1
|
Fadhar NF, Nyanasegran PK, Firdaus-Raih M, Nathan S, Jonet MA, Ng CL. Protein expression, purification, crystallization and crystallographic studies of BPSL0741 from Burkholderia pseudomallei. Acta Crystallogr F Struct Biol Commun 2024; 80:263-268. [PMID: 39259140 DOI: 10.1107/s2053230x24008197] [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: 06/19/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024] Open
Abstract
Burkholderia pseudomallei is the causative agent of the lethal disease melioidosis. This bacterium infects animals and humans and is increasingly resistant to multiple antibiotics. Recently, genes associated with survival of the bacterium in the infected host have been identified. One of these genes, bpsl0741, is annotated as a hypothetical protein of 185 amino acids. Here, recombinant BPSL0741 (rBPSL0741) protein was expressed, purified, verified by mass spectrometry, crystallized and analyzed by X-ray diffraction. rBPSL0741 was crystallized by vapor diffusion using a reservoir solution consisting of 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate pH 4.6, 30% PEG 4000. The crystals diffracted to 2.1 Å resolution using an in-house X-ray diffractometer and belonged to an orthorhombic space group, with unit-cell parameters a = 62.92, b = 64.57, c = 89.16 Å. The Matthews coefficient (VM) was calculated to be 2.18 Å3 Da-1, suggesting the presence of two molecules per asymmetric unit and an estimated solvent content of 43.5%. The crystal was deemed to be suitable for further structural studies, which are currently ongoing.
Collapse
Affiliation(s)
- Nurul Fadzillah Fadhar
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | | | - Mohd Firdaus-Raih
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Sheila Nathan
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Mohd Anuar Jonet
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000 Kajang, Selangor, Malaysia
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| |
Collapse
|
2
|
Kaewpan A, Duangurai T, Rungruengkitkun A, Muangkaew W, Kanjanapruthipong T, Jitprasutwit N, Ampawong S, Sukphopetch P, Chantratita N, Pumirat P. Burkholderia pseudomallei pathogenesis in human skin fibroblasts: A Bsa type III secretion system is involved in the invasion, multinucleated giant cell formation, and cellular damage. PLoS One 2022; 17:e0261961. [PMID: 35113856 PMCID: PMC8812868 DOI: 10.1371/journal.pone.0261961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
Burkholderia pseudomallei-a causative agent of melioidosis that is endemic in Southeast Asia and Northern Australia-is a Gram-negative bacterium transmitted to humans via inhalation, inoculation through skin abrasions, and ingestion. Melioidosis causes a range of clinical presentations including skin infection, pneumonia, and septicemia. Despite skin infection being one of the clinical symptoms of melioidosis, the pathogenesis of B. pseudomallei in skin fibroblasts has not yet been elucidated. In this study, we investigated B. pseudomallei pathogenesis in the HFF-1 human skin fibroblasts. On the basis of co-culture assays between different B. pseudomallei clinical strains and the HFF-1 human skin fibroblasts, we found that all B. pseudomallei strains have the ability to mediate invasion, intracellular replication, and multinucleated giant cell (MNGC) formation. Furthermore, all strains showed a significant increase in cytotoxicity in human fibroblasts, which coincides with the augmented expression of matrix metalloproteinase-2. Using B. pseudomallei mutants, we showed that the B. pseudomallei Bsa type III secretion system (T3SS) contributes to skin fibroblast pathogenesis, but O-polysaccharide, capsular polysaccharide, and short-chain dehydrogenase metabolism do not play a role in this process. Taken together, our findings reveal a probable connection for the Bsa T3SS in B. pseudomallei infection of skin fibroblasts, and this may be linked to the pathogenesis of cutaneous melioidosis.
Collapse
Affiliation(s)
- Anek Kaewpan
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Taksaon Duangurai
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Amporn Rungruengkitkun
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Watcharamat Muangkaew
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tapanee Kanjanapruthipong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Niramol Jitprasutwit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sumate Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Passanesh Sukphopetch
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Takenaka S, Kawashima T, Arita M. A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria. FEMS Microbiol Lett 2021; 368:6360976. [PMID: 34468734 PMCID: PMC8440127 DOI: 10.1093/femsle/fnab117] [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: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In prokaryotes, a major contributor to genomic evolution is the exchange of genes via horizontal gene transfer (HGT). Areas with a high density of HGT networks are defined as genetic exchange communities (GECs). Although some phenotypes associated with specific ecological niches are linked to GECs, little is known about the phenotypic influences on HGT in bacterial groups within a taxonomic family. Thanks to the published genome sequences and phenotype data of lactic acid bacteria (LAB), it is now possible to obtain more detailed information about the phenotypes that affect GECs. Here, we have investigated the relationship between HGT and internal and external environmental factors for 178 strains from 24 genera in the Lactobacillaceae family. We found a significant correlation between strains with high utilization of sugars and HGT bias. The result suggests that the phenotype of the utilization of a variety of sugars is key to the construction of GECs in this family. This feature is consistent with the fact that the Lactobacillaceae family contributes to the production of a wide variety of fermented foods by sharing niches such as those in vegetables, dairy products and brewing-related environments. This result provides the first evidence that phenotypes associated with ecological niches contribute to form GECs in the LAB family.
Collapse
Affiliation(s)
- Shinkuro Takenaka
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Takeshi Kawashima
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masanori Arita
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.,National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| |
Collapse
|
5
|
Lee HH, Park J, Jung H, Seo YS. Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. Microorganisms 2021; 9:1123. [PMID: 34067383 PMCID: PMC8224644 DOI: 10.3390/microorganisms9061123] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.
Collapse
Affiliation(s)
- Hyun-Hee Lee
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Jungwook Park
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
- Environmental Microbiology Research Team, Nakdonggang National Institute of Biological Resources (NNIBR), Sangju 37242, Korea
| | - Hyejung Jung
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (H.-H.L.); (J.P.); (H.J.)
| |
Collapse
|
6
|
Peng Z, Dottorini T, Hu Y, Li M, Yan S, Fanning S, Baker M, Xu J, Li F. Comparative Genomic Analysis of the Foodborne Pathogen Burkholderia gladioli pv. cocovenenans Harboring a Bongkrekic Acid Biosynthesis Gene Cluster. Front Microbiol 2021; 12:628538. [PMID: 34079526 PMCID: PMC8166232 DOI: 10.3389/fmicb.2021.628538] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
The environmental bacterium Burkholderia gladioli pv. cocovenenans (B. cocovenenans) has been linked to fatal food poisoning cases in Asia and Africa. Bongkrekic acid (BA), a mitochondrial toxin produced by B. cocovenenans, is thought to be responsible for these outbreaks. While there are over 80 species in the Burkholderia genus, B. cocovenenans is the only pathovar capable of producing BA and causing human death. However, the genomic features of B. gladioli and the evolution of the BA biosynthesis gene cluster, bon, in B. cocovenenans remain elusive. In this study, 239 whole genome sequences (WGSs) of B. gladioli, isolated from 12 countries collected over 100 years, were used to analyze the intra-species genomic diversity and phylogenetic relationships of B. gladioli and to explore the origin and evolution of the bon gene cluster. Our results showed that the genome-wide average nucleotide identity (ANI) values were above 97.29% for pairs of B. gladioli genomes. Thirty-six of the 239 (15.06%) B. gladioli genomes, isolated from corn, rice, fruits, soil, and patients from Asia, Europe, North America, and South America, contained the bon gene cluster and formed three clades within the phylogenetic tree. Pan- and core-genome analysis suggested that the BA biosynthesis genes were recently acquired. Comparative genome analysis of the bon gene cluster showed that complex recombination events contributed to this toxin biosynthesis gene cluster's evolution and formation. This study suggests that a better understanding of the genomic diversity and evolution of this lethal foodborne pathovar will potentially contribute to B. cocovenenans food poisoning outbreak prevention.
Collapse
Affiliation(s)
- Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Menghan Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Shaofei Yan
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Séamus Fanning
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, United Kingdom
| | - Jin Xu
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, Chinese Academy of Medical Sciences Research Unit (2019RU014), China National Center for Food Safety Risk Assessment, Beijing, China
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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: 4] [Impact Index Per Article: 1.3] [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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Amladi A, Devanga Ragupathi NK, Vasudevan K, Venkatesan M, Anandan S, Veeraraghavan B. First report of Burkholderia pseudomallei ST412 and ST734 clones harbouring blaOXA-57 but susceptible to imipenem in India. New Microbes New Infect 2019; 32:100613. [PMID: 31737280 PMCID: PMC6849412 DOI: 10.1016/j.nmni.2019.100613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/03/2019] [Accepted: 10/07/2019] [Indexed: 12/19/2022] Open
Abstract
Melioidosis caused by Burkholderia pseudomallei has become an important clinical threat, especially in Northern Australia and Southeast Asia. However, the genome information on this pathogen is limited. B. pseudomallei isolates identified from bloodstream infections from inpatients were subjected to whole-genome sequencing by IonTorrent PGM and MinION Oxford Nanopore sequencing technologies. Highly accurate complete genomes of two strains, VB3253 and VB2514, were obtained by a hybrid genome assembly method using both short and long DNA reads. Both isolates carried blaPenI and carbapenemase-encoding blaOXA-57 genes, although the isolates were susceptible to imipenem by E-test method with MIC 1 μg/mL. Multiple IS family transposases specific for all non-fermenting Gram-negative bacteria (NFGNBs)—especially IS3 and IS5, which facilitate mobilization of extended-spectrum β-lactamase (ESBL) and carbapenemase genes—were carried in these genomes. This further adds to the complexity of gene transmission. These IS families were identified only upon hybrid genome assembly and would otherwise be missed.
