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Seng R, Chomkatekaew C, Tandhavanant S, Saiprom N, Phunpang R, Thaipadungpanit J, Batty EM, Day NPJ, Chantratita W, Eoin West T, Thomson NR, Parkhill J, Chewapreecha C, Chantratita N. Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in Northeast Thailand. Nat Commun 2024; 15:5699. [PMID: 38972886 PMCID: PMC11228029 DOI: 10.1038/s41467-024-50067-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/28/2024] [Indexed: 07/09/2024] Open
Abstract
Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conduct a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identifies three dominant lineages, each with unique gene sets potentially enhancing bacterial fitness in the environment. We find that recombination drives lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage reveal increased expression of lineage-specific genes under environmental conditions in two out of three lineages. This underscores the potential importance of environmental persistence for these dominant lineages. The study also highlights the influence of environmental factors such as terrain slope, altitude, and river direction on the geographical dispersal of B. pseudomallei. Collectively, our findings suggest that environmental persistence may play a role in facilitating the spread of B. pseudomallei, and as a prerequisite for exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.
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Affiliation(s)
- Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth M Batty
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas P J Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T Eoin West
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Nicholas R Thomson
- Parasites and Microbes Wellcome Sanger Institute, Cambridge, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Parasites and Microbes Wellcome Sanger Institute, Cambridge, UK.
- Previous Affiliations: Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut University of Technology Thonburi, Bangkok, Thailand.
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Meumann EM, Limmathurotsakul D, Dunachie SJ, Wiersinga WJ, Currie BJ. Burkholderia pseudomallei and melioidosis. Nat Rev Microbiol 2024; 22:155-169. [PMID: 37794173 DOI: 10.1038/s41579-023-00972-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, is found in soil and water of tropical and subtropical regions globally. Modelled estimates of the global burden predict that melioidosis remains vastly under-reported, and a call has been made for it to be recognized as a neglected tropical disease by the World Health Organization. Severe weather events and environmental disturbance are associated with increased case numbers, and it is anticipated that, in some regions, cases will increase in association with climate change. Genomic epidemiological investigations have confirmed B. pseudomallei endemicity in newly recognized regions, including the southern United States. Melioidosis follows environmental exposure to B. pseudomallei and is associated with comorbidities that affect the immune response, such as diabetes, and with socioeconomic disadvantage. Several vaccine candidates are ready for phase I clinical trials. In this Review, we explore the global burden, epidemiology and pathophysiology of B. pseudomallei as well as current diagnostics, treatment recommendations and preventive measures, highlighting research needs and priorities.
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Affiliation(s)
- Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia.
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia.
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- NDM Centre for Global Health Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Willem J Wiersinga
- Division of Infectious Diseases, Center for Experimental Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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Seng R, Chomkatekaew C, Tandhavanant S, Saiprom N, Phunpang R, Thaipadungpanit J, Batty EM, Day NPJ, Chantratita W, West TE, Thomson NR, Parkhill J, Chewapreecha C, Chantratita N. Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in northeast Thailand. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543359. [PMID: 38106061 PMCID: PMC10723255 DOI: 10.1101/2023.06.02.543359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conducted a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identified three dominant lineages with unique gene sets enhancing bacterial fitness, indicating lineage-specific adaptation strategies. Crucially, recombination was found to drive lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage revealed heightened expression of lineage-specific genes in environmental versus infection conditions, notably under nutrient depletion, highlighting environmental persistence as a key factor in the success of dominant lineages. The study also revealed the role of environmental factors - slope of terrain, altitude, direction of rivers, and the northeast monsoons - in shaping B. pseudomallei geographical dispersal. Collectively, our findings highlight persistence in the environment as a pivotal element facilitating B. pseudomallei spread, and as a prelude to exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.
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Affiliation(s)
- Rathanin Seng
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chalita Chomkatekaew
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Sarunporn Tandhavanant
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Natnaree Saiprom
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Elizabeth M Batty
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas PJ Day
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - T. Eoin West
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Division of Pulmonary, Critical Care & Sleep Medicine, Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, UK
| | - Claire Chewapreecha
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Previous Affiliations: Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut University of Technology Thonburi, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Jayasinghearachchi HS, Muthugama TA, Masakorala J, Kulasekara US, Jayaratne K, Jayatunga DADN, De Silva AD, Corea EM. Burkholderia pseudomallei in soil and natural water bodies in rural Sri Lanka: A hidden threat to public health. Front Vet Sci 2023; 9:1045088. [PMID: 36733425 PMCID: PMC9888492 DOI: 10.3389/fvets.2022.1045088] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/12/2022] [Indexed: 01/19/2023] Open
Abstract
Burkholderia pseudomallei is the causative agent of the potentially fatal infection, melioidosis. This study provides the first evidence for the presence of B. pseudomallei in soil and water in Sri Lanka. Targeted sampling of soil and natural water sources was done between November 2019 and October 2020 over eight field visits encompassing the neighborhood of 28 culture and/or antibody-positive melioidosis patients in northwestern, western and southern Sri Lanka. A total of eight environmental isolates of B. pseudomallei (BPs-env1 to BPs-env8) were cultured from 116 soil and 117 natural water samples collected from 72 locations. The presence of B. pseudomallei in soil and natural water in these areas poses a risk of melioidosis for populations cultivating crops in such soils and using untreated water from these sources for drinking, bathing, and other domestic purposes. Identifying sites positive for B. pseudomallei may help to mitigate risk by raising public awareness of contaminated environmental sources and allowing soil and water remediation.
