Burkholderia: Molecular Microbiology and Genomics Chapter Abstracts
Chapter 1: Diversity and Role of Burkholderia spp.
Peter Vandamme, John Govan and John LiPuma
Abstract
The genus Burkholderia comprises more then 40 different species, which occupy a wide array of ecological niches. They occur in soil and water, in the plant rhizosphere and endophytically in roots and shoots, but also in and on fungal mycelia. A growing number of Burkholderia endosymbionts is reported in various animal species. Their biological and metabolic properties can be exploited for biocontrol, bioremediation and plant growth promotion purposes, but safety issues regarding human infections, especially in cystic fibrosis patients, have not been solved. Traditionally, Burkholderia species are known as plant pathogens and soil bacteria with two important exceptions, Burkholderia mallei and Burkholderia pseudomallei, which are primary pathogens for humans and animals. Our present knowledge on the natural diversity of members of this genus indicates that the range of interactions between these bacteria and their hosts is more complex, diverse, and, often, contradictory. Their host range can vary dramatically, and the type of interaction may be that of a pathogen; it can also be beneficial or may be host dependent. The present chapter documents this taxonomic and ecological complexity, the role of Burkholderia species in infections, and tools for the detection and identification of these bacteria.
Chapter 2: Epidemiology, Typing and Population Genetics of Burkholderia Species
Tom Coenye and John J. LiPuma
Abstract
The aim of this review is to provide a comparative overview of the various (mostly genotypic) methods used in epidemiological studies of Burkholderia species, including ribotyping, pulsed-field gel electrophoresis of genomic macrorestriction fragments, randomly amplified polymorphic DNA fingerprinting, Rep- and BOX-PCR fingerprinting, multilocus-based approaches and variable-number tandem repeat analysis. Subsequently, the epidemiology of the most-commonly encountered Burkholderia species is discussed. The focus will be on the Burkholderia cepacia complex and infection in people with cystic fibrosis and the epidemiology of Burkholderia pseudomallei and Burkholderia mallei. In the final section we discuss recent advances in our understanding of the population genetics of B. cepacia complex and B. pseudomallei, based on results obtained with multilocus-based approaches like multilocus sequence typing and multilocus restriction typing.
Chapter 3: Comparative Genomics of Burkholderia Species
Eshwar Mahenthiralingam and Pavel Drevinek
Abstract
Burkholderia species have large and unusual multireplicon genomes that encode a diverse range of phenotypic functions. Currently there are 9 finished and 17 draft Burkholderia genome sequences that may be accessed via curated public databases; another 6 genome projects have recently been initiated or completed outside of the public domain. Examination of the completed Burkholderia genomes demonstrates that they: (i) on average encode 7.5 Mb of DNA, and (ii) possess a minimum of two large chromosomal replicons. Burkholderia xenovorans and all members of the Burkholderia cepacia complex which have been sequenced also possess a third replicon. Ribosomal RNA operons together with the majority of essential house-keeping genes reside on the largest chromosomal replicon; all characterised second replicons also encode these essential operons defining them as chromosomal. However, the presence of essential genes on the third replicon is variable within the genus, with for example B. xenovorans lacking ribosomal RNA operons on its third replicon. Rapid evolution via the acquisition of foreign DNA is an inherent feature of nearly all Burkholderia species genomes with nearly 10% of the genome content comprising genomic islands. Burkholderia mallei is currently the only characterised member of the genus to show an alternative evolutionary path that has involved deletion, rearrangement and loss of genome content. Large numbers of plasmid-like genes, bacteriophages and insertion sequences also contribute to the genotypic plasticity and diversity of Burkholderia genomes. With a wealth genomic information now available for the genus, detailed characterisation of the ecology and pathogenesis of Burkholderia at the molecular level has been greatly enhanced.
Chapter 4: Antibiotic Resistance of Burkholderia spp.
Jane L. Burns
Abstract
Antibiotic resistance mechanisms reported in Burkholderia species parallel those seen in other Gram-negative bacilli. They include enzymatic modification, alteration in drug targets, and limited permeability. The most common drug modifying enzymes are the β-lactamases and aminoglycoside modifying enzymes. Altered drug targets include penicillin binding proteins, DNA gyrase, and dihydrofolate reductase. Permeability may be limited by antibiotic efflux pumps, porin structure or function, lipopolysaccharide structure or biofilm formation. Antibiotic resistance is an important facet of the management of infections caused by Burkholderia species.
Chapter 5: Polysaccharides of Burkholderia spp.