Collapse
Affiliation(s)
- A Amladi
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632 004, Tamil Nadu, India
| | - N K Devanga Ragupathi
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632 004, Tamil Nadu, India
| | - K Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632 004, Tamil Nadu, India
| | - M Venkatesan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632 004, Tamil Nadu, India
| | - S Anandan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632 004, Tamil Nadu, India
| | - B Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632 004, Tamil Nadu, India
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Shaw T, Tellapragada C, Kamath A, Kalwaje Eshwara V, Mukhopadhyay C. Implications of environmental and pathogen-specific determinants on clinical presentations and disease outcome in melioidosis patients. PLoS Negl Trop Dis 2019; 13:e0007312. [PMID: 31091290 PMCID: PMC6538188 DOI: 10.1371/journal.pntd.0007312] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 05/28/2019] [Accepted: 03/18/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Melioidosis is gaining recognition as an emerging infectious disease with diverse clinical manifestations and high-case fatality rates worldwide. However, the molecular epidemiology of the disease outside the endemic regions such as northeast part of Thailand and northern Australia remains unclear. METHODOLOGY/PRINCIPAL FINDINGS Clinical data and B. pseudomallei isolates obtained from 199 culture-confirmed cases of melioidosis diagnosed during 2006-2016 in South India were used to elucidate the host and pathogen specific variable virulence determinants associated with clinical presentations and disease outcome. Further, we determined the temporal variations and the influence of ecological factors on B.pseudomallei Lipopolysaccharide (LPS) genotypes causing infections. Severe forms of the disease were observed amongst 169 (85%) patients. Renal dysfunction and infection due to B.pseudomallei harboring BimABm variant had significant associations with severe forms of the disease. Diabetes mellitus, septicemic melioidosis and infection due to LPSB genotype were independent risk factors for mortality. LPSB (74%) and LPSA (20.6%) were the prevalent genotypes causing infections. Both genotypes demonstrated temporal variations and had significant correlations with rainfall and humidity. CONCLUSION/SIGNIFICANCE Our study findings suggest that the pathogen specific virulence traits under the influence of ecological factors are the key drivers for geographical variations in the molecular epidemiology of melioidosis.
Collapse
Affiliation(s)
- Tushar Shaw
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chaitanya Tellapragada
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Asha Kamath
- Department of Statistics, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vandana Kalwaje Eshwara
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chiranjay Mukhopadhyay
- Department of Microbiology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
15
|
Rahbar MR, Zarei M, Jahangiri A, Khalili S, Nezafat N, Negahdaripour M, Fattahian Y, Ghasemi Y. Trimeric autotransporter adhesins in Acinetobacter baumannii, coincidental evolution at work. INFECTION GENETICS AND EVOLUTION 2019; 71:116-127. [PMID: 30922803 DOI: 10.1016/j.meegid.2019.03.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/27/2019] [Accepted: 03/23/2019] [Indexed: 12/20/2022]
Abstract
Trimeric autotransporter (TAA), also known as type Vc secretion system, is expressed by many strains of Acinetobacter baumannii, an opportunistic pathogen, which is responsible for nosocomial infections worldwide. TAAs, are modular homotrimeric virulence factors, containing a signal peptide, complex stalk, and conserved membrane anchoring domain. The evolutionary mechanisms underlying the evolvement of these adhesins are not clear. Here, we showed that TAA genes were laterally acquired and underwent gene duplication and recombination. The heterogeneity of TAA nucleotide sequences, GC content, codon usage, and the probability of recombination and duplication events were assessed by MEGA7. Given the heterogeneity of sequences, we used all-against-all BLAST for clustering the TAAs. The pattern of distribution of TAAs are highly scattered; GC content and codon usage for these genes are variable. Multiple events of lateral gene transfer from the early history of Acinetobacter and the occurrence of gene duplication, gene loss, and recombination after acquiring the alien genes may explain the scattered pattern of distribution of TAAs. Additionally, this gene is not present in many clinical isolates of A. baumannii, thus is not a single virulence factor attributing to the infection. The advantage of harboring such genes might be adopting to different environments by developing the biofilm communities. We suggested that TAA genes were laterally acquired in the environmental context and incidentally provided some benefits at the infection site. Thus, coincidental evolution theory may be better suited for describing the evolution of TAA genes in A. baumannii genomes.
Collapse
Affiliation(s)
- Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahboubeh Zarei
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yaser Fattahian
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Sim SH, Ong CEL, Gan YH, Wang D, Koh VWH, Tan YK, Wong MSY, Chew JSW, Ling SF, Tan BZY, Ye AZ, Bay PCK, Wong WK, Fernandez CJ, Xie S, Jayarajah P, Tahar T, Oh PY, Luz S, Chien JMF, Tan TT, Chai LYA, Fisher D, Liu Y, Loh JJP, Tan GGY. Melioidosis in Singapore: Clinical, Veterinary, and Environmental Perspectives. Trop Med Infect Dis 2018; 3:tropicalmed3010031. [PMID: 30274428 PMCID: PMC6136607 DOI: 10.3390/tropicalmed3010031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 02/23/2018] [Accepted: 03/07/2018] [Indexed: 12/11/2022] Open
Abstract
Melioidosis is a notifiable infectious disease registered with the Ministry of Health (MOH) and Agri-Food & Veterinary Authority (AVA), Singapore. From a clinical perspective, increased awareness of the disease has led to early detection and treatment initiation, thus resulting in decreasing mortality rates in recent years. However, the disease still poses a threat to local pet, zoo and farm animals, where early diagnosis is a challenge. The lack of routine environmental surveillance studies also makes prevention of the disease in animals difficult. To date, there have been no reports that provide a complete picture of how the disease impacts the local human and animal populations in Singapore. Information on the distribution of Burkholderia pseudomallei in the environment is also lacking. The aim of this review is to provide a comprehensive overview of both published and unpublished clinical, veterinary and environmental studies on melioidosis in Singapore to achieve better awareness and management of the disease.
Collapse
Affiliation(s)
- Siew Hoon Sim
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Catherine Ee Ling Ong
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Yunn Hwen Gan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Dongling Wang
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Victor Wee Hong Koh
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Yian Kim Tan
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Michelle Su Yen Wong
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Janet Seok Wei Chew
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Sian Foong Ling
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Brian Zi Yan Tan
- Laboratories Group, Agri-Food & Veterinary Authority of Singapore, Singapore 718827, Singapore.
| | - Agnes Zhengyu Ye
- Laboratories Group, Agri-Food & Veterinary Authority of Singapore, Singapore 718827, Singapore.
| | - Patrick Chuan Kiat Bay
- Food Establishment Regulation Group, Agri-Food & Veterinary Authority of Singapore, Singapore 608550, Singapore.
| | - Wai Kwan Wong
- Laboratories Group, Agri-Food & Veterinary Authority of Singapore, Singapore 718827, Singapore.
| | | | - Shangzhe Xie
- Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore 729826, Singapore.
| | - Praveena Jayarajah
- Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore 729826, Singapore.
| | - Tasha Tahar
- Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore 729826, Singapore.
| | - Pei Yee Oh
- Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore 729826, Singapore.
| | - Sonja Luz
- Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore 729826, Singapore.
| | - Jaime Mei Fong Chien
- Department of Infectious Diseases, Singapore General Hospital, Singapore 169608, Singapore.
| | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore 169608, Singapore.
| | - Louis Yi Ann Chai
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore 119228, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
- National University Cancer Institute, Singapore 119074, Singapore.
| | - Dale Fisher
- Division of Infectious Diseases, Department of Medicine, National University Health System, Singapore 119228, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore.
| | - Yichun Liu
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Jimmy Jin Phang Loh
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| | - Gladys Gek Yen Tan
- Defence Medical and Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore.
| |
Collapse
|
18
|
Mangalea MR, Borlee GI, Borlee BR. The Current Status of Extracellular Polymeric Substances Produced by Burkholderia pseudomallei. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0118-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Burkholderia pseudomallei: Challenges for the Clinical Microbiology Laboratory. J Clin Microbiol 2016; 54:2866-2873. [PMID: 27654336 DOI: 10.1128/jcm.01636-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Melioidosis is a potentially fatal infection caused by the bacterium Burkholderia pseudomallei Clinical diagnosis of melioidosis can be challenging since there is no pathognomonic clinical syndrome, and the organism is often misidentified by methods used routinely in clinical laboratories. Although the disease is more prevalent in Thailand and northern Australia, sporadic cases may be encountered in areas where it is not endemic, including the United States. Since the organism is considered a tier 1 select agent according to the Centers for Disease Control and Prevention and the U.S. Department of Agriculture Animal and Plant Health Inspection Service, clinical laboratories must be proficient at rapidly recognizing isolates suspicious for B. pseudomallei, be able to safely perform necessary rule-out tests, and to refer suspect isolates to Laboratory Response Network reference laboratories. In this minireview, we report a case of melioidosis encountered at our institution and discuss the laboratory challenges encountered when dealing with clinical isolates suspicious for B. pseudomallei or clinical specimens from suspected melioidosis cases.
