dilution and plate dilution methods to define resistance or decreased susceptibilityaccording to CLSI guidelines. Select isolates were subjected to whole genome sequencing with an Illumina MiSeq V2 instrument and analysis using CLCBio Genomics Workbench v6.5. Molecular docking studies were carried out to understand binding mode analysis and orientation of ceftriaxone in the active site of PBP2. Biofilm formation measured by confocal laser scanning microscopy.
Results
Among the N. gonorrhoeae clinical isolates, two isolates had significant reduced susceptibility to ceftriaxone (MICs of 0.125 mg/L), which were isolated from urethral swab in male heterosexual patients. Both were multidrug resistance and strong biofilm producers with ceftriaxone tolerance (MBEC > 128 mg/L). One isolate was resistant to azithromycin (MIC of 1 mg/L), and other one remained susceptible (MIC of 0.5 mg/L). Reduced susceptibility to ceftriaxone associated with alterations in PBP2, PBP1, PorB, MtrR, and mtrR promoter region with one belonged to ST7235 and second one had new allele number of tbpB with new sequence type (ST). Ceftriaxone weakly occupy the active site of mosaic XXXIV penicillin-binding protein 2 (PBP2) variant in both. Molecular epidemiology results reviled that both isolates display similarities with isolates from UK, USA, and Netherlands.
Conclusion
This first cluster of genetically related gonococcal isolates with decreased ceftriaxone susceptibility may bring threat of treatment failure in Thailand. Also highlighted the importance of maintaining surveillance for antimicrobial resistance.
Disclosures
All Authors: No reported disclosures
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Affiliation(s)
- Dhammika Leshan Wannigama
- Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand, Bangkok, Krung Thep, Thailand
| | - Naris Kueakulpattana
- Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand, Bangkok, Krung Thep, Thailand
| | - Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand, Pathumwan, Krung Thep, Thailand
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand, Chiang Rai, Chiang Rai, Thailand
| | - Cameron Hurst
- Department of Statistic, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia, Brisbane, Queensland, Australia
| | - Vishnu Nayak Badavath
- Applied Medical Virology Research Unit, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand, Pathumwan, Krung Thep, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand, Pathumwan, Krung Thep, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand, Pathumwan, Krung Thep, Thailand
| | - Nipat Teeratakulpisan
- HIV-NAT, Thai Red Cross AIDS Research Centre, Bangkok, Thailand, Pathumwan, Krung Thep, Thailand
| | - Stephen J Kerr
- Chulalongkorn University, Pathumwan, Krung Thep, Thailand
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan, Yamagata, Yamagata, Japan
| | - Lachlan Pearson
- Centre for Heart Research, Westmead Institute for Medical Research, Sydney, New South Wales, Australia, Sydney, New South Wales, Australia
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand, Pathumwan, Krung Thep, Thailand
| | - Naphat Chantaravisoot
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand, Pathumwan, Krung Thep, Thailand
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany, Cologne, Nordrhein-Westfalen, Germany
| | - Tanittha Chatsuwan
- Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Pathumwan, Krung Thep, Thailand
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9
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Shein AMS, Wannigama DL, Higgins PG, Hurst C, Abe S, Hongsing P, Chantaravisoot N, Saethang T, Luk-in S, Liao T, Nilgate S, Rirerm U, Kueakulpattana N, Laowansiri M, Srisakul S, Muhummudaree N, Techawiwattanaboon T, Gan L, Xu C, Kupwiwat R, Phattharapornjaroen P, Rojanathanes R, Leelahavanichkul A, Chatsuwan T. Novel colistin-EDTA combination for successful eradication of colistin-resistant Klebsiella pneumoniae catheter-related biofilm infections. Sci Rep 2021; 11:21676. [PMID: 34737361 PMCID: PMC8568960 DOI: 10.1038/s41598-021-01052-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/20/2021] [Indexed: 12/20/2022] Open
Abstract
Development of an effective therapy to overcome colistin resistance in Klebsiella pneumoniae, a common pathogen causing catheter-related biofilm infections in vascular catheters, has become a serious therapeutic challenge that must be addressed urgently. Although colistin and EDTA have successful roles for eradicating biofilms, no in vitro and in vivo studies have investigated their efficacy in catheter-related biofilm infections of colistin-resistant K. pneumoniae. In this study, colistin resistance was significantly reversed in both planktonic and mature biofilms of colistin-resistant K. pneumoniae by a combination of colistin (0.25-1 µg/ml) with EDTA (12 mg/ml). This novel colistin-EDTA combination was also demonstrated to have potent efficacy in eradicating colistin-resistant K. pneumoniae catheter-related biofilm infections, and eliminating the risk of recurrence in vivo. Furthermore, this study revealed significant therapeutic efficacy of colistin-EDTA combination in reducing bacterial load in internal organs, lowering serum creatinine, and protecting treated mice from mortality. Altered in vivo expression of different virulence genes indicate bacterial adaptive responses to survive in hostile environments under different treatments. According to these data discovered in this study, a novel colistin-EDTA combination provides favorable efficacy and safety for successful eradication of colistin-resistant K. pneumonia catheter-related biofilm infections.