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Affiliation(s)
- Himali S. Jayasinghearachchi
- Institute for Combinatorial Advanced Research and Education, General Sir John Kotelawala Defense University, Dehiwala-Mount Lavinia, Sri Lanka,*Correspondence: Himali S. Jayasinghearachchi ✉
| | - Thilini A. Muthugama
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defense University, Dehiwala-Mount Lavinia, Sri Lanka
| | - Jayanthi Masakorala
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - Upeksha S. Kulasekara
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defense University, Dehiwala-Mount Lavinia, Sri Lanka
| | - Kumari Jayaratne
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defense University, Dehiwala-Mount Lavinia, Sri Lanka
| | - D. A. Dasun N. Jayatunga
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defense University, Dehiwala-Mount Lavinia, Sri Lanka
| | - Aruna D. De Silva
- Biomedical Laboratory 2, Faculty of Medicine, General Sir John Kotelawala Defense University, Dehiwala-Mount Lavinia, Sri Lanka
| | - Enoka M. Corea
- Department of Medical Microbiology and Immunology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka,Enoka M. Corea ✉
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Richter WR, Sunderman MM, Fulton ML, Willenberg Z, Serre S, Oudejans L, Wood J, Calfee MW. Decontamination efficacy of common liquid disinfectants against non-spore-forming biological agents in soil matrices. J Appl Microbiol 2022; 133:3659-3668. [PMID: 36056613 PMCID: PMC9748868 DOI: 10.1111/jam.15802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/20/2022] [Accepted: 08/28/2022] [Indexed: 11/28/2022]
Abstract
AIMS The purpose of this study was to evaluate decontamination efficacy, within three soil types, against Yersinia pestis, Burkholderia pseudomallei, and the Venezuelan Equine Encephalitis virus (VEEV). METHODS AND RESULTS One of three liquid disinfectants (dilute bleach, Virkon-S or Klozur One) was added to three soil types (sand, loam, or clay) and allowed contact for four pre-spike durations: 0, 15, 30 and 60 min. Y. pestis, B. pseudomallei, or VEEV was then spiked into the soil (10 microliters or approx. 1 × 107 CFU or PFU into 1 g soil) and decontamination efficacy assessed at post-spike contact times of 10 or 60 min at ambient environmental conditions. Across all soil types, sandy soil resulted in the least quenching to all three disinfectants tested as shown by sustained decontamination efficacy across all pre-spike and post-spike timepoints. Clay and loam soil types exhibited quenching effects on the hypochlorite and peroxygen based disinfectants (dilute bleach and Virkon S) and in general resulted in decreased efficacy with increased pre-spike contact time. The sodium persulfate (Klozur One) performance was the most consistent across all soil types and pre-spike contact times, resulting in greater efficacy with increased post-spike time. CONCLUSIONS Liquid disinfectants can provide high levels of decontamination in soil for both viral and non-spore-forming bacterial select agents. Hypochlorite and peroxygen based disinfectants used in soils containing higher organic content (loam or clay) may require extended contact times or re-application of liquid disinfectant, in as little as 15 min of application, to achieve a 6-log reduction. SIGNIFICANCE AND IMPACT OF THE STUDY These results provide information for the performance of three disinfectants in soil against non-spore-forming select agents. These data may aid response decision makers following a biological contamination incident by informing the selection of disinfectant as well as the re-application time to achieve effective site remediation.
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Affiliation(s)
| | | | | | | | - Shannon Serre
- US Environmental Protection Agency, TW Alexander Drive, Research Triangle Park, North Carolina, USA
| | - Lukas Oudejans
- US Environmental Protection Agency, TW Alexander Drive, Research Triangle Park, North Carolina, USA
| | - Joseph Wood
- US Environmental Protection Agency, TW Alexander Drive, Research Triangle Park, North Carolina, USA
| | - Michael W. Calfee
- US Environmental Protection Agency, TW Alexander Drive, Research Triangle Park, North Carolina, USA
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Richter W, Sunderman M, Willenberg Z, Calfee M, Serre S, Wood JP. Effectiveness of formaldehyde in various soil types as a wide area decontamination approach for Bacillus anthracis spores. PLoS One 2022; 17:e0277941. [PMID: 36399484 PMCID: PMC9674150 DOI: 10.1371/journal.pone.0277941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/07/2022] [Indexed: 11/20/2022] Open
Abstract
The purpose of this study was to evaluate and compare the decontamination efficacy of liquid formaldehyde solutions for three soil types (sand, loam, and clay) against spores of Bacillus anthracis (B.a.) and Bacillus atrophaeus. Approximately 1 x 108 colony forming units were inoculated into each sample. Through a series of six bench-scale experiments, two concentrations and two volumes of liquid formaldehyde solution were then added to the soil samples and allowed to remain in contact for either 24 or 48 hours. Decontamination efficacy was assessed at either 22° or 10°C with or without lids atop the sample jars. Complete inactivation (no spores recovered from the soil samples, typically providing > 7 log reduction) of B.a. occurred in all soil types in five of the six tests, while complete inactivation of B. atrophaeus was achieved in all soil types for three of the six tests. The results demonstrated a higher probability of complete inactivation of spores for samples that were covered, samples that received the higher volume of formaldehyde, and those contaminated with B.a. Overall, the use of liquid formaldehyde solution (2.5-5%) was highly effective in inactivating entire spore populations (typically > 107 CFU) for both B.a. and B. atrophaeus in the soil matrices studied. Covering the soil after application would allow for less formaldehyde solution to be used without impacting the overall efficacy of the process. The data from this study may aid in the selection of appropriate decontamination parameters when using liquid formaldehyde for soil remediation. The data may also aid in the decision to use B. atrophaeus as a surrogate for B.a. when performing further decontamination studies using liquid formalin solutions.
