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Li J, Tan J, Xiong X, Zhong Q, Lu W. Burkholderia thailandensis Isolated from Infected Wound, Southwest China, 2022. Emerg Infect Dis 2024; 30:1055-1057. [PMID: 38666739 PMCID: PMC11060469 DOI: 10.3201/eid3005.230743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2024] Open
Abstract
We report a clinical isolate of Burkholderia thailandensis 2022DZh obtained from a patient with an infected wound in southwest China. Genomic analysis indicates that this isolate clusters with B. thailandensis BPM, a human isolate from Chongqing, China. We recommend enhancing monitoring and surveillance for B. thailandensis infection in both humans and livestock.
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Kumar SP, Uthra KT, Chitra V, Damodharan N, Pazhani GP. Challenges and mitigation strategies associated with Burkholderia cepacia complex contamination in pharmaceutical manufacturing. Arch Microbiol 2024; 206:159. [PMID: 38483625 DOI: 10.1007/s00203-024-03921-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/15/2024] [Accepted: 03/02/2024] [Indexed: 03/19/2024]
Abstract
Burkholderia cepacia complex (BCC) is a Gram-negative, non-spore-forming bacterium with more than 20 opportunistic pathogenic species, most commonly found in soil and water. Due to their rapid mutation rates, these organisms are adaptable and possess high genomic plasticity. BCC can cause life-threatening infections in immunocompromised individuals, such as those with cystic fibrosis, chronic granulomatous disease, and neonates. BCC contamination is a significant concern in pharmaceutical manufacturing, frequently causing non-sterile product recalls. BCC has been found in purified water, cosmetics, household items, and even ultrasound gel used in veterinary practices. Pharmaceuticals, personal care products, and cleaning solutions have been implicated in numerous outbreaks worldwide, highlighting the risks associated with intrinsic manufacturing site contamination. Regulatory compliance, product safety, and human health protection depend on testing for BCC in pharmaceutical manufacturing. Identification challenges exist, with BCC often misidentified as other bacteria like non-lactose fermenting Escherichia coli or Pseudomonas spp., particularly in developing countries where reporting BCC in pharmaceuticals remains limited. This review comprehensively aims to address the organisms causing BCC contamination, genetic diversity, identification challenges, regulatory requirements, and mitigation strategies. Recommendations are proposed to aid pharmaceutical chemists in managing BCC-associated risks and implementing prevention strategies within manufacturing processes.
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Affiliation(s)
- Sethuraman Prem Kumar
- Department of Pharmaceutical Quality Assurance, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Karupanagounder Thangaraj Uthra
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603 203, India
| | - Vellapandian Chitra
- Department of Pharmacology, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Narayanasamy Damodharan
- Department of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Gururaja Perumal Pazhani
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603 203, India.
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Kim B, Han SR, Lee H, Oh TJ. Insights into group-specific pattern of secondary metabolite gene cluster in Burkholderia genus. Front Microbiol 2024; 14:1302236. [PMID: 38293557 PMCID: PMC10826400 DOI: 10.3389/fmicb.2023.1302236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Burkholderia is a versatile strain that has expanded into several genera. It has been steadily reported that the genome features of Burkholderia exhibit activities ranging from plant growth promotion to pathogenicity across various isolation areas. The objective of this study was to investigate the secondary metabolite patterns of 366 Burkholderia species through comparative genomics. Samples were selected based on assembly quality assessment and similarity below 80% in average nucleotide identity. Duplicate samples were excluded. Samples were divided into two groups using FastANI analysis. Group A included B. pseudomallei complex. Group B included B. cepacia complex. The limitations of MLST were proposed. The detection of genes was performed, including environmental and virulence-related genes. In the pan-genome analysis, each complex possessed a similar pattern of cluster for orthologous groups. Group A (n = 185) had 14,066 cloud genes, 2,465 shell genes, 682 soft-core genes, and 2,553 strict-core genes. Group B (n = 181) had 39,867 cloud genes, 4,986 shell genes, 324 soft-core genes, 222 core genes, and 2,949 strict-core genes. AntiSMASH was employed to analyze the biosynthetic gene cluster (BGC). The results were then utilized for network analysis using BiG-SCAPE and CORASON. Principal component analysis was conducted and a table was constructed using the results obtained from antiSMASH. The results were divided into Group A and Group B. We expected the various species to show similar patterns of secondary metabolite gene clusters. For in-depth analysis, a network analysis of secondary metabolite gene clusters was conducted, exemplified by BiG-SCAPE analysis. Depending on the species and complex, Burkholderia possessed several kinds of siderophore. Among them, ornibactin was possessed in most Burkholderia and was clustered into 4,062 clans. There was a similar pattern of gene clusters depending on the species. NRPS_04014 belonged to siderophore BGCs including ornibactin and indigoidine. However, it was observed that each family included a similar species. This suggests that, besides siderophores being species-specific, the ornibactin gene cluster itself might also be species-specific. The results suggest that siderophores are associated with environmental adaptation, possessing a similar pattern of siderophore gene clusters among species, which could provide another perspective on species-specific environmental adaptation mechanisms.
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Affiliation(s)
- Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
| | - So-Ra Han
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
| | - Hyun Lee
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Division of Computer Science and Engineering, SunMoon University, Asan, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan, Republic of Korea
- Genome-Based BioIT Convergence Institute, Asan, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan, Republic of Korea
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Moran CL, Debowski A, Vrielink A, Stubbs K, Sarkar-Tyson M. N-acetyl-β-hexosaminidase activity is important for chitooligosaccharide metabolism and biofilm formation in Burkholderia pseudomallei. Environ Microbiol 2024; 26:e16571. [PMID: 38178319 DOI: 10.1111/1462-2920.16571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Burkholderia pseudomallei is a saprophytic Gram-negative bacillus that can cause the disease melioidosis. Although B. pseudomallei is a recognised member of terrestrial soil microbiomes, little is known about its contribution to the saprophytic degradation of polysaccharides within its niche. For example, while chitin is predicted to be abundant within terrestrial soils the chitinolytic capacity of B. pseudomallei is yet to be defined. This study identifies and characterises a putative glycoside hydrolase, bpsl0500, which is expressed by B. pseudomallei K96243. Recombinant BPSL0500 was found to exhibit activity against substrate analogues and GlcNAc disaccharides relevant to chitinolytic N-acetyl-β-d-hexosaminidases. In B. pseudomallei, bpsl0500 was found to be essential for both N-acetyl-β-d-hexosaminidase activity and chitooligosaccharide metabolism. Furthermore, bpsl0500 was also observed to significantly affect biofilm deposition. These observations led to the identification of BPSL0500 activity against model disaccharide linkages that are present in biofilm exopolysaccharides, a feature that has not yet been described for chitinolytic enzymes. The results in this study indicate that chitinolytic N-acetyl-β-d-hexosaminidases like bpsl0500 may facilitate biofilm disruption as well as chitin assimilation, providing dual functionality for saprophytic bacteria such as B. pseudomallei within the competitive soil microbiome.