Collapse
|
21
|
D'haeseleer P, Johnson SL, Davenport KW, Chain PS, Schoeniger J, Ray D, Sinha A, Williams KP, Peña J, Branda SS, El-Etr S. Genome Sequence of the Historical Clinical Isolate Burkholderia pseudomallei PHLS 6. GENOME ANNOUNCEMENTS 2016; 4:e00649-16. [PMID: 27365360 PMCID: PMC4929523 DOI: 10.1128/genomea.00649-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022]
Abstract
Here, we present the draft genome sequence of Burkholderia pseudomallei PHLS 6, a virulent clinical strain isolated from a melioidosis patient in Bangladesh in 1960. The draft genome consists of 39 contigs and is 7,322,181 bp long.
Collapse
Affiliation(s)
- Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | | | | | - Patrick S Chain
- Los Alamos National Laboratory (LANL), Los Alamos, New Mexico, USA
| | - Joe Schoeniger
- Sandia National Laboratories (SNL), Livermore, California, USA
| | - Debjit Ray
- Sandia National Laboratories (SNL), Livermore, California, USA
| | - Anupama Sinha
- Sandia National Laboratories (SNL), Livermore, California, USA
| | | | - José Peña
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Steven S Branda
- Sandia National Laboratories (SNL), Livermore, California, USA
| | - Sahar El-Etr
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| |
Collapse
|
22
|
Sahoo M, Lantier L, Re F. Role of Canonical and Non-canonical Inflammasomes During Burkholderia Infection. Curr Top Microbiol Immunol 2016; 397:199-214. [PMID: 27460811 DOI: 10.1007/978-3-319-41171-2_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Burkholderia pseudomallei is a Gram-negative flagellate bacterium that causes melioidosis, a disease endemic to Southeast Asia and other tropical regions. Following infection of macrophages and other non-phagocytic cell types, B. pseudomallei or B. thailandensis (a related species that causes disease in mice but not humans) are able to escape the phagosome and replicate in the host cell cytoplasm. Resistance to infection with Burkholderia is dependent on the Nlrp3 and Nlrc4 inflammasomes and the non-canonical caspase-11 inflammasome. Nlrc4 mediates protection through induction of pyroptosis in the early phase of infection. As the infection progresses and as IL-18-dependent IFNγ production increases, caspase-11-dependent pyroptosis acquires a preponderant protective role. Production of IL-1β and IL-18 during infection is primarily mediated by Nlrp3. IL-18 is essential for survival because of its ability to induce IFNγ production, which in turn activates macrophage microbicidal functions and primes for caspase-11 expression. In contrast, during melioidosis, IL-1β has deleterious effects due to excessive recruitment of neutrophils to the lung and consequent tissue damage.
Collapse
Affiliation(s)
- Manoranjan Sahoo
- Department of Microbiology & Immunology, Rosalind Franklin University of Medicine and Science, 3333, Green Bay Road, North Chicago, IL, 60064, USA
| | - Louis Lantier
- Department of Microbiology & Immunology, Rosalind Franklin University of Medicine and Science, 3333, Green Bay Road, North Chicago, IL, 60064, USA
| | - Fabio Re
- Department of Microbiology & Immunology, Rosalind Franklin University of Medicine and Science, 3333, Green Bay Road, North Chicago, IL, 60064, USA.
| |
Collapse
|
23
|
Spring-Pearson SM, Stone JK, Doyle A, Allender CJ, Okinaka RT, Mayo M, Broomall SM, Hill JM, Karavis MA, Hubbard KS, Insalaco JM, McNew LA, Rosenzweig CN, Gibbons HS, Currie BJ, Wagner DM, Keim P, Tuanyok A. Pangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates. PLoS One 2015; 10:e0140274. [PMID: 26484663 PMCID: PMC4613141 DOI: 10.1371/journal.pone.0140274] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/23/2015] [Indexed: 11/19/2022] Open
Abstract
The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is ‘open’, with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.
Collapse
Affiliation(s)
- Senanu M. Spring-Pearson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Joshua K. Stone
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Adina Doyle
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Christopher J. Allender
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Richard T. Okinaka
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Mark Mayo
- Menzies School of Health Research and Infectious Disease Department, Royal Darwin Hospital. Darwin, Northern Territory, Australia
| | - Stacey M. Broomall
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Jessica M. Hill
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Mark A. Karavis
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Kyle S. Hubbard
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Joseph M. Insalaco
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Lauren A. McNew
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - C. Nicole Rosenzweig
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Henry S. Gibbons
- BioSciences Division, Edgewood Chemical Biological Center, Aberdeen Proving Ground, MD, United States of America
| | - Bart J. Currie
- Menzies School of Health Research and Infectious Disease Department, Royal Darwin Hospital. Darwin, Northern Territory, Australia
| | - David M. Wagner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
| | - Paul Keim
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
- * E-mail:
| | - Apichai Tuanyok
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011, United States of America
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL, United States of America
| |
Collapse
|
24
|
Youenou B, Favre-Bonté S, Bodilis J, Brothier E, Dubost A, Muller D, Nazaret S. Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles. Genome Biol Evol 2015; 7:2484-505. [PMID: 26276674 PMCID: PMC4607518 DOI: 10.1093/gbe/evv161] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Stenotrophomonas maltophilia, a ubiquitous Gram-negative γ-proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain's phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance-nodulation-division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.
Collapse
Affiliation(s)
- Benjamin Youenou
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sabine Favre-Bonté
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Josselin Bodilis
- EA4312 Laboratoire de Microbiologie Signaux et Microenvironnement, Université de Rouen, Mont-Saint-Aignan, France
| | - Elisabeth Brothier
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Audrey Dubost
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| | - Sylvie Nazaret
- Université de Lyon, France; Research Group on Environmental Multi-Resistance and Efflux Pump, CNRS, Ecole Nationale Vétérinaire de Lyon, and Université Lyon 1, UMR 5557 Ecologie Microbienne, Villeurbanne, France
| |
Collapse
|
25
|
Lau SKP, Lam CW, Curreem SOT, Lee KC, Chow WN, Lau CCY, Sridhar S, Wong SCY, Martelli P, Hui SW, Yuen KY, Woo PCY. Metabolomic profiling of Burkholderia pseudomallei using UHPLC-ESI-Q-TOF-MS reveals specific biomarkers including 4-methyl-5-thiazoleethanol and unique thiamine degradation pathway. Cell Biosci 2015; 5:26. [PMID: 26097677 PMCID: PMC4475313 DOI: 10.1186/s13578-015-0018-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is an emerging pathogen that causes melioidosis, a serious and potentially fatal disease which requires prolonged antibiotics to prevent relapse. However, diagnosis of melioidosis can be difficult, especially in culture-negative cases. While metabolomics represents an uprising tool for studying infectious diseases, there were no reports on its applications to B. pseudomallei. To search for potential specific biomarkers, we compared the metabolomics profiles of culture supernatants of B. pseudomallei (15 strains), B. thailandensis (3 strains), B. cepacia complex (14 strains), P. aeruginosa (4 strains) and E. coli (3 strains), using ultra-high performance liquid chromatography-electrospray ionization-quadruple time-of-flight mass spectrometry (UHPLC-ESI-Q-TOF-MS). Multi- and univariate analyses were used to identify specific metabolites in B. pseudomallei. RESULTS Principal component and partial-least squares discrimination analysis readily distinguished the metabolomes between B. pseudomallei and other bacterial species. Using multi-variate and univariate analysis, eight metabolites with significantly higher levels in B. pseudomallei were identified. Three of the eight metabolites were identified by MS/MS, while five metabolites were unidentified against database matching, suggesting that they may be potentially novel compounds. One metabolite, m/z 144.048, was identified as 4-methyl-5-thiazoleethanol, a degradation product of thiamine (vitamin B1), with molecular formula C6H9NOS by database searches and confirmed by MS/MS using commercially available authentic chemical standard. Two metabolites, m/z 512.282 and m/z 542.2921, were identified as tetrapeptides, Ile-His-Lys-Asp with molecular formula C22H37N7O7 and Pro-Arg-Arg-Asn with molecular formula C21H39N11O6, respectively. To investigate the high levels of 4-methyl-5-thiazoleethanol in B. pseudomallei, we compared the thiamine degradation pathways encoded in genomes of B. pseudomallei and B. thailandensis. While both B. pseudomallei and B. thailandensis possess thiaminase I which catalyzes degradation of thiamine to 4-methyl-5-thiazoleethanol, thiM, which encodes hydroxyethylthiazole kinase responsible for degradation of 4-methyl-5-thiazoleethanol, is present and expressed in B. thailandensis as detected by PCR/RT-PCR, but absent or not expressed in all B. pseudomallei strains. This suggests that the high 4-methyl-5-thiazoleethanol level in B. pseudomallei is likely due to the absence of hydroxyethylthiazole kinase and hence reduced downstream degradation. CONCLUSION Eight novel biomarkers, including 4-methyl-5-thiazoleethanol and two tetrapeptides, were identified in the culture supernatant of B. pseudomallei.