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Affiliation(s)
- William Richter
- Battelle Memorial Institute, Columbus, OH, United States of America
| | | | | | - Michael Calfee
- US Environmental Protection Agency, Research Triangle Park, NC, United States of America
| | - Shannon Serre
- US Environmental Protection Agency, Research Triangle Park, NC, United States of America
| | - Joseph P. Wood
- US Environmental Protection Agency, Research Triangle Park, NC, United States of America,* E-mail:
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Shaw T, Assig K, Tellapragada C, Wagner GE, Choudhary M, Göhler A, Eshwara VK, Steinmetz I, Mukhopadhyay C. Environmental Factors Associated With Soil Prevalence of the Melioidosis Pathogen Burkholderia pseudomallei: A Longitudinal Seasonal Study From South West India. Front Microbiol 2022; 13:902996. [PMID: 35847064 PMCID: PMC9283100 DOI: 10.3389/fmicb.2022.902996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Melioidosis is a seasonal infectious disease in tropical and subtropical areas caused by the soil bacterium Burkholderia pseudomallei. In many parts of the world, including South West India, most cases of human infections are reported during times of heavy rainfall, but the underlying causes of this phenomenon are not fully understood. India is among the countries with the highest predicted melioidosis burden globally, but there is very little information on the environmental distribution of B. pseudomallei and its determining factors. The present study aimed (i) to investigate the prevalence of B. pseudomallei in soil in South West India, (ii) determine geochemical factors associated with B. pseudomallei presence and (iii) look for potential seasonal patterns of B. pseudomallei soil abundance. Environmental samplings were performed in two regions during the monsoon and post-monsoon season and summer from July 2016 to November 2018. We applied direct quantitative real time PCR (qPCR) together with culture protocols to overcome the insufficient sensitivity of solely culture-based B. pseudomallei detection from soil. A total of 1,704 soil samples from 20 different agricultural sites were screened for the presence of B. pseudomallei. Direct qPCR detected B. pseudomallei in all 20 sites and in 30.2% (517/1,704) of all soil samples, whereas only two samples from two sites were culture-positive. B. pseudomallei DNA-positive samples were negatively associated with the concentration of iron, manganese and nitrogen in a binomial logistic regression model. The highest number of B. pseudomallei-positive samples (42.6%, p < 0.0001) and the highest B. pseudomallei loads in positive samples [median 4.45 × 103 genome equivalents (GE)/g, p < 0.0001] were observed during the monsoon season and eventually declined to 18.9% and a median of 1.47 × 103 GE/g in summer. In conclusion, our study from South West India shows a wide environmental distribution of B. pseudomallei, but also considerable differences in the abundance between sites and within single sites. Our results support the hypothesis that nutrient-depleted habitats promote the presence of B. pseudomallei. Most importantly, the highest B. pseudomallei abundance in soil is seen during the rainy season, when melioidosis cases occur.
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Affiliation(s)
- Tushar Shaw
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Faculty of Life and Allied Health Sciences, Ramaiah University of Applied Sciences, Bengaluru, India
| | - Karoline Assig
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Chaitanya Tellapragada
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Gabriel E. Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Madhu Choudhary
- ICAR-Central Soil Salinity Research Institute (CSSRI), Karnal, India
| | - André Göhler
- German Federal Institute for Risk Assessment, Berlin, Germany
| | - Vandana Kalwaje Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Centre for Antimicrobial Resistance and Education, Manipal Academy of Higher Education, Manipal, India
| | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
- *Correspondence: Ivo Steinmetz,
| | - Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
- Centre for Emerging and Tropical Diseases, Manipal Academy of Higher Education, Manipal, India
- Chiranjay Mukhopadhyay,
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Pongmala K, Pierret A, Oliva P, Pando A, Davong V, Rattanavong S, Silvera N, Luangraj M, Boithias L, Xayyathip K, Menjot L, Macouin M, Rochelle-Newall E, Robain H, Vongvixay A, Simpson AJH, Dance DAB, Ribolzi O. Distribution of Burkholderia pseudomallei within a 300-cm deep soil profile: implications for environmental sampling. Sci Rep 2022; 12:8674. [PMID: 35606475 PMCID: PMC9126866 DOI: 10.1038/s41598-022-12795-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/12/2022] [Indexed: 01/02/2023] Open
Abstract
The environmental distribution of Burkholderia pseudomallei, the causative agent of melioidosis, remains poorly understood. B. pseudomallei is known to have the ability to occupy a variety of environmental niches, particularly in soil. This paper provides novel information about a putative association of soil biogeochemical heterogeneity and the vertical distribution of B. pseudomallei. We investigated (1) the distribution of B. pseudomallei along a 300-cm deep soil profile together with the variation of a range of soil physico-chemical properties; (2) whether correlations between the distribution of B. pseudomallei and soil physico-chemical properties exist and (3) when they exist, what such correlations indicate with regards to the environmental conditions conducive to the occurrence of B. pseudomallei in soils. Unexpectedly, the highest concentrations of B. pseudomallei were observed between 100 and 200 cm below the soil surface. Our results indicate that unravelling the environmental conditions favorable to B. pseudomallei entails considering many aspects of the actual complexity of soil. Important recommendations regarding environmental sampling for B. pseudomallei can be drawn from this work, in particular that collecting samples down to the water table is of foremost importance, as groundwater persistence appears to be a controlling factor of the occurrence of B. pseudomallei in soil.