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Affiliation(s)
- Clare L Moran
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Aleksandra Debowski
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Keith Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
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Grund M, Choi SJ, Powell L, Lukomski S. Intranasal immunization with a Bucl8-based vaccine ameliorates bacterial burden and pathological inflammation, and promotes an IgG2a/b dominant response in an outbred mouse model of Burkholderia infection. Front Immunol 2023; 14:1177650. [PMID: 37545515 PMCID: PMC10399622 DOI: 10.3389/fimmu.2023.1177650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Burkholderia pseudomallei is a gram-negative bacterium that is the etiological agent of the tropical disease melioidosis. Currently, there is no licensed vaccine for melioidosis, but numerous candidates are being tested for protective efficacy and characterization of the elicited immune response. Our lab has previously reported the immunogenicity of a Bucl8-protein-based peptide antigen, designated L1-CRM197 (Cross-reacting material 197). When given subcutaneously, this vaccine formulation promoted a strong Th2 (IgG1) antibody response, however immunization did not protect from death. In this study, we hypothesized that an intranasally administered L1-CRM197 vaccine would induce protective mucosal immunity. To evaluate vaccine efficacy, we developed a surrogate Burkholderia infection model that employs outbred CD-1 mice which imitates the immunogenetic diversity of humans. Mice were immunized with either L1-CRM197 adjuvanted with fluorinated cyclic diguanosine monophosphate (FCDG) or with FCDG-only control. These mice were then challenged intranasally with an infectious dose of a luminescent strain of B. thailandensis E264 two weeks post-immunization, and correlates of protection were assessed in euthanized mice on days 1, 2, 3, and 7 post-infection. Overall, intranasal vaccination, compared to subcutaneous administration, induced a stronger Th1 (IgG2a/2b) to Th2 (IgG1) antibody response and promoted anti-L1 nasal, pulmonary, and systemic IgA. Additionally, sera IgG from L1-CRM197-vaccinated mice recognized whole-cell B. thailandensis and B. pseudomallei, a select agent exempt strain Bp82. Vaccination ameliorated disease indicators, including luminescent signal and bacterial cell counts, weight and temperature loss, and organ weight, which negatively correlated with IgG2a antibody levels and mucosa-stimulating cytokines IL-13 and IL-9. L1-CRM197-vaccinated mice also had earlier resolution of inflammatory and tissue-damaging cytokines compared to the FCDG-only controls. These results suggest a balanced humoral and cell-mediated response, along with mucosa-based immunity are beneficial for protection. Future efforts should further assess mucosal cellular and humoral mechanisms of protection and test such protection, using aerosolized B. pseudomallei select agent strain(s).
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Affiliation(s)
| | | | | | - Slawomir Lukomski
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, United States
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Kumar R, Barbhuiya RI, Bohra V, Wong JWC, Singh A, Kaur G. Sustainable rhamnolipids production in the next decade - Advancing with Burkholderia thailandensis as a potent biocatalytic strain. Microbiol Res 2023; 272:127386. [PMID: 37094547 DOI: 10.1016/j.micres.2023.127386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 03/27/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
Rhamnolipids are one of the most promising eco-friendly green glycolipids for bio-replacements of commercially available fossil fuel-based surfactants. However, the current industrial biotechnology practices cannot meet the required standards due to the low production yields, expensive biomass feedstocks, complicated processing, and opportunistic pathogenic nature of the conventional rhamnolipid producer strains. To overcome these problems, it has become important to realize non-pathogenic producer substitutes and high-yielding strategies supporting biomass-based production. We hereby review the inherent characteristics of Burkholderia thailandensis E264 which favor its competence towards such sustainable rhamnolipid biosynthesis. The underlying biosynthetic networks of this species have unveiled unique substrate specificity, carbon flux control and rhamnolipid congener profile. Acknowledging such desirable traits, the present review provides critical insights towards metabolism, regulation, upscaling, and applications of B. thailandensis rhamnolipids. Identification of their unique and naturally inducible physiology has proved to be beneficial for achieving previously unmet redox balance and metabolic flux requirements in rhamnolipids production. These developments in part are targeted by the strategic optimization of B. thailandensis valorizing low-cost substrates ranging from agro-industrial byproducts to next generation (waste) fractions. Accordingly, safer bioconversions can propel the industrial rhamnolipids in advanced biorefinery domains to promote circular economy, reduce carbon footprint and increased applicability as both social and environment friendly bioproducts.
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Affiliation(s)
- Rajat Kumar
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | | | - Varsha Bohra
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Jonathan W C Wong
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong; Institute of Bioresources and Agriculture and Sino-Forest Applied Research Centre for Pearl River Delta Environment, Hong Kong Baptist University, Kowloon Tong, Hong Kong
| | - Ashutosh Singh
- School of Engineering, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Guneet Kaur
- School of Engineering, University of Guelph, Guelph, ON N1G2W1, Canada.
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7
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Somprasong N, Hagen JP, Sahl JW, Webb JR, Hall CM, Currie BJ, Wagner DM, Keim P, Schweizer HP. A conserved active site PenA β-lactamase Ambler motif specific for Burkholderia pseudomallei/B. mallei is likely responsible for intrinsic amoxicillin-clavulanic acid sensitivity and facilitates a simple diagnostic PCR assay for melioidosis. Int J Antimicrob Agents 2023; 61:106714. [PMID: 36640845 DOI: 10.1016/j.ijantimicag.2023.106714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/23/2022] [Accepted: 12/31/2022] [Indexed: 01/13/2023]
Abstract
Burkholderia pseudomallei is a soil- and water-dwelling Gram-negative bacterium that causes melioidosis in humans and animals. Amoxicillin-clavulanic acid (AMC) susceptibility has been hailed as an integral part of the screening algorithm for identification of B. pseudomallei, but the molecular basis for the inherent AMC susceptibility of this bacterium remains undefined. This study showed that B. pseudomallei (and the closely-related B. mallei) wild-type strains are the only Burkholderia spp. that contain a 70STSK73 PenA Ambler motif. This motif was present in >99.5% of 1820 analysed B. pseudomallei strains and 100% of 83 analysed B. mallei strains, and is proposed as the likely cause for their inherent AMC sensitivity. The authors developed a polymerase chain reaction (PCR) assay that specifically amplifies the penA70ST(S/F)K73-containing region from B. pseudomallei and B. mallei, but not from the remaining B. pseudomallei complex species or the 70STFK73 region from the closely-related penB of B. cepacia complex species. The abundance and purity of the 193-bp PCR fragment from putative B. pseudomallei isolates from clinical and environmental samples is likely sufficient for reliable confirmation of the presence of B. pseudomallei. The PCR assay is designed to be especially suited for use in resource-constrained areas. While not further explored in this study, the assay may allow diagnosis of putative B. mallei in culture isolates from animal and human samples.