Joanna B. Goldberg
Abstract
Bacterial polysaccharides are generally excellent targets for vaccine development as they are surface exposed and often the most protective antigens expressed on a pathogen. Polysaccharides can be potent virulence factors responsible for avoidance of the host immune response, elicitation of an inflammatory response, or attachment to host cells. For this review, we will focus on species of Burkholderia that are associated with human disease. Members of the Burkholderia cepacia complex (Bcc) are important pathogens in immunocompromised patients including those with cystic fibrosis and chronic granulomatous disease. The genetically similar Burkholderia mallei and Burkholderia pseudomallei are the causative agents of glanders and meliodosis, respectively. Genomic sequences of model isolates of these and other Burkholderia species are currently being generated. While a wealth of in silico information will be emerging from the analysis of the genome sequences of Burkholderia species, including the detection and analysis of genes homologous to those encoding proteins involved in polysaccharide synthesis, this will not be the focus of this review. Instead we will update the topic of Bcc polysaccharides since it was last reviewed (Vinion-Dubiel and Goldberg, 2003), as well as summarize the literature on other members of the genera Burkholderia.
Chapter 6: Interaction of Burkholderia Species With the Phagocytic System
Kelly L. MacDonald and David P. Speert
Abstract
Burkholderia cepacia complex and Burkholderia pseudomallei are important human pathogens that subvert the phagocytic system, processes which may enhance disease in susceptible individuals. The human phagocytic system is an essential component of the immune response and is comprised mainly of neutrophils, macrophages and dendritic cells, highly specialized cells which bind and internalize microbes through the sophisticated process of phagocytosis. The ultimate goal of the phagocytic system is to kill or control infectious microbes and to orchestrate an appropriate immune response to eradicate the infection. Though many differences in the virulence and pathogenicity of B. cepacia complex and B. pseudomallei have been identified, these organisms both impair the elegant phagocytic system using some common strategies. This chapter will summarize the current knowledge of interactions between phagocytic cells and bacteria within the genus Burkholderia and will provide speculation on how these interactions may enhance the bacterial pathogenesis in humans.
Chapter 7: Beneficial Interactions of Burkholderia spp. With Plants
Jacques Balandreau and Patrick Mavingui
Abstract
Burkholderia species are widespread in nature, particularly in the plant environment. Abundance of Burkholderia cells on roots is commonly 100 to 1000 times higher than in bulk soil. This stimulatory effect of roots is more prominent than in most heterotrophic bacteria indicating that it reflects not only a nutritional effect, but probably a special ability to cope with selective pressures exerted by the plant environment. Burkholderia rhizosphere inhabitants commonly comprise B. ambifaria, B. caribensis, B. cenocepacia, B. glathei, B. graminis, B. hospita, B. phenazinium, B. pyrrocinia, B. tropica, B. unamae, and B. vietnamiensis. Some species have a closer relationship with their host plants, being internal tissues colonizers. In the case of teosintle and maize, a symbiosis was suggested to have evolved in America. In Rubiaceae leaves another symbiosis is known. The case of Burkholderia colonisation of legume nodules is a further proof of the ability of Burkholderia to undergo a beneficial coevolution with plants. These associations usually benefit both partners and are clearly different from pathogenic interactions caused by distinct taxa.
Chapter 8: The Phytopathogenic Burkholderia
Carlos F. Gonzalez, Vittorio Venturi and Amanda S. Engledow
Abstract
Members of the genus Burkholderia are versatile organisms that occupy a surprisingly wide range of ecological niches. The phytopathogenic species of the genus Burkholderia are the etiological agents of disease for a variety of plants, and cause such symptoms as wilt, rot, blight, or canker. They were originally described and placed in the genus Pseudomonas; however, using a polyphasic taxonomic approach P. andropogonis, P. caryophylli, P. cepacia, P. gladioli, P. glumae, and P. plantarii have all been transferred to the genus Burkholderia. The phytopathogenic Burkholderia have evolved a spectrum of extracellular factors which permit them to cause disease in a variety of hosts. The pathogens B. cepacia and B. gladioli produce extracellular factors that allow them to obtain nutrition by affecting cell membranes and the structural integrity of plant tissue. B. andropogonis, B. glumae and B. plantarii produce non-host specific toxins that allow the pathogen to access nutrients for growth and further proliferation. B. caryophylli a vascular wilting pathogen infects via wounding, and the vascular dysfunction induced by this extensive colonization causes wilting symptoms and eventual plant death. Genomic analysis of the phytopathogenic Burkholderia will provide insights on mechanisms involved in adaptation and pathogenesis.
