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Korneev KV, Arbatsky NP, Molinaro A, Palmigiano A, Shaikhutdinova RZ, Shneider MM, Pier GB, Kondakova AN, Sviriaeva EN, Sturiale L, Garozzo D, Kruglov AA, Nedospasov SA, Drutskaya MS, Knirel YA, Kuprash DV. Structural Relationship of the Lipid A Acyl Groups to Activation of Murine Toll-Like Receptor 4 by Lipopolysaccharides from Pathogenic Strains of Burkholderia mallei, Acinetobacter baumannii, and Pseudomonas aeruginosa. Front Immunol 2015; 6:595. [PMID: 26635809 PMCID: PMC4655328 DOI: 10.3389/fimmu.2015.00595] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/06/2015] [Indexed: 11/13/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is required for activation of innate immunity upon recognition of lipopolysaccharide (LPS) of Gram-negative bacteria. The ability of TLR4 to respond to a particular LPS species is important since insufficient activation may not prevent bacterial growth while excessive immune reaction may lead to immunopathology associated with sepsis. Here, we investigated the biological activity of LPS from Burkholderia mallei that causes glanders, and from the two well-known opportunistic pathogens Acinetobacter baumannii and Pseudomonas aeruginosa (causative agents of nosocomial infections). For each bacterial strain, R-form LPS preparations were purified by hydrophobic chromatography and the chemical structure of lipid A, an LPS structural component, was elucidated by HR-MALDI-TOF mass spectrometry. The biological activity of LPS samples was evaluated by their ability to induce production of proinflammatory cytokines, such as IL-6 and TNF, by bone marrow-derived macrophages. Our results demonstrate direct correlation between the biological activity of LPS from these pathogenic bacteria and the extent of their lipid A acylation.
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Affiliation(s)
- Kirill V Korneev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia ; Biological Faculty, Lomonosov Moscow State University , Moscow , Russia
| | - Nikolay P Arbatsky
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Moscow , Russia
| | - Antonio Molinaro
- Department of Chemical Sciences, Università di Napoli Federico II , Naples , Italy
| | - Angelo Palmigiano
- CNR Institute for Polymers Composites and Biomaterials , Catania , Italy
| | | | - Mikhail M Shneider
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences , Moscow , Russia
| | - Gerald B Pier
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - Anna N Kondakova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Moscow , Russia
| | - Ekaterina N Sviriaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia ; Biological Faculty, Lomonosov Moscow State University , Moscow , Russia
| | - Luisa Sturiale
- CNR Institute for Polymers Composites and Biomaterials , Catania , Italy
| | - Domenico Garozzo
- CNR Institute for Polymers Composites and Biomaterials , Catania , Italy
| | - Andrey A Kruglov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia ; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Sergei A Nedospasov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia ; Biological Faculty, Lomonosov Moscow State University , Moscow , Russia ; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow , Russia
| | - Marina S Drutskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia
| | - Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences , Moscow , Russia
| | - Dmitry V Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Moscow , Russia ; Biological Faculty, Lomonosov Moscow State University , Moscow , Russia
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Sim SH, Yu Y, Lin CH, Karuturi RKM, Wuthiekanun V, Tuanyok A, Chua HH, Ong C, Paramalingam SS, Tan G, Tang L, Lau G, Ooi EE, Woods D, Feil E, Peacock SJ, Tan P. The core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis. PLoS Pathog 2008; 4:e1000178. [PMID: 18927621 PMCID: PMC2564834 DOI: 10.1371/journal.ppat.1000178] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 09/16/2008] [Indexed: 11/19/2022] Open
Abstract
Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, can exhibit significant ecological flexibility that is likely reflective of a dynamic genome. Using whole-genome Bp microarrays, we examined patterns of gene presence and absence across 94 South East Asian strains isolated from a variety of clinical, environmental, or animal sources. 86% of the Bp K96243 reference genome was common to all the strains representing the Bp “core genome”, comprising genes largely involved in essential functions (eg amino acid metabolism, protein translation). In contrast, 14% of the K96243 genome was variably present across the isolates. This Bp accessory genome encompassed multiple genomic islands (GIs), paralogous genes, and insertions/deletions, including three distinct lipopolysaccharide (LPS)-related gene clusters. Strikingly, strains recovered from cases of human melioidosis clustered on a tree based on accessory gene content, and were significantly more likely to harbor certain GIs compared to animal and environmental isolates. Consistent with the inference that the GIs may contribute to pathogenesis, experimental mutation of BPSS2053, a GI gene, reduced microbial adherence to human epithelial cells. Our results suggest that the Bp accessory genome is likely to play an important role in microbial adaptation and virulence. Melioidosis is a serious infectious disease of humans caused by Burkholderia pseudomallei, a soil bacterium endemic to many areas in South East Asia. Besides humans, B. pseudomallei is also capable of infecting many other species and can be isolated from diverse environmental sources including soil, water, and air. In this study, we used DNA microarrays to probe the stability of the B. pseudomallei genome in a large panel of clinical, animal, and environmental strains. We found that evidence of a highly dynamic B. pseudomallei genome, with up to 14% being variably present across different strains. Surprisingly, strains recovered from human patients were significantly associated with the presence of “genomic islands”, corresponding to regions of DNA directly acquired from other microorganisms. Genes on these genomic islands may thus play an important role in the pathogenesis of human melioidosis.
