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Gassiep I, Chatfield MD, Permana B, Burnard D, Bauer MJ, Cuddihy T, Forde BM, Mayer-Coverdale J, Norton RE, Harris PNA. The Genomic Epidemiology of Clinical Burkholderia pseudomallei Isolates in North Queensland, Australia. Pathogens 2024; 13:584. [PMID: 39057811 PMCID: PMC11279585 DOI: 10.3390/pathogens13070584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/26/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Background:Burkholderia pseudomallei, the causative agent of melioidosis, is highly genetically recombinant, resulting in significant genomic diversity. Multiple virulence factors have been associated with specific disease presentations. To date, there are limited data relating to genomic diversity and virulence factors associated with melioidosis cases in North Queensland, Australia. Aim: To describe the genetic diversity of B. pseudomallei and identify virulence factors associated with clinical risk factors and patient outcomes. Methods: Whole genome sequencing of clinical isolates was performed and analysed with clinical data obtained from a retrospective melioidosis cohort study. Results: Fifty-nine distinct sequence types (STs) were identified from the 128 clinical isolates. Six STs comprised 64/128 (50%) isolates. Novel STs accounted for 38/59 (64%) STs, with ST TSV-13 as the most prevalent (n = 7), and were less likely to possess an LPS A genotype or YLF gene cluster (p < 0.001). These isolates were most likely to be found outside the inner city (aOR: 4.0, 95% CI: 1.7-9.0, p = 0.001). ST TSV-13 was associated with increased mortality (aOR: 6.1, 95% CI: 1.2-30.9, p = 0.03). Patients with a history of alcohol excess were less likely to be infected by fhaB3 (aOR 0.2, 95% CI: 0.1-0.7, p = 0.01) or YLF (aOR: 0.4, 95% CI: 0.2-0.9, p = 0.04) positive isolates. Conclusions: There are a significant number of novel sequence types in Townsville, Australia. An emerging novel ST appears to have an association with geographic location and mortality. Ongoing investigation is required to further understand the impact of this ST on the Townsville region.
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Affiliation(s)
- Ian Gassiep
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Brisbane, QLD 4029, Australia; (M.D.C.); (B.P.); (M.J.B.); (B.M.F.); (J.M.-C.); (P.N.A.H.)
- Department of Infectious Diseases, Mater Hospital Brisbane, Brisbane, QLD 4101, Australia
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Brisbane, QLD 4029, Australia
| | - Mark D. Chatfield
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Brisbane, QLD 4029, Australia; (M.D.C.); (B.P.); (M.J.B.); (B.M.F.); (J.M.-C.); (P.N.A.H.)
| | - Budi Permana
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Brisbane, QLD 4029, Australia; (M.D.C.); (B.P.); (M.J.B.); (B.M.F.); (J.M.-C.); (P.N.A.H.)
| | - Delaney Burnard
- Queensland Cyber Infrastructure Foundation, Brisbane, QLD 4067, Australia;
| | - Michelle J. Bauer
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Brisbane, QLD 4029, Australia; (M.D.C.); (B.P.); (M.J.B.); (B.M.F.); (J.M.-C.); (P.N.A.H.)
| | - Thom Cuddihy
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD 4067, Australia;
| | - Brian M. Forde
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Brisbane, QLD 4029, Australia; (M.D.C.); (B.P.); (M.J.B.); (B.M.F.); (J.M.-C.); (P.N.A.H.)
- Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, QLD 4067, Australia;
| | - Johanna Mayer-Coverdale
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Brisbane, QLD 4029, Australia; (M.D.C.); (B.P.); (M.J.B.); (B.M.F.); (J.M.-C.); (P.N.A.H.)
- Sullivan Nicolaides Pathology, Brisbane, QLD 4006, Australia
- Herston Infectious Diseases Institute, Royal Brisbane and Woman’s Hospital, Herston, Brisbane, QLD 4029, Australia
| | - Robert E. Norton
- Pathology Queensland, Townsville University Hospital, Townsville, QLD 4814, Australia;
- Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Patrick N. A. Harris
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Brisbane, QLD 4029, Australia; (M.D.C.); (B.P.); (M.J.B.); (B.M.F.); (J.M.-C.); (P.N.A.H.)
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Brisbane, QLD 4029, Australia
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Wainwright BJ, Leon J, Vilela E, Hickman KJE, Caldwell J, Aimone B, Bischoff P, Ohran M, Morelli MW, Arlyza IS, Marwayana ON, Zahn G. Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria. ENVIRONMENTAL MICROBIOME 2024; 19:23. [PMID: 38637894 PMCID: PMC11027274 DOI: 10.1186/s40793-024-00568-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line. RESULTS We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community. CONCLUSION Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.
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Affiliation(s)
- Benjamin J Wainwright
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| | - Josh Leon
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Ernie Vilela
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - K J E Hickman
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jensen Caldwell
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Behlee Aimone
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Porter Bischoff
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Marissa Ohran
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Magnolia W Morelli
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Irma S Arlyza
- Research Center for Oceanography, National Research and Innovation Agency (BRIN), Jl. Pasir Putih I, Ancol Timur, Jakarta, 14430, Indonesia
| | - Onny N Marwayana
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta-Bogor KM 46, Cibinong, Bogor, 16911, Indonesia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA), 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
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Yadav PK, Singh S, Paul M, Kumar S, Ponmariappan S, Thavaselvam D. Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices. Ann Clin Microbiol Antimicrob 2024; 23:30. [PMID: 38600514 PMCID: PMC11007888 DOI: 10.1186/s12941-024-00693-4] [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: 06/05/2023] [Accepted: 03/29/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Melioidosis, caused by the category B biothreat agent Burkholderia pseudomallei, is a disease with a high mortality rate and requires an immediate culture-independent diagnosis for effective disease management. In this study, we developed a highly sensitive qPCR assay for specific detection of Burkholderia pseudomallei and melioidosis disease diagnosis based on a novel target sequence. METHODS An extensive in-silico analysis was done to identify a novel and highly conserved sequence for developing a qPCR assay. The specificity of the developed assay was analyzed with 65 different bacterial cultures, and the analytical sensitivity of the assay was determined with the purified genomic DNA of B. pseudomallei. The applicability of the assay for B. pseudomallei detection in clinical and environmental matrices was evaluated by spiking B. pseudomallei cells in the blood, urine, soil, and water along with suitable internal controls. RESULTS A novel 85-nucleotide-long sequence was identified using in-silico tools and employed for the development of the highly sensitive and specific quantitative real-time PCR assay S664. The assay S664 was found to be highly specific when evaluated with 65 different bacterial cultures related and non-related to B. pseudomallei. The assay was found to be highly sensitive, with a detection limit of 3 B. pseudomallei genome equivalent copies per qPCR reaction. The detection limit in clinical matrices was found to be 5 × 102 CFU/mL for both human blood and urine. In environmental matrices, the detection limit was found to be 5 × 101 CFU/mL of river water and 2 × 103 CFU/gm of paddy field soil. CONCLUSIONS The findings of the present study suggest that the developed assay S664 along with suitable internal controls has a huge diagnostic potential and can be successfully employed for specific, sensitive, and rapid molecular detection of B. pseudomallei in various clinical and environmental matrices.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o DGLS, Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, India.
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Weeratunga MP, Mayo M, Kaestli M, Currie BJ. Melioidosis Knowledge Awareness in Three Distinct Groups in the Tropical Northern Territory of Australia. Trop Med Infect Dis 2024; 9:71. [PMID: 38668532 PMCID: PMC11054246 DOI: 10.3390/tropicalmed9040071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Melioidosis is a potentially life-threatening infection. This study aimed to assess the melioidosis knowledge among distinct participant groups in the tropical Top End of the Northern Territory (NT) of Australia. Participants were categorised into three groups: NT medical students and health research staff (Group 1: Hi-Ed), Aboriginal Rangers and Aboriginal Healthcare Workers (Group 2: Rangers/AHWs), and patients with a history of melioidosis infection (Group 3: Patients). A questionnaire was developed to collect data on demographics, risk and protective factor awareness, and knowledge acquisition sources. We used responses to calculate indices for risk knowledge (RKI), protective knowledge (PKI), overall melioidosis knowledge (MKI), and information sources (ISI). We found that 93.6% of participants in Group 1 (Hi-Ed) said that they had heard of melioidosis, followed by 81.5% in Group 3 (Patients), and 72.0% in Group 2 (Rangers/AHWs). Group 1 (Hi-Ed) participants demonstrated greater knowledge of risk-increasing behaviours but had gaps in knowledge of clinical risks like diabetes. Multiple regression revealed that the number of resources used was the only significant predictor of MKI. There are varying melioidosis knowledge levels across different NT participant groups. Targeted educational interventions are needed to enhance melioidosis awareness. A weblink with an interactive summary of our analysis can be found under Results part.
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Affiliation(s)
- Madusha P. Weeratunga
- Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (M.P.W.); (M.M.); (M.K.)
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT 0810, Australia
- Northern Territory Medical Program, Flinders and Charles Darwin University, Darwin, NT 0810, Australia
| | - Mark Mayo
- Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (M.P.W.); (M.M.); (M.K.)
| | - Mirjam Kaestli
- Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (M.P.W.); (M.M.); (M.K.)
| | - Bart J. Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (M.P.W.); (M.M.); (M.K.)
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT 0810, Australia
- Northern Territory Medical Program, Flinders and Charles Darwin University, Darwin, NT 0810, Australia
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5
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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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Yadav PK, Paul M, Singh S, Kumar S, Ponmariappan S, Thavaselvam D. Development of a Novel Internally Controlled HrpB1 Gene-Based Real-Time qPCR Assay for Detection of Burkholderia pseudomallei. Mol Diagn Ther 2024; 28:101-112. [PMID: 38085447 DOI: 10.1007/s40291-023-00686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2023] [Indexed: 01/14/2024]
Abstract
BACKGROUND Melioidosis, caused by category B bioterrorism agent Burkholderia pseudomallei, is a seasonal disease of tropical and subtropical regions with a high mortality rate. An early and culture-independent detection of B. pseudomallei is required for the appropriate disease management and prevention. The present study is designed to identify novel and unique sequences of B. pseudomallei and development of quantitative polymerase chain reaction (qPCR) assay. METHODS A novel B. pseudomallei-specific target sequence was identified by in silico analysis for the qPCR assay development. The specificity of the developed assay was assessed using purified DNA of 65 different bacterial cultures, and the sensitivity was estimated using a cloned target gene. Further, a type III secretion protein HrpB1 (HrpB1) gene-based duplex qPCR assay incorporating suitable extraction and amplification control was developed, and its viability was assessed in different clinical and environmental matrices for the detection of B. pseudomallei. RESULTS In this study, an 80-nucleotide-long B. pseudomallei-specific region within the gene HrpB1 was identified by computational analysis. The developed HrpB1-based qPCR assay was highly specific for B. pseudomallei detection when evaluated with 65 different bacterial cultures. The sensitivity of the qPCR assay with the HrpB1-recombinant plasmid was found to be five copies per qPCR reaction. The assay's detection limit was found to be 5 × 102 CFU/mL for human blood and urine, 5 × 101 CFU/mL in river water, and 2 × 103 CFU/gm in paddy field soil. CONCLUSION The results of the study showed the applicability of a novel HrpB1-based qPCR assay for sensitive and specific detection of B. pseudomallei in diverse clinical and environmental samples.