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Affiliation(s)
- Aye Mya Sithu Shein
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Interdisciplinary Program of Medical Microbiology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.1012.20000 0004 1936 7910School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA Australia
| | - Paul G. Higgins
- grid.6190.e0000 0000 8580 3777Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany ,German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Cameron Hurst
- grid.1049.c0000 0001 2294 1395Statistics, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Shuichi Abe
- grid.417323.00000 0004 1773 9434Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Parichart Hongsing
- grid.411554.00000 0001 0180 5757Mae Fah Luang University Hospital, Chiang Rai, Thailand ,grid.411554.00000 0001 0180 5757School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Naphat Chantaravisoot
- grid.7922.e0000 0001 0244 7875Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thammakorn Saethang
- grid.9723.f0000 0001 0944 049XDepartment of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sirirat Luk-in
- grid.10223.320000 0004 1937 0490Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Tingting Liao
- grid.7922.e0000 0001 0244 7875Department of Physiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Center of Excellence for Microcirculation, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sumanee Nilgate
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ubolrat Rirerm
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naris Kueakulpattana
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Matchima Laowansiri
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sukrit Srisakul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Netchanok Muhummudaree
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Teerasit Techawiwattanaboon
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Chula Vaccine Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Lin Gan
- grid.490170.bDepartment of General Surgery, Fuling Center Hospital of Chongqing City, Chongqing, China
| | - Chenchen Xu
- grid.412676.00000 0004 1799 0784In-Patient Pharmacy, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rosalyn Kupwiwat
- grid.412434.40000 0004 1937 1127Chulabhorn International College of Medicine, Thammasat University, Thammasat University Hospital, Bangkok, Thailand
| | - Phatthranit Phattharapornjaroen
- grid.10223.320000 0004 1937 0490Department of Emergency Medicine, Center of Excellence, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand ,grid.8761.80000 0000 9919 9582Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - Rojrit Rojanathanes
- grid.7922.e0000 0001 0244 7875Center of Excellence in Materials and Bio-Interfaces, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand ,grid.7922.e0000 0001 0244 7875Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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10
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Kueakulpattana N, Wannigama DL, Luk-In S, Hongsing P, Hurst C, Badavath VN, Jenjaroenpun P, Wongsurawat T, Teeratakulpisan N, Kerr SJ, Abe S, Phattharapornjaroen P, Shein AMS, Saethang T, Chantaravisoot N, Amarasiri M, Higgins PG, Chatsuwan T. Multidrug-resistant Neisseria gonorrhoeae infection in heterosexual men with reduced susceptibility to ceftriaxone, first report in Thailand. Sci Rep 2021; 11:21659. [PMID: 34737332 PMCID: PMC8569152 DOI: 10.1038/s41598-021-00675-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/15/2021] [Indexed: 12/01/2022] Open
Abstract
The global rapid emergence of azithromycin/ceftriaxone resistant Neisseria gonorrhoeae threatens current recommend azithromycin/ceftriaxone dual therapy for gonorrhea to ensure effective treatment. Here, we identified the first two N. gonorrhoeae isolates with decreased ceftriaxone susceptibility in Thailand. Among 134 N. gonorrhoeae isolates collected from Thai Red Cross Anonymous Clinic, Bangkok, two isolates (NG-083 and NG-091) from urethral swab in male heterosexual patients had reduced susceptibility to ceftriaxone (MICs of 0.125 mg/L). Both were multidrug resistant and strong biofilm producers with ceftriaxone tolerance (MBEC > 128 mg/L). NG-083 and NG-091 remained susceptible to azithromycin (MIC of 1 mg/L and 0.5 mg/L, respectively). Reduced susceptibility to ceftriaxone was associated with alterations in PBP2, PBP1, PorB, MtrR, and mtrR promoter region. NG-083 belonged to sequence type (ST) 7235 and NG-091 has new allele number of tbpB with new ST. Molecular docking revealed ceftriaxone weakly occupied the active site of mosaic XXXIV penicillin-binding protein 2 variant in both isolates. Molecular epidemiology results revealed that both isolates display similarities with isolates from UK, USA, and The Netherlands. These first two genetically related gonococcal isolates with decreased ceftriaxone susceptibility heralds the threat of treatment failure in Thailand, and importance of careful surveillance.