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Chewapreecha C, Pensar J, Chattagul S, Pesonen M, Sangphukieo A, Boonklang P, Potisap C, Koosakulnirand S, Feil EJ, Dunachie S, Chantratita N, Limmathurotsakul D, Peacock SJ, Day NPJ, Parkhill J, Thomson NR, Sermswan RW, Corander J. Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. Mol Biol Evol 2022; 39:6400259. [PMID: 34662416 PMCID: PMC8760936 DOI: 10.1093/molbev/msab306] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and subtropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies (2,011 genomes), condition-wide transcriptome analyses (82 diverse conditions), and a gene knockout assay to uncover signals of "co-selection"-that is a combination of genetic markers that have been repeatedly selected together through B. pseudomallei evolution. These enabled us to identify 13,061 mutation pairs under co-selection in distinct genes and noncoding RNA. Genes under co-selection displayed marked expression correlation when B. pseudomallei was subjected to physical stress conditions, highlighting the conditions as one of the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed a BPSL1661 role under nutrient deprivation, and explored the functional basis of co-selection gene network surrounding BPSL1661 in facilitating the bacterial survival under nutrient depletion. Our findings suggest that nutrient-limited conditions have been the common selection pressure acting on this species, and allelic variation of BPSL1661 may have promoted B. pseudomallei survival during harsh environmental conditions by facilitating bacterial adherence to different surfaces, cells, or living hosts.
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Affiliation(s)
- Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Parasites and Microbes Programme, Wellcome Sanger Insitute, Hinxton, United Kingdom
- Bioinformatics & Systems Biology Program, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Corresponding authors: E-mails: ; ;
| | - Johan Pensar
- Department of Mathematics, University of Oslo, Oslo, Norway
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Supaksorn Chattagul
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Apiwat Sangphukieo
- Bioinformatics & Systems Biology Program, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Phumrapee Boonklang
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chotima Potisap
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
| | - Sirikamon Koosakulnirand
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Edward J Feil
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Susanna Dunachie
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Narisara Chantratita
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nick P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Insitute, Hinxton, United Kingdom
| | - Rasana W Sermswan
- Melioidosis Research Center, Khon Kaen University, Khon Kaen, Thailand
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Corresponding authors: E-mails: ; ;
| | - Jukka Corander
- Parasites and Microbes Programme, Wellcome Sanger Insitute, Hinxton, United Kingdom
- Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Corresponding authors: E-mails: ; ;
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10
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Swe MMM, Win MM, Cohen J, Phyo AP, Lin HN, Soe K, Amorncha P, Wah TT, Win KKN, Ling C, Parker DM, Dance DAB, Ashley EA, Smithuis F. Geographical distribution of Burkholderia pseudomallei in soil in Myanmar. PLoS Negl Trop Dis 2021; 15:e0009372. [PMID: 34029325 PMCID: PMC8143414 DOI: 10.1371/journal.pntd.0009372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/07/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is a Gram-negative bacterium found in soil and water in many tropical countries. It causes melioidosis, a potentially fatal infection first described in 1911 in Myanmar. Melioidosis is a common cause of sepsis and death in South and South-east Asia, but it is rarely diagnosed in Myanmar. We conducted a nationwide soil study to identify areas where B. pseudomallei is present. METHODOLOGY/PRINCIPAL FINDINGS We collected soil samples from 387 locations in all 15 states and regions of Myanmar between September 2017 and June 2019. At each site, three samples were taken at each of three different depths (30, 60 and 90 cm) and were cultured for B. pseudomallei separately, along with a pooled sample from each site (i.e. 10 cultures per site). We used a negative binomial regression model to assess associations between isolation of B. pseudomallei and environmental factors (season, soil depth, soil type, land use and climate zones). B. pseudomallei was isolated in 7 of 15 states and regions. Of the 387 sites, 31 (8%) had one or more positive samples and of the 3,870 samples cultured, 103 (2.7%) tested positive for B. pseudomallei. B. pseudomallei was isolated more frequently during the monsoon season [RR-2.28 (95% CI: 0.70-7.38)] and less in the hot dry season [RR-0.70 (95% CI: 0.19-2.56)] compared to the cool dry season, and in the tropical monsoon climate zone [RR-2.26; 95% CI (0.21-6.21)] compared to the tropical dry winter climate zone. However, these associations were not statistically significant. B. pseudomallei was detected at all three depths and from various soil types (clay, silt and sand). Isolation was higher in agricultural land (2.2%), pasture land (8.5%) and disused land (5.8%) than in residential land (0.4%), but these differences were also not significant. CONCLUSION/SIGNIFICANCE This study confirms a widespread distribution of B. pseudomallei in Myanmar. Clinical studies should follow to obtain a better picture of the burden of melioidosis in Myanmar.
