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Ghazali AK, Firdaus-Raih M, Uthaya Kumar A, Lee WK, Hoh CC, Nathan S. Transitioning from Soil to Host: Comparative Transcriptome Analysis Reveals the Burkholderia pseudomallei Response to Different Niches. Microbiol Spectr 2023; 11:e0383522. [PMID: 36856434 PMCID: PMC10100664 DOI: 10.1128/spectrum.03835-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
Burkholderia pseudomallei, a soil and water saprophyte, is responsible for the tropical human disease melioidosis. A hundred years since its discovery, there is still much to learn about B. pseudomallei proteins that are essential for the bacterium's survival in and interaction with the infected host, as well as their roles within the bacterium's natural soil habitat. To address this gap, bacteria grown under conditions mimicking the soil environment were subjected to transcriptome sequencing (RNA-seq) analysis. A dual RNA-seq approach was used on total RNA from spleens isolated from a B. pseudomallei mouse infection model at 5 days postinfection. Under these conditions, a total of 1,434 bacterial genes were induced, with 959 induced in the soil environment and 475 induced in bacteria residing within the host. Genes encoding metabolism and transporter proteins were induced when the bacteria were present in soil, while virulence factors, metabolism, and bacterial defense mechanisms were upregulated during active infection of mice. On the other hand, capsular polysaccharide and quorum-sensing pathways were inhibited during infection. In addition to virulence factors, reactive oxygen species, heat shock proteins, siderophores, and secondary metabolites were also induced to assist bacterial adaptation and survival in the host. Overall, this study provides crucial insights into the transcriptome-level adaptations which facilitate infection by soil-dwelling B. pseudomallei. Targeting novel therapeutics toward B. pseudomallei proteins required for adaptation provides an alternative treatment strategy given its intrinsic antimicrobial resistance and the absence of a vaccine. IMPORTANCE Burkholderia pseudomallei, a soil-dwelling bacterium, is the causative agent of melioidosis, a fatal infectious disease of humans and animals. The bacterium has a large genome consisting of two chromosomes carrying genes that encode proteins with important roles for survival in diverse environments as well as in the infected host. While a general mechanism of pathogenesis has been proposed, it is not clear which proteins have major roles when the bacteria are in the soil and whether the same proteins are key to successful infection and spread. To address this question, we grew the bacteria in soil medium and then in infected mice. At 5 days postinfection, bacteria were recovered from infected mouse organs and their gene expression was compared against that of bacteria grown in soil medium. The analysis revealed a list of genes expressed under soil growth conditions and a different set of genes encoding proteins which may be important for survival, replication, and dissemination in an infected host. These proteins are a potential resource for understanding the full adaptation mechanism of this pathogen. In the absence of a vaccine for melioidosis and with treatment being reliant on combinatorial antibiotic therapy, these proteins may be ideal targets for designing antimicrobials to treat 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
| | - Mohd Firdaus-Raih
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Asqwin Uthaya Kumar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Wei-Kang Lee
- Codon Genomics Sdn. Bhd., Seri Kembangan, Selangor, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics Sdn. Bhd., Seri Kembangan, 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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Yimthin T, Cliff JM, Phunpang R, Ekchariyawat P, Kaewarpai T, Lee JS, Eckold C, Andrada M, Thiansukhon E, Tanwisaid K, Chuananont S, Morakot C, Sangsa N, Silakun W, Chayangsu S, Buasi N, Day N, Lertmemongkolchai G, Chantratita W, Eoin West T, Chantratita N. Blood transcriptomics to characterize key biological pathways and identify biomarkers for predicting mortality in melioidosis. Emerg Microbes Infect 2021; 10:8-18. [PMID: 33256556 PMCID: PMC7832033 DOI: 10.1080/22221751.2020.1858176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Melioidosis is an often lethal tropical disease caused by the Gram-negative bacillus, Burkholderia pseudomallei. The study objective was to characterize transcriptomes in melioidosis patients and identify genes associated with outcome. Whole blood RNA-seq was performed in a discovery set of 29 melioidosis patients and 3 healthy controls. Transcriptomic profiles of patients who did not survive to 28 days were compared with patients who survived and healthy controls, showing 65 genes were significantly up-regulated and 218 were down-regulated in non-survivors compared to survivors. Up-regulated genes were involved in myeloid leukocyte activation, Toll-like receptor cascades and reactive oxygen species metabolic processes. Down-regulated genes were hematopoietic cell lineage, adaptive immune system and lymphocyte activation pathways. RT-qPCR was performed for 28 genes in a validation set of 60 melioidosis patients and 20 healthy controls, confirming differential expression. IL1R2, GAS7, S100A9, IRAK3, and NFKBIA were significantly higher in non-survivors compared with survivors (P < 0.005) and healthy controls (P < 0.0001). The AUROCC of these genes for mortality discrimination ranged from 0.80-0.88. In survivors, expression of IL1R2, S100A9 and IRAK3 genes decreased significantly over 28 days (P < 0.05). These findings augment our understanding of this severe infection, showing expression levels of specific genes are potential biomarkers to predict melioidosis outcomes.