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Affiliation(s)
- Pranjal Kumar Yadav
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Moumita Paul
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Suchetna Singh
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Sanjay Kumar
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India.
| | - S Ponmariappan
- Biodetector Development Test and Evaluation Division, Defence Research & Development Establishment, Defence Research and Development Organization, Jhansi Road, Gwalior, Madhya Pradesh, 474 002, India
| | - Duraipandian Thavaselvam
- O/o Director General Life Science (DGLS), Defence Research and Development Organization, Ministry of Defence, SSPL Campus, Timarpur, New Delhi, 110 054, India.
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Jilani MSA, Farook S, Bhattacharjee A, Barai L, Ahsan CR, Haq JA, Tuanyok A. Phylogeographic characterization of Burkholderia pseudomallei isolated from Bangladesh. PLoS Negl Trop Dis 2023; 17:e0011823. [PMID: 38060593 PMCID: PMC10729972 DOI: 10.1371/journal.pntd.0011823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/19/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Burkholderia pseudomallei possesses a diverse set of genes which encode a vast array of biological functions reflecting its clinical, ecological and phenotypic diversity. Strain variation is linked to geographic location as well as pattern of land uses. This soil-dwelling Gram-negative pathogen causes melioidosis, a tropical disease endemic in northern Australia and Southeast Asian regions including Bangladesh. Phylogeographic analyses of B. pseudomallei isolates by molecular typing techniques could be used to examine the diversity of this organism as well as to track melioidosis epidemics. METHODS In this study, 22 B. pseudomallei isolates, of which 20 clinical and two soil isolates were analyzed, utilizing Real-time PCR assay and multilocus sequence typing (MLST). The sequences were then submitted to PubMLST database for analysis and construction of phylogenetic tree. FINDINGS A total of 12 different sequence types (STs) that includes four novel STs were identified for the first time. Strains having STs 1005, 1007 and 56 were the most widespread STs frequently isolated in Bangladesh. ST 1005, ST 56, ST 1007 and ST 211 have been detected not only in Bangladesh but are also present in many Southeast Asian countries. SIGNIFICANCE ST 1005 was detected in both soil and clinical samples of Gazipur. Most prevalent, ST 56 has been previously reported from Myanmar, Thailand, Cambodia and Vietnam, confirming the persistence of the genotype over the entire continent. Further large-scale study is necessary to find out the magnitude of the infection and its different reservoirs in the environment along with phylogeographic association.
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Affiliation(s)
| | - Saika Farook
- Department of Microbiology, Ibrahim Medical College, Dhaka, Bangladesh
| | - Arittra Bhattacharjee
- Bioinformatics Division, National Institute of Biotechnology, Savar, Dhaka, Bangladesh
| | - Lovely Barai
- Department of Microbiology, BIRDEM General Hospital, Dhaka, Bangladesh
| | | | | | - Apichai Tuanyok
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
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Guterres H, Gusmao C, Pinheiro M, Martins J, Odio G, Maia C, da Conceicao V, Soares M, Osorio C, da Silva ES, Tilman A, Givney R, Oakley T, Yan J, Toto L, Amaral E, James R, Buising K, Mayo M, Kaestli M, Webb JR, Baird RW, Currie BJ, Francis JR, Muhi S. Melioidosis in Timor-Leste: First Case Description and Phylogenetic Analysis. Open Forum Infect Dis 2023; 10:ofad405. [PMID: 37577114 PMCID: PMC10414804 DOI: 10.1093/ofid/ofad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis, has not yet been reported in Timor-Leste, a sovereign state northwest of Australia. In the context of improved access to diagnostic resources and expanding clinical networks in the Australasian region, we report the first 3 cases of culture-confirmed melioidosis in Timor-Leste. These cases describe a broad range of typical presentations, including sepsis, pneumonia, multifocal abscesses, and cutaneous infection. Phylogenetic analysis revealed that the Timor-Leste isolates belong to the Australasian clade of B. pseudomallei, rather than the Asian clade, consistent with the phylogeographic separation across the Wallace Line. This study underscores an urgent need to increase awareness of this pathogen in Timor-Leste and establish diagnostic laboratories with improved culture capacity in regional hospitals. Clinical suspicion should prompt appropriate sampling and communication with laboratory staff to target diagnostic testing. Local antimicrobial guidelines have recently been revised to include recommendations for empiric treatment of severe sepsis.
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Affiliation(s)
| | - Celia Gusmao
- National Hospital Guido Valadares, Dili, Timor-Leste
| | | | - Joana Martins
- National Hospital Guido Valadares, Dili, Timor-Leste
| | - Gustavo Odio
- National Hospital Guido Valadares, Dili, Timor-Leste
| | | | - Virginia da Conceicao
- National Health Laboratory, Dili, Timor-Leste
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Messias Soares
- National Health Laboratory, Dili, Timor-Leste
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | | | | | | | - Rodney Givney
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Tessa Oakley
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jennifer Yan
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Lucia Toto
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Elfiana Amaral
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Rodney James
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kirsty Buising
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mark Mayo
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Jessica R Webb
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Robert W Baird
- Territory Pathology, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Bart J Currie
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Joshua R Francis
- Menzies School of Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Stephen Muhi
- Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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9
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Currie BJ, Meumann EM, Kaestli M. The Expanding Global Footprint of Burkholderia pseudomallei and Melioidosis. Am J Trop Med Hyg 2023; 108:1081-1083. [PMID: 37160279 PMCID: PMC10540122 DOI: 10.4269/ajtmh.23-0223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/14/2023] [Indexed: 05/11/2023] Open
Affiliation(s)
- Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Program, Darwin, Northern Territory, Australia
| | - Ella M. Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital and Northern Territory Medical Program, Darwin, Northern Territory, Australia
- Sullivan Nicolaides Pathology, Brisbane, Queensland, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
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10
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Subspecific Nomenclature of Giardia duodenalis in the Light of a Compared Population Genomics of Pathogens. Pathogens 2023; 12:pathogens12020249. [PMID: 36839521 PMCID: PMC9960469 DOI: 10.3390/pathogens12020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Genetic and genomic data have long recognized that the species Giardia duodenalis is subdivided into at least eight genetic clusters that have been named "assemblages" by specialists in the field. Some of these assemblages have been given the status of species, with Linnean binames. In the framework of the predominant clonal evolution model (PCE), we have shown that, from an evolutionary point of view, G. duodenalis assemblages are equatable to "near-clades", that is to say: clades whose discreteness is somewhat clouded by occasional genetic exchange, but remain discrete and stable in space and time. The implications of this evolutionary status for the species described within G. duodenalis are discussed in light of the most recent genetic and genomic studies. The pattern of this species' subspecific genetic variability and genetic clustering appears to be very similar to the ones of various parasitic, fungal and bacteria species. This underlines the relevance of a compared population genomics of pathogenic species allowed by the broad framework of the PCE model.
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11
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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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12
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Alsowayeh N, Albutti A. Designing a novel chimeric multi-epitope vaccine against Burkholderia pseudomallei, a causative agent of melioidosis. Front Med (Lausanne) 2022; 9:945938. [PMID: 36330071 PMCID: PMC9623267 DOI: 10.3389/fmed.2022.945938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/20/2022] [Indexed: 06/04/2024] Open
Abstract
Burkholderia pseudomallei, a gram-negative soil-dwelling bacterium, is primarily considered a causative agent of melioidosis infection in both animals and humans. Despite the severity of the disease, there is currently no licensed vaccine on the market. The development of an effective vaccine against B. pseudomallei could help prevent the spread of infection. The purpose of this study was to develop a multi-epitope-based vaccine against B. pseudomallei using advanced bacterial pan-genome analysis. A total of four proteins were prioritized for epitope prediction by using multiple subtractive proteomics filters. Following that, a multi-epitopes based chimeric vaccine construct was modeled and joined with an adjuvant to improve the potency of the designed vaccine construct. The structure of the construct was predicted and analyzed for flexibility. A population coverage analysis was performed to evaluate the broad-spectrum applicability of B. pseudomallei. The computed combined world population coverage was 99.74%. Molecular docking analysis was applied further to evaluate the binding efficacy of the designed vaccine construct with the human toll-like receptors-5 (TLR-5). Furthermore, the dynamic behavior and stability of the docked complexes were investigated using molecular dynamics simulation, and the binding free energy determined for Vaccine-TLR-5 was delta total -168.3588. The docking result revealed that the vaccine construct may elicit a suitable immunological response within the host body. Hence, we believe that the designed in-silico vaccine could be helpful for experimentalists in the formulation of a highly effective vaccine for B. pseudomallei.
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Affiliation(s)
- Noorah Alsowayeh
- Department of Biology, College of Education (Majmaah), Majmaah University, Al Majmaah, Saudi Arabia
| | - Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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13
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Meumann EM, Krause VL, Baird R, Currie BJ. Using Genomics to Understand the Epidemiology of Infectious Diseases in the Northern Territory of Australia. Trop Med Infect Dis 2022; 7:tropicalmed7080181. [PMID: 36006273 PMCID: PMC9413455 DOI: 10.3390/tropicalmed7080181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
The Northern Territory (NT) is a geographically remote region of northern and central Australia. Approximately a third of the population are First Nations Australians, many of whom live in remote regions. Due to the physical environment and climate, and scale of social inequity, the rates of many infectious diseases are the highest nationally. Molecular typing and genomic sequencing in research and public health have provided considerable new knowledge on the epidemiology of infectious diseases in the NT. We review the applications of genomic sequencing technology for molecular typing, identification of transmission clusters, phylogenomics, antimicrobial resistance prediction, and pathogen detection. We provide examples where these methodologies have been applied to infectious diseases in the NT and discuss the next steps in public health implementation of this technology.
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Affiliation(s)
- Ella M. Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
- Correspondence:
| | - Vicki L. Krause
- Northern Territory Centre for Disease Control, Northern Territory Government, Darwin 0810, Australia
| | - Robert Baird
- Territory Pathology, Royal Darwin Hospital, Darwin 0810, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0810, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin 0810, Australia
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14
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Jibrin MO, Timilsina S, Minsavage GV, Vallad GE, Roberts PD, Goss EM, Jones JB. Bacterial Spot of Tomato and Pepper in Africa: Diversity, Emergence of T5 Race, and Management. Front Microbiol 2022; 13:835647. [PMID: 35509307 PMCID: PMC9058171 DOI: 10.3389/fmicb.2022.835647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial spot disease was first reported from South Africa by Ethel M. Doidge in 1920. In the ensuing century after the initial discovery, the pathogen has gained global attention in plant pathology research, providing insights into host-pathogen interactions, pathogen evolution, and effector discovery, such as the first discovery of transcription activation-like effectors, among many others. Four distinct genetic groups, including Xanthomonas euvesicatoria (proposed name: X. euvesicatoria pv. euvesicatoria), Xanthomonas perforans (proposed name: X. euvesicatoria pv. perforans), Xanthomonas gardneri (proposed name: Xanthomonas hortorum pv. gardneri), and Xanthomonas vesicatoria, are known to cause bacterial spot disease. Recently, a new race of a bacterial spot pathogen, race T5, which is a product of recombination between at least two Xanthomonas species, was reported in Nigeria. In this review, our focus is on the progress made on the African continent, vis-à-vis progress made in the global bacterial spot research community to provide a body of information useful for researchers in understanding the diversity, evolutionary changes, and management of the disease in Africa.