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Affiliation(s)
- Nawarat Somprasong
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Johannah P Hagen
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Carina M Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA
| | - Bart J Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Infectious Diseases and Northern Territory Medical Programme, Royal Darwin Hospital, Darwin, Northern Territory, Australia
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Herbert P Schweizer
- The Pathogen and Microbiome Institute, Northern Arizona University, 1395 S Knoles Dr. Flagstaff, AZ 86001-4073, USA; Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.
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Surface Motility Favors Codependent Interaction between Pseudomonas aeruginosa and Burkholderia cenocepacia. mSphere 2022; 7:e0015322. [PMID: 35862793 PMCID: PMC9429929 DOI: 10.1128/msphere.00153-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Interactions between different bacterial species shape bacterial communities and their environments. The opportunistic pathogens Pseudomonas aeruginosa and Burkholderia cenocepacia both can colonize the lungs of individuals affected by cystic fibrosis. Using the social surface behavior called swarming motility as a study model, we noticed intricate interactions between B. cenocepacia K56-2 and P. aeruginosa PA14. While strain K56-2 does not swarm under P. aeruginosa favorable swarming conditions, co-inoculation with a nonmotile PA14 flagellum-less ΔfliC mutant restored spreading for both strains. We show that P. aeruginosa provides the wetting agent rhamnolipids allowing K56-2 to perform swarming motility, while aflagellated PA14 appears to “hitchhike” along with K56-2 cells in the swarming colony. IMPORTANCEPseudomonas aeruginosa and Burkholderia cenocepacia are important opportunistic pathogens often found together in the airways of persons with cystic fibrosis. Laboratory cocultures of both species often ends with one taking over the other. We used a surface motility assay to study the social interactions between populations of these bacterial species. Under our conditions, B. cenocepacia cannot swarm without supplementation of the wetting agent produced by P. aeruginosa. In a mixed colony of both species, an aflagellated mutant of P. aeruginosa provides the necessary wetting agent to B. cenocepacia, allowing both bacteria to swarm and colonize a surface. We highlight this peculiar interaction where both bacteria set aside their antagonistic tendencies to travel together.
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Hall CM, Baker AL, Sahl JW, Mayo M, Scholz HC, Kaestli M, Schupp J, Martz M, Settles EW, Busch JD, Sidak-Loftis L, Thomas A, Kreutzer L, Georgi E, Schweizer HP, Warner JM, Keim P, Currie BJ, Wagner DM. Expanding the Burkholderia pseudomallei Complex with the Addition of Two Novel Species: Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. Appl Environ Microbiol 2022; 88:e0158321. [PMID: 34644162 PMCID: PMC8752149 DOI: 10.1128/aem.01583-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Distinct Burkholderia strains were isolated from soil samples collected in tropical northern Australia (Northern Territory and the Torres Strait Islands, Queensland). Phylogenetic analysis of 16S rRNA and whole genome sequences revealed these strains were distinct from previously described Burkholderia species and assigned them to two novel clades within the B. pseudomallei complex (Bpc). Because average nucleotide identity and digital DNA-DNA hybridization calculations are consistent with these clades representing distinct species, we propose the names Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov. Strains assigned to B. mayonis sp. nov. include type strain BDU6T (=TSD-80; LMG 29941; ASM152374v2) and BDU8. Strains assigned to B. savannae sp. nov. include type strain MSMB266T (=TSD-82; LMG 29940; ASM152444v2), MSMB852, BDU18, and BDU19. Comparative genomics revealed unique coding regions for both putative species, including clusters of orthologous genes associated with phage. Type strains of both B. mayonis sp. nov. and B. savannae sp. nov. yielded biochemical profiles distinct from each other and from other species in the Bpc, and profiles also varied among strains within B. mayonis sp. nov. and B. savannae sp. nov. Matrix-assisted laser desorption ionization time-of-flight (MLST) analysis revealed a B. savannae sp. nov. cluster separate from other species, whereas B. mayonis sp. nov. strains did not form a distinct cluster. Neither B. mayonis sp. nov. nor B. savannae sp. nov. caused mortality in mice when delivered via the subcutaneous route. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species currently within the Bpc. IMPORTANCEBurkholderia species can be important sources of novel natural products, and new species are of interest to diverse scientific disciplines. Although many Burkholderia species are saprophytic, Burkholderia pseudomallei is the causative agent of the disease melioidosis. Understanding the genomics and virulence of the closest relatives to B. pseudomallei, i.e., the other species within the B. pseudomallei complex (Bpc), is important for identifying robust diagnostic targets specific to B. pseudomallei and for understanding the evolution of virulence in B. pseudomallei. Two proposed novel species, B. mayonis sp. nov. and B. savannae sp. nov., were isolated from soil samples collected from multiple locations in northern Australia. The two proposed species belong to the Bpc but are phylogenetically distinct from all other members of this complex. The addition of B. mayonis sp. nov. and B. savannae sp. nov. results in a total of eight species within this significant complex of bacteria that are available for future studies.