Collapse
Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital, Pok Fu Lam, Hong Kong ; Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Shirly O T Curreem
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Wang-Ngai Chow
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Candy C Y Lau
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Sally C Y Wong
- Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | - Suk-Wai Hui
- Ocean Park Corporation, Aqua City, Hong Kong
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital, Pok Fu Lam, Hong Kong ; Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Room 423, University Pathology Building, Queen Mary Hospital, Pok Fu Lam, Hong Kong ; Research Centre of Infection and Immunology, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Carol Yu Centre for Infection, The University of Hong Kong, Pok Fu Lam, Hong Kong ; Department of Microbiology, The University of Hong Kong, Pok Fu Lam, Hong Kong
| |
Collapse
|
26
|
Challacombe JF, Stubben CJ, Klimko CP, Welkos SL, Kern SJ, Bozue JA, Worsham PL, Cote CK, Wolfe DN. Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates. PLoS One 2014; 9:e115951. [PMID: 25536074 PMCID: PMC4275268 DOI: 10.1371/journal.pone.0115951] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 12/01/2014] [Indexed: 11/18/2022] Open
Abstract
Infection by the Gram-negative pathogen Burkholderia pseudomallei results in the disease melioidosis, acquired from the environment in parts of southeast Asia and northern Australia. Clinical symptoms of melioidosis range from acute (fever, pneumonia, septicemia, and localized infection) to chronic (abscesses in various organs and tissues, most commonly occurring in the lungs, liver, spleen, kidney, prostate and skeletal muscle), and persistent infections in humans are difficult to cure. Understanding the basic biology and genomics of B. pseudomallei is imperative for the development of new vaccines and therapeutic interventions. This formidable task is becoming more tractable due to the increasing number of B. pseudomallei genomes that are being sequenced and compared. Here, we compared three B. pseudomallei genomes, from strains MSHR668, K96243 and 1106a, to identify features that might explain why MSHR668 is more virulent than K96243 and 1106a in a mouse model of B. pseudomallei infection. Our analyses focused on metabolic, virulence and regulatory genes that were present in MSHR668 but absent from both K96243 and 1106a. We also noted features present in K96243 and 1106a but absent from MSHR668, and identified genomic differences that may contribute to variations in virulence noted among the three B. pseudomallei isolates. While this work contributes to our understanding of B. pseudomallei genomics, more detailed experiments are necessary to characterize the relevance of specific genomic features to B. pseudomallei metabolism and virulence. Functional analyses of metabolic networks, virulence and regulation shows promise for examining the effects of B. pseudomallei on host cell metabolism and will lay a foundation for future prediction of the virulence of emerging strains. Continued emphasis in this area will be critical for protection against melioidosis, as a better understanding of what constitutes a fully virulent Burkholderia isolate may provide for better diagnostic and medical countermeasure strategies.
Collapse
Affiliation(s)
- Jean F. Challacombe
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States of America
- * E-mail:
| | - Chris J. Stubben
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, United States of America
| | - Christopher P. Klimko
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Susan L. Welkos
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Steven J. Kern
- US Army Medical Research Institute of Infectious Diseases, Biostatistics Division, Fort Detrick, MD, United States of America
| | - Joel A. Bozue
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Patricia L. Worsham
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Christopher K. Cote
- US Army Medical Research Institute of Infectious Diseases, Bacteriology Division, Fort Detrick, MD, United States of America
| | - Daniel N. Wolfe
- Defense Threat Reduction Agency, Chemical and Biological Technologies Department, Fort Belvoir, VA, United States of America
| |
Collapse
|
27
|
Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy. J Clin Microbiol 2014; 53:323-6. [PMID: 25392354 PMCID: PMC4290968 DOI: 10.1128/jcm.02574-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei isolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.
Collapse
|
28
|
Nandi T, Holden MTG, Holden MTG, Didelot X, Mehershahi K, Boddey JA, Beacham I, Peak I, Harting J, Baybayan P, Guo Y, Wang S, How LC, Sim B, Essex-Lopresti A, Sarkar-Tyson M, Nelson M, Smither S, Ong C, Aw LT, Hoon CH, Michell S, Studholme DJ, Titball R, Chen SL, Parkhill J, Tan P. Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles. Genome Res 2014; 25:129-41. [PMID: 25236617 PMCID: PMC4317168 DOI: 10.1101/gr.177543.114] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.
Collapse
Affiliation(s)
- Tannistha Nandi
- Genome Institute of Singapore, Singapore, 138672, Republic of Singapore
| | | | - Mathew T G Holden
- The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, United Kingdom
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, W2 1PG, United Kingdom
| | - Kurosh Mehershahi
- Department of Medicine, National University of Singapore, Singapore, 119074 Republic of Singapore
| | - Justin A Boddey
- Institute for Glycomics, Griffith University (Gold Coast Campus), Southport, Queensland, QLD 4222, Australia
| | - Ifor Beacham
- Institute for Glycomics, Griffith University (Gold Coast Campus), Southport, Queensland, QLD 4222, Australia
| | - Ian Peak
- Institute for Glycomics, Griffith University (Gold Coast Campus), Southport, Queensland, QLD 4222, Australia
| | - John Harting
- Pacific Biosciences, Menlo Park, California 94025, USA
| | | | - Yan Guo
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Susana Wang
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Lee Chee How
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Bernice Sim
- Genome Institute of Singapore, Singapore, 138672, Republic of Singapore
| | - Angela Essex-Lopresti
- Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom
| | - Mitali Sarkar-Tyson
- Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom
| | - Michelle Nelson
- Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom
| | - Sophie Smither
- Defence Science and Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, United Kingdom
| | - Catherine Ong
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, 117510, Republic of Singapore
| | - Lay Tin Aw
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, 117510, Republic of Singapore
| | - Chua Hui Hoon
- Genome Institute of Singapore, Singapore, 138672, Republic of Singapore
| | - Stephen Michell
- Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom
| | | | - Richard Titball
- Biosciences, University of Exeter, Exeter, EX4 4QD, United Kingdom; Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, WC1E 7HT, United Kingdom
| | - Swaine L Chen
- Genome Institute of Singapore, Singapore, 138672, Republic of Singapore; Department of Medicine, National University of Singapore, Singapore, 119074 Republic of Singapore
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, United Kingdom
| | - Patrick Tan
- Genome Institute of Singapore, Singapore, 138672, Republic of Singapore; Duke-NUS Graduate Medical School Singapore, Singapore, 169857, Republic of Singapore; Cancer Science Institute of Singapore, National University of Singapore, 117599, Republic of Singapore
| |
Collapse
|
29
|
A Burkholderia pseudomallei outer membrane vesicle vaccine provides protection against lethal sepsis. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2014; 21:747-54. [PMID: 24671550 DOI: 10.1128/cvi.00119-14] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The environmental Gram-negative encapsulated bacillus Burkholderia pseudomallei is the causative agent of melioidosis, a disease associated with high morbidity and mortality rates in areas of Southeast Asia and northern Australia in which the disease is endemic. B. pseudomallei is also classified as a tier I select agent due to the high level of lethality of the bacterium and its innate resistance to antibiotics, as well as the lack of an effective vaccine. Gram-negative bacteria, including B. pseudomallei, secrete outer membrane vesicles (OMVs) which are enriched with multiple protein, lipid, and polysaccharide antigens. Previously, we demonstrated that immunization with multivalent B. pseudomallei-derived OMVs protects highly susceptible BALB/c mice against an otherwise lethal aerosol challenge. In this work, we evaluated the protective efficacy of OMV immunization against intraperitoneal challenge with a heterologous strain because systemic infection with phenotypically diverse environmental B. pseudomallei strains poses another hazard and a challenge to vaccine development. We demonstrated that B. pseudomallei OMVs derived from strain 1026b afforded significant protection against septicemic infection with B. pseudomallei strain K96243. OMV immunization induced robust OMV-, lipopolysaccharide-, and capsular polysaccharide-specific serum IgG (IgG1, IgG2a, and IgG3) and IgM antibody responses. OMV-immune serum promoted bacterial killing in vitro, and passive transfer of B. pseudomallei OMV immune sera protected naive mice against a subsequent challenge. These results indicate that OMV immunization provides antibody-mediated protection against acute, rapidly lethal sepsis in mice. B. pseudomallei-derived OMVs may represent an efficacious multivalent vaccine strategy against melioidosis.