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Affiliation(s)
- Mustafa Ojonuba Jibrin
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, United States
- Department of Crop Protection, Ahmadu Bello University, Zaria, Nigeria
| | - Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Gerald V. Minsavage
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
| | - Garry E. Vallad
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Pamela D. Roberts
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- UF/IFAS Southwest Florida Research and Education Center, Immokalee, FL, United States
| | - Erica M. Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Jeffrey B. Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, United States
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15
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McLaughlin HP, Gulvik CA, Sue D. In silico analyses of penicillin binding proteins in Burkholderia pseudomallei uncovers SNPs with utility for phylogeography, species differentiation, and sequence typing. PLoS Negl Trop Dis 2022; 16:e0009882. [PMID: 35417451 PMCID: PMC9037935 DOI: 10.1371/journal.pntd.0009882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/25/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022] Open
Abstract
Burkholderia pseudomallei causes melioidosis. Sequence typing this pathogen can reveal geographical origin and uncover epidemiological associations. Here, we describe B. pseudomallei genes encoding putative penicillin binding proteins (PBPs) and investigate their utility for determining phylogeography and differentiating closely related species. We performed in silico analysis to characterize 10 PBP homologs in B. pseudomallei 1026b. As PBP active site mutations can confer β-lactam resistance in Gram-negative bacteria, PBP sequences in two resistant B. pseudomallei strains were examined for similar alterations. Sequence alignments revealed single amino acid polymorphisms (SAAPs) unique to the multidrug resistant strain Bp1651 in the transpeptidase domains of two PBPs, but not directly within the active sites. Using BLASTn analyses of complete assembled genomes in the NCBI database, we determined genes encoding PBPs were conserved among B. pseudomallei (n = 101) and Burkholderia mallei (n = 26) strains. Within these genes, single nucleotide polymorphisms (SNPs) useful for predicting geographic origin of B. pseudomallei were uncovered. SNPs unique to B. mallei were also identified. Based on 11 SNPs identified in two genes encoding predicted PBP-3s, a dual-locus sequence typing (DLST) scheme was developed. The robustness of this typing scheme was assessed using 1,523 RefSeq genomes from B. pseudomallei (n = 1,442) and B. mallei (n = 81) strains, resulting in 32 sequence types (STs). Compared to multi-locus sequence typing (MLST), the DLST scheme demonstrated less resolution to support the continental separation of Australian B. pseudomallei strains. However, several STs were unique to strains originating from a specific country or region. The phylogeography of Western Hemisphere B. pseudomallei strains was more highly resolved by DLST compared to internal transcribed spacer (ITS) typing, and all B. mallei strains formed a single ST. Conserved genes encoding PBPs in B. pseudomallei are useful for strain typing, can enhance predictions of geographic origin, and differentiate strains of closely related Burkholderia species. Burkholderia pseudomallei causes the life-threatening disease melioidosis and is considered a biological threat and select agent by the United States government. This soil-dwelling bacterium is commonly found in regions of southeast Asia and northern Australia, but it is also detected in other tropical and sub-tropical areas around the world. With a predicted global burden of 165,000 annual cases and mortality rate that can exceed 40% without prompt and appropriate antibiotic treatment, understanding the epidemiology of melioidosis and mechanisms of antibiotic resistance in B. pseudomallei can benefit public health and safety. Recently, we identified ten conserved genes encoding putative penicillin binding proteins (PBPs) in B. pseudomallei. Here, we examined B. pseudomallei PBP sequences for amino acid mutations that may contribute to β-lactam resistance. We also uncovered nucleotide mutations with utility to predict the geographical origin of B. pseudomallei strains and to differentiate closely related Burkholderia species. Based on 11 informative single nucleotide polymorphisms in two genes each encoding a PBP-3, we developed a simple, targeted dual-locus typing approach.
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Affiliation(s)
- Heather P. McLaughlin
- Biodefense Research and Development Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Christopher A. Gulvik
- Zoonoses and Select Agent Laboratory, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - David Sue
- Biodefense Research and Development Laboratory, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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16
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Roe C, Vazquez AJ, Phillips PD, Allender CJ, Bowen RA, Nottingham RD, Doyle A, Wongsuwan G, Wuthiekanun V, Limmathurotsakul D, Peacock S, Keim P, Tuanyok A, Wagner DM, Sahl JW. Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand. PLoS Negl Trop Dis 2022; 16:e0010172. [PMID: 35143500 PMCID: PMC8865643 DOI: 10.1371/journal.pntd.0010172] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 02/23/2022] [Accepted: 01/14/2022] [Indexed: 11/24/2022] Open
Abstract
Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although the global genomic diversity of clinical B. pseudomallei isolates has been investigated, there is limited understanding of its genomic diversity across small geographic scales, especially in soil. In this study, we obtained 288 B. pseudomallei isolates from a single soil sample (~100g; intensive site 2, INT2) collected at a depth of 30cm from a site in Ubon Ratchathani Province, Thailand. We sequenced the genomes of 169 of these isolates that represent 7 distinct sequence types (STs), including a new ST (ST1820), based on multi-locus sequence typing (MLST) analysis. A core genome SNP phylogeny demonstrated that all identified STs share a recent common ancestor that diverged an estimated 796-1260 years ago. A pan-genomics analysis demonstrated recombination between clades and intra-MLST phylogenetic and gene differences. To identify potential differential virulence between STs, groups of BALB/c mice (5 mice/isolate) were challenged via subcutaneous injection (500 CFUs) with 30 INT2 isolates representing 5 different STs; over the 21-day experiment, eight isolates killed all mice, 2 isolates killed an intermediate number of mice (1-2), and 20 isolates killed no mice. Although the virulence results were largely stratified by ST, one virulent isolate and six attenuated isolates were from the same ST (ST1005), suggesting that variably conserved genomic regions may contribute to virulence. Genomes from the animal-challenged isolates were subjected to a bacterial genome-wide association study to identify genomic regions associated with differential virulence. One associated region is a unique variant of Hcp1, a component of the type VI secretion system, which may result in attenuation. The results of this study have implications for comprehensive sampling strategies, environmental exposure risk assessment, and understanding recombination and differential virulence in B. pseudomallei.
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Affiliation(s)
- Chandler Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adam J. Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul D. Phillips
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Chris J. Allender
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard A. Bowen
- Department of Biological Sciences, Colorado State University, Ft. Collins, Colorado, United States of America
| | - Roxanne D. Nottingham
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adina Doyle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Gumphol Wongsuwan
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | | | - Sharon Peacock
- Department of Medicine, University of Cambridge, Cambridge, England
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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17
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Leishmania and the Model of Predominant Clonal Evolution. Microorganisms 2021; 9:microorganisms9112409. [PMID: 34835534 PMCID: PMC8620605 DOI: 10.3390/microorganisms9112409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 01/23/2023] Open
Abstract
As it is the case for other pathogenic microorganisms, the respective impact of clonality and genetic exchange on Leishmania natural populations has been the object of lively debates since the early 1980s. The predominant clonal evolution (PCE) model states that genetic exchange in these parasites’ natural populations may have a high relevance on an evolutionary scale, but is not sufficient to erase a persistent phylogenetic signal and the existence of bifurcating trees. Recent data based on high-resolution markers and genomic polymorphisms fully confirm the PCE model down to a microevolutionary level.
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18
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Zheng H, Qin J, Chen H, Hu H, Zhang X, Yang C, Wu Y, Li Y, Li S, Kuang H, Zhou H, Shen D, Song K, Song Y, Zhao T, Yang R, Tan Y, Cui Y. Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis. Microb Genom 2021; 7. [PMID: 34762026 PMCID: PMC8743561 DOI: 10.1099/mgen.0.000659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative soil-dwelling bacillus that causes melioidosis, a frequently fatal infectious disease, in tropical and subtropical regions. Previous studies have identified the overall genetic and evolutionary characteristics of B. pseudomallei on a global scale, including its origin and transmission routes. However, beyond its known hyperendemicity foci in northern Australia and Southeast Asia, the distribution and genetic characteristics of B. pseudomallei in most tropical regions remain poorly understood, including in southern China. Here, we sequenced the genomes of 122 B. pseudomallei strains collected from Hainan, an island in southern China, in 2002–2018, to investigate the population structure, relationships with global strains, local epidemiology, and virulence and antimicrobial-resistance factors. A phylogenetic analysis and hierarchical clustering divided the Hainan strains into nine phylogenic groups (PGs), 80 % of which were concentrated within five major groups (group 1: corresponding to minor sequence types [STs], 12.3 %; group 3: ST46 and ST50, 31.1 %; group 9: ST58, 13.1 %; group 11: ST55, 8.2 %; group 15: mainly ST658, 15.6%). A phylogenetic analysis that included global strains suggested that B. pseudomallei in Hainan originated from Southeast Asian countries, transmitted in multiple historical importation events. We also identified several mutual transmission events between Hainan and Southeast Asian countries in recent years, including three importation events from Thailand and Singapore to Hainan and three exportation events from Hainan to Singapore, Malaysia, and Taiwan island. A statistical analysis of the temporal distribution showed that the Hainan strains of groups 3, 9, and 15 have dominated the disease epidemic locally in the last 5 years. The spatial distribution of the Hainan strains demonstrated that some PGs are distributed in different cities on Hainan island, and by combining phylogenic and geographic distribution information, we detected 21 between-city transmission events, indicating its frequent local transmission. The detection of virulence factor genes showed that 56 % of the Hainan strains in group 1 encode a B. pseudomallei-specific adherence factor, boaB, confirming the specific pathogenic characteristics of the Hainan strains in group 1. An analysis of the antimicrobial-resistance potential of B. pseudomallei showed that various kinds of alterations were identified in clinically relevant antibiotic resistance factors, such as AmrR, PenA and PBP3, etc. Our results clarify the population structure, local epidemiology, and pathogenic characteristics of B. pseudomallei in Hainan, providing further insight into its regional and global transmission networks and improving our knowledge of its global phylogeography.
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Affiliation(s)
- Hongyuan Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Jingliang Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, 230032, PR China
| | - Hai Chen
- Department of Clinical Laboratory, Sanya People's Hospital, Sanya, Hainan Province, 572000, PR China
| | - Hongyan Hu
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yuanli Li
- Department of Clinical Laboratory, Sanya People's Hospital, Sanya, Hainan Province, 572000, PR China
| | - Sha Li
- Department of Clinical Laboratory, Sanya People's Hospital, Sanya, Hainan Province, 572000, PR China
| | - Huihui Kuang
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Hanwang Zhou
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Dingxia Shen
- Department of Laboratory Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, Hainan Province, 572000, PR China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Tongyan Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, PR China.,School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui Province, 230032, PR China
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19
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Watthanaworawit W, Roberts T, Hopkins J, Gassiep I, Norton R, Robinson MT, Silisouk J, Sar P, Sao S, Amornchai P, Limmathurotsakul D, Wuthiekanun V, Nosten F, Simpson AJH, Turner P, Ling CL. A multi-country study using MALDI-TOF mass spectrometry for rapid identification of Burkholderia pseudomallei. BMC Microbiol 2021; 21:213. [PMID: 34266382 PMCID: PMC8283998 DOI: 10.1186/s12866-021-02276-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 06/21/2021] [Indexed: 11/10/2022] Open
Abstract
Background Burkholderia pseudomallei is the bacterial causative agent of melioidosis, a difficult disease to diagnose clinically with high mortality if not appropriately treated. Definitive diagnosis requires isolation and identification of the organism. With the increased adoption of MALDI-TOF MS for the identification of bacteria, we established a method for rapid identification of B. pseudomallei using the Vitek MS, a system that does not currently have B. pseudomallei in its in-vitro diagnostic database. Results A routine direct spotting method was employed to create spectra and SuperSpectra. An initial B. pseudomallei SuperSpectrum was created at Shoklo Malaria Research Unit (SMRU) from 17 reference isolates (46 spectra). When tested, this initial SMRU SuperSpectrum was able to identify 98.2 % (54/55) of Asian isolates, but just 46.7 % (35/75) of Australian isolates. Using spectra (430) from different reference and clinical isolates, two additional SMRU SuperSpectra were created. Using the combination of all SMRU SuperSpectra with seven existing SuperSpectra from Townsville, Australia 119 (100 %) Asian isolates and 31 (100 %) Australian isolates were correctly identified. In addition, no misidentifications were obtained when using these 11 SuperSpectra when tested with 34 isolates of other bacteria including the closely related species Burkholderia thailandensis and Burkholderia cepacia. Conclusions This study has established a method for identification of B. pseudomallei using Vitek MS, and highlights the impact of geographical differences between strains for identification using this technique. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02276-1.