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Affiliation(s)
- Carina M. Hall
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Anthony L. Baker
- Discipline of Biomedicine and Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Mark Mayo
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | | | - Mirjam Kaestli
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - James Schupp
- Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Madison Martz
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Erik W. Settles
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Joseph D. Busch
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Lindsay Sidak-Loftis
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Astrid Thomas
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Lisa Kreutzer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Enrico Georgi
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Herbert P. Schweizer
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Jeffrey M. Warner
- Discipline of Biomedicine and Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bart J. Currie
- Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
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10
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Mullins AJ, Mahenthiralingam E. The Hidden Genomic Diversity, Specialized Metabolite Capacity, and Revised Taxonomy of Burkholderia Sensu Lato. Front Microbiol 2021; 12:726847. [PMID: 34650530 PMCID: PMC8506256 DOI: 10.3389/fmicb.2021.726847] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Burkholderia sensu lato is a collection of closely related genera within the family Burkholderiaceae that includes species of environmental, industrial, biotechnological, and clinical importance. Multiple species within the complex are the source of diverse specialized metabolites, many of which have been identified through genome mining of their biosynthetic gene clusters (BGCs). However, the full, true genomic diversity of these species and genera, and their biosynthetic capacity have not been investigated. This study sought to cluster and classify over 4000 Burkholderia sensu lato genome assemblies into distinct genomic taxa representing named and uncharacterized species. We delineated 235 species groups by average nucleotide identity analyses that formed seven distinct phylogenomic clades, representing the genera of Burkholderia sensu lato: Burkholderia, Paraburkholderia, Trinickia, Caballeronia, Mycetohabitans, Robbsia, and Pararobbisa. A total of 137 genomic taxa aligned with named species possessing a sequenced type strain, while 93 uncharacterized species groups were demarcated. The 95% ANI threshold proved capable of delineating most genomic species and was only increased to resolve several closely related species. These analyses enabled the assessment of species classifications of over 4000 genomes, and the correction of over 400 genome taxonomic assignments in public databases into existing and uncharacterized genomic species groups. These species groups were genome mined for BGCs, their specialized metabolite capacity calculated per species and genus, and the number of distinct BGCs per species estimated through kmer-based de-replication. Mycetohabitans species dedicated a larger proportion of their relatively small genomes to specialized metabolite biosynthesis, while Burkholderia species harbored more BGCs on average per genome and possessed the most distinct BGCs per species compared to the remaining genera. Exploring the hidden genomic diversity of this important multi-genus complex contributes to our understanding of their taxonomy and evolutionary relationships, and supports future efforts toward natural product discovery.
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Gassiep I, Burnard D, Bauer MJ, Norton RE, Harris PN. Diagnosis of melioidosis: the role of molecular techniques. Future Microbiol 2021; 16:271-288. [PMID: 33595347 DOI: 10.2217/fmb-2020-0202] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.
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Affiliation(s)
- Ian Gassiep
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Department of Infectious Diseases, Mater Hospital Brisbane, South Brisbane, Queensland, 4101, Australia
| | - Delaney Burnard
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Michelle J Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia
| | - Robert E Norton
- Pathology Queensland, Townsville University Hospital, Townsville, Queensland, 4814, Australia
| | - Patrick N Harris
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Queensland, 4029, Australia.,Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, Queensland, 4029, Australia
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12
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Detection and differentiation of Burkholderia species with pathogenic potential in environmental soil samples. PLoS One 2021; 16:e0245175. [PMID: 33411797 PMCID: PMC7790303 DOI: 10.1371/journal.pone.0245175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/22/2020] [Indexed: 01/12/2023] Open
Abstract
The Burkholderia pseudomallei phylogenetic cluster includes B. pseudomallei, B. mallei, B. thailandensis, B. oklahomensis, B. humptydooensis and B. singularis. Regarded as the only pathogenic members of this group, B. pseudomallei and B. mallei cause the diseases melioidosis and glanders, respectively. Additionally, variant strains of B. pseudomallei and B. thailandensis exist that include the geographically restricted B. pseudomallei that express a B. mallei-like BimA protein (BPBM), and B. thailandensis that express a B. pseudomallei-like capsular polysaccharide (BTCV). To establish a PCR-based assay for the detection of pathogenic Burkholderia species or their variants, five PCR primers were designed to amplify species-specific sequences within the bimA (Burkholderiaintracellular motility A) gene. Our multiplex PCR assay could distinguish pathogenic B. pseudomallei and BPBM from the non-pathogenic B. thailandensis and the BTCV strains. A second singleplex PCR successfully discriminated the BTCV from B. thailandensis. Apart from B. humptydooensis, specificity testing against other Burkholderia spp., as well as other Gram-negative and Gram-positive bacteria produced a negative result. The detection limit of the multiplex PCR in soil samples artificially spiked with known quantities of B. pseudomallei and B. thailandensis were 5 and 6 CFU/g soil, respectively. Furthermore, comparison between standard bacterial culture and the multiplex PCR to detect B. pseudomallei from 34 soil samples, collected from an endemic area of melioidosis, showed high sensitivity and specificity. This robust, sensitive, and specific PCR assay will be a useful tool for epidemiological study of B. pseudomallei and closely related members with pathogenic potential in soil.
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13
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Amiss AS, Webb JR, Mayo M, Currie BJ, Craik DJ, Henriques ST, Lawrence N. Safer In Vitro Drug Screening Models for Melioidosis Therapy Development. Am J Trop Med Hyg 2020; 103:1846-1851. [PMID: 32975176 DOI: 10.4269/ajtmh.20-0248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Melioidosis is a neglected tropical disease caused by the Gram-negative soil bacterium Burkholderia pseudomallei. Current antibiotic regimens used to treat melioidosis are prolonged and expensive, and often ineffective because of intrinsic and acquired antimicrobial resistance. Efforts to develop new treatments for melioidosis are limited by the risks associated with handling pathogenic B. pseudomallei, which restricts research to facilities with biosafety level three containment. Closely related nonpathogenic Burkholderia can be investigated under less stringent biosafety level two containment, and we hypothesized that they could be used as model organisms for developing therapies that would also be effective against B. pseudomallei. We used microbroth dilution assays to compare drug susceptibility profiles of three B. pseudomallei strains and five nonpathogenic Burkholderia strains. Burkholderia humptydooensis, Burkholderia thailandensis, and Burkholderia territorii had similar susceptibility profiles to pathogenic B. pseudomallei that support their potential as safer in vitro models for developing new melioidosis therapies.