Collapse
|
30
|
Sarovich DS, Price EP, Webb JR, Ward LM, Voutsinos MY, Tuanyok A, Mayo M, Kaestli M, Currie BJ. Variable virulence factors in Burkholderia pseudomallei (melioidosis) associated with human disease. PLoS One 2014; 9:e91682. [PMID: 24618705 PMCID: PMC3950250 DOI: 10.1371/journal.pone.0091682] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 02/14/2014] [Indexed: 11/18/2022] Open
Abstract
Burkholderia pseudomallei is a Gram-negative environmental bacterium that causes melioidosis, a potentially life-threatening infectious disease affecting mammals, including humans. Melioidosis symptoms are both protean and diverse, ranging from mild, localized skin infections to more severe and often fatal presentations including pneumonia, septic shock with multiple internal abscesses and occasionally neurological involvement. Several ubiquitous virulence determinants in B. pseudomallei have already been discovered. However, the molecular basis for differential pathogenesis has, until now, remained elusive. Using clinical data from 556 Australian melioidosis cases spanning more than 20 years, we identified a Burkholderia mallei-like actin polymerization bimA(Bm) gene that is strongly associated with neurological disease. We also report that a filamentous hemagglutinin gene, fhaB3, is associated with positive blood cultures but is negatively correlated with localized skin lesions without sepsis. We show, for the first time, that variably present virulence factors play an important role in the pathogenesis of melioidosis. Collectively, our study provides a framework for assessing other non-ubiquitous bacterial virulence factors and their association with disease, such as candidate loci identified from large-scale microbial genome-wide association studies.
Collapse
Affiliation(s)
- Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Linda M. Ward
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Marcos Y. Voutsinos
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Apichai Tuanyok
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, University of Hawai’i, Honolulu, Hawai’i, 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
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Infectious Diseases Department, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| |
Collapse
|
31
|
Genome-wide saturation mutagenesis of Burkholderia pseudomallei K96243 predicts essential genes and novel targets for antimicrobial development. mBio 2014; 5:e00926-13. [PMID: 24520057 PMCID: PMC3950516 DOI: 10.1128/mbio.00926-13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei is the causative agent of melioidosis, an often fatal infectious disease for which there is no vaccine. B. pseudomallei is listed as a tier 1 select agent, and as current therapeutic options are limited due to its natural resistance to most antibiotics, the development of new antimicrobial therapies is imperative. To identify drug targets and better understand the complex B. pseudomallei genome, we sought a genome-wide approach to identify lethal gene targets. As B. pseudomallei has an unusually large genome spread over two chromosomes, an extensive screen was required to achieve a comprehensive analysis. Here we describe transposon-directed insertion site sequencing (TraDIS) of a library of over 106 transposon insertion mutants, which provides the level of genome saturation required to identify essential genes. Using this technique, we have identified a set of 505 genes that are predicted to be essential in B. pseudomallei K96243. To validate our screen, three genes predicted to be essential, pyrH, accA, and sodB, and a gene predicted to be nonessential, bpss0370, were independently investigated through the generation of conditional mutants. The conditional mutants confirmed the TraDIS predictions, showing that we have generated a list of genes predicted to be essential and demonstrating that this technique can be used to analyze complex genomes and thus be more widely applied. Burkholderia pseudomallei is a lethal human pathogen that is considered a potential bioterrorism threat and has limited treatment options due to an unusually high natural resistance to most antibiotics. We have identified a set of genes that are required for bacterial growth and thus are excellent candidates against which to develop potential novel antibiotics. To validate our approach, we constructed four mutants in which gene expression can be turned on and off conditionally to confirm that these genes are required for the bacteria to survive.
Collapse
|
32
|
Ooi WF, Ong C, Nandi T, Kreisberg JF, Chua HH, Sun G, Chen Y, Mueller C, Conejero L, Eshaghi M, Ang RML, Liu J, Sobral BW, Korbsrisate S, Gan YH, Titball RW, Bancroft GJ, Valade E, Tan P. The condition-dependent transcriptional landscape of Burkholderia pseudomallei. PLoS Genet 2013; 9:e1003795. [PMID: 24068961 PMCID: PMC3772027 DOI: 10.1371/journal.pgen.1003795] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/29/2013] [Indexed: 12/25/2022] Open
Abstract
Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7.2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array expression data of Bp exposed to >80 diverse physical, chemical, and biological conditions. Our results provide direct experimental support for the strand-specific expression of 5,467 Sanger protein-coding genes, 1,041 operons, and 766 non-coding RNAs. A large proportion of these transcripts displayed condition-dependent expression, consistent with them playing functional roles. The two Bp chromosomes exhibited dramatically different transcriptional landscapes — Chr 1 genes were highly and constitutively expressed, while Chr 2 genes exhibited mosaic expression where distinct subsets were expressed in a strongly condition-dependent manner. We identified dozens of cis-regulatory motifs associated with specific condition-dependent expression programs, and used the condition compendium to elucidate key biological processes associated with two complex pathogen phenotypes — quorum sensing and in vivo infection. Our results demonstrate the utility of a Bp condition-compendium as a community resource for biological discovery. Moreover, the observation that significant portions of the Bp virulence machinery can be activated by specific in vitro cues provides insights into Bp's capacity as an “accidental pathogen”, where genetic pathways used by the bacterium to survive in environmental niches may have also facilitated its ability to colonize human hosts. Bacterial transcriptomes are dynamic, context-specific and condition-dependent. Infection by the soil bacterium, Burkholderia pseudomallei, causes melioidosis, an often fatal infectious disease of humans and animals. Possessing a large multi-chromosomal genome, B. pseudomallei is able to persist and survive in a multitude of environments. To obtain a comprehensive overview of B. pseudomallei expressed transcripts, we initiated whole-genome transcriptome profiling covering a broad spectrum of conditions and exposures — a so-called “condition compendium”. Using the compendium, we confirmed many previously-annotated genes and operons, and also identified hundreds of novel transcripts including anti-sense transcripts and non-coding RNAs. By systematically examining genes exhibiting highly similar expression patterns, we ascribed putative functions to previously uncharacterized genes, and identified novel regulatory elements controlling these expression patterns. We also used the compendium to elucidate candidate virulence pathways associated with quorum-sensing and infection in mice. Our study showcases the power of a B. pseudomallei condition compendium as a valuable resource for understanding microbial physiology and the pathogenesis of melioidosis.
Collapse
Affiliation(s)
- Wen Fong Ooi
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | - Catherine Ong
- 2DMERI@DSO, DSO National Laboratories, Singapore, Republic of Singapore
| | - Tannistha Nandi
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Hui Hoon Chua
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | - Guangwen Sun
- School of Applied Science, Republic Polytechnic, Singapore, Republic of Singapore
| | - Yahua Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Claudia Mueller
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Laura Conejero
- Department of Immunology and Infection, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Majid Eshaghi
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | - Roy Moh Lik Ang
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | - Jianhua Liu
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | - Bruno W. Sobral
- Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, Virginia, United States of America
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yunn Hwen Gan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Richard W. Titball
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Gregory J. Bancroft
- Department of Immunology and Infection, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Eric Valade
- Institut de Recherche Biomédicale des Armées/CRSSA, La Tronche, France
- Ecole du Val-de-Grâce, Paris, France
| | - Patrick Tan
- Genome Institute of Singapore, Singapore, Republic of Singapore
- Duke-NUS Graduate Medical School, Singapore, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Republic of Singapore
- * E-mail:
| |
Collapse
|
33
|
An improved method for oriT-directed cloning and functionalization of large bacterial genomic regions. Appl Environ Microbiol 2013; 79:4869-78. [PMID: 23747708 DOI: 10.1128/aem.00994-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have made significant improvements to a broad-host-range system for the cloning and manipulation of large bacterial genomic regions based on site-specific recombination between directly repeated oriT sites during conjugation. Using two suicide capture vectors carrying flanking homology regions, oriT sites are recombined on either side of the target region. Using a broad-host-range conjugation helper plasmid, the region between the oriT sites is conjugated into an Escherichia coli recipient strain, where it is circularized and maintained as a chimeric mini-F vector. The cloned target region is functionalized in multiple ways to accommodate downstream manipulation. The target region is flanked with Gateway attB sites for recombination into other vectors and by rare 18-bp I-SceI restriction sites for subcloning. The Tn7-functionalized target can also be inserted at a naturally occurring chromosomal attTn7 site(s) or maintained as a broad-host-range plasmid for complementation or heterologous expression studies. We have used the oriTn7 capture technique to clone and complement Burkholderia pseudomallei genomic regions up to 140 kb in size and have created isogenic Burkholderia strains with various combinations of genomic islands. We believe this system will greatly aid the cloning and genetic analysis of genomic islands, biosynthetic gene clusters, and large open reading frames.