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Affiliation(s)
- Myo Maung Maung Swe
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Mo Mo Win
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Joshua Cohen
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
| | | | | | - Kyaw Soe
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
| | - Premjit Amorncha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University Bangkok, Thailand
| | - Thin Thin Wah
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Kyi Kyi Nyein Win
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Clare Ling
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Shoklo Malaria Research Unit (SMRU), Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Daniel M. Parker
- Department of Population Health and Disease Prevention Program in Public Health, University of California, Irvine, CA, United States of America
| | - David A. B. Dance
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Lao People’s Democratic Republic
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elizabeth A. Ashley
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Lao People’s Democratic Republic
| | - Frank Smithuis
- Myanmar Oxford Clinical Research Unit, Yangon, Myanmar
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
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11
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Abstract
The causative agent of melioidosis, Burkholderia pseudomallei, a tier 1 select agent, is endemic in Southeast Asia and northern Australia, with increased incidence associated with high levels of rainfall. Increasing reports of this condition have occurred worldwide, with estimates of up to 165,000 cases and 89,000 deaths per year. The ecological niche of the organism has yet to be clearly defined, although the organism is associated with soil and water. The culture of appropriate clinical material remains the mainstay of laboratory diagnosis. Identification is best done by phenotypic methods, although mass spectrometric methods have been described. Serology has a limited diagnostic role. Direct molecular and antigen detection methods have limited availability and sensitivity. Clinical presentations of melioidosis range from acute bacteremic pneumonia to disseminated visceral abscesses and localized infections. Transmission is by direct inoculation, inhalation, or ingestion. Risk factors for melioidosis include male sex, diabetes mellitus, alcohol abuse, and immunosuppression. The organism is well adapted to intracellular survival, with numerous virulence mechanisms. Immunity likely requires innate and adaptive responses. The principles of management of this condition are drainage and debridement of infected material and appropriate antimicrobial therapy. Global mortality rates vary between 9% and 70%. Research into vaccine development is ongoing.
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Affiliation(s)
- I Gassiep
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - M Armstrong
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
| | - R Norton
- Pathology Queensland, Townsville Hospital, Townsville, Queensland, Australia
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
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12
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Kaestli M, O'Donnell M, Rose A, Webb JR, Mayo M, Currie BJ, Gibb K. Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia. PLoS Negl Trop Dis 2019; 13:e0007672. [PMID: 31487283 PMCID: PMC6728021 DOI: 10.1371/journal.pntd.0007672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/29/2019] [Indexed: 12/11/2022] Open
Abstract
In the wet-dry tropics of Northern Australia, drinking water in remote communities is mostly sourced from bores accessing groundwater. Many aquifers contain naturally high levels of iron and some are shallow with surface water intrusion in the wet season. Therefore, environmental bacteria such as iron-cycling bacteria promoting biofilm formation in pipes or opportunistic pathogens can occur in these waters. An opportunistic pathogen endemic to northern Australia and Southeast Asia and emerging worldwide is Burkholderia pseudomallei. It causes the frequently fatal disease melioidosis in humans and animals. As we know very little about the microbial composition of drinking water in remote communities, this study aimed to provide a first snapshot of the microbiota and occurrence of opportunistic pathogens in bulk water and biofilms from the source and through the distribution system of three remote water supplies with varying iron levels. Using 16s-rRNA gene sequencing, we found that the geochemistry of the groundwater had a substantial impact on the untreated microbiota. Different iron-cycling bacteria reflected differences in redox status and nutrients. We cultured and sequenced B. pseudomallei from bores with elevated iron and from a multi-species biofilm which also contained iron-oxidizing Gallionella, nitrifying Nitrospira and amoebae. Gallionella are increasingly used in iron-removal filters in water supplies and more research is needed to examine these interactions. Similar to other opportunistic pathogens, B. pseudomallei occurred in water with low organic carbon levels and with low heterotrophic microbial growth. No B. pseudomallei were detected in treated water; however, abundant DNA of another opportunistic pathogen group, non-tuberculous mycobacteria was recovered from treated parts of one supply. Results from this study will inform future studies to ultimately improve management guidelines for water supplies in the wet-dry tropics. Water providers in the wet-dry tropics of Northern Australia face additional challenges to keep drinking water microbiologically safe. The source water is often rich in iron-cycling bacteria leading to excessive biofilm formation in pipes and it can also contain the emerging opportunistic pathogen Burkholderia pseudomallei causing the severe disease melioidosis in humans and animals. We know very little about the ecology of microbes in remote community water supplies, so to start to fill this gap we assessed the microbial composition from the source to the distribution of three remote water supplies. We not only found that the geochemistry of the source water had a substantial impact on the composition of the iron-cycling bacteria but B. pseudomallei was cultured from source water with low organic carbon but elevated iron levels and from a multi-species biofilm linked to iron bacteria. No B. pseudomallei were detected in treated water; however, abundant DNA of another opportunistic pathogen group, non-tuberculous mycobacteria, was recovered from treated parts of one water supply. This work lays the foundation for future studies to ultimately improve management guidelines for water supplies in the wet-dry tropics.