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Affiliation(s)
- Wanitda Watthanaworawit
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Jill Hopkins
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ian Gassiep
- University of Queensland Centre for Clinical Research, Herston, Queensland, Australia
| | - Robert Norton
- Pathology, Townsville Hospital, Townsville, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Australia
| | - Matthew T Robinson
- 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
| | - Joy Silisouk
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Poda Sar
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sena Sao
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Premjit Amornchai
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Francois Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew J H Simpson
- 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
| | - Paul Turner
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Clare L Ling
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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20
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Meumann EM, Kaestli M, Mayo M, Ward L, Rachlin A, Webb JR, Kleinecke M, Price EP, Currie BJ. Emergence of Burkholderia pseudomallei Sequence Type 562, Northern Australia. Emerg Infect Dis 2021; 27:1057-1067. [PMID: 33754984 PMCID: PMC8007296 DOI: 10.3201/eid2704.202716] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since 2005, the range of Burkholderia pseudomallei sequence type 562 (ST562) has expanded in northern Australia. During 2005–2019, ST562 caused melioidosis in 61 humans and 3 animals. Cases initially occurred in suburbs surrounding a creek before spreading across urban Darwin, Australia and a nearby island community. In urban Darwin, ST562 caused 12% (53/440) of melioidosis cases, a proportion that increased during the study period. We analyzed 2 clusters of cases with epidemiologic links and used genomic analysis to identify previously unassociated cases. We found that ST562 isolates from Hainan Province, China, and Pingtung County, Taiwan, were distantly related to ST562 strains from Australia. Temporal genomic analysis suggested a single ST562 introduction into the Darwin region in ≈1988. The origin and transmission mode of ST562 into Australia remain uncertain.
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21
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Gassiep I, Burnard D, Bauer MJ, Norton RE, Harris PN. Diagnosis of melioidosis: the role of molecular techniques. Future Microbiol 2021; 16:271-288. [PMID: 33595347 DOI: 10.2217/fmb-2020-0202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.
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Affiliation(s)
- Ian Gassiep
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Department of Infectious Diseases, Mater Hospital Brisbane, South Brisbane, Queensland, 4101, Australia
| | - Delaney Burnard
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Michelle J Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Robert E Norton
- Pathology Queensland, Townsville University Hospital, Townsville, Queensland, 4814, Australia
| | - Patrick N Harris
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, Queensland, 4029, Australia
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22
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Abstract
B. pseudomallei causes significant morbidity and mortality, but its geographic prevalence and genetic diversity are not well characterized, especially in the Western Hemisphere. A better understanding of the genetic relationships among clinical and environmental isolates will improve knowledge of the population structure of this bacterium as well as the ability to conduct epidemiological investigations of cases of melioidosis. Burkholderia pseudomallei is a Gram-negative bacterium that causes the sapronotic disease melioidosis. An outbreak in 2003 in the state of Ceara, Brazil, resulted in subsequent surveillance and environmental sampling which led to the recognition of B. pseudomallei as an endemic pathogen in that area. From 2003 to 2015, 24 clinical and 12 environmental isolates were collected across Ceara along with one from the state of Alagoas. Using next-generation sequencing, multilocus sequence typing, and single nucleotide polymorphism analysis, we characterized the genomic diversity of this collection to better understand the population structure of B. pseudomallei associated with Ceara. We found that the isolates in this collection form a distinct subclade compared to other examples from the Western Hemisphere. Substantial genetic diversity among the clinical and environmental isolates was observed, with 14 sequence types (STs) identified among the 37 isolates. Of the 31,594 core single-nucleotide polymorphisms (SNPs) identified, a high proportion (59%) were due to recombination. Because recombination events do not follow a molecular clock, the observation of high occurrence underscores the importance of identifying and removing recombination SNPs prior to evolutionary reconstructions and inferences in public health responses to B. pseudomallei outbreaks. Our results suggest long-term B. pseudomallei prevalence in this recently recognized region of melioidosis endemicity. IMPORTANCEB. pseudomallei causes significant morbidity and mortality, but its geographic prevalence and genetic diversity are not well characterized, especially in the Western Hemisphere. A better understanding of the genetic relationships among clinical and environmental isolates will improve knowledge of the population structure of this bacterium as well as the ability to conduct epidemiological investigations of cases of melioidosis.
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23
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Ghazali AK, Eng SA, Khoo JS, Teoh S, Hoh CC, Nathan S. Whole-genome comparative analysis of Malaysian Burkholderia pseudomallei clinical isolates. Microb Genom 2021; 7. [PMID: 33565959 PMCID: PMC8208702 DOI: 10.1099/mgen.0.000527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei, a soil-dwelling Gram-negative bacterium, is the causative agent of the endemic tropical disease melioidosis. Clinical manifestations of B. pseudomallei infection range from acute or chronic localized infection in a single organ to fulminant septicaemia in multiple organs. The diverse clinical manifestations are attributed to various factors, including the genome plasticity across B. pseudomallei strains. We previously characterized B. pseudomallei strains isolated in Malaysia and noted different levels of virulence in model hosts. We hypothesized that the difference in virulence might be a result of variance at the genome level. In this study, we sequenced and assembled four Malaysian clinical B. pseudomallei isolates, UKMR15, UKMPMC2000, UKMD286 and UKMH10. Phylogenomic analysis showed that Malaysian subclades emerged from the Asian subclade, suggesting that the Malaysian strains originated from the Asian region. Interestingly, the low-virulence strain, UKMH10, was the most distantly related compared to the other Malaysian isolates. Genomic island (GI) prediction analysis identified a new island of 23 kb, GI9c, which is present in B. pseudomallei and Burkholderia mallei, but not Burkholderia thailandensis. Genes encoding known B. pseudomallei virulence factors were present across all four genomes, but comparative analysis of the total gene content across the Malaysian strains identified 104 genes that are absent in UKMH10. We propose that these genes may encode novel virulence factors, which may explain the reduced virulence of this strain. Further investigation on the identity and role of these 104 proteins may aid in understanding B. pseudomallei pathogenicity to guide the design of new therapeutics for treating melioidosis.
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Affiliation(s)
- Ahmad-Kamal Ghazali
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Su-Anne Eng
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Jia-Shiun Khoo
- Codon Genomics S/B, 26, Jalan Dutamas 7, Taman Dutamas Balakong, Selangor, Malaysia
| | - Seddon Teoh
- Codon Genomics S/B, 26, Jalan Dutamas 7, Taman Dutamas Balakong, Selangor, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics S/B, 26, Jalan Dutamas 7, Taman Dutamas Balakong, Selangor, Malaysia
| | - Sheila Nathan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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24
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Using Land Runoff to Survey the Distribution and Genetic Diversity of Burkholderia pseudomallei in Vientiane, Laos. Appl Environ Microbiol 2021; 87:AEM.02112-20. [PMID: 33257313 PMCID: PMC7851688 DOI: 10.1128/aem.02112-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Melioidosis is a disease of significant public health importance that is being increasingly recognized globally. The majority of cases arise through direct percutaneous exposure to its etiological agent, Burkholderia pseudomallei In the Lao People's Democratic Republic (Laos), the presence and environmental distribution of B. pseudomallei are not well characterized, though recent epidemiological surveys of the bacterium have indicated that B. pseudomallei is widespread throughout the environment in the center and south of the country and that rivers can act as carriers and potential sentinels for the bacterium. The spatial and genetic distribution of B. pseudomallei within Vientiane Capital, from where the majority of cases diagnosed to date have originated, remains an important knowledge gap. We sampled surface runoff from drain catchment areas throughout urban Vientiane to determine the presence and local population structure of the bacterium. B. pseudomallei was detected in drainage areas throughout the capital, indicating it is widespread in the environment and that exposure rates in urban Vientiane are likely more frequent than previously thought. Whole-genome comparative analysis demonstrated that Lao B. pseudomallei isolates are highly genetically diverse, suggesting the bacterium is well-established and not a recent introduction. Despite the wide genome diversity, one environmental survey isolate was highly genetically related to a Lao melioidosis patient isolate collected 13 years prior to the study. Knowledge gained from this study will augment understanding of B. pseudomallei phylogeography in Asia and enhance public health awareness and future implementation of infection control measures within Laos.IMPORTANCE The environmental bacterium B. pseudomallei is the etiological agent of melioidosis, a tropical disease with one model estimating a global annual incidence of 165,000 cases and 89,000 deaths. In the Lao People's Democratic Republic (Laos), the environmental distribution and population structure of B. pseudomallei remain relatively undefined, particularly in Vientiane Capital from where most diagnosed cases have originated. We used surface runoff as a proxy for B. pseudomallei dispersal in the environment and performed whole-genome sequencing (WGS) to examine the local population structure. Our data confirmed that B. pseudomallei is widespread throughout Vientiane and that surface runoff might be useful for future environmental monitoring of the bacterium. B. pseudomallei isolates were also highly genetically diverse, suggesting the bacterium is well-established and endemic in Laos. These findings can be used to improve awareness of B. pseudomallei in the Lao environment and demonstrates the epidemiological and phylogeographical insights that can be gained from WGS.
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25
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Chomkatekaew C, Boonklang P, Sangphukieo A, Chewapreecha C. An Evolutionary Arms Race Between Burkholderia pseudomallei and Host Immune System: What Do We Know? Front Microbiol 2021; 11:612568. [PMID: 33552023 PMCID: PMC7858667 DOI: 10.3389/fmicb.2020.612568] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
A better understanding of co-evolution between pathogens and hosts holds promise for better prevention and control strategies. This review will explore the interactions between Burkholderia pseudomallei, an environmental and opportunistic pathogen, and the human host immune system. B. pseudomallei causes "Melioidosis," a rapidly fatal tropical infectious disease predicted to affect 165,000 cases annually worldwide, of which 89,000 are fatal. Genetic heterogeneities were reported in both B. pseudomallei and human host population, some of which may, at least in part, contribute to inter-individual differences in disease susceptibility. Here, we review (i) a multi-host-pathogen characteristic of the interaction; (ii) selection pressures acting on B. pseudomallei and human genomes with the former being driven by bacterial adaptation across ranges of ecological niches while the latter are driven by human encounter of broad ranges of pathogens; (iii) the mechanisms that generate genetic diversity in bacterial and host population particularly in sequences encoding proteins functioning in host-pathogen interaction; (iv) reported genetic and structural variations of proteins or molecules observed in B. pseudomallei-human host interactions and their implications in infection outcomes. Together, these predict bacterial and host evolutionary trajectory which continues to generate genetic diversity in bacterium and operates host immune selection at the molecular level.