Chapter 9: Biodegradation of Organic Anthropogenic Pollutants by Burkholderia Species
Vincent J. Denef
Abstract
In this chapter, the capacities of Burkholderia species to degrade organic anthropogenic pollutants are reviewed. Both from isolation studies as well as from diversity typing studies, the relevance of this genus in the degradation of an array of aromatic pollutants, including several priority pollutants, has been shown. We also present an overview of the research aimed at improving the potential of isolated strains to be utilized in bioremediation efforts. This includes (1) the increase of the knowledge base, by use of biochemical, genetic and functional genomic means; (2) the bio-engineering of the wild type strains; (3) the use of multi-species approaches; and (4) the manipulation of environmental parameters. Considering the presence of multiple species with malign properties in this genus, we shortly reflect on the relationship of strains with biodegradative potential with known pathogenic strains.
Chapter 10: Molecular Mechanisms of Virulence of Burkholderia pseudomallei and Burkholderia mallei
Donald E. Woods
Abstract
Burkholderia pseudomallei and Burkholderia mallei are the causative agents of meliodosis and glanders, respectively. Melioidosis is recognized as an important health problem in Southeast Asia and Northern Australia, and it poses a concern due to increased travel and military involvement in endemic regions. Isolated cases of melioidosis have been identified in a number of other regions as well. Although glanders has been eradicated from North America and Western Europe, the disease still persists in South America, Eastern Europe, Africa and Asia. In addition, both B. pseudomallei and B. mallei are classified as category B biological agents, and B. mallei has been utilized as an agent of biological warfare. Due to the importance of these diseases in endemic areas and the fact that the causative agents are not well characterized on a molecular level, there has been an increased interest in the identification and characterization of virulence determinants in these organisms. This review focuses on the recent advances in the understanding of the pathogenesis of disease caused by B. pseudomallei and B. mallei and describes molecular mechanisms of virulence for these organisms.
Chapter 11: Model Systems of Burkholderia cepacia Complex Infection
Pamela A. Sokol
Abstract
The Burkholderia cepacia complex causes infections in a diverse range of species including humans, animals, nematodes and plants. A variety of infection models have been developed to investigate both host specific and conserved mechanisms of pathogenicity. These include models for chronic and acute respiratory infection, cystic fibrosis, chronic granulomatous disease, pulmonary clearance, nematode killing, and virulence in onions and alfalfa. Models have been used to determine the virulence of different species of the complex and mutants to understand the importance of specific genes in disease. Infection models have also been applied to studies of host response, gene therapy, antimicrobial delivery, and immunization for prevention of Bcc lung disease.
Chapter 12: Social Behaviour of Members of the Genus Burkholderia: Quorum Sensing and Biofilms
Kathrin Riedel and Leo Eberl
Abstract
The view of bacteria as solitary life forms has strong roots in the tradition of culturing bacteria as suspensions in liquid media. In their natural environments, however, bacteria form surface-associated, structured and co-operative consortia, referred to as biofilms. Bacteria living in biofilms do interact with each other in various ways, sometimes even entering obligate mutualistic relationships. In this chapter two aspects of social behaviour in Burkholderia, namely biofilm formation and quorum sensing (QS), are reviewed and existing links between these two social phenomena are discussed.
Chapter 13: Intracellular Survival of Burkholderia cepacia Complex Isolates
Miguel A. Valvano, Kendra E. Maloney, Julie Lamothe, and Soledad Saldías
Abstract
Burkholderia cepacia complex (Bcc) species are important opportunistic pathogens that infect the airways of patients with cystic fibrosis. Bcc members are multi-drug resistant bacteria that have been associated with the "cepacia syndrome", characterized by rapid lung deterioration, acute necrotizing pneumonia and septicemia. This syndrome contributes to higher morbidity and mortality in patients with cystic fibrosis. Extra pulmonary dissemination of the infection sets Bcc species apart from other opportunistic pathogens in cystic fibrosis. To date, very little is known about the virulence factors involved in the persistence of the bacteria within the airway and how the bacteria interact with the CF lung environment. Several groups have reported that Bcc isolates can survive within epithelial cells, amoebae, and macrophages. We hypothesize that Bcc species can resist killing by phagocytic cells and the interactions between bacteria and phagocytic cells plays a major role in pulmonary infection and contributes to the persistent inflammation observed in patients with cystic fibrosis. Intracellular survival of Bcc and other Burkholderia species outside the complex can also occur in the environmental setting, particularly as endosymbiontic associations with fungi and plants. This chapter reviews the current understanding of the molecular and cellular biology of intracellular survival of Bcc species in different niches including epithelial cells, macrophages, amoebae, fungi, and plant tissues.
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