Collapse
|
34
|
Kvitko BH, Cox CR, DeShazer D, Johnson SL, Voorhees KJ, Schweizer HP. φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity. BMC Microbiol 2012; 12:289. [PMID: 23217012 PMCID: PMC3548686 DOI: 10.1186/1471-2180-12-289] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 11/28/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example φK96243, φ1026b and φ52237. RESULTS We have isolated a P2-like bacteriophage, φX216, which infects 78% of all B. pseudomallei strains tested. φX216 also infects B. mallei, but not other Burkholderia species, including the closely related B. thailandensis and B. oklahomensis. The nature of the φX216 host receptor remains unclear but evidence indicates that in B. mallei φX216 uses lipopolysaccharide O-antigen but a different receptor in B. pseudomallei. The 37,637 bp genome of φX216 encodes 47 predicted open reading frames and shares 99.8% pairwise identity and an identical strain host range with bacteriophage φ52237. Closely related P2-like prophages appear to be widely distributed among B. pseudomallei strains but both φX216 and φ52237 readily infect prophage carrying strains. CONCLUSIONS The broad strain infectivity and high specificity for B. pseudomallei and B. mallei indicate that φX216 will provide a good platform for the development of phage-based diagnostics for these bacteria.
Collapse
Affiliation(s)
- Brian H Kvitko
- Department of Microbiology, Colorado State University, IDRC at Foothills Campus, Fort Collins, CO 80523-0922, USA
| | | | | | | | | | | |
Collapse
|
35
|
Butt A, Müller C, Harmer N, Titball RW. Identification of type II toxin-antitoxin modules in Burkholderia pseudomallei. FEMS Microbiol Lett 2012; 338:86-94. [PMID: 23082999 DOI: 10.1111/1574-6968.12032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/16/2012] [Accepted: 10/18/2012] [Indexed: 11/30/2022] Open
Abstract
Type II toxin-antitoxin (TA) systems are believed to be widely distributed amongst bacteria although their biological functions are not clear. We have identified eight candidate TA systems in the genome of the human pathogen Burkholderia pseudomallei. Five of these were located in genome islands. Of the candidate toxins, BPSL0175 (RelE1) or BPSS1060 (RelE2) caused growth to cease when expressed in Escherichia coli, whereas expression of BPSS0390 (HicA) or BPSS1584 (HipA) (in an E. coli ΔhipBA background) caused a reduction in the number of culturable bacteria. The cognate antitoxins could restore growth and culturability of cells.
Collapse
Affiliation(s)
- Aaron Butt
- Department of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | | |
Collapse
|
36
|
Ricaldi JN, Fouts DE, Selengut JD, Harkins DM, Patra KP, Moreno A, Lehmann JS, Purushe J, Sanka R, Torres M, Webster NJ, Vinetz JM, Matthias MA. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PLoS Negl Trop Dis 2012; 6:e1853. [PMID: 23145189 PMCID: PMC3493377 DOI: 10.1371/journal.pntd.0001853] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/25/2012] [Indexed: 12/25/2022] Open
Abstract
The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010T and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics. Leptospirosis is one of the most common diseases transmitted by animals worldwide and is important because it is a major cause of febrile illness in tropical areas and also occurs in epidemic form associated with natural disasters and flooding. The mechanisms through which Leptospira cause disease are not well understood. In this study we have sequenced the genomes of two strains of Leptospira licerasiae isolated from a person and a marsupial in the Peruvian Amazon. These strains were thought to be able to cause only mild disease in humans. We have compared these genomes with other leptospires that can cause severe illness and death and another leptospire that does not infect humans or animals. These comparisons have allowed us to demonstrate similarities among the disease-causing Leptospira. Studying genes that are common among infectious strains will allow us to identify genetic factors necessary for infecting, causing disease and determining the severity of disease. We have also found that L. licerasiae seems to be able to uptake and incorporate genetic information from other bacteria found in the environment. This information will allow us to begin to understand how Leptospira species have evolved.
Collapse
Affiliation(s)
- Jessica N. Ricaldi
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Derrick E. Fouts
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jeremy D. Selengut
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Derek M. Harkins
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Kailash P. Patra
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Angelo Moreno
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Jason S. Lehmann
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Janaki Purushe
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ravi Sanka
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Michael Torres
- Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nicholas J. Webster
- Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Joseph M. Vinetz
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Departamento de Ciencias Celulares y Moleculares, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
- * E-mail: (JMV); (MAM)
| | - Michael A. Matthias
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- * E-mail: (JMV); (MAM)
| |
Collapse
|
37
|
Bacterial gene loss as a mechanism for gain of antimicrobial resistance. Curr Opin Microbiol 2012; 15:583-7. [PMID: 23022568 PMCID: PMC3712167 DOI: 10.1016/j.mib.2012.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 07/23/2012] [Accepted: 07/30/2012] [Indexed: 11/22/2022]
Abstract
Acquisition of exogenous DNA by pathogenic bacteria represents the basis for much of the acquired antimicrobial resistance in pathogenic bacteria. A more extreme mechanism to avoid the effect of an antibiotic is to delete the drug target, although this would be predicted to be rare since drug targets are often essential genes. Here, we review and discuss the description of a novel mechanism of resistance to the cephalosporin drug ceftazidime caused by loss of a penicillin-binding protein (PBP) in a Gram-negative bacillus (Burkholderia pseudomallei). This organism causes melioidosis across south-east Asia and northern Australia, and is usually treated with two or more weeks of ceftazidime followed by oral antibiotics for three to six months. Comparison of clinical isolates from six patients with melioidosis found initial ceftazidime-susceptible isolates and subsequent ceftazidime-resistant variants. The latter failed to grow on commonly used culture media, rendering these isolates difficult to detect in the diagnostic laboratory. Genomic analysis using pulsed-field gel electrophoresis and array based genomic hybridisation revealed a large-scale genomic deletion comprising 49 genes in the ceftazidime-resistant strains. Mutational analysis of wild-type B. pseudomallei demonstrated that ceftazidime resistance was due to deletion of a gene encoding a PBP 3 present within the region of genomic loss. This provides one explanation for ceftazidime treatment failure, and may be a frequent but undetected event in patients with melioidosis.
Collapse
|
38
|
Affiliation(s)
- W Joost Wiersinga
- Department of Medicine, Division of Infectious Diseases, Academic Medical Center, Amsterdam, The Netherlands.
| | | | | |
Collapse
|
39
|
Segerman B. The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories. Front Cell Infect Microbiol 2012; 2:116. [PMID: 22973561 PMCID: PMC3434323 DOI: 10.3389/fcimb.2012.00116] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 08/20/2012] [Indexed: 11/13/2022] Open
Abstract
Strains within a bacterial species typically have a set of conserved core genes and a variable set of accessory genes. The accessory genes often appear to move laterally between strains, thereby forming new trait combinations. Sometimes, genetic material also moves laterally between species, thereby resulting in diffuse borders between them. The growing number of genome sequences offers new possibilities to study these processes. Ten species for which abundant genomic data exists were here selected for analysis of the species border integrity. The average core genome similarities and relative core genome sizes (RCGSs) were determined for strain pairs within the species and for strain pairs crossing the species border. The variability within the species as well as the border integrity varies for different bacterial species. Some have very distinct borders while others are more or less indefinable. From the growing amount of genomic data, it becomes even clearer that the concept of bacterial species is, in many cases, far from absolute.