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Affiliation(s)
- Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia.,Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - Alea Rose
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R Webb
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bart J Currie
- Global and Tropical Health, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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13
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Presence of Burkholderia pseudomallei in the 'Granary of Myanmar'. Trop Med Infect Dis 2019; 4:tropicalmed4010008. [PMID: 30621177 PMCID: PMC6473437 DOI: 10.3390/tropicalmed4010008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/27/2018] [Accepted: 12/27/2018] [Indexed: 12/11/2022] Open
Abstract
Melioidosis is a frequently fatal infectious disease caused by the Gram negative bacillus Burkholderia pseudomallei. Although it was originally discovered in Myanmar, the disease disappeared from sight for many decades. This study focuses on detection of B. pseudomallei in soil in selected sampling sites in an attempt to start to fill the gaps in the current status of our knowledge of the geographical distribution of B. pseudomallei in soil in Myanmar. This cross-sectional study consists of 400 soil samples from 10 selected study townships from two major paddy growing regions. Bacterial isolation was done using a simplified method for the isolation of Burkholderia pseudomallei from soil. In this study, only 1% (4/400) of soil samples were found to be positive; two of four were found at 90 cm depth and another two positive samples were found at 30 cm and 60 cm. This survey has confirmed the presence of environmental B. pseudomallei in Myanmar indicating that the conditions are in place for melioidosis acquisition.
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14
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Dong S, Wu L, Long F, Wu Q, Liu X, Pei H, Xu K, Lu Y, Wang Y, Lin Y, Xia Q. The prevalence and distribution of Burkholderia pseudomallei in rice paddy within Hainan, China. Acta Trop 2018; 187:165-168. [PMID: 30096286 DOI: 10.1016/j.actatropica.2018.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 07/25/2018] [Accepted: 08/06/2018] [Indexed: 11/16/2022]
Abstract
Melioidosis is an infectious disease caused by Burkholderia pseudomallei, mainly found in Southeast Asia and northern Australia. In Hainan, sporadic cases were first described in 1990; since then, more cases have been identified. No systematic study has yet been done to detect the environmental source of the organism and its true extent in Hainan. This study is aimed to confirm the prevalence of B. pseudomallei in soil samples in Hainan. 1080 soil samples from 18 different counties were collected from 3 sampling points of 360 sites. They were screened for the presence of B. pseudomallei by Ashdown selective media. Suspected colonies of B. pseudomallei were confirmed by biochemical test and a specific PCR assay. 48 of 360 sites (13.3%) were positive for B. pseudomallei, including all coastal counties in Hainan Island. This study revealed the prevalence and distribution of B. pseudomallei in the soil environment in Hainan Island of southern China and may be helpful to understand the distribution of B. pseudomallei and to access its epidemiological importance.
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Affiliation(s)
- Sufang Dong
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Lixian Wu
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Fuquan Long
- Department of STD, Shanghai Dermatology Hospital, Shanghai 200443, China
| | - Qiang Wu
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Xiang Liu
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Hua Pei
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Ke Xu
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Yajun Lu
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Ying Wang
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China
| | - Yingzi Lin
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China.
| | - Qianfeng Xia
- Laboratory of Tropical Biomedicine and Biotechnology, School of Tropical Medicine and Laboratory Medicine, Hainan Medical University, Haikou 571199, China.
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15
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Soil characteristics influencing the spatial distribution of melioidosis in Far North Queensland, Australia. Epidemiol Infect 2018; 146:1602-1607. [PMID: 29970213 DOI: 10.1017/s0950268818001188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The environmental bacterium, Burkholderia pseudomallei, is responsible for the potentially fatal disease melioidosis. Factors responsible for the temporospatial distribution of cases are incompletely understood, although a combination of rainfall, groundwater levels and the physicochemical properties of soil are important. The distribution of culture-positive cases of melioidosis from 1996 to 2016 in Far North Queensland, Australia, was investigated to determine the association with different soil types and landforms in Cairns, the region's largest city. Cases were clustered on alluvial fan landforms of strongly bleached gradational textured and yellow massive gradational textured soils indicating these soils are more suitable for B. pseudomallei and risk of melioidosis infection is higher in these areas, cases were less frequent on other soil types on alluvial fan landforms (despite comparable population density) and beach ridges. This indicates that the combination of these soils might be more suitable for B. pseudomallei, increasing the risk of disease in these locations. Sociodemographic characterisics of the population in cluster locations were considered. Knowledge of local soil characteristics may help predict cases of melioidosis and inform public health strategies to prevent the disease. Because melioidosis case clusters were identified, testing for the presence of B. pseudomallei across the study area is a useful target of future research.
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16
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Melioidosis: An Australian Perspective. Trop Med Infect Dis 2018; 3:tropicalmed3010027. [PMID: 30274424 PMCID: PMC6136632 DOI: 10.3390/tropicalmed3010027] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 12/16/2022] Open
Abstract
Burkholderia pseudomallei is endemic in northern Australia, with cases of melioidosis most commonly occurring during the wet season in individuals with diabetes, hazardous alcohol use, and chronic kidney disease. Pneumonia is the most common presentation and the majority of patients are bacteraemic—however, infection may involve almost any organ, with the skin and soft tissues, genitourinary system, visceral organs, and bone and joints affected most commonly. Central nervous system involvement is rarer, but has a high attributable mortality. Increased awareness of the disease amongst healthcare providers, ready access to appropriate antibiotic therapy and high-quality intensive care services has resulted in a sharp decline in the case fatality rate over the last 20 years. Further improvement in clinical outcomes will require a greater understanding of the disease′s pathophysiology, its optimal management, and more effective strategies for its prevention.