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Affiliation(s)
- Siew Hoon Sim
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore
| | - Yiting Yu
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | - Chi Ho Lin
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Apichai Tuanyok
- Faculty of Medicine, University of Calgary Health Sciences Centre, Calgary, Alberta, Canada
| | - Hui Hoon Chua
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | - Catherine Ong
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore
| | | | - Gladys Tan
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore
| | - Lynn Tang
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore
| | - Gary Lau
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore
| | - Eng Eong Ooi
- Defense Medical and Environmental Research Institute, DSO National Laboratories, Singapore, Republic of Singapore
| | - Donald Woods
- Faculty of Medicine, University of Calgary Health Sciences Centre, Calgary, Alberta, Canada
| | - Edward Feil
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Sharon J. Peacock
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Clinical Vaccinology and Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, United Kingdom
- * E-mail: (SJP); (PT)
| | - Patrick Tan
- Genome Institute of Singapore, Singapore, Republic of Singapore
- Duke-NUS Graduate Medical School Singapore, Singapore, Republic of Singapore
- * E-mail: (SJP); (PT)
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A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. J Bacteriol 2007; 189:9044-9. [PMID: 17933898 PMCID: PMC2168593 DOI: 10.1128/jb.01264-07] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei is the etiologic agent of melioidosis. Many disease manifestations are associated with melioidosis, and the mechanisms causing this variation are unknown; genomic differences among strains offer one explanation. We compared the genome sequences of two strains of B. pseudomallei: the original reference strain K96243 from Thailand and strain MSHR305 from Australia. We identified a variable homologous region between the two strains. This region was previously identified in comparisons of the genome of B. pseudomallei strain K96243 with the genome of strain E264 from the closely related B. thailandensis. In that comparison, K96243 was shown to possess a horizontally acquired Yersinia-like fimbrial (YLF) gene cluster. Here, we show that the homologous genomic region in B. pseudomallei strain 305 is similar to that previously identified in B. thailandensis strain E264. We have named this region in B. pseudomallei strain 305 the B. thailandensis-like flagellum and chemotaxis (BTFC) gene cluster. We screened for these different genomic components across additional genome sequences and 571 B. pseudomallei DNA extracts obtained from regions of endemicity. These alternate genomic states define two distinct groups within B. pseudomallei: all strains contained either the BTFC gene cluster (group BTFC) or the YLF gene cluster (group YLF). These two groups have distinct geographic distributions: group BTFC is dominant in Australia, and group YLF is dominant in Thailand and elsewhere. In addition, clinical isolates are more likely to belong to group YLF, whereas environmental isolates are more likely to belong to group BTFC. These groups should be further characterized in an animal model.