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Affiliation(s)
- Anna S Amiss
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Bart J Currie
- Northern Territory Medical Program, Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Australia.,Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Sónia Troeira Henriques
- Queensland University of Technology, School of Biomedical Sciences, Institute of Healthy and Biomedical Innovation, and Translational Research Institute, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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14
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Laroucau K, Aaziz R, Vorimore F, Varghese K, Deshayes T, Bertin C, Delannoy S, Sami AM, Al Batel M, El Shorbagy M, Almutawaa KAW, Alanezi SJ, Alazemi YSN, Guernier-Cambert V, Wernery U. A genetic variant of Burkholderia mallei detected in Kuwait: Consequences for the PCR diagnosis of glanders. Transbound Emerg Dis 2020; 68:960-963. [PMID: 33245616 DOI: 10.1111/tbed.13777] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 11/26/2022]
Abstract
Glanders is a contagious zoonotic disease caused by Burkholderia mallei. Following the detection of glanders positive horses using the OIE complement fixation test, the tissues of two horses were analysed by PCR. While PCR systems targeting the Burkholderia pseudomallei complex gave positive signals, the species-specific PCR systems targeting B. mallei (fliP-IS407A) and B. pseudomallei (orf11)-the OIE recommended targets-resulted in negative signals. However, the presence of B. mallei in these tissues was confirmed with a recently described B. mallei-specific real-time PCR system and genotyping with MLST- and SNP-based methods, performed on the most positive tissue, identified a genotype closely related to B. mallei strains recently isolated in the Middle East. This study leads to recommendations regarding the use of PCR systems for the molecular diagnosis of glanders, especially in regions where the circulating B. mallei strains have not yet been fully genetically characterized.
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Affiliation(s)
- Karine Laroucau
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Rachid Aaziz
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Fabien Vorimore
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Koshy Varghese
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Thomas Deshayes
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Claire Bertin
- Laboratory for Animal Health, Bacterial Zoonosis Unit, European and OIE Reference Laboratory for Glanders, Paris-Est University, ANSES, Maisons-Alfort, France
| | - Sabine Delannoy
- Food Research Laboratory, IdentyPath Platform, University Paris-Est, ANSES, Maisons-Alfort, France
| | - Attia M Sami
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Maha Al Batel
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Mamdouh El Shorbagy
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Khaled A W Almutawaa
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Saad J Alanezi
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Yousef S N Alazemi
- Veterinary Diagnostic Laboratory Centre & Animal Health Department, Agriculture Affairs & Fish Resources Authority (PAAF), Kuwait
| | - Vanina Guernier-Cambert
- Agricultural Research Service, National Animal Disease Center, United States Department of Agriculture, Ames, IA, USA
| | - Ulrich Wernery
- Central Veterinary Research Laboratory, OIE Reference Laboratory for Glanders, Dubai, United Arab Emirates
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15
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Hammerl JA, Volkmar S, Jacob D, Klein I, Jäckel C, Hertwig S. The Burkholderia thailandensis Phages ΦE058 and ΦE067 Represent Distinct Prototypes of a New Subgroup of Temperate Burkholderia Myoviruses. Front Microbiol 2020; 11:1120. [PMID: 32528458 PMCID: PMC7266877 DOI: 10.3389/fmicb.2020.01120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/05/2020] [Indexed: 12/03/2022] Open
Abstract
Burkholderia mallei and B. pseudomallei are highly pathogenic species which are closely related, but diverse regarding their prophage content. While temperate phages have not yet been isolated from B. mallei, several phages of B. pseudomallei, and its non-pathogenic relative B. thailandensis have been described. In this study we isolated two phages from B. pseudomallei and three phages from B. thailandensis and determined their morphology, host range, and relationship. All five phages belong to the family Myoviridae, but some of them revealed different host specificities. DNA-DNA hybridization experiments indicated that the phages belong to two groups. One group, composed of ΦE058 (44,121 bp) and ΦE067 (43,649 bp), represents a new subgroup of Burkholderia myoviruses that is not related to known phages. The genomes of ΦE058 and ΦE067 are similar but also show some striking differences. Repressor proteins differ clearly allowing the phages to form plaques on hosts containing the respective other phage. The tail fiber proteins exhibited some minor deviations in the C-terminal region, which may account for the ability of ΦE058, but not ΦE067, to lyse B. mallei, B. pseudomallei, and B. thailandensis. In addition, the integrases and attachment sites of the phages are not related. While ΦE058 integrates into the Burkholderia chromosome within an intergenic region, the ΦE067 prophage resides in the selC tRNA gene for selenocysteine. Experiments on the structure of phage DNA isolated from particles suggest that the ΦE058 and ΦE067 genomes have a circular conformation.
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Affiliation(s)
- Jens A Hammerl
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Daniela Jacob
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Iris Klein
- Centre for Biological Threats and Special Pathogens (ZBS 2), Robert Koch Institute, Berlin, Germany
| | - Claudia Jäckel
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Stefan Hertwig
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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16
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Shakya M, Ahmed SA, Davenport KW, Flynn MC, Lo CC, Chain PSG. Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life. Sci Rep 2020; 10:1723. [PMID: 32015354 PMCID: PMC6997174 DOI: 10.1038/s41598-020-58356-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/06/2020] [Indexed: 12/02/2022] Open
Abstract
There is growing interest in reconstructing phylogenies from the copious amounts of genome sequencing projects that target related viral, bacterial or eukaryotic organisms. To facilitate the construction of standardized and robust phylogenies for disparate types of projects, we have developed a complete bioinformatic workflow, with a web-based component to perform phylogenetic and molecular evolutionary (PhaME) analysis from sequencing reads, draft assemblies or completed genomes of closely related organisms. Furthermore, the ability to incorporate raw data, including some metagenomic samples containing a target organism (e.g. from clinical samples with suspected infectious agents), shows promise for the rapid phylogenetic characterization of organisms within complex samples without the need for prior assembly.
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Affiliation(s)
- Migun Shakya
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA.
| | - Sanaa A Ahmed
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Karen W Davenport
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Mark C Flynn
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Chien-Chi Lo
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, MS-M888, Los Alamos, NM, 87545, USA.
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17
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French CT, Bulterys PL, Woodward CL, Tatters AO, Ng KR, Miller JF. Virulence from the rhizosphere: ecology and evolution of Burkholderia pseudomallei-complex species. Curr Opin Microbiol 2020; 54:18-32. [PMID: 32028234 DOI: 10.1016/j.mib.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Christopher T French
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Northern Arizona University, Department of Biological Sciences, Pathogen and Microbiome Institute 1395 S Knoles Drive, Flagstaff, AZ 86011, United States.