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Affiliation(s)
| | | | - Apiwat Sangphukieo
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
| | - Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Bangkok, Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, United Kingdom
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26
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Webb JR, Win MM, Zin KN, Win KKN, Wah TT, Ashley EA, Smithuis F, Swe MMM, Mayo M, Currie BJ, Dance DAB. Myanmar Burkholderia pseudomallei strains are genetically diverse and originate from Asia with phylogenetic evidence of reintroductions from neighbouring countries. Sci Rep 2020; 10:16260. [PMID: 33004984 PMCID: PMC7530998 DOI: 10.1038/s41598-020-73545-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/11/2020] [Indexed: 02/08/2023] Open
Abstract
Melioidosis was first identified in Myanmar in 1911 but for the last century it has remained largely unreported there. Burkholderia pseudomallei was first isolated from the environment of Myanmar in 2016, confirming continuing endemicity. Recent genomic studies showed that B. pseudomallei originated in Australia and spread to Asia, with phylogenetic evidence of repeated reintroduction of B. pseudomallei across countries bordered by the Mekong River and the Malay Peninsula. We present the first whole-genome sequences of B. pseudomallei isolates from Myanmar: nine clinical and seven environmental isolates. We used large-scale comparative genomics to assess the genetic diversity, phylogeography and potential origins of B. pseudomallei in Myanmar. Global phylogenetics demonstrated that Myanmar isolates group in two distantly related clades that reside in a more ancestral Asian clade with high amounts of genetic diversity. The diversity of B. pseudomallei from Myanmar and divergence within our global phylogeny suggest that the original introduction of B. pseudomallei to Myanmar was not a recent event. Our study provides new insights into global patterns of B. pseudomallei dissemination, most notably the dynamic nature of movement of B. pseudomallei within densely populated Southeast Asia. The role of anthropogenic influences in both ancient and more recent dissemination of B. pseudomallei to Myanmar and elsewhere in Southeast Asia and globally requires further study.
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Affiliation(s)
- Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia.
| | - Mo Mo Win
- Department of Medical Research, Yangon, Myanmar
| | - Khwar Nyo Zin
- Microbiology Laboratory, Yangon General Hospital, Yangon, Myanmar
| | | | | | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Frank Smithuis
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Myanmar-Oxford Clinical Research Unit, Yangon, Myanmar
| | - Myo Maung Maung Swe
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, NT, Australia
| | - David A B Dance
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford, UK
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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27
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Somprasong N, Hall CM, Webb JR, Sahl JW, Wagner DM, Keim P, Currie BJ, Schweizer HP. Burkholderia ubonensis Meropenem Resistance: Insights into Distinct Properties of Class A β-Lactamases in Burkholderia cepacia Complex and Burkholderia pseudomallei Complex Bacteria. mBio 2020; 11:e00592-20. [PMID: 32291300 PMCID: PMC7157819 DOI: 10.1128/mbio.00592-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Burkholderia pseudomallei, the founding member of the B. pseudomallei complex (Bpc), is a biothreat agent and causes melioidosis, a disease whose treatment mainly relies on ceftazidime and meropenem. The concern is that B. pseudomallei could enhance its drug resistance repertoire by the acquisition of DNA from resistant near-neighbor species. Burkholderia ubonensis, a member of the B. cepacia complex (Bcc), is commonly coisolated from environments where B. pseudomallei is present. Unlike B. pseudomallei, in which significant primary carbapenem resistance is rare, it is not uncommon in B. ubonensis, but the underlying mechanisms are unknown. We established that carbapenem resistance in B. ubonensis is due to an inducible class A PenB β-lactamase, as has been shown for other Bcc bacteria. Inducibility is not sufficient for high-level resistance but also requires other determinants, such as a PenB that is more robust than that present in susceptible isolates, as well as other resistance factors. Curiously and diagnostic for the two complexes, both Bpc and Bcc bacteria contain distinct annotated PenA class A β-lactamases. However, the protein from Bcc bacteria is missing its essential active-site serine and, therefore, is not a β-lactamase. Regulated expression of a transcriptional penB'-lacZ (β-galactosidase) fusion in the B. pseudomallei surrogate B. thailandensis confirms that although Bpc bacteria lack an inducible β-lactamase, they contain the components required for responding to aberrant peptidoglycan synthesis resulting from β-lactam challenge. Understanding the diversity of antimicrobial resistance in Burkholderia species is informative about how the challenges arising from potential resistance transfer between them can be met.IMPORTANCEBurkholderia pseudomallei causes melioidosis, a tropical disease that is highly fatal if not properly treated. Our data show that, in contrast to B. pseudomallei, B. ubonensis β-lactam resistance is fundamentally different because intrinsic resistance is mediated by an inducible class A β-lactamase. This includes resistance to carbapenems. Our work demonstrates that studies with near-neighbor species are informative about the diversity of antimicrobial resistance in Burkholderia and can also provide clues about the potential of resistance transfer between bacteria inhabiting the same environment. Knowledge about potential adverse challenges resulting from the horizontal transfer of resistance genes between members of the two complexes enables the design of effective countermeasures.
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Affiliation(s)
- Nawarat Somprasong
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bart J Currie
- Global and Tropical Heath Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Northern Territory, Australia
- Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Herbert P Schweizer
- Department of Molecular Genetics & Microbiology, College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
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28
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Whole-genome sequencing of Burkholderia pseudomallei from an urban melioidosis hot spot reveals a fine-scale population structure and localised spatial clustering in the environment. Sci Rep 2020; 10:5443. [PMID: 32214186 PMCID: PMC7096523 DOI: 10.1038/s41598-020-62300-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/17/2019] [Indexed: 11/12/2022] Open
Abstract
Melioidosis is a severe disease caused by the environmental bacterium Burkholderia pseudomallei that affects both humans and animals throughout northern Australia, Southeast Asia and increasingly globally. While there is a considerable degree of genetic diversity amongst isolates, B. pseudomallei has a robust global biogeographic structure and genetic populations are spatially clustered in the environment. We examined the distribution and local spread of B. pseudomallei in Darwin, Northern Territory, Australia, which has the highest recorded urban incidence of melioidosis globally. We sampled soil and land runoff throughout the city centre and performed whole-genome sequencing (WGS) on B. pseudomallei isolates. By combining phylogenetic analyses, Bayesian clustering and spatial hot spot analysis our results demonstrate that some sequence types (STs) are widespread in the urban Darwin environment, while others are highly spatially clustered over a small geographic scale. This clustering matches the spatial distribution of clinical cases for one ST. Results also demonstrate a greater overall isolate diversity recovered from drains compared to park soils, further supporting the role drains may play in dispersal of B. pseudomallei STs in the environment. Collectively, knowledge gained from this study will allow for better understanding of B. pseudomallei phylogeography and melioidosis source attribution, particularly on a local level.
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29
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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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30
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Pearson T, Sahl JW, Hepp CM, Handady K, Hornstra H, Vazquez AJ, Settles E, Mayo M, Kaestli M, Williamson CHD, Price EP, Sarovich DS, Cook JM, Wolken SR, Bowen RA, Tuanyok A, Foster JT, Drees KP, Kidd TJ, Bell SC, Currie BJ, Keim P. Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection. PLoS Pathog 2020; 16:e1008298. [PMID: 32134991 PMCID: PMC7077878 DOI: 10.1371/journal.ppat.1008298] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 03/17/2020] [Accepted: 01/02/2020] [Indexed: 12/14/2022] Open
Abstract
Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314's airways over a >16-year period, and also sampled the patient's home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host.
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Affiliation(s)
- Talima Pearson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal M. Hepp
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Karthik Handady
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heidie Hornstra
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Adam J. Vazquez
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erik Settles
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Charles H. D. Williamson
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Derek S. Sarovich
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Cook
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Spenser R. Wolken
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Richard A. Bowen
- Department of Biomedical Sciences, Colorado State University, Colorado, United States of America
| | - Apichai Tuanyok
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey T. Foster
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Kevin P. Drees
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Timothy J. Kidd
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C. Bell
- Department of Thoracic Medicine, The Prince Charles Hospital, Chermside, and QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - Paul Keim
- Pathogen & Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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French CT, Bulterys PL, Woodward CL, Tatters AO, Ng KR, Miller JF. Virulence from the rhizosphere: ecology and evolution of Burkholderia pseudomallei-complex species. Curr Opin Microbiol 2020; 54:18-32. [PMID: 32028234 DOI: 10.1016/j.mib.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Christopher T French
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Northern Arizona University, Department of Biological Sciences, Pathogen and Microbiome Institute 1395 S Knoles Drive, Flagstaff, AZ 86011, United States.
| | - Philip L Bulterys
- Department of Pathology, Stanford University, Lane Building, L235, 300 Pasteur Drive, Stanford, CA, 94305, United States
| | - Cora L Woodward
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Avery O Tatters
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Ken R Ng
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Jeff F Miller
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, 611 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States
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Aziz A, Currie BJ, Mayo M, Sarovich DS, Price EP. Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality. Microb Genom 2020; 6:e000326. [PMID: 31958055 PMCID: PMC7067207 DOI: 10.1099/mgen.0.000326] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/18/2019] [Indexed: 01/13/2023] Open
Abstract
Human-to-human transmission of the melioidosis bacterium, Burkholderia pseudomallei, is exceedingly rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing (WGS) to characterize one such unusual B. pseudomallei transmission event, which occurred between a breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types (STs)-259 and -261 were identified in the mother's sputum from both the primary culture sweep and in purified colonies, confirming an unusual polyclonal infection in this patient. In contrast, primary culture sweeps of the mother's breast milk and the child's cerebrospinal fluid and blood samples contained only ST-259, indicating monoclonal transmission to the child. Analysis of purified ST-259 isolates showed no genetic variation between mother and baby isolates, providing the strongest possible evidence of B. pseudomallei human-to-human transmission, probably via breastfeeding. Next, phylogenomic analysis of all isolates, including the mother's mixed ST-259/ST-261 sputum sample, was performed to investigate the effects of mixtures on phylogenetic inference. Inclusion of this mixture caused a dramatic reduction in the number of informative SNPs, resulting in branch collapse of ST-259 and ST-261 isolates, and several instances of incorrect topology in a global B. pseudomallei phylogeny, resulting in phylogenetic incongruence. Although phylogenomics can provide clues about the presence of mixtures within WGS datasets, our results demonstrate that this methodology can lead to phylogenetic misinterpretation if mixed genomes are not correctly identified and omitted. Using current bioinformatic tools, we demonstrate a robust method for bacterial mixture identification and strain parsing that avoids these pitfalls.