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Affiliation(s)
- Thatcha Yimthin
- Faculty of Tropical Medicine, Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand
| | - Jacqueline Margaret Cliff
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Rungnapa Phunpang
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Peeraya Ekchariyawat
- Faculty of Tropical Medicine, Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand.,Faculty of Public Health, Department of Microbiology, Mahidol University, Bangkok, Thailand
| | - Taniya Kaewarpai
- Faculty of Tropical Medicine, Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand
| | - Ji-Sook Lee
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Clare Eckold
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Megan Andrada
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | | | | | | | - Chumpol Morakot
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | | | | | | | - Noppol Buasi
- Department of Medicine, Sisaket Hospital, Sisaket, Thailand
| | - Nicholas Day
- Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.,Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ganjana Lertmemongkolchai
- Faculty of Associated Medical Science, Department of Clinical Immunology, Khon Kaen University, Khon Kaen, Thailand.,The Centre for Research and Development of Medical Diagnostic Laboratories, Khon Kaen University, Khon Kaen, Thailand
| | - Wasun Chantratita
- Faculty of Medicine Ramathibodi Hospital, Center for Medical Genomics, Mahidol University, Bangkok, Thailand
| | - T Eoin West
- Division of Pulmonary and Critical Care Medicine, Harborview Medical Center, University of Washington, Seattle, Washington, USA
| | - Narisara Chantratita
- Faculty of Tropical Medicine, Department of Microbiology and Immunology, Mahidol University, Bangkok, Thailand.,Faculty of Tropical Medicine, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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Burkholderia pseudomallei pathogenesis and survival in different niches. Biochem Soc Trans 2020; 48:569-579. [PMID: 32167134 DOI: 10.1042/bst20190836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 01/16/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of melioidosis, a disease of the tropics with high clinical mortality rates. To date, no vaccines are approved for melioidosis and current treatment relies on antibiotics. Conversely, common misdiagnosis and high pathogenicity of Bp hamper efforts to fight melioidosis. This bacterium can be isolated from a wide range of niches such as waterlogged fields, stagnant water bodies, salt water bodies and from human and animal clinical specimens. Although extensive studies have been undertaken to elucidate pathogenesis mechanisms of Bp, little is known about how a harmless soil bacterium adapts to different environmental conditions, in particular, the shift to a human host to become a highly virulent pathogen. The bacterium has a large genome encoding an armory of factors that assist the pathogen in surviving under stressful conditions and assuming its role as a deadly intracellular pathogen. This review presents an overview of what is currently known about how the pathogen adapts to different environments. With in-depth understanding of Bp adaptation and survival, more effective therapies for melioidosis can be developed by targeting related genes or proteins that play a major role in the bacteria's survival.
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Peng D, Pang F, Cao R, Zhu S, Yang X, Nie X, Zhang Z, Li B, Huang H, Li Y, Li G, Du L, Wang F. Upregulation of Immune Process-Associated Genes in RAW264.7 Macrophage Cells in Response to Burkholderia pseudomallei Infection. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1235097. [PMID: 29967766 PMCID: PMC6008862 DOI: 10.1155/2018/1235097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/22/2018] [Accepted: 05/06/2018] [Indexed: 12/19/2022]
Abstract
Melioidosis is a severe and fatal tropical zoonosis, which is triggered by Burkholderia pseudomallei. To better understand the host's response to infection of B. pseudomallei, an RNA-Seq technology was used to confirm differentially expressed genes (DEGs) in RAW264.7 cells infected with B. pseudomallei. In total, 4668 DEGs were identified across three time points (4, 8, and 11 hours after infection). Short Time-Series Expression Miner (STEM) analysis revealed the temporal gene expression profiles and identified seven significant patterns in a total of 26 profiles. Kyoto Encyclopedia of Genes and Genomes (KEGG) was utilized to confirm significantly enriched immune process-associated pathways, and 10 DEGs, including Ccl9, Ifnb1, Tnfα, Ptgs2, Tnfaip3, Zbp1, Ccl5, Ifi202b, Nfkbia, and Nfkbie, were mapped to eight immune process-associated pathways. Subsequent quantitative real-time PCR assays confirmed that the 10 DEGs were all upregulated during infection. Overall, the results showed that B. pseudomallei infection can initiate a time-series upregulation of immune process-associated DEGs in RAW264.7 macrophage cells. The discovery of this article helps us better understand the biological function of the immune process-associated genes during B. pseudomallei infection and may aid in the development of prophylaxis and treatment protocols for melioidosis.