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Affiliation(s)
- Naris Kueakulpattana
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, King, Thailand.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, King, Thailand.,School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Mae Fah Luang University, Chiang Rai, 57100, Thailand.,School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Cameron Hurst
- Department of Statistic, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Vishnu Nayak Badavath
- Institute for Drug Research, The Hebrew University, Jerusalem, 9112001, Israel.,Chitkara College of Pharmacy, Chitkara University, Punjab, 140401, India
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | | | - Stephen J Kerr
- HIV-NAT, Thai Red Cross AIDS Research Centre, Bangkok, Thailand.,Center of Excellence in Biostatistics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Phatthranit Phattharapornjaroen
- Department of Emergency Medicine, Center of Excellence, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Aye Mya Sithu Shein
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, King, Thailand.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Naphat Chantaravisoot
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Mohan Amarasiri
- Laboratory of Environmental HygieneDepartment of Health Science, School of Allied Health Sciences, Kitasato University, Sagamihara-Minami, KitasatoKanagawa, 252-0373, Japan
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Centre for Infection Research, Partner Site Bonn-Cologne, Cologne, Germany
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, King, Thailand. .,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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11
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Wannigama DL, Amarasiri M, Hurst C, Phattharapornjaroen P, Abe S, Hongsing P, Rad SMAH, Pearson L, Saethang T, Luk-In S, Kueakulpattana N, Storer RJ, Ounjai P, Jacquet A, Leelahavanichkul A, Chatsuwan T. Tracking COVID-19 with wastewater to understand asymptomatic transmission. Int J Infect Dis 2021; 108:296-299. [PMID: 33989774 PMCID: PMC8111879 DOI: 10.1016/j.ijid.2021.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION SARS-CoV-2 RNA is excreted in feces of most patients, therefore viral load in wastewater can be used as a surveillance tool to develop an early warning system to help and manage future pandemics. METHODS We collected wastewater from 24 random locations at Bangkok city center and 26 nearby suburbs from July to December 2020. SARS-CoV-2 RNA copy numbers were measured using real-time polymerase chain reaction (PCR). RESULTS SARS-CoV-2 RNA was detected in wastewater from both the city center and suburbs. Except for July, there were no significant differences in copy numbers between the city center and suburbs. Between October and November, a sharp rise in copy number was observed in both places followed by two to three times increase in December, related to SARS-CoV-2 cases reported for same month. CONCLUSIONS Our study provided the first dataset related to SARS-CoV-2 viral RNA in the wastewater of Bangkok. Our results suggest that wastewater could be used as a complementary source for detecting viral RNA and predicting upcoming outbreaks and waves.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Mohan Amarasiri
- Laboratory of Environmental Hygiene, Department of Health Science, School of Allied Health Sciences, Graduate School of Medical Sciences, Kitasato University, Kitasato, Sagamihara-Minami, Kanagawa, Japan
| | - Cameron Hurst
- Statistics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Faculty of Public Health, Thammasat University, Rangsit, Khlong Luang District, Pathum Thani Thailand
| | - Phatthranit Phattharapornjaroen
- Department of Emergency Medicine, Center of Excellence, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand; Institute of Clinical Sciences, Department of Surgery, Sahlgrenska Academy, Gothenburg University, 40530 Gothenburg, Sweden
| | - Shuichi Abe
- Department of Infectious Diseases and Infection Control, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Parichart Hongsing
- Mae Fah Luang University Hospital, Chiang Rai, Thailand; School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - S M Ali Hosseini Rad
- Department of Microbiology and Immunology, University of Otago, Dunedin 9010, Otago, New Zealand; Center of Excellence in Immunology and Immune-Mediated Diseases, Chulalongkorn University, Bangkok 10330, Thailand
| | - Lachlan Pearson
- Centre for Heart Research, Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Thammakorn Saethang
- Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Sirirat Luk-In
- Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Naris Kueakulpattana
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Alain Jacquet
- Chula Vaccine Research Center, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Asada Leelahavanichkul
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Translational Research in Inflammation and Immunology Research Unit (TRIRU), Department of Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand; Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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12
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Thim-uam A, Prabakaran T, Tansakul M, Makjaroen J, Wongkongkathep P, Chantaravisoot N, Saethang T, Leelahavanichkul A, Benjachat T, Paludan SR, Pisitkun T, Pisitkun P. Erratum: STING Mediates Lupus via the Activation of Conventional Dendritic Cell Maturation and Plasmacytoid Dendritic Cell Differentiation. iScience 2020; 23:101706. [PMID: 33196029 PMCID: PMC7644739 DOI: 10.1016/j.isci.2020.101706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1016/j.isci.2020.101530.].
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13
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Thim-Uam A, Prabakaran T, Tansakul M, Makjaroen J, Wongkongkathep P, Chantaravisoot N, Saethang T, Leelahavanichkul A, Benjachat T, Paludan S, Pisitkun T, Pisitkun P. STING Mediates Lupus via the Activation of Conventional Dendritic Cell Maturation and Plasmacytoid Dendritic Cell Differentiation. iScience 2020; 23:101530. [PMID: 33083760 PMCID: PMC7502826 DOI: 10.1016/j.isci.2020.101530] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/15/2020] [Accepted: 09/01/2020] [Indexed: 12/17/2022] Open
Abstract
Signaling through stimulator of interferon genes (STING) leads to the production of type I interferons (IFN-Is) and inflammatory cytokines. A gain-of-function mutation in STING was identified in an autoinflammatory disease (STING-associated vasculopathy with onset in infancy; SAVI). The expression of cyclic GMP-AMP, DNA-activated cGAS-STING pathway, increased in a proportion of patients with SLE. The STING signaling pathway may be a candidate for targeted therapy in SLE. Here, we demonstrated that disruption of STING signaling ameliorated lupus development in Fcgr2b-deficient mice. Activation of STING promoted maturation of conventional dendritic cells and differentiation of plasmacytoid dendritic cells via LYN interaction and phosphorylation. The inhibition of LYN decreased the differentiation of STING-activated dendritic cells. Adoptive transfer of STING-activated bone marrow-derived dendritic cells into the FCGR2B and STING double-deficiency mice restored lupus phenotypes. These findings provide evidence that the inhibition of STING signaling may be a candidate targeted treatment for a subset of patients with SLE.