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Affiliation(s)
- Ammar Aziz
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, NT, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, QLD, Australia
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33
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Rachlin A, Shilton C, Webb JR, Mayo M, Kaestli M, Kleinecke M, Rigas V, Benedict S, Gurry I, Currie BJ. Melioidosis fatalities in captive slender-tailed meerkats (Suricata suricatta): combining epidemiology, pathology and whole-genome sequencing supports variable mechanisms of transmission with one health implications. BMC Vet Res 2019; 15:458. [PMID: 31856823 PMCID: PMC6921467 DOI: 10.1186/s12917-019-2198-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/27/2019] [Indexed: 12/29/2022] Open
Abstract
Background Melioidosis is a tropical infectious disease which is being increasingly recognised throughout the globe. Infection occurs in humans and animals, typically through direct exposure to soil or water containing the environmental bacterium Burkholderia pseudomallei. Case clusters of melioidosis have been described in humans following severe weather events and in exotic animals imported into melioidosis endemic zones. Direct transmission of B. pseudomallei between animals and/or humans has been documented but is considered extremely rare. Between March 2015 and October 2016 eight fatal cases of melioidosis were reported in slender-tailed meerkats (Suricata suricatta) on display at a Wildlife Park in Northern Australia. To further investigate the melioidosis case cluster we sampled the meerkat enclosure and adjacent park areas and performed whole-genome sequencing (WGS) on all culture-positive B. pseudomallei environmental and clinical isolates. Results WGS confirmed that the fatalities were caused by two different B. pseudomallei sequence types (STs) but that seven of the meerkat isolates were highly similar on the whole-genome level. Used concurrently with detailed pathology data, our results demonstrate that the seven cases originated from a single original source, but routes of infection varied amongst meerkats belonging to the clonal outbreak cluster. Moreover, in some instances direct transmission may have transpired through wounds inflicted while fighting. Conclusions Collectively, this study supports the use of high-resolution WGS to enhance epidemiological investigations into transmission modalities and pathogenesis of melioidosis, especially in the instance of a possible clonal outbreak scenario in exotic zoological collections. Such findings from an animal outbreak have important One Health implications.
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Affiliation(s)
- Audrey Rachlin
- Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina NT, 0811, Australia.
| | - Cathy Shilton
- Department of Primary Industry and Resources, Berrimah Veterinary Laboratory, Berrimah Farm, Makagon Road, Berrimah, Northern Territory, 0828, Australia
| | - Jessica R Webb
- Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina NT, 0811, Australia
| | - Mark Mayo
- Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina NT, 0811, Australia
| | - Mirjam Kaestli
- Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina NT, 0811, Australia.,Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, 0811, Australia
| | - Mariana Kleinecke
- Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina NT, 0811, Australia
| | - Vanessa Rigas
- Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina NT, 0811, Australia
| | - Suresh Benedict
- Department of Primary Industry and Resources, Berrimah Veterinary Laboratory, Berrimah Farm, Makagon Road, Berrimah, Northern Territory, 0828, Australia
| | - Ian Gurry
- Parap Veterinary Hospital, Parap, Darwin, Northern Territory, 0820, Australia
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, Casuarina NT, 0811, Australia.,Royal Darwin Hospital and Northern Territory Medical Program, Darwin, Northern Territory, 0811, Australia
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Chewapreecha C, Mather AE, Harris SR, Hunt M, Holden MTG, Chaichana C, Wuthiekanun V, Dougan G, Day NPJ, Limmathurotsakul D, Parkhill J, Peacock SJ. Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei. Commun Biol 2019; 2:428. [PMID: 31799430 PMCID: PMC6874650 DOI: 10.1038/s42003-019-0678-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023] Open
Abstract
The environmental bacterium Burkholderia pseudomallei causes melioidosis, an important endemic human disease in tropical and sub-tropical countries. This bacterium occupies broad ecological niches including soil, contaminated water, single-cell microbes, plants and infection in a range of animal species. Here, we performed genome-wide association studies for genetic determinants of environmental and human adaptation using a combined dataset of 1,010 whole genome sequences of B. pseudomallei from Northeast Thailand and Australia, representing two major disease hotspots. With these data, we identified 47 genes from 26 distinct loci associated with clinical or environmental isolates from Thailand and replicated 12 genes in an independent Australian cohort. We next outlined the selective pressures on the genetic loci (dN/dS) and the frequency at which they had been gained or lost throughout their evolutionary history, reflecting the bacterial adaptability to a wide range of ecological niches. Finally, we highlighted loci likely implicated in human disease.
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Affiliation(s)
- Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, 10150 Thailand
- Wellcome Sanger Institute, Hinxton, CB10 1SA UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich, NR4 7UQ UK
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | | | - Martin Hunt
- Wellcome Sanger Institute, Hinxton, CB10 1SA UK
| | | | - Chutima Chaichana
- Department of Mathematics, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Nicholas P. J. Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF UK
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
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35
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Hall CM, Jaramillo S, Jimenez R, Stone NE, Centner H, Busch JD, Bratsch N, Roe CC, Gee JE, Hoffmaster AR, Rivera-Garcia S, Soltero F, Ryff K, Perez-Padilla J, Keim P, Sahl JW, Wagner DM. Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico. PLoS Negl Trop Dis 2019; 13:e0007727. [PMID: 31487287 PMCID: PMC6748447 DOI: 10.1371/journal.pntd.0007727] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis. The global burden and distribution of melioidosis is poorly understood, including in the Caribbean. B. pseudomallei was previously isolated from humans and soil in eastern Puerto Rico but the abundance and distribution of B. pseudomallei in Puerto Rico as a whole has not been thoroughly investigated. METHODOLOGY/PRINCIPAL FINDINGS We collected 600 environmental samples (500 soil and 100 water) from 60 sites around Puerto Rico. We identified B. pseudomallei by isolating it via culturing and/or using PCR to detect its DNA within complex DNA extracts. Only three adjacent soil samples from one site were positive for B. pseudomallei with PCR; we obtained 55 isolates from two of these samples. The 55 B. pseudomallei isolates exhibited fine-scale variation in the core genome and contained four novel genomic islands. Phylogenetic analyses grouped Puerto Rico B. pseudomallei isolates into a monophyletic clade containing other Caribbean isolates, which was nested inside a larger clade containing all isolates from Central/South America. Other Burkholderia species were commonly observed in Puerto Rico; we cultured 129 isolates from multiple soil and water samples collected at numerous sites around Puerto Rico, including representatives of B. anthina, B. cenocepacia, B. cepacia, B. contaminans, B. glumae, B. seminalis, B. stagnalis, B. ubonensis, and several unidentified novel Burkholderia spp. CONCLUSIONS/SIGNIFICANCE B. pseudomallei was only detected in three soil samples collected at one site in north central Puerto Rico with only two of those samples yielding isolates. All previous human and environmental B. pseudomallei isolates were obtained from eastern Puerto Rico. These findings suggest B. pseudomallei is ecologically established and widely dispersed in the environment in Puerto Rico but rare. Phylogeographic patterns suggest the source of B. pseudomallei populations in Puerto Rico and elsewhere in the Caribbean may have been Central or South America.
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Affiliation(s)
- Carina M. Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sierra Jaramillo
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Rebecca Jimenez
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Nathan E. Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heather Centner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Joseph D. Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nicole Bratsch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jay E. Gee
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex R. Hoffmaster
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sarai Rivera-Garcia
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Fred Soltero
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Kyle Ryff
- Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico, United States of America
| | - Janice Perez-Padilla
- Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico, United States of America
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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Rachlin A, Kleinecke M, Kaestli M, Mayo M, Webb JR, Rigas V, Shilton C, Benedict S, Dyrting K, Currie BJ. A cluster of melioidosis infections in hatchling saltwater crocodiles ( Crocodylus porosus) resolved using genome-wide comparison of a common north Australian strain of Burkholderia pseudomallei. Microb Genom 2019; 5. [PMID: 31433287 PMCID: PMC6755496 DOI: 10.1099/mgen.0.000288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative saprophytic bacillus and the aetiological agent of melioidosis, a disease of public-health importance throughout Southeast Asia and northern Australia. Infection can occur in humans and a wide array of animal species, though zoonotic transmission and case clusters are rare. Despite its highly plastic genome and extensive strain diversity, fine-scale investigations into the population structure of B. pseudomallei indicate there is limited geographical dispersal amongst sequence types (STs). In the ‘Top End’ of northern Australia, five STs comprise 90 % of the overall abundance, the most prevalent and widespread of which is ST-109. In May 2016, ST-109 was implicated in two fatal cases of melioidosis in juvenile saltwater crocodiles at a wildlife park near Darwin, Australia. To determine the probable source of infection, we sampled the crocodile enclosures and analysed the phylogenetic relatedness of crocodile and culture-positive ST-109 environmental park isolates against an additional 135 ST-109 B. pseudomallei isolates from the Top End. Collectively, our whole-genome sequencing (WGS) and pathology findings confirmed B. pseudomallei detected in the hatchling incubator as the likely source of infection, with zero SNPs identified between clinical and environmental isolates. Our results also demonstrate little variation across the ST-109 genome, with SNPs in recombinogenic regions and one suspected case of ST homoplasy accounting for nearly all observed diversity. Collectively, this study supports the use of WGS for outbreak source attribution in highly recombinogenic pathogens, and confirms the epidemiological and phylogenetic insights that can be gained from high-resolution sequencing platforms.
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Affiliation(s)
- Audrey Rachlin
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
- *Correspondence: Audrey Rachlin,
| | - Mariana Kleinecke
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Mirjam Kaestli
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Mark Mayo
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Jessica R. Webb
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Vanessa Rigas
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Cathy Shilton
- Berrimah Veterinary Laboratory, Department of Primary Industry, Fisheries and Mines, Berrimah Farm, Makagon Road, Berrimah, Northern Territory 0828, Australia
| | - Suresh Benedict
- Berrimah Veterinary Laboratory, Department of Primary Industry, Fisheries and Mines, Berrimah Farm, Makagon Road, Berrimah, Northern Territory 0828, Australia
| | - Kitman Dyrting
- Berrimah Veterinary Laboratory, Department of Primary Industry, Fisheries and Mines, Berrimah Farm, Makagon Road, Berrimah, Northern Territory 0828, Australia
| | - Bart J. Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Royal Darwin Hospital and Northern Territory Medical Program, Darwin, Northern Territory 0811, Australia
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Webb JR, Rachlin A, Rigas V, Sarovich DS, Price EP, Kaestli M, Ward LM, Mayo M, Currie BJ. Tracing the environmental footprint of the Burkholderia pseudomallei lipopolysaccharide genotypes in the tropical "Top End" of the Northern Territory, Australia. PLoS Negl Trop Dis 2019; 13:e0007369. [PMID: 31348781 PMCID: PMC6701815 DOI: 10.1371/journal.pntd.0007369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/20/2019] [Accepted: 07/04/2019] [Indexed: 11/18/2022] Open
Abstract
The Tier 1 select agent Burkholderia pseudomallei is an environmental bacterium that causes melioidosis, a high mortality disease. Variably present genetic markers used to elucidate strain origin, relatedness and virulence in B. pseudomallei include the Burkholderia intracellular motility factor A (bimA) and filamentous hemagglutinin 3 (fhaB3) gene variants. Three lipopolysaccharide (LPS) O-antigen types in B. pseudomallei have been described, which vary in proportion between Australian and Asian isolates. However, it remains unknown if these LPS types can be used as genetic markers for geospatial analysis within a contiguous melioidosis-endemic region. Using a combination of whole-genome sequencing (WGS), statistical analysis and geographical mapping, we examined if the LPS types can be used as geographical markers in the Northern Territory, Australia. The clinical isolates revealed that LPS A prevalence was highest in the Darwin and surrounds (n = 660; 96% being LPS A and 4% LPS B) and LPS B in the Katherine and Katherine remote and East Arnhem regions (n = 79; 60% being LPS A and 40% LPS B). Bivariate logistics regression of 999 clinical B. pseudomallei isolates revealed that the odds of getting a clinical isolate with LPS B was highest in East Arnhem in comparison to Darwin and surrounds (OR 19.5, 95% CI 9.1-42.0; p<0.001). This geospatial correlation was subsequently confirmed by geographically mapping the LPS type from 340 environmental Top End strains. We also found that in the Top End, the minority bimA genotype bimABm has a similar remote region geographical footprint to that of LPS B. In addition, correlation of LPS type with multi-locus sequence typing (MLST) was strong, and where multiple LPS types were identified within a single sequence type, WGS confirmed homoplasy of the MLST loci. The clinical, sero-diagnostic and vaccine implications of geographically-based B. pseudomallei LPS types, and their relationships to regional and global dispersal of melioidosis, require global collaborations with further analysis of larger clinically and geospatially-linked datasets.