Collapse
Affiliation(s)
- Bo Segerman
- National Veterinary Institute Uppsala, Sweden.
| |
Collapse
|
40
|
Genomic islands as a marker to differentiate between clinical and environmental Burkholderia pseudomallei. PLoS One 2012; 7:e37762. [PMID: 22675491 PMCID: PMC3365882 DOI: 10.1371/journal.pone.0037762] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 04/24/2012] [Indexed: 11/19/2022] Open
Abstract
Burkholderia pseudomallei, as a saprophytic bacterium that can cause a severe sepsis disease named melioidosis, has preserved several extra genes in its genome for survival. The sequenced genome of the organism showed high diversity contributed mainly from genomic islands (GIs). Comparative genome hybridization (CGH) of 3 clinical and 2 environmental isolates, using whole genome microarrays based on B. pseudomallei K96243 genes, revealed a difference in the presence of genomic islands between clinical and environmental isolates. The largest GI, GI8, of B. pseudomallei was observed as a 2 sub-GI named GIs8.1 and 8.2 with distinguishable %GC content and unequal presence in the genome. GIs8.1, 8.2 and 15 were found to be more common in clinical isolates. A new GI, GI16c, was detected on chromosome 2. Presences of GIs8.1, 8.2, 15 and 16c were evaluated in 70 environmental and 64 clinical isolates using PCR assays. A combination of GIs8.1 and 16c (positivity of either GI) was detected in 70% of clinical isolates and 11.4% of environmental isolates (P<0.001). Using BALB/c mice model, no significant difference of time to mortality was observed between K96243 isolate and three isolates without GIs under evaluation (P>0.05). Some virulence genes located in the absent GIs and the difference of GIs seems to contribute less to bacterial virulence. The PCR detection of 2 GIs could be used as a cost effective and rapid tool to detect potentially virulent isolates that were contaminated in soil.
Collapse
|
41
|
Hayden HS, Lim R, Brittnacher MJ, Sims EH, Ramage ER, Fong C, Wu Z, Crist E, Chang J, Zhou Y, Radey M, Rohmer L, Haugen E, Gillett W, Wuthiekanun V, Peacock SJ, Kaul R, Miller SI, Manoil C, Jacobs MA. Evolution of Burkholderia pseudomallei in recurrent melioidosis. PLoS One 2012; 7:e36507. [PMID: 22615773 PMCID: PMC3352902 DOI: 10.1371/journal.pone.0036507] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/02/2012] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei, the etiologic agent of human melioidosis, is capable of causing severe acute infection with overwhelming septicemia leading to death. A high rate of recurrent disease occurs in adult patients, most often due to recrudescence of the initial infecting strain. Pathogen persistence and evolution during such relapsing infections are not well understood. Bacterial cells present in the primary inoculum and in late infections may differ greatly, as has been observed in chronic disease, or they may be genetically similar. To test these alternative models, we conducted whole-genome comparisons of clonal primary and relapse B. pseudomallei isolates recovered six months to six years apart from four adult Thai patients. We found differences within each of the four pairs, and some, including a 330 Kb deletion, affected substantial portions of the genome. Many of the changes were associated with increased antibiotic resistance. We also found evidence of positive selection for deleterious mutations in a TetR family transcriptional regulator from a set of 107 additional B. pseudomallei strains. As part of the study, we sequenced to base-pair accuracy the genome of B. pseudomallei strain 1026b, the model used for genetic studies of B. pseudomallei pathogenesis and antibiotic resistance. Our findings provide new insights into pathogen evolution during long-term infections and have important implications for the development of intervention strategies to combat recurrent melioidosis.
Collapse
Affiliation(s)
- Hillary S Hayden
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Liguori AP, Warrington SD, Ginther JL, Pearson T, Bowers J, Glass MB, Mayo M, Wuthiekanun V, Engelthaler D, Peacock SJ, Currie BJ, Wagner DM, Keim P, Tuanyok A. Diversity of 16S-23S rDNA internal transcribed spacer (ITS) reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors. PLoS One 2011; 6:e29323. [PMID: 22195045 PMCID: PMC3237603 DOI: 10.1371/journal.pone.0029323] [Citation(s) in RCA: 28] [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: 07/04/2011] [Accepted: 11/24/2011] [Indexed: 11/19/2022] Open
Abstract
Length polymorphisms within the 16S-23S ribosomal DNA internal transcribed spacer (ITS) have been described as stable genetic markers for studying bacterial phylogenetics. In this study, we used these genetic markers to investigate phylogenetic relationships in Burkholderia pseudomallei and its near-relative species. B. pseudomallei is known as one of the most genetically recombined bacterial species. In silico analysis of multiple B. pseudomallei genomes revealed approximately four homologous rRNA operons and ITS length polymorphisms therein. We characterized ITS distribution using PCR and analyzed via a high-throughput capillary electrophoresis in 1,191 B. pseudomallei strains. Three major ITS types were identified, two of which were commonly found in most B. pseudomallei strains from the endemic areas, whereas the third one was significantly correlated with worldwide sporadic strains. Interestingly, mixtures of the two common ITS types were observed within the same strains, and at a greater incidence in Thailand than Australia suggesting that genetic recombination causes the ITS variation within species, with greater recombination frequency in Thailand. In addition, the B. mallei ITS type was common to B. pseudomallei, providing further support that B. mallei is a clone of B. pseudomallei. Other B. pseudomallei near-neighbors possessed unique and monomorphic ITS types. Our data shed light on evolutionary patterns of B. pseudomallei and its near relative species.
Collapse
Affiliation(s)
- Andrew P. Liguori
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Stephanie D. Warrington
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jennifer L. Ginther
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Talima Pearson
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jolene Bowers
- Division of Pathogen Genomics, The Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
| | - Mindy B. Glass
- Bacterial Zoonoses Branch, Division of Foodborne, Bacterial and Mycotic Diseases, National Center for Zoonotic, Vector-Borne and Enteric Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Mark Mayo
- Charles Darwin University, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - David Engelthaler
- Division of Pathogen Genomics, The Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America
| | | | - Bart J. Currie
- Charles Darwin University, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - David M. Wagner
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
| |
Collapse
|
43
|
Goldfarb KC, Karaoz U, Hanson CA, Santee CA, Bradford MA, Treseder KK, Wallenstein MD, Brodie EL. Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance. Front Microbiol 2011; 2:94. [PMID: 21833332 PMCID: PMC3153052 DOI: 10.3389/fmicb.2011.00094] [Citation(s) in RCA: 238] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 04/18/2011] [Indexed: 02/01/2023] Open
Abstract
Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeled DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin–protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.
Collapse
Affiliation(s)
- Katherine C Goldfarb
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Lee SH, Ooi SK, Mahadi NM, Tan MW, Nathan S. Complete killing of Caenorhabditis elegans by Burkholderia pseudomallei is dependent on prolonged direct association with the viable pathogen. PLoS One 2011; 6:e16707. [PMID: 21408228 PMCID: PMC3049773 DOI: 10.1371/journal.pone.0016707] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/12/2011] [Indexed: 11/19/2022] Open
Abstract
Background Burkholderia pseudomallei is the causative agent of melioidosis, a disease of significant morbidity and mortality in both human and animals in endemic areas. Much remains to be known about the contributions of genotypic variations within the bacteria and the host, and environmental factors that lead to the manifestation of the clinical symptoms of melioidosis. Methodology/Principal Findings In this study, we showed that different isolates of B. pseudomallei have divergent ability to kill the soil nematode Caenorhabditis elegans. The rate of nematode killing was also dependent on growth media: B. pseudomallei grown on peptone-glucose media killed C. elegans more rapidly than bacteria grown on the nematode growth media. Filter and bacteria cell-free culture filtrate assays demonstrated that the extent of killing observed is significantly less than that observed in the direct killing assay. Additionally, we showed that B. pseudomallei does not persistently accumulate within the C. elegans gut as brief exposure to B. pseudomallei is not sufficient for C. elegans infection. Conclusions/Significance A combination of genetic and environmental factors affects virulence. In addition, we have also demonstrated that a Burkholderia-specific mechanism mediating the pathogenic effect in C. elegans requires proliferating B. pseudomallei to continuously produce toxins to mediate complete killing.
Collapse
Affiliation(s)
- Song-Hua Lee
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Soon-Keat Ooi
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Nor Muhammad Mahadi
- UKM-MTDC Technology Centre, Malaysia Genome Institute, UKM Bangi, Selangor, Malaysia
| | - Man-Wah Tan
- Department of Genetics and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
- UKM-MTDC Technology Centre, Malaysia Genome Institute, UKM Bangi, Selangor, Malaysia
- * E-mail:
| |
Collapse
|
45
|
Genome-wide analysis reveals loci encoding anti-macrophage factors in the human pathogen Burkholderia pseudomallei K96243. PLoS One 2010; 5:e15693. [PMID: 21203527 PMCID: PMC3008741 DOI: 10.1371/journal.pone.0015693] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 11/22/2010] [Indexed: 11/19/2022] Open
Abstract
Burkholderia pseudomallei is an important human pathogen whose infection biology is still poorly understood. The bacterium is endemic to tropical regions, including South East Asia and Northern Australia, where it causes melioidosis, a serious disease associated with both high mortality and antibiotic resistance. B. pseudomallei is a Gram-negative facultative intracellular pathogen that is able to replicate in macrophages. However despite the critical nature of its interaction with macrophages, few anti-macrophage factors have been characterized to date. Here we perform a genome-wide gain of function screen of B. pseudomallei strain K96243 to identify loci encoding factors with anti-macrophage activity. We identify a total of 113 such loci scattered across both chromosomes, with positive gene clusters encoding transporters and secretion systems, enzymes/toxins, secondary metabolite, biofilm, adhesion and signal response related factors. Further phenotypic analysis of four of these regions shows that the encoded factors cause striking cellular phenotypes relevant to infection biology, including apoptosis, formation of actin 'tails' and multi-nucleation within treated macrophages. The detailed analysis of the remaining host of loci will facilitate genetic dissection of the interaction of this important pathogen with host macrophages and thus further elucidate this critical part of its infection cycle.