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Affiliation(s)
- Arthid Thim-Uam
- Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand.,Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | | | - Mookmanee Tansakul
- Section for Translational Medicine Program, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Jiradej Makjaroen
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Piriya Wongkongkathep
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Naphat Chantaravisoot
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Thammakorn Saethang
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Asada Leelahavanichkul
- Center of Excellence in Immunology and Immune-mediated Diseases, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Thitima Benjachat
- Center of Excellence in Immunology and Immune-mediated Diseases, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
| | - Søren Paludan
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand.,Epithelial Systems Biology Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Prapaporn Pisitkun
- Section for Translational Medicine Program, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand.,Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, 270 Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
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14
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Tansakul M, Thim-Uam A, Saethang T, Makjaroen J, Wongprom B, Pisitkun T, Pisitkun P. Deficiency of STING Promotes Collagen-Specific Antibody Production and B Cell Survival in Collagen-Induced Arthritis. Front Immunol 2020; 11:1101. [PMID: 32582187 PMCID: PMC7283782 DOI: 10.3389/fimmu.2020.01101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
The levels of interferon-alpha are high in the serum and synovial fluid of rheumatoid arthritis (RA) patients. Activation of the stimulator of type I interferon genes (STING) mediates the productions of type I interferon and promotes chronic inflammation. STING plays a significant role in autoimmune lupus mice. However, the function of STING in collagen-induced arthritis (CIA) model has never been described. This study aimed to test the function of STING in CIA. The Sting-deficient mice developed arthritis comparable to WT mice. The levels of anti-collagen antibody from Sting-deficient mice were significantly higher than the WT mice. The B cells derived from Sting-deficient mice showed better survival than WT mice in response to the B cell receptor (BCR) stimulation. Activation of STING also induced B cell death, especially in activated B cells. This study demonstrated that the inhibition of STING promotes anti-collagen antibodies and B cell survival, which suggested that STING acts as a negative regulator of B cell function in the CIA model.
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Affiliation(s)
- Mookmanee Tansakul
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Arthid Thim-Uam
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Thammakorn Saethang
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jiradej Makjaroen
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Benjawan Wongprom
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Prapaporn Pisitkun
- Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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15
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Wannigama DL, Hurst C, Hongsing P, Pearson L, Saethang T, Chantaravisoot N, Singkham-In U, Luk-In S, Storer RJ, Chatsuwan T. A rapid and simple method for routine determination of antibiotic sensitivity to biofilm populations of Pseudomonas aeruginosa. Ann Clin Microbiol Antimicrob 2020; 19:8. [PMID: 32169075 PMCID: PMC7071750 DOI: 10.1186/s12941-020-00350-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/26/2020] [Indexed: 02/07/2023] Open
Abstract
Treatment of infections by Pseudomonas aeruginosa forming biofilms after antimicrobial testing on planktonic bacteria can result in substantial failure. Therefore, we offer a robust and simple experimental platform to test the impact of antimicrobials on biofilms. Antibiotic response patterns varied uniquely within biofilm formation capacity and minimal biofilm eradication concentrations (MBECs) has a significantly better discriminatory power than minimum inhibitory concentrations (MICs) to differentiate the overall efficiency of antibiotics to eradicate biofilm. Our resazurin-based 96-well-plate platform is able to emulate bacterial responses to antibiotics under biofilm conditions in a fast, simple, and cost-effective screening method adaptable to automation, and warrants trials in the clinic.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand.,School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, WA, Australia.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Cameron Hurst
- Department of Statistics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Center of Excellence in Biostatistics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Parichart Hongsing
- School of Integrative Medicine, Mae Fah Luang University, Chiang Rai, Thailand
| | - Lachlan Pearson
- Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Centre for Heart Research, Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Thammakorn Saethang
- Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Naphat Chantaravisoot
- Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Uthaibhorn Singkham-In
- Department of Microbiology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirirat Luk-In