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Affiliation(s)
- Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- * E-mail:
| | - Audrey Rachlin
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Vanessa Rigas
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Linda M. Ward
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Department of Infectious Diseases and Northern Territory Medical Program, Royal Darwin Hospital, Darwin, Northern Territory, Australia
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Gee JE, Elrod MG, Gulvik CA, Haselow DT, Waters C, Liu L, Hoffmaster AR. Burkholderia thailandensis Isolated from Infected Wound, Arkansas, USA. Emerg Infect Dis 2019; 24:2091-2094. [PMID: 30334705 PMCID: PMC6199988 DOI: 10.3201/eid2411.180821] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The bacterium Burkholderia thailandensis, a member of the Burkholderia pseudomallei complex, is generally considered nonpathogenic; however, on rare occasions, B. thailandensis infections have been reported. We describe a clinical isolate of B. thailandensis, BtAR2017, recovered from a patient with an infected wound in Arkansas, USA, in 2017.
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Louca S, Mazel F, Doebeli M, Parfrey LW. A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol 2019; 17:e3000106. [PMID: 30716065 PMCID: PMC6361415 DOI: 10.1371/journal.pbio.3000106] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/21/2018] [Indexed: 12/17/2022] Open
Abstract
The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs. A massive survey of Earth's Bacteria and Archaea reveals that their diversity is orders of magnitude lower than previously thought. The study also indicates that extinctions played an important role in prokaryotic evolution. The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- * E-mail:
| | - Florent Mazel
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Michael Doebeli
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Wegener Parfrey
- Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
- Department of Zoology, University of British Columbia, Vancouver, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
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40
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Aziz A, Sarovich DS, Harris TM, Kaestli M, McRobb E, Mayo M, Currie BJ, Price EP. Suspected cases of intracontinental Burkholderia pseudomallei sequence type homoplasy resolved using whole-genome sequencing. Microb Genom 2019; 3. [PMID: 29208140 PMCID: PMC5729916 DOI: 10.1099/mgen.0.000139] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium that causes melioidosis, a disease of high mortality in humans and animals. Multilocus sequence typing (MLST) is a popular and portable genotyping method that has been used extensively to characterise the genetic diversity of B. pseudomallei populations. MLST has been central to our understanding of the underlying phylogeographical signal present in the B. pseudomallei genome, revealing distinct populations on both the intra- and the inter-continental level. However, due to its high recombination rate, it is possible for B. pseudomallei isolates to share the same multilocus sequence type (ST) despite being genetically and geographically distinct, with two cases of ‘ST homoplasy’ recently reported between Cambodian and Australian B. pseudomallei isolates. This phenomenon can dramatically confound conclusions about melioidosis transmission patterns and source attribution, a critical issue for bacteria such as B. pseudomallei that are of concern due to their potential for use as bioweapons. In this study, we used whole-genome sequencing to identify the first reported instances of intracontinental ST homoplasy, which involved ST-722 and ST-804 B. pseudomallei isolates separated by large geographical distances. In contrast, a third suspected homoplasy case was shown to be a true long-range (460 km) dispersal event between a remote Australian island and the Australian mainland. Our results show that, whilst a highly useful and portable method, MLST can occasionally lead to erroneous conclusions about isolate origin and disease attribution. In cases where a shared ST is identified between geographically distant locales, whole-genome sequencing should be used to resolve strain origin.
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Affiliation(s)
- Ammar Aziz
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Derek S Sarovich
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia.,2Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Tegan M Harris
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Mirjam Kaestli
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia.,3Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Australia
| | - Evan McRobb
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Mark Mayo
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Bart J Currie
- 1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Erin P Price
- 2Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,1Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
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Baker AL, Pearson T, Sahl JW, Hepp C, Price EP, Sarovich DS, Mayo M, Tuanyok A, Currie BJ, Keim P, Warner J. Burkholderia pseudomallei distribution in Australasia is linked to paleogeographic and anthropogenic history. PLoS One 2018; 13:e0206845. [PMID: 30395628 PMCID: PMC6218070 DOI: 10.1371/journal.pone.0206845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 10/20/2018] [Indexed: 12/30/2022] Open
Abstract
Burkholderia pseudomallei is the environmental bacillus that causes melioidosis; a disease clinically significant in Australia and Southeast Asia but emerging in tropical and sub-tropical regions around the globe. Previous studies have placed the ancestral population of the organism in Australia with a single lineage disseminated to Southeast Asia. We have previously characterized B. pseudomallei isolates from New Guinea and the Torres Strait archipelago; remote regions that share paleogeographic ties with Australia. These studies identified regional biogeographical boundaries. In this study, we utilize whole-genome sequencing to reconstruct ancient evolutionary relationships and ascertain correlations between paleogeography and present-day distribution of this bacterium in Australasia. Our results indicate that B. pseudomallei from New Guinea fall into a single clade within the Australian population. Furthermore, clades from New Guinea are region-specific; an observation possibly linked to limited recent anthropogenic influence in comparison to mainland Australia and Southeast Asia. Isolates from the Torres Strait archipelago were distinct yet scattered among those from mainland Australia. These results provide evidence that the New Guinean and Torres Strait lineages may be remnants of an ancient portion of the Australian population. Rising sea levels isolated New Guinea and the Torres Strait Islands from each other and the Australian mainland, and may have allowed long-term isolated evolution of these lineages, providing support for a theory of microbial biogeography congruent with that of macro flora and fauna. Moreover, these findings indicate that contemporary microbial biogeography theories should consider recent and ongoing impacts of globalisation and human activity.
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Affiliation(s)
- Anthony L. Baker
- Tasmanian Institute of Agriculture (TIA), University of Tasmania, Sandy Bay, Tasmania, Australia
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- * E-mail:
| | - Talima Pearson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Crystal Hepp
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Informatics and Computing, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Apichai Tuanyok
- College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey Warner
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
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Sadiq MA, Hassan L, Aziz SA, Zakaria Z, Musa HI, Amin MM, Othman N. Phylogenetic Diversity of Burkholderia pseudomallei isolated from veterinary cases and the environments in Peninsular Malaysia. Vet Anim Sci 2018; 6:21-28. [PMID: 32734049 PMCID: PMC7386693 DOI: 10.1016/j.vas.2018.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 07/30/2018] [Indexed: 12/01/2022] Open
Abstract
This study was designed to determine the genotype and the phylogeny of Burkholderia pseudomallei isolated from veterinary cases and from the animal environments in Peninsular Malaysia. The Malaysian B. pseudomallei population were then compared to those found elsewhere. A total of 113 isolates from veterinary cases (35) and the environment (56 from soil and 22 from water) were characterized using multilocus sequence typing (MLST). Two novel alleles, allele 97 and 69 of the gene locus ace and lepA respectively were recovered. Isolates were resolved into 12 distinct sequence types (STs) out of which five were novel, namely ST1130, ST1131, ST1338, ST1339 and ST1367. The isolates from veterinary cases co-clustered with those from the environment. B. pseudomallei isolates in this study were highly clonal and have descended from a common ancestor clonal complex (CC) 48 found in Southeast Asia. This study shows that veterinary case isolates are often caused by similar STs, with similar populations found in the direct animal environment and those previously reported to cause human infections in Malaysia and elsewhere. Isolates of B. pseudomallei from human infections have been given more attention, with a comparatively lower focus on isolates from animals and the farm environment. This study highlighted the genotype and phylogeny of B. pseudomallei isolated from animals and the environment and their relations to the isolates from human cases reported in Malaysia and elsewhere. Most STs reported in this study, from veterinary cases and animal environment are similar to those previously reported as causing human infections in Malaysia and elsewhere. Therefore, even though direct zoonosis is uncommon, monitoring melioidosis occurrences in animals can provide insights on the bacterial strains infecting humans.
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Affiliation(s)
- Muhammad Abubakar Sadiq
- Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), 44300 UPM Serdang, Selangor Darul Ehsan, Malaysia.,Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Maiduguri, P.M.B 1069, Maiduguri, Borno State, Nigeria
| | - Latiffah Hassan
- Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), 44300 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Saleha Abdul Aziz
- Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), 44300 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Zunita Zakaria
- Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), 44300 UPM Serdang, Selangor Darul Ehsan, Malaysia
| | - Hassan Ismail Musa
- Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), 44300 UPM Serdang, Selangor Darul Ehsan, Malaysia.,Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Maiduguri, P.M.B 1069, Maiduguri, Borno State, Nigeria
| | - Maswati Mat Amin
- Makmal Veterinar Kawasan Bukit Tengah, Peti Surat 63, 14007 Bukit Mertajam, Seberang Perai Tengah, Pulau Pinang, Malaysia
| | - Norlida Othman
- Makmal Veterinar Kawasan Kota Bharu, Jabatan Perkhidmatan Veterinar 16150 Kubang Kerian, Kota Bharu, Kelantan, Malaysia
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Fleshman A, Mullins K, Sahl J, Hepp C, Nieto N, Wiggins K, Hornstra H, Kelly D, Chan TC, Phetsouvanh R, Dittrich S, Panyanivong P, Paris D, Newton P, Richards A, Pearson T. Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity. Microb Genom 2018; 4. [PMID: 30035711 PMCID: PMC6202447 DOI: 10.1099/mgen.0.000199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.
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Affiliation(s)
- Amy Fleshman
- 1Northern Arizona University, Flagstaff, AZ, USA
| | | | - Jason Sahl
- 1Northern Arizona University, Flagstaff, AZ, USA
| | - Crystal Hepp
- 1Northern Arizona University, Flagstaff, AZ, USA
| | - Nathan Nieto
- 1Northern Arizona University, Flagstaff, AZ, USA
| | | | | | - Daryl Kelly
- 2Naval Medical Research Center, Silver Spring, MD, USA.,3The Ohio State University, Columbus, OH, USA
| | | | - Rattanaphone Phetsouvanh
- 4Lao-Oxford-Mahosot Hospital-Wellcome Trust, Research Unit, Mahosot Hospital, Vientiane, Vientiane, Lao People's Democratic Republic
| | - Sabine Dittrich
- 5University of Oxford, Centre for Tropical Medicine and Global Health, Oxford, UK.,6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,7Foundation of Innovative New Diagnostics, Geneva, Switzerland
| | - Phonepasith Panyanivong
- 6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Daniel Paris
- 8Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.,9Swiss Tropical and Public Health Institute, Basel, Switzerland.,10University of Basel, Basel, Switzerland
| | - Paul Newton
- 5University of Oxford, Centre for Tropical Medicine and Global Health, Oxford, UK.,6Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Allen Richards
- 2Naval Medical Research Center, Silver Spring, MD, USA.,11Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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Steinmetz I, Wagner GE, Kanyala E, Sawadogo M, Soumeya H, Teferi M, Andargie E, Yeshitela B, Yaba Atsé-Achi L, Sanogo M, Bonfoh B, Rakotozandrindrainy R, Pongombo Shongo C, Shongoya Pongombo M, Kasamba Ilunga E, Lichtenegger S, Assig K, May J, Bertherat E, Owusu M, Owusu-Dabo E, Adu-Sarkodie Y. Melioidosis in Africa: Time to Uncover the True Disease Load. Trop Med Infect Dis 2018; 3:E62. [PMID: 30274458 PMCID: PMC6073667 DOI: 10.3390/tropicalmed3020062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 02/05/2023] Open
Abstract
Melioidosis is an often fatal infectious disease with a protean clinical spectrum, caused by the environmental bacterial pathogen Burkholderia pseudomallei. Although the disease has been reported from some African countries in the past, the present epidemiology of melioidosis in Africa is almost entirely unknown. Therefore, the common view that melioidosis is rare in Africa is not evidence-based. A recent study concludes that large parts of Africa are environmentally suitable for B. pseudomallei. Twenty-four African countries and three countries in the Middle East were predicted to be endemic, but no cases of melioidosis have been reported yet. In this study, we summarize the present fragmentary knowledge on human and animal melioidosis and environmental B. pseudomallei in Africa and the Middle East. We propose that systematic serological studies in man and animals together with environmental investigations on potential B. pseudomallei habitats are needed to identify risk areas for melioidosis. This information can subsequently be used to target raising clinical awareness and the implementation of simple laboratory algorithms for the isolation of B. pseudomallei from clinical specimens. B. pseudomallei was most likely transferred from Asia to the Americas via Africa, which is shown by phylogenetic analyses. More data on the virulence and genomic characteristics of African B. pseudomallei isolates will contribute to a better understanding of the global evolution of the pathogen and will also help to assess potential differences in disease prevalence and outcome.