| | - Philip L Bulterys
- Department of Pathology, Stanford University, Lane Building, L235, 300 Pasteur Drive, Stanford, CA, 94305, United States
| | - Cora L Woodward
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Avery O Tatters
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Ken R Ng
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Jeff F Miller
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, 611 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States
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18
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Hall CM, Jaramillo S, Jimenez R, Stone NE, Centner H, Busch JD, Bratsch N, Roe CC, Gee JE, Hoffmaster AR, Rivera-Garcia S, Soltero F, Ryff K, Perez-Padilla J, Keim P, Sahl JW, Wagner DM. Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico. PLoS Negl Trop Dis 2019; 13:e0007727. [PMID: 31487287 PMCID: PMC6748447 DOI: 10.1371/journal.pntd.0007727] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/17/2019] [Accepted: 08/23/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis. The global burden and distribution of melioidosis is poorly understood, including in the Caribbean. B. pseudomallei was previously isolated from humans and soil in eastern Puerto Rico but the abundance and distribution of B. pseudomallei in Puerto Rico as a whole has not been thoroughly investigated. METHODOLOGY/PRINCIPAL FINDINGS We collected 600 environmental samples (500 soil and 100 water) from 60 sites around Puerto Rico. We identified B. pseudomallei by isolating it via culturing and/or using PCR to detect its DNA within complex DNA extracts. Only three adjacent soil samples from one site were positive for B. pseudomallei with PCR; we obtained 55 isolates from two of these samples. The 55 B. pseudomallei isolates exhibited fine-scale variation in the core genome and contained four novel genomic islands. Phylogenetic analyses grouped Puerto Rico B. pseudomallei isolates into a monophyletic clade containing other Caribbean isolates, which was nested inside a larger clade containing all isolates from Central/South America. Other Burkholderia species were commonly observed in Puerto Rico; we cultured 129 isolates from multiple soil and water samples collected at numerous sites around Puerto Rico, including representatives of B. anthina, B. cenocepacia, B. cepacia, B. contaminans, B. glumae, B. seminalis, B. stagnalis, B. ubonensis, and several unidentified novel Burkholderia spp. CONCLUSIONS/SIGNIFICANCE B. pseudomallei was only detected in three soil samples collected at one site in north central Puerto Rico with only two of those samples yielding isolates. All previous human and environmental B. pseudomallei isolates were obtained from eastern Puerto Rico. These findings suggest B. pseudomallei is ecologically established and widely dispersed in the environment in Puerto Rico but rare. Phylogeographic patterns suggest the source of B. pseudomallei populations in Puerto Rico and elsewhere in the Caribbean may have been Central or South America.
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Affiliation(s)
- Carina M. Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sierra Jaramillo
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Rebecca Jimenez
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Nathan E. Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Heather Centner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Joseph D. Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nicole Bratsch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Chandler C. Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jay E. Gee
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alex R. Hoffmaster
- Bacterial Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sarai Rivera-Garcia
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Fred Soltero
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, San Juan, Puerto Rico, United States of America
| | - Kyle Ryff
- Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico, United States of America
| | - Janice Perez-Padilla
- Dengue Branch, Centers for Disease Control and Prevention, San Juan, Puerto Rico, United States of America
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jason W. Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- * E-mail:
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19
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Trottmann F, Franke J, Richter I, Ishida K, Cyrulies M, Dahse H, Regestein L, Hertweck C. Cyclopropanol Warhead in Malleicyprol Confers Virulence of Human‐ and Animal‐Pathogenic
Burkholderia
Species. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Jakob Franke
- Institute of Organic Chemistry, BMWZ Leibniz University Hannover 30167 Hannover Germany
| | - Ingrid Richter
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
| | - Michael Cyrulies
- Department Bio Pilot Plant Leibniz Institute for Natural Product Research and Infection Biology (HKI) 07745 Jena Germany
| | - Hans‐Martin Dahse
- Department Infection Biology Leibniz Institute for Natural Product Research and Infection Biology (HKI) 07745 Jena Germany
| | - Lars Regestein
- Department Bio Pilot Plant Leibniz Institute for Natural Product Research and Infection Biology (HKI) 07745 Jena Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry Leibniz Institute for Natural Product Research and Infection Biology (HKI) Beutenbergstr. 11a 07745 Jena Germany
- Natural Product Chemistry Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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20
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Trottmann F, Franke J, Richter I, Ishida K, Cyrulies M, Dahse HM, Regestein L, Hertweck C. Cyclopropanol Warhead in Malleicyprol Confers Virulence of Human- and Animal-Pathogenic Burkholderia Species. Angew Chem Int Ed Engl 2019; 58:14129-14133. [PMID: 31353766 PMCID: PMC6790655 DOI: 10.1002/anie.201907324] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/20/2019] [Indexed: 12/16/2022]
Abstract
Burkholderia species such as B. mallei and B. pseudomallei are bacterial pathogens causing fatal infections in humans and animals (glanders and melioidosis), yet knowledge on their virulence factors is limited. While pathogenic effects have been linked to a highly conserved gene locus (bur/mal) in the B. mallei group, the metabolite associated to the encoded polyketide synthase, burkholderic acid (syn. malleilactone), could not explain the observed phenotypes. By metabolic profiling and molecular network analyses of the model organism B. thailandensis, the primary products of the cryptic pathway were identified as unusual cyclopropanol-substituted polyketides. First, sulfomalleicyprols were identified as inactive precursors of burkholderic acid. Furthermore, a highly reactive upstream metabolite, malleicyprol, was discovered and obtained in two stabilized forms. Cell-based assays and a nematode infection model showed that the rare natural product confers cytotoxicity and virulence.
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Affiliation(s)
- Felix Trottmann
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Jakob Franke
- Institute of Organic Chemistry, BMWZ, Leibniz University Hannover, 30167, Hannover, Germany
| | - Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Keishi Ishida
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Michael Cyrulies
- Department Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany
| | - Hans-Martin Dahse
- Department Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany
| | - Lars Regestein
- Department Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), 07745, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany.,Natural Product Chemistry, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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21
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Birnie E, van ’t Hof S, Bijnsdorp A, Mansaray Y, Huizenga E, van der Ende A, Hugenholtz F, Grobusch MP, Wiersinga WJ. Identification of Burkholderia thailandensis with novel genotypes in the soil of central Sierra Leone. PLoS Negl Trop Dis 2019; 13:e0007402. [PMID: 31199807 PMCID: PMC6623504 DOI: 10.1371/journal.pntd.0007402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/11/2019] [Accepted: 04/18/2019] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The soil-dwelling bacillus Burkholderia pseudomallei is the etiological-agent of the neglected and life-threatening emerging infection melioidosis. The distribution of B. pseudomallei in West Africa is unknown. In the present study we aimed to determine whether B. pseudomallei and B. thailandensis are present in the environment of central Sierra Leone. METHODOLOGY/PRINCIPAL FINDINGS In June-July 2017, we conducted an environmental surveillance study-designed in accordance with existing consensus guidelines-in central Sierra Leone. A total of 1,000 soil samples (100 per site) were collected and cultured. B. pseudomallei was not identified in the soil, but we identified seven novel B. thailandensis sequence types with multi-locus sequence typing (MLST) and 16S rRNA gene sequence analyses. CONCLUSIONS/SIGNIFICANCE The presence of B. pseudomallei was not demonstrated, however, multiple novel B. thailandensis sequence types were identified. More environmental and sequencing studies are needed to further understand the genetic diversity, evolution and virulence of these emerging organisms.