- Department of Microbiology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand.,Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, King Chulalongkorn Memorial Hospital, Chulalongkorn University, Bangkok, Thailand. .,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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16
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Saethang T, Hodge K, Yang CR, Zhao Y, Kimkong I, Knepper MA, Pisitkun T. PTM-Logo: a program for generation of sequence logos based on position-specific background amino-acid probabilities. Bioinformatics 2019; 35:5313-5314. [PMID: 31318409 DOI: 10.1093/bioinformatics/btz568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/29/2019] [Accepted: 07/16/2019] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Identification of the amino-acid motifs in proteins that are targeted for post-translational modifications (PTMs) is of great importance in understanding regulatory networks. Information about targeted motifs can be derived from mass spectrometry data that identify peptides containing specific PTMs such as phosphorylation, ubiquitylation and acetylation. Comparison of input data against a standardized 'background' set allows identification of over- and under-represented amino acids surrounding the modified site. Conventionally, calculation of targeted motifs assumes a random background distribution of amino acids surrounding the modified position. However, we show that probabilities of amino acids depend on (i) the type of the modification and (ii) their positions relative to the modified site. Thus, software that identifies such over- and under-represented amino acids should make appropriate adjustments for these effects. Here we present a new program, PTM-Logo, that generates representations of these amino acid preferences ('logos') based on position-specific amino-acid probability backgrounds calculated either from user-input data or curated databases. AVAILABILITY AND IMPLEMENTATION PTM-Logo is freely available online at http://sysbio.chula.ac.th/PTMLogo/ or https://hpcwebapps.cit.nih.gov/PTMLogo/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thammakorn Saethang
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Computer Science, Kasetsart University, Bangkok, Thailand
| | - Kenneth Hodge
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA
| | - Yue Zhao
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA
| | - Ingorn Kimkong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA
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17
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Vanichtantikul A, Hodge KG, Somparn P, Saethang T, Triratanachat S, Pisitkun T, Lertkhachonsuk R. Corrigendum to "Proteomic identification of predictive biomarkers for malignant transformation in complete hydatidiform moles" [Placenta 77 (2019) 58-64]. Placenta 2019; 85:80. [PMID: 31300166 DOI: 10.1016/j.placenta.2019.06.387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Asama Vanichtantikul
- Placental Related Disease Research Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Kenneth G Hodge
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Poorichaya Somparn
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Thammakorn Saethang
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Surang Triratanachat
- Division of Gynecologic Cytopathology, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Trairak Pisitkun
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Ruangsak Lertkhachonsuk
- Placental Related Disease Research Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand.
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18
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Wannigama DL, Hurst C, Pearson L, Saethang T, Singkham-In U, Luk-In S, Storer RJ, Chatsuwan T. Simple fluorometric-based assay of antibiotic effectiveness for Acinetobacter baumannii biofilms. Sci Rep 2019; 9:6300. [PMID: 31004100 PMCID: PMC6474882 DOI: 10.1038/s41598-019-42353-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/27/2019] [Indexed: 02/07/2023] Open
Abstract
Despite strengthened antimicrobial therapy, biofilm infections of Acinetobacter baumannii are associated with poor prognosis and limited therapeutic options. Assessing antibiotics on planktonic bacteria can result in failure against biofilm infections. Currently, antibiotics to treat biofilm infections are administered empirically, usually without considering the susceptibility of the biofilm objectively before beginning treatment. For effective therapy to resolve biofilm infections it is essential to assess the efficacy of commonly used antibiotics against biofilms. Here, we offer a robust and simple assay to assess the efficacy of antibiotics against biofilms. In the present work, we carefully optimized the incubation time, detection range, and fluorescence reading mode for resazurin-based viability staining of biofilms in 96-well-plates and determined minimal biofilm eradication concentrations (MBECs) for A. baumannii isolates from patients with chronic infection. By applying this assay, we demonstrated that antibiotic response patterns varied uniquely within the biofilm formation of various clinical samples. MBEC-50 and 75 have significant discriminatory power over minimum inhibitory concentrations for planktonic suspensions to differentiate the overall efficiency of an antibiotic to eradicate a biofilm. The present assay is an ideal platform on which to assess the efficacy of antibiotics against biofilms in vitro to pave the way for more effective therapy.