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Affiliation(s)
- Ivo Steinmetz
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8036 Graz, Austria.
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine of Greifswald, KöR, 17475 Greifswald, Germany.
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8036 Graz, Austria.
| | - Estelle Kanyala
- Departement UFR/Science de la Santé, Université d'Ouagadougou, BP 7021, Ouagadougou, Burkina Faso.
| | - Mamadou Sawadogo
- Departement UFR/Science de la Santé, Université d'Ouagadougou, BP 7021, Ouagadougou, Burkina Faso.
| | - Hema Soumeya
- Centre Muraz, 01 BP 390 Bobo Dioulasso, Burkina Faso.
| | - Mekonnen Teferi
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, P.O. Box 1005 Addis Ababa, Ethiopia.
| | - Emawayish Andargie
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, P.O. Box 1005 Addis Ababa, Ethiopia.
| | - Biruk Yeshitela
- Armauer Hansen Research Institute, Jimma Road, ALERT Compound, P.O. Box 1005 Addis Ababa, Ethiopia.
| | - Louise Yaba Atsé-Achi
- Laboratoire Central Vétérinaire de Bingerville, LANADA, P.O. Box 206 Bingerville, Cote D'Ivoire.
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), 01 BP 1303 Abidjan, Cote D'Ivoire.
| | - Moussa Sanogo
- Laboratoire Central Vétérinaire de Bingerville, LANADA, P.O. Box 206 Bingerville, Cote D'Ivoire.
| | - Bassirou Bonfoh
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS), 01 BP 1303 Abidjan, Cote D'Ivoire.
| | | | - Célestin Pongombo Shongo
- Democratic Republic of the Congo, Université de Lubumbashi, 1825 Lubumbashi, Republic of the Congo.
| | - Mick Shongoya Pongombo
- Democratic Republic of the Congo, Université de Lubumbashi, 1825 Lubumbashi, Republic of the Congo.
| | - Eric Kasamba Ilunga
- Democratic Republic of the Congo, Université de Lubumbashi, 1825 Lubumbashi, Republic of the Congo.
| | - Sabine Lichtenegger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8036 Graz, Austria.
| | - Karoline Assig
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8036 Graz, Austria.
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine of Greifswald, KöR, 17475 Greifswald, Germany.
| | - Jürgen May
- Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany.
| | - Eric Bertherat
- Department of Infectious Hazard Management, World Health Organization, Geneva 27, Switzerland.
| | - Michael Owusu
- College of Health Sciences, Kwame Nkrumah University of Science and Technology, 00233 Kumasi, Ghana.
| | - Ellis Owusu-Dabo
- College of Health Sciences, Kwame Nkrumah University of Science and Technology, 00233 Kumasi, Ghana.
- Kumasi Centre for Collaborative Research, 00233 Kumasi, Ghana.
| | - Yaw Adu-Sarkodie
- College of Health Sciences, Kwame Nkrumah University of Science and Technology, 00233 Kumasi, Ghana.
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Trinh TT, Nguyen LDN, Nguyen TV, Tran CX, Le AV, Nguyen HV, Assig K, Lichtenegger S, Wagner GE, Do CD, Steinmetz I. Melioidosis in Vietnam: Recently Improved Recognition but still an Uncertain Disease Burden after Almost a Century of Reporting. Trop Med Infect Dis 2018; 3:E39. [PMID: 30274435 PMCID: PMC6073866 DOI: 10.3390/tropicalmed3020039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 01/09/2023] Open
Abstract
The first cases of human melioidosis were described in Vietnam in the 1920s, almost a century ago. It was in Vietnam in the thirties that the saprophytic nature of B. pseudomallei was first recognized. Although a significant number of French and U.S. soldiers acquired the disease during the Vietnam wars, indigenous cases in the Vietnamese population were only sporadically reported over many decades. After reunification in 1975, only two retrospective studies reported relatively small numbers of indigenous cases from single tertiary care hospitals located in the biggest cities in the South and the North, respectively. Studies from provincial hospitals throughout the country were missing until the Research Network on Melioidosis and Burkholderia pseudomallei (RENOMAB) project started in 2014. From then on seminars, workshops, and national scientific conferences on melioidosis have been conducted to raise awareness among physicians and clinical laboratory staff. This led to the recognition of a significant number of cases in at least 36 hospitals in 26 provinces and cities throughout Vietnam. Although a widespread distribution of melioidosis has now been documented, there are still challenges to understand the true epidemiology of the disease. Establishment of national guidelines for diagnosis, management, and reporting of the disease together with more investigations on animal melioidosis, genomic diversity of B. pseudomallei and its environmental distribution are required.
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Affiliation(s)
- Trung T Trinh
- Institute of Microbiology and Biotechnology, Vietnam National University, Hanoi 100000, Vietnam.
| | - Linh D N Nguyen
- Department of Academic Affairs, Phan Chau Trinh University, Quang Nam 560000, Vietnam.
| | - Trung V Nguyen
- Department of Medical Microbiology, Hanoi Medical University, Hanoi 100000, Vietnam.
- National Hospital for Tropical Diseases, Hanoi 100000, Vietnam.
| | - Chuong X Tran
- Department of Infectious Diseases, Hue University of Medicine and Pharmacy, Hue 530000, Vietnam.
| | - An V Le
- Department of Medical Microbiology, Hue University of Medicine and Pharmacy, Hue 530000, Vietnam.
| | - Hao V Nguyen
- Department of Infectious Diseases, University of Medicine and Pharmacy, Ho Chi Minh 700000, Vietnam.
- Hospital for Tropical Diseases, Ho Chi Minh 700000, Vietnam.
| | - Karoline Assig
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria.
| | - Sabine Lichtenegger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria.
| | - Gabriel E Wagner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria.
| | - Cuong D Do
- Department of Infectious Diseases, Bach Mai Hospital, Hanoi 100000, Vietnam.
| | - Ivo Steinmetz
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, 8010 Graz, Austria.
- Friedrich Loeffler Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany.
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Gee JE, Gulvik CA, Elrod MG, Batra D, Rowe LA, Sheth M, Hoffmaster AR. Phylogeography of Burkholderia pseudomallei Isolates, Western Hemisphere. Emerg Infect Dis 2018. [PMID: 28628442 PMCID: PMC5512505 DOI: 10.3201/eid2307.161978] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The bacterium Burkholderia pseudomallei causes melioidosis, which is mainly associated with tropical areas. We analyzed single-nucleotide polymorphisms (SNPs) among genome sequences from isolates of B. pseudomallei that originated in the Western Hemisphere by comparing them with genome sequences of isolates that originated in the Eastern Hemisphere. Analysis indicated that isolates from the Western Hemisphere form a distinct clade, which supports the hypothesis that these isolates were derived from a constricted seeding event from Africa. Subclades have been resolved that are associated with specific regions within the Western Hemisphere and suggest that isolates might be correlated geographically with cases of melioidosis. One isolate associated with a former World War II prisoner of war was believed to represent illness 62 years after exposure in Southeast Asia. However, analysis suggested the isolate originated in Central or South America.
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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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Global Burden and Challenges of Melioidosis. Trop Med Infect Dis 2018; 3:tropicalmed3010013. [PMID: 30274411 PMCID: PMC6136634 DOI: 10.3390/tropicalmed3010013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 01/23/2018] [Accepted: 01/24/2018] [Indexed: 11/26/2022] Open
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Norris MH, Heacock-Kang Y, Zarzycki-Siek J, Bluhm AP, McMillan IA, Schweizer HP, Hoang TT. Burkholderia pseudomallei natural competency and DNA catabolism: Identification and characterization of relevant genes from a constructed fosmid library. PLoS One 2017; 12:e0189018. [PMID: 29253888 PMCID: PMC5734746 DOI: 10.1371/journal.pone.0189018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 11/18/2017] [Indexed: 11/19/2022] Open
Abstract
Burkholderia spp. are genetically and physiologically diverse. Some strains are naturally transformable and capable of DNA catabolism. Burkholderia pseudomallei (Bp) strains 1026b and K96243 and B. thailandensis strain E264 are able to utilize DNA as a sole carbon source for growth, while only strains 1026b and E264 are naturally transformable. In this study, we constructed low-copy broad-host-range fosmid library, containing Bp strain 1026b chromosomal DNA fragments, and employed a novel positive selection approach to identify genes responsible for DNA uptake and DNA catabolism. The library was transferred to non-competent Bp K96243 and B. cenocepacia (Bc) K56-2, harboring chromosomally-inserted FRT-flanked sacB and pheS counter-selection markers. The library was incubated with DNA encoding Flp recombinase, followed by counter-selection on sucrose and chlorinated phenylalanine, to select for clones that took up flp-DNA, transiently expressed Flp, and excised the sacB-pheS cassette. Putative clones that survived the counter-selection were subsequently incubated with gfp-DNA and bacteria were visualized via fluorescent microscopy to confirm natural competency. Fosmid sequencing identified several 1026b genes implicated in DNA uptake, which were validated using chromosomal mutants. One of the naturally competent clones selected in Bc K56-2 enabled Bc, Bp and B. mallei to utilize DNA as a sole carbon source, and all fosmids were used to successfully create mutations in non-naturally-competent B. mallei and Bp strains.
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Affiliation(s)
- Michael H. Norris
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, United States of America
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States of America
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Yun Heacock-Kang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Jan Zarzycki-Siek
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Andrew P. Bluhm
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Ian A. McMillan
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, United States of America
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States of America
| | - Herbert P. Schweizer
- Department of Molecular Genetics and Microbiology, College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Tung T. Hoang
- Department of Microbiology, University of Hawaii at Manoa, Honolulu, HI, United States of America
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, United States of America
- * E-mail:
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Pal V, Saxena A, Singh S, Kumar S, Goel AK. Development of a TaqMan Real-Time Polymerase Chain Reaction Assay for Detection of Burkholderia mallei. J Equine Vet Sci 2017. [DOI: 10.1016/j.jevs.2017.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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