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Duangsonk K, Gal D, Mayo M, Hart CA, Currie BJ, Winstanley C. Use of a variable amplicon typing scheme reveals considerable variation in the accessory genomes of isolates of Burkholderia pseudomallei. J Clin Microbiol 2006; 44:1323-34. [PMID: 16597858 PMCID: PMC1448637 DOI: 10.1128/jcm.44.4.1323-1334.2006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Melioidosis, a disease caused by the bacterium Burkholderia pseudomallei, is endemic in southeast Asia and northern Australia. We used suppression subtractive hybridization (SSH) to identify sequences that varied between two B. pseudomallei isolates from Australia and determined the distribution of 45 SSH-derived sequences among a panel of B. pseudomallei and B. thailandensis isolates. Sequences exhibiting variable prevalence were included in a variable amplicon typing (VAT) scheme designed to score the presence or absence of 14 PCR amplicons. VAT analysis was carried out with 48 isolates from Thailand, which were typed by multilocus sequence typing (MLST), and 44 isolates from Australia of known MLST type. The VAT scheme could be used to divide the 48 isolates from Thailand into 23 VAT types and the 44 isolates from Australia into 36 VAT types. Some of the sequences included in the VAT scheme were more commonly PCR positive among isolates from Australia than among isolates from Thailand, and vice versa. No isolate from Australia was PCR positive for genomic island 11 or a putative transposase sequence, whereas four SSH-derived sequences were far more prevalent among the Australian isolates. Analysis based on the VAT scheme indicated that the isolates clustered into groups, some of which were mainly or exclusively from one geographical origin. One cluster included Australian isolates that were mostly associated with severe disease, including rare neurological melioidosis, suggesting that the content of the accessory genome may play an important role in determining the clinical manifestation of the disease.
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Affiliation(s)
- Kwanjit Duangsonk
- Division of Medical Microbiology, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, United Kingdom.
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Fushan A, Monastyrskaya G, Abaev I, Sverdlov E. Genomic fingerprinting of Burkholderia pseudomallei and B. mallei pathogens with DNA array based on interspecies sequence differences obtained by subtractive hybridization. Res Microbiol 2006; 157:684-92. [PMID: 16621455 DOI: 10.1016/j.resmic.2006.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 02/13/2006] [Accepted: 02/23/2006] [Indexed: 11/30/2022]
Abstract
The ability to rapidly and efficiently identify causative agents of dangerous human and animal diseases is a prerequisite to diagnosis, prophylaxis and therapy. Such identification systems can be developed based on DNA markers enabling differentiation between various bacterial strains. One source of these markers is genetic polymorphism. An efficient method for detecting the most stable polymorphisms without knowledge of genomic sequences is subtractive hybridization. In this work we report an approach to typing of Burkholderia pseudomallei and B. mallei that cause melioidosis and glanders, respectively. Typing is based on hybridization of bacterial genomes with a DNA array of genomic markers obtained using subtractive hybridization. The array comprised 55 DNA fragments which distinguished the genomes of B. pseudomallei C-141 and B. mallei C-5 strains, and it was used to test 28 radioactively labeled B. pseudomallei strains and 8 B. mallei strains. Each strain was characterized by a specific hybridization pattern, and the results were analyzed using cluster analysis. 18 patterns specific to B. pseudomallei and 6 patterns specific to B. mallei were found to be unique. The data allowed us to differentiate most studied B. pseudomallei variants from one another and from B. mallei strains. It was concluded that DNA markers obtained by subtractive hybridization can be potentially useful for molecular typing of B. pseudomallei and B. mallei strains, as well as for their molecular diagnosis. The method reported can be easily adapted for use both with DNA arrays and DNA microarrays with fluorescent probes.
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Affiliation(s)
- Alexey Fushan
- Laboratory of Structure and Functions of Human Genes, M. M. Shemyakin & Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997, Moscow, Russia.
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Novak RT, Glass MB, Gee JE, Gal D, Mayo MJ, Currie BJ, Wilkins PP. Development and evaluation of a real-time PCR assay targeting the type III secretion system of Burkholderia pseudomallei. J Clin Microbiol 2006; 44:85-90. [PMID: 16390953 PMCID: PMC1351940 DOI: 10.1128/jcm.44.1.85-90.2006] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we report on the development of a discriminatory real-time assay for the rapid identification of Burkholderia pseudomallei isolates and the evaluation of this assay for sensitivity against related species and detection in spiked human blood samples. The assay targets a 115-base-pair region within orf2 of the B. pseudomallei type III secretion system gene cluster and distinguishes B. pseudomallei from other microbial species. Assay performance was evaluated with 224 geographically, temporally, and clinically diverse B. pseudomallei isolates from the Centers for Disease Control and Prevention strain collection. This represents the first real-time PCR for rapid and sensitive identification of B. pseudomallei that has been tested for cross-reactivity with 23 Burkholderia mallei, 5 Burkholderia thailandensis, and 35 Burkholderia and 76 non-Burkholderia organisms which have historically presented diagnostic challenges. The assay performed with 100% specificity. The limit of detection was found to be 76 femtograms of DNA (equivalent to 5.2 x 10(3) genome equivalents per ml) in a single PCR. In spiked human blood, the assay could detect as few as 8.4 x 10(3) CFU per ml. This rapid assay is a valuable tool for identification of B. pseudomallei and may improve diagnosis in regions endemic for melioidosis.