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Affiliation(s)
- Dhammika Leshan Wannigama
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Cameron Hurst
- Center of Excellence in Biostatistics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Statistics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Lachlan Pearson
- Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Snowy River Vet Clinic and Veterinary Hospital, Orbost, Victoria, Australia
| | - Thammakorn Saethang
- Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Computer Science, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Uthaibhorn Singkham-In
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sirirat Luk-In
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand.,Interdisciplinary Program of Medical Microbiology, Graduate School, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Robin James Storer
- Office of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tanittha Chatsuwan
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand. .,Antimicrobial Resistance and Stewardship Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
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19
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Wannigama D, Hurst C, Pearson L, Saethang T, Singkham-in U, Luk-in S, Storer R, Chatsuwan T. A SIMPLE ANTIBIOTIC SUSCEPTIBILITY ASSAY FOR PSEUDOMONAS AERUGINOSA AND ACINETOBACTER BAUMANNII BIOFILM COULD LEAD TO EFFECTIVE TREATMENT SELECTION FOR CHRONIC LUNG INFECTIONS. Chest 2019. [DOI: 10.1016/j.chest.2019.02.351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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20
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Vanichtantikul A, Hodge KG, Somparn P, Saethang T, Triratanachat S, Pisitkun T, Lertkhachonsuk R. Proteomic identification of predictive biomarkers for malignant transformation in complete hydatidiform moles. Placenta 2019; 77:58-64. [PMID: 30827356 DOI: 10.1016/j.placenta.2019.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 12/11/2018] [Accepted: 02/04/2019] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Protein expression in cells are associated with oncogenesis. This study aims to explore proteomic profiles and discover potential biomarkers that can predict malignant transformation of hydatidiform mole. METHODS Retrospective analysis was done in 14 cases of remission hydatidiform mole and 14 cases of hydatidiform mole who later developed malignancy (GTN group). Molar tissues were retrieved from -70 °C frozen tissue. Subsequently, a large-scale proteomic analysis was performed to identify proteins and compare their abundance levels in the preserved molar tissues from these two groups using a dimethyl-labeling technique coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS A total of 2,153 proteins were identified from all samples. 22 and 10 proteins were significantly up-regulated and down-regulated, respectively, in the GTN group compared with the mole group. These altered proteins were found in several biological groups such as cell-cell adhesion, secreted proteins, and ribonucleoproteins. Several hormone-related proteins were among the most up-regulated proteins in the GTN group including choriogonadotropin subunit beta (β-hCG) and alpha (α-hCG), growth/differentiation factor 15, as well as both pregnancy-specific beta-1-glycoproteins 2 and 3. In contrast, protein S100-A11 and l-lactate dehydrogenase A chain, were down-regulated in molar tissue from most patients in the GTN group. DISCUSSION This study identified a set of differentially expressed proteins in molar tissues that could potentially be further examined as predictive biomarkers for the malignant transformation of CHMs. A molar proteome database was constructed and can be accessible online at http://sysbio.chula.ac.th/Database/GTD_DB/Supplementary_Data.xlsx.
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Affiliation(s)
- Asama Vanichtantikul
- Placental Related Disease Research Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Kenneth G Hodge
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Poorichaya Somparn
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Thammakorn Saethang
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Surang Triratanachat
- Division of Gynecologic Cytopathology, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Trairak Pisitkun
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Thailand
| | - Ruangsak Lertkhachonsuk
- Placental Related Disease Research Unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Thailand.
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21
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Saethang T, Hodge K, Kimkong I, Payne DM, Knepper MA, Pisitkun T. AbDesigner3D: a structure-guided tool for peptide-based antibody production. Bioinformatics 2018; 34:2158-2160. [PMID: 29408997 DOI: 10.1093/bioinformatics/bty055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/31/2018] [Indexed: 11/13/2022] Open
Abstract
Summary We present AbDesigner3D, a new tool for identification of optimal immunizing peptides for antibody production using a peptide-based strategy. AbDesigner3D integrates 3D structural data from the Protein Data Bank (PDB) with UniProt data, which includes basic sequence data, post-translational modification sites, SNP occurrences and more. Other features, such as uniqueness and conservation scores, are calculated based on sequences from UniProt. The 3D visualization capabilities allow an intuitive interface, while an abundance of quantitative output simplifies the process of comparing immunogen peptides. Important quantitative features added in this tool include calculation and display of accessible surface area (ASA) and protein-protein interacting residues (PPIR). The specialized data visualization features of AbDesigner3D will greatly assist users to optimize their choice of immunizing peptides. Availability and implementation AbDesigner3D is freely available at http://sysbio.chula.ac.th/AbDesigner3D or https://hpcwebapps.cit.nih.gov/AbDesigner3D/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Thammakorn Saethang
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kenneth Hodge
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ingorn Kimkong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - D Michael Payne
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, USA
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22