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Affiliation(s)
- Dongmei Peng
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Feng Pang
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Ruiyong Cao
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Shu Zhu
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Xiaojian Yang
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Xin Nie
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Zhenxing Zhang
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Baobao Li
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Haifeng Huang
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Yaying Li
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Guohua Li
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Li Du
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
| | - Fengyang Wang
- College of Animal Science and Technology, College of Tropical Agriculture and Forestry, Hainan University, Hainan Key Lab of Tropical Animal Reproduction & Breeding and Epidemic Disease Research, Haidian Island, Haikou 570228, China
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Nathan S, Chieng S, Kingsley PV, Mohan A, Podin Y, Ooi MH, Mariappan V, Vellasamy KM, Vadivelu J, Daim S, How SH. Melioidosis in Malaysia: Incidence, Clinical Challenges, and Advances in Understanding Pathogenesis. Trop Med Infect Dis 2018; 3:E25. [PMID: 30274422 PMCID: PMC6136604 DOI: 10.3390/tropicalmed3010025] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/18/2018] [Accepted: 02/18/2018] [Indexed: 12/12/2022] Open
Abstract
Malaysia is an endemic hot spot for melioidosis; however, a comprehensive picture of the burden of disease, clinical presentations, and challenges faced in diagnosis and treatment of melioidosis is not available. This review provides a nonexhaustive overview of epidemiological data, clinical studies, risk factors, and mortality rates from available literature and case reports. Clinical patterns of melioidosis are generally consistent with those from South and Southeast Asia in terms of common primary presentations with diabetes as a major risk factor. Early diagnosis and appropriate management of Malaysian patients is a key limiting factor, which needs to be addressed to reduce serious complications and high mortality and recurrence rates. Promoting awareness among the local healthcare personnel is crucial to improving diagnostics and early treatment, as well as educating the Malaysian public on disease symptoms and risk factors. A further matter of urgency is the need to make this a notifiable disease and the establishment of a national melioidosis registry. We also highlight local studies on the causative agent, Burkholderia pseudomallei, with regards to bacteriology and identification of virulence factors as well as findings from host⁻pathogen interaction studies. Collectively, these studies have uncovered new correlations and insights for further understanding of the disease.
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Affiliation(s)
- Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
| | - Sylvia Chieng
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia.
| | | | - Anand Mohan
- Department of Paediatrics, Bintulu Hospital, Bintulu 97000, Malaysia.
| | - Yuwana Podin
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Kota Samarahan 94300, Malaysia.
| | - Mong-How Ooi
- Institute of Health and Community Medicine, Universiti Malaysia Sarawak, Kota Samarahan 94300, Malaysia.
- Department of Paediatrics, Sarawak General Hospital, Kuching 93586, Malaysia.
| | - Vanitha Mariappan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Kumutha Malar Vellasamy
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Jamuna Vadivelu
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Sylvia Daim
- Department of Pathobiology and Medical Diagnostics, Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia.
| | - Soon-Hin How
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University Malaysia, Kuantan 25200, Malaysia.
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Vander Broek CW, Stevens JM. Type III Secretion in the Melioidosis Pathogen Burkholderia pseudomallei. Front Cell Infect Microbiol 2017; 7:255. [PMID: 28664152 PMCID: PMC5471309 DOI: 10.3389/fcimb.2017.00255] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/31/2017] [Indexed: 02/03/2023] Open
Abstract
Burkholderia pseudomallei is a Gram-negative intracellular pathogen and the causative agent of melioidosis, a severe disease of both humans and animals. Melioidosis is an emerging disease which is predicted to be vastly under-reported. Type III Secretion Systems (T3SSs) are critical virulence factors in Gram negative pathogens of plants and animals. The genome of B. pseudomallei encodes three T3SSs. T3SS-1 and -2, of which little is known, are homologous to Hrp2 secretion systems of the plant pathogens Ralstonia and Xanthomonas. T3SS-3 is better characterized and is homologous to the Inv/Mxi-Spa secretion systems of Salmonella spp. and Shigella flexneri, respectively. Upon entry into the host cell, B. pseudomallei requires T3SS-3 for efficient escape from the endosome. T3SS-3 is also required for full virulence in both hamster and murine models of infection. The regulatory cascade which controls T3SS-3 expression and the secretome of T3SS-3 have been described, as well as the effect of mutations of some of the structural proteins. Yet only a few effector proteins have been functionally characterized to date and very little work has been carried out to understand the hierarchy of assembly, secretion and temporal regulation of T3SS-3. This review aims to frame current knowledge of B. pseudomallei T3SSs in the context of other well characterized model T3SSs, particularly those of Salmonella and Shigella.
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Affiliation(s)
- Charles W Vander Broek
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothian, United Kingdom
| | - Joanne M Stevens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghMidlothian, United Kingdom
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