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Affiliation(s)
- Ryan T Novak
- Meningitis and Special Pathogens Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, CDC, Atlanta, GA 30333, USA
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U'Ren JM, Van Ert MN, Schupp JM, Easterday WR, Simonson TS, Okinaka RT, Pearson T, Keim P. Use of a real-time PCR TaqMan assay for rapid identification and differentiation of Burkholderia pseudomallei and Burkholderia mallei. J Clin Microbiol 2005; 43:5771-4. [PMID: 16272516 PMCID: PMC1287822 DOI: 10.1128/jcm.43.11.5771-5774.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2005] [Revised: 07/19/2005] [Accepted: 08/24/2005] [Indexed: 11/20/2022] Open
Abstract
A TaqMan allelic-discrimination assay designed around a synonymous single-nucleotide polymorphism was used to genotype Burkholderia pseudomallei and Burkholderia mallei isolates. The assay rapidly identifies and discriminates between these two highly pathogenic bacteria and does not cross-react with genetic near neighbors, such as Burkholderia thailandensis and Burkholderia cepacia.
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Affiliation(s)
- Jana M U'Ren
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2447482 DOI: 10.1002/cfg.421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Fushan A, Monastyrskaya G, Abaev I, Kostina M, Filyukova O, Pecherskih E, Sverdlov E. Genome-wide identification and mapping of variable sequences in the genomes of Burkholderia mallei and Burkholderia pseudomallei. Res Microbiol 2004; 156:278-88. [PMID: 15748995 DOI: 10.1016/j.resmic.2004.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2004] [Revised: 09/16/2004] [Accepted: 09/20/2004] [Indexed: 11/21/2022]
Abstract
Burkholderia mallei and Burkholderia pseudomallei, closely related Gram-negative bacteria, are the causative agents of such serious infectious diseases of humans and animals as glanders and melioidosis, respectively. Despite numerous studies of these pathogens, the detailed mechanisms of their pathogenesis is still poorly understood. One of the serious obstacles to revealing factors responsible for pathogenicity lies in the considerable natural variability of B. pseudomallei and B. mallei, which is also a challenge to development of rapid and efficient diagnostic tools facilitating unambiguous identification of the infectious agents. To gain a deeper insight into B. mallei and B. pseudomallei interspecies divergence and intraspecies polymorphism, we compared the genomes of B. mallei C-5 and B. pseudomallei C-141 strains using a subtractive hybridization technique. A library of DNA fragments specific for B. mallei C-5 and absent from B. pseudomallei C-141 was obtained and analyzed. Some of the differential sequences detected were also not found in the recently sequenced genome of B. pseudomallei K96243. However, a multitude of B. mallei C-5 sequences absent from the B. pseudomallei C-141 genome were detected in the genome of B. pseudomallei K96243. On the other hand, some sequences identified as constituents of the B. mallei C-5 genome were not found in the genome of B. mallei ATCC 23344. Some of the differential DNA fragments displayed similarity to different mobile elements that have not yet been described for B. mallei, whereas the others matched fragments of various prophages, or, when translated into protein sequences, components of active transport systems and different enzymes. A substantial proportion of the differential clones had no database matches either at the nucleotide or amino acid sequence level. The results suggest great genome-wide intra- and interspecies variability of B. mallei and B. pseudomallei. The differences identified may be useful as molecular signatures for identification of B. mallei strains.
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Affiliation(s)
- Alexey Fushan
- Laboratory of Structure and Functions of Human Genes, M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 GSP, Moscow V-437, Russia.
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