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Cannizzaro L, Rossoni G, Savi F, Altomare A, Marinello C, Saethang T, Carini M, Payne DM, Pisitkun T, Aldini G, Leelahavanichkul A. Regulatory landscape of AGE-RAGE-oxidative stress axis and its modulation by PPARγ activation in high fructose diet-induced metabolic syndrome. Nutr Metab (Lond) 2017; 14:5. [PMID: 28101123 PMCID: PMC5237238 DOI: 10.1186/s12986-016-0149-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/29/2016] [Indexed: 12/26/2022] Open
Abstract
Background The AGE-RAGE-oxidative stress (AROS) axis is involved in the onset and progression of metabolic syndrome induced by a high-fructose diet (HFD). PPARγ activation is known to modulate metabolic syndrome; however a systems-level investigation looking at the protective effects of PPARγ activation as related to the AROS axis has not been performed. The aim of this work is to simultaneously characterize multiple molecular parameters within the AROS axis, using samples taken from different body fluids and tissues of a rat model of HFD-induced metabolic syndrome, in the presence or absence of a PPARγ agonist, Rosiglitazone (RGZ). Methods Rats were fed with 60% HFD for the first half of the treatment duration (21 days) then continued with either HFD alone or HFD plus RGZ for the second half. Results Rats receiving HFD alone showed metabolic syndrome manifestations including hypertension, dyslipidemia, increased glucose levels and insulin resistance, as well as abnormal kidney and inflammatory parameters. Systolic blood pressure, plasma triglyceride and glucose levels, plasma creatinine, and albuminuria were significantly improved in the presence of RGZ. The following molecular parameters of the AROS axis were significantly upregulated in our rat model: carboxymethyl lysine (CML) in urine and liver; carboxyethyl lysine (CEL) in urine; advanced glycation end products (AGEs) in plasma; receptor for advanced glycation end products (RAGE) in liver and kidney; advanced oxidation protein products (AOPP) in plasma; and 4-hydroxynonenal (HNE) in plasma, liver, and kidney. Conversely, with RGZ administration, the upregulation of AOPP and AGEs in plasma, CML and CEL in urine, RAGE in liver as well as HNE in plasma and liver was significantly counteracted/prevented. Conclusions Our data demonstrate (i) the systems-level regulatory landscape of HFD-induced metabolic syndrome involving multiple molecular parameters, including HNE, AGEs and their receptor RAGE, and (ii) attenuation of metabolic syndrome by PPARγ modulation. Electronic supplementary material The online version of this article (doi:10.1186/s12986-016-0149-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luca Cannizzaro
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand ; Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Giuseppe Rossoni
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Vanvitelli 32, 20129 Milan, Italy
| | - Federica Savi
- Pathological Anatomy Unit (U.O.C. Anatomia Patologica), ASST Santi Paolo e Carlo, Via di Rudinì 8, 20142 Milan, Italy
| | - Alessandra Altomare
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Cristina Marinello
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Thammakorn Saethang
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Marina Carini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - D Michael Payne
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Trairak Pisitkun
- Systems Biology Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Giancarlo Aldini
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli 25, 20133 Milan, Italy
| | - Asada Leelahavanichkul
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330 Thailand
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Wisetsathorn S, Tantithavorn V, Hirankarn N, Tangkijvanich P, Saethang T, Kimkong I. Gene polymorphisms of autophagy machinery and the risk of hepatitis B virus-related hepatocellular carcinoma in a Thai population. ScienceAsia 2017. [DOI: 10.2306/scienceasia1513-1874.2017.43.362] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Saethang T, Payne DM, Avihingsanon Y, Pisitkun T. A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions. BMC Bioinformatics 2016; 17:307. [PMID: 27534850 PMCID: PMC4989344 DOI: 10.1186/s12859-016-1165-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 08/05/2016] [Indexed: 02/02/2023] Open
Abstract
Background One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR can either interfere with or facilitate the interaction between proteins. The ability to predict whether sites of protein modifications are inside or outside of PPIRs would be useful in further elucidating the regulatory mechanisms by which modifications of specific proteins regulate their cellular functions. Results Using two of the comprehensive databases for protein-protein interaction and protein modification site data (PDB and PhosphoSitePlus, respectively), we created new databases that map PTMs to their locations inside or outside of PPIRs. The mapped PTMs represented only 5 % of all known PTMs. Thus, in order to predict localization within or outside of PPIRs for the vast majority of PTMs, a machine learning strategy was used to generate predictive models from these mapped databases. For the three mapped PTM databases which had sufficient numbers of modification sites for generating models (acetylation, phosphorylation, and ubiquitylation), the resulting models yielded high overall predictive performance as judged by a combined performance score (CPS). Among the multiple properties of amino acids that were used in the classification tasks, hydrophobicity was found to contribute substantially to the performance of the final predictive models. Compared to the other classifiers we also evaluated, the SVM provided the best performance overall. Conclusions These models are the first to predict whether PTMs are located inside or outside of PPIRs, as demonstrated by their high predictive performance. The models and data presented here should be useful in prioritizing both known and newly identified PTMs for further studies to determine the functional relationship between specific PTMs and protein-protein interactions. The implemented R package is available online (http://sysbio.chula.ac.th/PtmPPIR). Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1165-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thammakorn Saethang
- Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok, 10330, Thailand
| | - D Michael Payne
- Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok, 10330, Thailand
| | - Yingyos Avihingsanon
- Department of Medicine, Division of Nephrology, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok, 10330, Thailand.
| | - Trairak Pisitkun
- Systems Biology Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok, 10330, Thailand. .,Epithelial Systems Biology Laboratory, NHLBI, National Institutes of Health, Bethesda, MD, 20892-1603, USA.