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17
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Physicochemical and Biological Factors of Soil and the Potential Use of Antagonistic Microbes for Biocontrol of Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0125-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Burkholderia pseudomallei in a lowland rice paddy: seasonal changes and influence of soil depth and physico-chemical properties. Sci Rep 2017; 7:3031. [PMID: 28596557 PMCID: PMC5465195 DOI: 10.1038/s41598-017-02946-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/27/2017] [Indexed: 11/18/2022] Open
Abstract
Melioidosis, a severe infection with the environmental bacterium Burkholderia pseudomallei, is being recognised increasingly frequently. What determines its uneven distribution within endemic areas is poorly understood. We cultured soil from a rice field in Laos for B. pseudomallei at different depths on 4 occasions over a 13-month period. We also measured physical and chemical parameters in order to identify associated characteristics. Overall, 195 of 653 samples (29.7%) yielded B. pseudomallei. A higher prevalence of B. pseudomallei was found at soil depths greater than the 30 cm currently recommended for B. pseudomallei environmental sampling. B. pseudomallei was associated with a high soil water content and low total nitrogen, carbon and organic matter content. Our results suggested that a sampling grid of 25 five metre square quadrats (i.e. 25 × 25 m) should be sufficient to detect B. pseudomallei at a given location if samples are taken at a soil depth of at least 60 cm. However, culture of B. pseudomallei in environmental samples is difficult and liable to variation. Future studies should both rely on molecular approaches and address the micro-heterogeneity of soil when investigating physico-chemical associations with the presence of B. pseudomallei.
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19
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Chuah CJ, Tan EKH, Sermswan RW, Ziegler AD. Hydrological connectivity and Burkholderia pseudomallei prevalence in wetland environments: investigating rice-farming community's risk of exposure to melioidosis in North-East Thailand. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:287. [PMID: 28536911 DOI: 10.1007/s10661-017-5988-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
In our analysis of 136 water samples from wetland environments (rice paddies, natural wetland sites, man-made water bodies) in rural areas of North-East Thailand, Burkholderia pseudomallei was most prevalent in rice paddies (15 of the 30 positive sites). The high prevalence in the water of rice fields is indicative of the inherent vulnerability of farmers in rural agricultural areas in this area of Thailand and likely other locations in the tropics. Nearly all B. pseudomallei-positive sites were found within the vicinity of a large wetland associated with the Chi River, in the month of July 2014. Positive samples were found in water ranging in pH from 5.9 to 8.7, salinity ranging from 0.04 to 1.58 ppt, nitrate ranging from 0 to 10.8 ppm, and iron ranging from 0.003 to 1.519 ppm. Of these variables, only iron content was statistically higher in B. pseudomallei-positive versus B. pseudomallei-negative sites, suggesting that increasing concentrations of iron may encourage the growth of this bacterium, which is responsible for melioidosis. Our results, when combined with data from other published studies, support the notion that B. pseudomallei can exist in a wide range of environmental conditions. Thus, we argue that health safety education is a more appropriate means of addressing farmer vulnerability than chemical or physical alterations to fields at large scales. Further, it may be important to investigate melioidosis through transdisciplinary approaches that consider the complex social and ecological contexts in which the disease occurs.
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Affiliation(s)
- C Joon Chuah
- Institute of Water Policy, National University of Singapore, Singapore, Singapore.
- Department of Geography, National University of Singapore, Singapore, Singapore.
| | - Esther K H Tan
- Department of Geography, National University of Singapore, Singapore, Singapore
| | - Rasana W Sermswan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Alan D Ziegler
- Department of Geography, National University of Singapore, Singapore, Singapore
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20
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Portacci K, Rooney AP, Dobos R. Assessing the potential forBurkholderia pseudomalleiin the southeastern United States. J Am Vet Med Assoc 2017; 250:153-159. [DOI: 10.2460/javma.250.2.153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Soil Nutrient Depletion Is Associated with the Presence of Burkholderia pseudomallei. Appl Environ Microbiol 2016; 82:7086-7092. [PMID: 27694236 PMCID: PMC5118919 DOI: 10.1128/aem.02538-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 09/23/2016] [Indexed: 12/02/2022] Open
Abstract
Burkholderia pseudomallei is a soil-dwelling bacterium and the cause of melioidosis, which kills an estimated 89,000 people per year worldwide. Agricultural workers are at high risk of infection due to repeated exposure to the bacterium. Little is known about the soil physicochemical properties associated with the presence or absence of the organism. Here, we evaluated the soil physicochemical properties and presence of B. pseudomallei in 6,100 soil samples collected from 61 rice fields in Thailand. The presence of B. pseudomallei was negatively associated with the proportion of clay, proportion of moisture, level of salinity, percentage of organic matter, presence of cadmium, and nutrient levels (phosphorus, potassium, calcium, magnesium, and iron). The presence of B. pseudomallei was not associated with the level of soil acidity (P = 0.54). In a multivariable logistic regression model, the presence of B. pseudomallei was negatively associated with the percentage of organic matter (odds ratio [OR], 0.06; 95% confidence interval [CI], 0.01 to 0.47; P = 0.007), level of salinity (OR, 0.06; 95% CI, 0.01 to 0.74; P = 0.03), and percentage of soil moisture (OR, 0.81; 95% CI, 0.66 to 1.00; P = 0.05). Our study suggests that B. pseudomallei thrives in rice fields that are nutrient depleted. Some agricultural practices result in a decline in soil nutrients, which may impact the presence and amount of B. pseudomallei bacteria in affected areas. IMPORTANCEBurkholderia pseudomallei is an environmental Gram-negative bacillus and the cause of melioidosis. Humans acquire the disease following skin inoculation, inhalation, or ingestion of the bacterium in the environment. The presence of B. pseudomallei in soil defines geographic regions where humans and livestock are at risk of melioidosis, yet little is known about the soil properties associated with the presence of the organism. We evaluated the soil properties and presence of B. pseudomallei in 61 rice fields in East, Central, and Northeast Thailand. We demonstrated that the organism was more commonly found in soils with lower levels of organic matter and nutrients, including phosphorus, potassium, calcium, magnesium, and iron. We also demonstrated that crop residue burning after harvest, which can reduce soil nutrients, was not uncommon. Some agricultural practices result in a decline in soil nutrients, which may impact the presence and amount of B. pseudomallei bacteria in affected areas.