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Affiliation(s)
- Emma Birnie
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Lion Heart Medical Centre, Yele, Sierra Leone
- * E-mail:
| | - Senne van ’t Hof
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | | | | | - Arie van der Ende
- Department of Medical Microbiology, Amsterdam UMC, location AMC, Amsterdam, the Netherlands
| | - Floor Hugenholtz
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Martin P. Grobusch
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Infectious Diseases, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Masanga Medical Research Unit, Masanga, Sierra Leone
| | - W. Joost Wiersinga
- Center for Experimental and Molecular Medicine (CEMM), Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Infectious Diseases, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands
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22
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DeShazer D. A novel contact-independent T6SS that maintains redox homeostasis via Zn 2+ and Mn 2+ acquisition is conserved in the Burkholderia pseudomallei complex. Microbiol Res 2019; 226:48-54. [PMID: 31284944 DOI: 10.1016/j.micres.2019.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Accepted: 05/30/2019] [Indexed: 12/21/2022]
Abstract
The Burkholderia pseudomallei complex consists of six phylogenetically related Gram-negative bacterial species that include environmental saprophytes and mammalian pathogens. These microbes possess multiple type VI secretion systems (T6SS) that provide a fitness advantage in diverse niches by translocating effector molecules into prokaryotic and eukaryotic cells in a contact-dependent manner. Several recent studies have elucidated the regulation and function of T6SS-2, a novel contact-independent member of the T6SS family. Expression of the T6SS-2 gene cluster is repressed by OxyR, Zur and TctR and is activated by GvmR and reactive oxygen species (ROS). The last two genes of the T6SS-2 gene cluster encode a zincophore (TseZ) and a manganeseophore (TseM) that are exported into the extracellular milieu in a contact-independent fashion when microbes encounter oxidative stress. TseZ and TseM bind Zn2+ and Mn2+, respectively, and deliver them to bacteria where they provide protection against the lethal effects of ROS. The TonB-dependent transporters that interact with TseZ and TseM, and actively transport Zn2+ and Mn2+ across the outer membrane, have also been identified. Finally, T6SS-2 provides a contact-independent growth advantage in nutrient limited environments and is critical for virulence in Galleria mellonella larvae, but is dispensable for virulence in rodent models of infection.
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Affiliation(s)
- David DeShazer
- Bacteriology Division, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, USA.
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Gee JE, Elrod MG, Gulvik CA, Haselow DT, Waters C, Liu L, Hoffmaster AR. Burkholderia thailandensis Isolated from Infected Wound, Arkansas, USA. Emerg Infect Dis 2019; 24:2091-2094. [PMID: 30334705 PMCID: PMC6199988 DOI: 10.3201/eid2411.180821] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The bacterium Burkholderia thailandensis, a member of the Burkholderia pseudomallei complex, is generally considered nonpathogenic; however, on rare occasions, B. thailandensis infections have been reported. We describe a clinical isolate of B. thailandensis, BtAR2017, recovered from a patient with an infected wound in Arkansas, USA, in 2017.
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Impact of Binge Alcohol Intoxication on the Humoral Immune Response during Burkholderia spp. Infections. Microorganisms 2019; 7:microorganisms7050125. [PMID: 31075819 PMCID: PMC6560430 DOI: 10.3390/microorganisms7050125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/02/2019] [Accepted: 05/05/2019] [Indexed: 11/17/2022] Open
Abstract
Burkholderia pseudomallei, the causative agent of melioidosis can occur in healthy humans, yet binge alcohol use is progressively being recognized as a major risk factor. Currently, no experimental studies have investigated the effects of binge alcohol on the adaptive immune system during an active infection. In this study, we used B. thailandensis and B. vietnamiensis, to investigate the impact of a single binge alcohol episode on the humoral response during infection. Eight-week-old female C57BL/6 mice were administered alcohol comparable to human binge drinking (4.4 g/kg) or PBS intraperitoneally 30 min before intranasal infection. Mice infected with B. thailandensis had a 100% survival rate, while those infected with B. vietnamiensis had a 33% survivability rate when a binge alcohol dose was administered. B. thailandensis was detected in blood of mice administered alcohol at only 7 days post infection (PI), while those infected with B. vietnamiensis and receiving alcohol were found throughout the 28-day infection as well as in tissues at day 28 PI. Binge alcohol elevated IgM and delayed IgG specific to the whole cell lysate (WCL) of B. vietnamiensis but not B. thailandensis infections. Differences in immunogenicity of B. pseudomallei near-neighbors provide a framework for novel insights into the effects of binge alcohol's suppression of the humoral immune response that can cause opportunistic infections in otherwise healthy hosts.
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Gislason AS, Turner K, Domaratzki M, Cardona ST. Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia. Microb Genom 2019; 3. [PMID: 29208119 PMCID: PMC5729917 DOI: 10.1099/mgen.0.000140] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations. Five hundred and eight genes were not significantly disrupted, suggesting that these genes are essential for survival in rich, undefined medium. Comparison of the B. cenocepacia K56-2 essential genome with that of the closely related B. cenocepacia J2315 revealed partial overlapping, suggesting that some essential genes are strain-specific. Furthermore, 158 essential genes were conserved in B. cenocepacia and two species belonging to the Burkholderia pseudomallei complex, B. pseudomallei K96243 and Burkholderia thailandensis E264. Porins, including OpcC, a lysophospholipid transporter, LplT, and a protein involved in the modification of lipid A with aminoarabinose were found to be essential in Burkholderia genomes but not in other bacterial essential genomes identified so far. Our results highlight the existence of cell envelope processes that are uniquely essential in species of the genus Burkholderia for which the essential genomes have been identified by Tn-seq.