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Tho Dang X, Hirose O, Hung Bui D, Saethang T, Anh Tran V, Anh T. Nguyen L, Kien T. Le T, Kubo M, Yamada Y, Satou K. A Novel Over-Sampling Method and its Application to Cancer Classification from Gene Expression Data. CBIJ 2013. [DOI: 10.1273/cbij.13.19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Xuan Tho Dang
- Graduate School of Natural Science and Technology, Kanazawa University
| | - Osamu Hirose
- Institute of Science and Engineering, Kanazawa University
| | - Duong Hung Bui
- Faculty of Information Technology, Vietnam Trade Union University
| | | | - Vu Anh Tran
- Graduate School of Natural Science and Technology, Kanazawa University
| | - Lan Anh T. Nguyen
- Graduate School of Natural Science and Technology, Kanazawa University
| | - Tu Kien T. Le
- Graduate School of Natural Science and Technology, Kanazawa University
| | - Mamoru Kubo
- Institute of Science and Engineering, Kanazawa University
| | - Yoichi Yamada
- Institute of Science and Engineering, Kanazawa University
| | - Kenji Satou
- Institute of Science and Engineering, Kanazawa University
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Saethang T, Hirose O, Kimkong I, Tran VA, Dang XT, Nguyen LAT, Le TKT, Kubo M, Yamada Y, Satou K. EpicCapo: epitope prediction using combined information of amino acid pairwise contact potentials and HLA-peptide contact site information. BMC Bioinformatics 2012; 13:313. [PMID: 23176036 PMCID: PMC3548761 DOI: 10.1186/1471-2105-13-313] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 11/15/2012] [Indexed: 11/10/2022] Open
Abstract
Background Epitope identification is an essential step toward synthetic vaccine development since epitopes play an important role in activating immune response. Classical experimental approaches are laborious and time-consuming, and therefore computational methods for generating epitope candidates have been actively studied. Most of these methods, however, are based on sophisticated nonlinear techniques for achieving higher predictive performance. The use of these techniques tend to diminish their interpretability with respect to binding potential: that is, they do not provide much insight into binding mechanisms. Results We have developed a novel epitope prediction method named EpicCapo and its variants, EpicCapo+ and EpicCapo+REF. Nonapeptides were encoded numerically using a novel peptide-encoding scheme for machine learning algorithms by utilizing 40 amino acid pairwise contact potentials (referred to as AAPPs throughout this paper). The predictive performances of EpicCapo+ and EpicCapo+REF outperformed other state-of-the-art methods without losing interpretability. Interestingly, the most informative AAPPs estimated by our study were those developed by Micheletti and Simons while previous studies utilized two AAPPs developed by Miyazawa & Jernigan and Betancourt & Thirumalai. In addition, we found that all amino acid positions in nonapeptides could effect on performances of the predictive models including non-anchor positions. Finally, EpicCapo+REF was applied to identify candidates of promiscuous epitopes. As a result, 67.1% of the predicted nonapeptides epitopes were consistent with preceding studies based on immunological experiments. Conclusions Our method achieved high performance in testing with benchmark datasets. In addition, our study identified a number of candidates of promiscuous CTL epitopes consistent with previously reported immunological experiments. We speculate that our techniques may be useful in the development of new vaccines. The R implementation of EpicCapo+REF is available at
http://pirun.ku.ac.th/~fsciiok/EpicCapoREF.zip. Datasets are available at
http://pirun.ku.ac.th/~fsciiok/Datasets.zip.
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Affiliation(s)
- Thammakorn Saethang
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan.
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Saethang T, Hirose O, Kimkong I, Tran VA, Dang XT, Nguyen LAT, Le TKT, Kubo M, Yamada Y, Satou K. PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors. J Immunol Methods 2012; 387:293-302. [PMID: 23058674 DOI: 10.1016/j.jim.2012.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/17/2012] [Indexed: 12/11/2022]
Abstract
Prediction of peptide immunogenicity is a promising approach for novel vaccine discovery. Conventionally, epitope prediction methods have been developed to accelerate the process of vaccine production by searching for candidate peptides from pathogenic proteins. However, recent studies revealed that peptides with high binding affinity to major histocompatibility complex molecules (MHCs) do not always result in high immunogenicity. Therefore, it is promising to predict the peptide immunogenicity rather than epitopes in order to discover new vaccines more effectively. To this end, we developed a novel T-cell reactivity predictor which we call PAAQD. Nonapeptides were encoded numerically, using combining information of amino acid pairwise contact potentials (AAPPs) and quantum topological molecular similarity (QTMS) descriptors. Encoded data were used in the construction of our classification model. Our numerical experiments suggested that the predictive performance of PAAQD is at least comparable with POPISK, one of the pioneering techniques for T-cell reactivity prediction. Also, our experiment suggested that the first and eighth positions of nonapeptides are the most important for immunogenicity and most of the anchor residues in epitope prediction were not important in T-cell reactivity prediction. The R implementation of PAAQD is available at http://pirun.ku.ac.th/~fsciiok/PAAQD.rar.
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Affiliation(s)
- Thammakorn Saethang
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan.
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Abstract
This article reports the use of a successful strategy for teaching non-critical care nurses how to safely administer critical cardiovascular drugs. The use of a gaming technique to accomplish this, accompanied by a caricature case study, is described in detail. Participants' evaluations evidenced a high degree of satisfaction and enjoyment in learning the pharmacological content. Readers can adapt this game to other learning topics for rapid and effective learning of material specific to their institutions.
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Affiliation(s)
- T Saethang
- Henry Medical Center, Stockbridge, Georgia, USA
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