Collapse
|
46
|
Sim BMQ, Chantratita N, Ooi WF, Nandi T, Tewhey R, Wuthiekanun V, Thaipadungpanit J, Tumapa S, Ariyaratne P, Sung WK, Sem XH, Chua HH, Ramnarayanan K, Lin CH, Liu Y, Feil EJ, Glass MB, Tan G, Peacock SJ, Tan P. Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates. Genome Biol 2010; 11:R89. [PMID: 20799932 PMCID: PMC2945791 DOI: 10.1186/gb-2010-11-8-r89] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/12/2010] [Accepted: 08/27/2010] [Indexed: 11/10/2022] Open
Abstract
Background Burkholderia thailandensis is a non-pathogenic environmental saprophyte closely related to Burkholderia pseudomallei, the causative agent of the often fatal animal and human disease melioidosis. To study B. thailandensis genomic variation, we profiled 50 isolates using a pan-genome microarray comprising genomic elements from 28 Burkholderia strains and species. Results Of 39 genomic regions variably present across the B. thailandensis strains, 13 regions corresponded to known genomic islands, while 26 regions were novel. Variant B. thailandensis isolates exhibited isolated acquisition of a capsular polysaccharide biosynthesis gene cluster (B. pseudomallei-like capsular polysaccharide) closely resembling a similar cluster in B. pseudomallei that is essential for virulence in mammals; presence of this cluster was confirmed by whole genome sequencing of a representative variant strain (B. thailandensis E555). Both whole-genome microarray and multi-locus sequence typing analysis revealed that the variant strains formed part of a phylogenetic subgroup distinct from the ancestral B. thailandensis population and were associated with atypical isolation sources when compared to the majority of previously described B. thailandensis strains. In functional assays, B. thailandensis E555 exhibited several B. pseudomallei-like phenotypes, including colony wrinkling, resistance to human complement binding, and intracellular macrophage survival. However, in murine infection assays, B. thailandensis E555 did not exhibit enhanced virulence relative to other B. thailandensis strains, suggesting that additional factors are required to successfully colonize and infect mammals. Conclusions The discovery of such novel variant strains demonstrates how unbiased genomic surveys of non-pathogenic isolates can reveal insights into the development and emergence of new pathogenic species.
Collapse
|
47
|
Comparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins. BMC Genomics 2010; 11:369. [PMID: 20537180 PMCID: PMC2890568 DOI: 10.1186/1471-2164-11-369] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 06/10/2010] [Indexed: 11/17/2022] Open
Abstract
Background Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important role in the emergence of new pathogenic strains within this family. Data from the sequenced genomes of strains in this family could show how the genes encoded by all these strains, known as the pangenome, are distributed. Information about the core, accessory and panproteome of this family can show how, for example, genes encoding virulence-associated proteins are distributed and help us understand how virulence emerges. Results We deduced the complete set of orthologs for eleven strains from this family. The core proteome consists of 1,882 orthologous groups, which is 28% of the 6,629 orthologous groups in this family. There were 4,411 accessory orthologous groups (i.e., proteins that occurred in from 2 to 10 proteomes) and 5,584 unique proteins (encoded once on only one of the eleven genomes). Proteins that have been associated with virulence in V. cholerae were widely distributed across the eleven genomes, but the majority was found only on the genomes of the two V. cholerae strains examined. Conclusions The proteomes are reflective of the differing evolutionary trajectories followed by different strains to similar phenotypes. The composition of the proteomes supports the notion that genetic exchange among species of the Vibrionaceae is widespread and that this exchange aids these species in adapting to their environments.
Collapse
|
48
|
A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog 2010; 6:e1000845. [PMID: 20368977 PMCID: PMC2848565 DOI: 10.1371/journal.ppat.1000845] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 03/03/2010] [Indexed: 11/19/2022] Open
Abstract
Certain environmental microorganisms can cause severe human infections, even in the absence of an obvious requirement for transition through an animal host for replication ("accidental virulence"). To understand this process, we compared eleven isolate genomes of Burkholderia pseudomallei (Bp), a tropical soil microbe and causative agent of the human and animal disease melioidosis. We found evidence for the existence of several new genes in the Bp reference genome, identifying 282 novel genes supported by at least two independent lines of supporting evidence (mRNA transcripts, database homologs, and presence of ribosomal binding sites) and 81 novel genes supported by all three lines. Within the Bp core genome, 211 genes exhibited significant levels of positive selection (4.5%), distributed across many cellular pathways including carbohydrate and secondary metabolism. Functional experiments revealed that certain positively selected genes might enhance mammalian virulence by interacting with host cellular pathways or utilizing host nutrients. Evolutionary modifications improving Bp environmental fitness may thus have indirectly facilitated the ability of Bp to colonize and survive in mammalian hosts. These findings improve our understanding of the pathogenesis of melioidosis, and establish Bp as a model system for studying the genetics of accidental virulence.
Collapse
|
49
|
Losada L, Ronning CM, DeShazer D, Woods D, Fedorova N, Kim HS, Shabalina SA, Pearson TR, Brinkac L, Tan P, Nandi T, Crabtree J, Badger J, Beckstrom-Sternberg S, Saqib M, Schutzer SE, Keim P, Nierman WC. Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements. Genome Biol Evol 2010; 2:102-16. [PMID: 20333227 PMCID: PMC2839346 DOI: 10.1093/gbe/evq003] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2010] [Indexed: 11/25/2022] Open
Abstract
Burkholderia mallei (Bm), the causative agent of the
predominately equine disease glanders, is a genetically uniform species that is
very closely related to the much more diverse species Burkholderia
pseudomallei (Bp), an opportunistic human pathogen and the primary
cause of melioidosis. To gain insight into the relative lack of genetic
diversity within Bm, we performed whole-genome comparative analysis of seven Bm
strains and contrasted these with eight Bp strains. The Bm core genome (shared
by all seven strains) is smaller in size than that of Bp, but the inverse is
true for the variable gene sets that are distributed across strains.
Interestingly, the biological roles of the Bm variable gene sets are much more
homogeneous than those of Bp. The Bm variable genes are found mostly in
contiguous regions flanked by insertion sequence (IS) elements, which appear to
mediate excision and subsequent elimination of groups of genes that are under
reduced selection in the mammalian host. The analysis suggests that the Bm
genome continues to evolve through random IS-mediated recombination events, and
differences in gene content may contribute to differences in virulence observed
among Bm strains. The results are consistent with the view that Bm recently
evolved from a single strain of Bp upon introduction into an animal host
followed by expansion of IS elements, prophage elimination, and genome
rearrangements and reduction mediated by homologous recombination across IS
elements.
Collapse
|
50
|
Within-host evolution of Burkholderia pseudomallei in four cases of acute melioidosis. PLoS Pathog 2010; 6:e1000725. [PMID: 20090837 PMCID: PMC2799673 DOI: 10.1371/journal.ppat.1000725] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 12/14/2009] [Indexed: 11/19/2022] Open
Abstract
Little is currently known about bacterial pathogen evolution and adaptation within the host during acute infection. Previous studies of Burkholderia pseudomallei, the etiologic agent of melioidosis, have shown that this opportunistic pathogen mutates rapidly both in vitro and in vivo at tandemly repeated loci, making this organism a relevant model for studying short-term evolution. In the current study, B. pseudomallei isolates cultured from multiple body sites from four Thai patients with disseminated melioidosis were subjected to fine-scale genotyping using multilocus variable-number tandem repeat analysis (MLVA). In order to understand and model the in vivo variable-number tandem repeat (VNTR) mutational process, we characterized the patterns and rates of mutations in vitro through parallel serial passage experiments of B. pseudomallei. Despite the short period of infection, substantial divergence from the putative founder genotype was observed in all four melioidosis cases. This study presents a paradigm for examining bacterial evolution over the short timescale of an acute infection. Further studies are required to determine whether the mutational process leads to phenotypic alterations that impact upon bacterial fitness in vivo. Our findings have important implications for future sampling strategies, since colonies in a single clinical sample may be genetically heterogeneous, and organisms in a culture taken late in the infective process may have undergone considerable genetic change compared with the founder inoculum.
Collapse
|