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Affiliation(s)
- April S Gislason
- 1Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Keith Turner
- 2Monsanto Company, 700 Chesterfield Parkway W, Chesterfield, MO, 63017, USA
| | - Mike Domaratzki
- 3Department of Computer Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Silvia T Cardona
- 4Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
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A mouse model of binge alcohol consumption and Burkholderia infection. PLoS One 2018; 13:e0208061. [PMID: 30485380 PMCID: PMC6261616 DOI: 10.1371/journal.pone.0208061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Binge drinking, an increasingly common form of alcohol consumption, is associated with increased mortality and morbidity; yet, its effects on the immune system's ability to defend against infectious agents are poorly understood. Burkholderia pseudomallei, the causative agent of melioidosis can occur in healthy humans, yet binge alcohol use is progressively being recognized as a major risk factor. Although our previous studies demonstrated that binge alcohol exposure results in reduced alveolar macrophage function and increased Burkholderia virulence in vitro, no experimental studies have investigated the outcomes of binge alcohol on Burkholderia spp. infection in vivo. PRINCIPAL FINDINGS In this study, we used the close genetic relatives of B. pseudomallei, B. thailandensis E264 and B. vietnamiensis, as useful BSL-2 model systems. Eight-week-old female C57BL/6 mice were administered alcohol comparable to human binge drinking episodes (4.4 g/kg) or PBS intraperitoneally 30 min before a non-lethal intranasal infection. In an initial B. thailandensis infection (3 x 105), bacteria accumulated in the lungs and disseminated to the spleen in alcohol administered mice only, compared with PBS treated mice at 24 h PI. The greatest bacterial load occurred with B. vietnamiensis (1 x 106) in lungs, spleen, and brain tissue by 72 h PI. Pulmonary cytokine expression (TNF-α, GM-CSF) decreased, while splenic cytokine (IL-10) increased in binge drunk mice. Increased lung and brain permeability was observed as early as 2 h post alcohol administration in vivo. Trans-epithelial electrical resistance (TEER) was significantly decreased, while intracellular invasion of non-phagocytic cells increased with 0.2% v/v alcohol exposure in vitro. CONCLUSIONS Our results indicate that a single binge alcohol dose suppressed innate immune functions and increased the ability of less virulent Burkholderia strains to disseminate through increased barrier permeability and intracellular invasion of non-phagocytic cells.
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Misra HS, Maurya GK, Kota S, Charaka VK. Maintenance of multipartite genome system and its functional significance in bacteria. J Genet 2018; 97:1013-1038. [PMID: 30262715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacteria are unicellular organisms that do not show compartmentalization of the genetic material and other cellular organelles as seen in higher organisms. Earlier, bacterial genomes were defined as single circular chromosome and extrachromosomal plasmids. Recently, many bacteria were found harbouringmultipartite genome system and the numbers of copies of genome elements including chromosomes vary from one to several per cell. Interestingly, it is noticed that majority of multipartite genome-harbouring bacteria are either stress tolerant or pathogens. Further, it is observed that the secondary genomes in these bacteria encode proteins that are involved in bacterial genome maintenance and also contribute to higher stress tolerance, and pathogenicity in pathogenic bacteria. Surprisingly, in some bacteria the genes encoding the proteins of classical homologous recombination pathways are present only on the secondary chromosomes, and some do not have either of the classical homologous recombination pathways. This review highlights the presence of ploidy and multipartite genomes in bacterial system, the underlying mechanisms of genome maintenance and the possibilities of these features contributing to higher abiotic and biotic stress tolerance in these bacteria.
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Affiliation(s)
- Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
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Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 67:4291-4293. [PMID: 29130433 DOI: 10.1099/ijsem.0.002415] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Price EP, Sarovich DS, Webb JR, Hall CM, Jaramillo SA, Sahl JW, Kaestli M, Mayo M, Harrington G, Baker AL, Sidak-Loftis LC, Settles EW, Lummis M, Schupp JM, Gillece JD, Tuanyok A, Warner J, Busch JD, Keim P, Currie BJ, Wagner DM. Phylogeographic, genomic, and meropenem susceptibility analysis of Burkholderia ubonensis. PLoS Negl Trop Dis 2017; 11:e0005928. [PMID: 28910350 PMCID: PMC5614643 DOI: 10.1371/journal.pntd.0005928] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 09/26/2017] [Accepted: 09/03/2017] [Indexed: 01/02/2023] Open
Abstract
The bacterium Burkholderia ubonensis is commonly co-isolated from environmental specimens harbouring the melioidosis pathogen, Burkholderia pseudomallei. B. ubonensis has been reported in northern Australia and Thailand but not North America, suggesting similar geographic distribution to B. pseudomallei. Unlike most other Burkholderia cepacia complex (Bcc) species, B. ubonensis is considered non-pathogenic, although its virulence potential has not been tested. Antibiotic resistance in B. ubonensis, particularly towards drugs used to treat the most severe B. pseudomallei infections, has also been poorly characterised. This study examined the population biology of B. ubonensis, and includes the first reported isolates from the Caribbean. Phylogenomic analysis of 264 B. ubonensis genomes identified distinct clades that corresponded with geographic origin, similar to B. pseudomallei. A small proportion (4%) of strains lacked the 920kb chromosome III replicon, with discordance of presence/absence amongst genetically highly related strains, demonstrating that the third chromosome of B. ubonensis, like other Bcc species, probably encodes for a nonessential pC3 megaplasmid. Multilocus sequence typing using the B. pseudomallei scheme revealed that one-third of strains lack the "housekeeping" narK locus. In comparison, all strains could be genotyped using the Bcc scheme. Several strains possessed high-level meropenem resistance (≥32 μg/mL), a concern due to potential transmission of this phenotype to B. pseudomallei. In silico analysis uncovered a high degree of heterogeneity among the lipopolysaccharide O-antigen cluster loci, with at least 35 different variants identified. Finally, we show that Asian B. ubonensis isolate RF23-BP41 is avirulent in the BALB/c mouse model via a subcutaneous route of infection. Our results provide several new insights into the biology of this understudied species.
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Affiliation(s)
- Erin P. Price
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Derek S. Sarovich
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
- Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Jessica R. Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Carina M. Hall
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Sierra A. Jaramillo
- 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
| | - Mirjam Kaestli
- 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
| | - Glenda Harrington
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - Anthony L. Baker
- Environmental and Public Health Microbiology Research Group, Microbiology and Immunology, James Cook University, Townsville, Queensland, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Lindsay C. Sidak-Loftis
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Erik W. Settles
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Madeline Lummis
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - James M. Schupp
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - John D. Gillece
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Apichai Tuanyok
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jeffrey Warner
- Environmental and Public Health Microbiology Research Group, Microbiology and Immunology, James Cook University, Townsville, Queensland, Australia
| | - Joseph D. Busch
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
- Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia
| | - David M. Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America
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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]
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