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22
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Musa HI, Hassan L, Shamsuddin ZH, Panchadcharam C, Zakaria Z, Abdul Aziz S. Physicochemical Properties Influencing Presence of Burkholderia pseudomallei in Soil from Small Ruminant Farms in Peninsular Malaysia. PLoS One 2016; 11:e0162348. [PMID: 27635652 PMCID: PMC5026356 DOI: 10.1371/journal.pone.0162348] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 08/22/2016] [Indexed: 11/18/2022] Open
Abstract
Soil is considered to be a major reservoir of Burkholderia pseudomallei in the environment. This paper investigates soil physicochemical properties that may influence presence of B. pseudomallei in soil samples from small ruminant farms in Peninsular Malaysia. Soil samples were collected from the farms and cultured for B. pseudomallei. The texture, organic matter and water contents, pH, elemental contents, cation exchange capacities, carbon, sulfur and nitrogen contents were determined. Analysis of soil samples that were positive and negative for B. pseudomallei using multivariable logistic regression found that the odds of bacterial isolation from soil was significantly higher for samples with higher contents of iron (OR = 1.01, 95%CI = 1.00-1.02, p = 0.03), water (OR = 1.28, 95%CI = 1.05-1.55, p = 0.01) and clay (OR = 1.54, 95%CI = 1.15-2.06, p = 0.004) compared to the odds of isolation in samples with lower contents of the above variables. These three factors may have favored the survival of B. pseudomallei because iron regulates expression of respiratory enzymes, while water is essential for soil ecology and agent's biological processes and clay retains water and nutrients.
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Affiliation(s)
- Hassan Ismail Musa
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Maiduguri, Borno State, Nigeria
| | - Latiffah Hassan
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- * E-mail:
| | - Zulkifli Hj. Shamsuddin
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | | | - Zunita Zakaria
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Saleha Abdul Aziz
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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23
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Ribolzi O, Rochelle-Newall E, Dittrich S, Auda Y, Newton PN, Rattanavong S, Knappik M, Soulileuth B, Sengtaheuanghoung O, Dance DAB, Pierret A. Land use and soil type determine the presence of the pathogen Burkholderia pseudomallei in tropical rivers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:7828-7839. [PMID: 26758304 PMCID: PMC4846699 DOI: 10.1007/s11356-015-5943-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/07/2015] [Indexed: 06/05/2023]
Abstract
Burkholderia pseudomallei is the bacterium that causes melioidosis in humans. While B. pseudomallei is known to be endemic in South East Asia (SEA), the occurrence of the disease in other parts of the tropics points towards a potentially large global distribution. We investigated the environmental factors that influence the presence (and absence) of B. pseudomallei in a tropical watershed in SEA. Our main objective was to determine whether there is a link between the presence of the organism in the hydrographic network and the upstream soil and land-use type. The presence of B. pseudomallei was determined using a specific quantitative real-time PCR assay following enrichment culture. Land use, soil, geomorphology, and environmental data were then analyzed using partial least squares discriminant analysis (PLSDA) to compare the B. pseudomallei positive and negative sites. Soil type in the surrounding catchment and turbidity had a strong positive influence on the presence (acrisols and luvisols) or absence (ferralsols) of B. pseudomallei. Given the strong apparent links between soil characteristics, water turbidity, and the presence/absence of B. pseudomallei, actions to raise public awareness about factors increasing the risk of exposure should be undertaken in order to reduce the incidence of melioidosis in regions of endemicity.
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Affiliation(s)
- Olivier Ribolzi
- Géosciences Environnement Toulouse (GET), UMR 5563, (IRD, CNRS, UPS), Université de Toulouse, UPS (OMP), CNRS, Toulouse, France.
| | - Emma Rochelle-Newall
- iEES-Paris (IRD-UPMC-CNRS-INRA-UDD-UPEC), Sorbonne Universités, UPMC Univ Paris 06, Institut de Recherche pour le Développement (IRD), case 23, 4 place Jussieu, Paris cedex, 75252, France
| | - Sabine Dittrich
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Yves Auda
- Géosciences Environnement Toulouse (GET), UMR 5563, (IRD, CNRS, UPS), Université de Toulouse, UPS (OMP), CNRS, Toulouse, France
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Michael Knappik
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bounsamai Soulileuth
- Institute of Ecology and Environmental Science-Paris, Institut de Recherche pour le Développement (IRD), Vientiane, Lao People's Democratic Republic
| | - Oloth Sengtaheuanghoung
- Department of Agricultural Land Management (DALaM), P.O. Box 4199, Ban Nogviengkham, Xaythany District, Vientiane, Lao People's Democratic Republic
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alain Pierret
- Institute of Ecology and Environmental Science-Paris, Institut de Recherche pour le Développement (IRD), Vientiane, Lao People's Democratic Republic
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