Burkholderia: From Genomes to Function
"this Burkholderia book is something special" (Biospektrum)
"a useful source of information" (Fungal Diversity)
Caister Academic Press
Tom Coenye and Eshwar Mahenthiralingam
Laboratorium voor Farmaceutische Microbiologie, Universiteit Gent, Belgium and Cardiff School of Biosciences, Cardiff, UK; respectively
viii + 254
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Burkholderia are a multi-faceted group of bacteria with considerable genetic and metabolic diversity and very versatile lifestyles. Some species are regarded as beneficial as they possess traits such as an ability to promote plant growth or kill pest organisms or fix nitrogen or degrade man-made pollutants. Others, however, are important pathogens and include species such as B. mallei and B. pseudomallei, considered to be potential biological weapons. The application of high-throughput sequencing and 'omics' technologies in recent years has allowed research on Burkholderia species to advance at an unprecedented pace permitting fascinating new insights into the molecular and cellular biology of this highly variable group of bacteria.
In this book leading international investigators review key advances in Burkholderia research to provide timely overview. The topics covered include: genomic taxonomy and biodiversity, comparative genomics, molecular epidemiology, transcriptomics, proteomics, molecular pathogenesis of virulence in B. mallei/B. pseudomallei and the Burkholderia cepacia complex, molecular basis of phytopathogenicity and antibiotic resistance, signalling and biofilms, and the genomic biology of Burkholderia phages. The theme underpinning each chapter is the use of DNA/protein sequence data and post-genomic technologies to understand Burkholderia biology. Essential reading for everyone working with these and related bacteria.
"this Burkholderia book is something special. It impresses with its timeliness and quality. Leading Burkholderia experts have put together new knowledge, not only their own work, but also presenting current knowledge ... the genus Burkholderia is presented very comprehensively and in many new facets ... recommended as high-quality reading for all microbiologists, medical, hygienic and quality managers as well as advanced students " from Biospektrum (2014) 20:474.
"This fascinating book consists of eleven chapters covering the key advances in research ... should be available in all schools, university libraries and research laboratories dealing with microbiology. It is also a useful source of information for epidemiologists, ecologists, pharmaceutical microbiologists and anyone studying bacteria." from Fungal Diversity (December 2014)
Table of contents
Introduction. Burkholderia: From Genomes to Function, and on to the Future
Eshwar Mahenthiralingam and Tom Coenye
Burkholderia is an enigmatic Gram negative bacterial genus that has attracted researchers from multiple disciplines. Burkholderia species possess considerable genetic and metabolic versatility allowing them to exist in a wide range of environmental settings as free-living or host-associated microorganisms. From a research standpoint, their interactions can be divided into either those that are beneficial or those that are problematic, often with the same Burkholderia species capable of both functions. The beneficial traits of Burkholderia are largely environmental and include their ability to promote plant growth, kill pest organisms, fix nitrogen, and degrade man-made pollutants. Pathogenicity towards multiple host organisms is the fundamental negative attribute for which Burkholderia have been widely researched, however, new problematic areas such as industrial contamination are emerging. We have summarised key advances in the biology of Burkholderia bacteria, many of which have been characterised as a result of greatly improved genomic and molecular resources for these bacteria.
1. Genomic Taxonomy and Biodiversity of the Burkholderia cepacia Complex
Peter Vandamme, Bart Verheyde, Charlotte Peeters and Peter Dawyndt
The Burkholderia cepacia complex is a group of closely related bacteria with conflicting biological properties and for which an unusually large amount of taxonomic data is available. These bacteria therefore represent a unique opportunity to evaluate traditional polyphasic taxonomic practices by means of novel whole-genome sequence based parameters. The present state-of-the-art demonstrates that taxonomists can replace DNA-DNA hybridization experiments as the pivotal instrument for species level demarcation and 16S rRNA sequence analysis for studying phylogeny by superior whole-genome sequence based alternatives in the frame of polyphasic taxonomic studies.
2. Comparative Genomics in the Genus Burkholderia
Pimlapas Leekitcharoenphon, Gregory S. Buzard and David W. Ussery
The Burkholderia genus contains over 60 species that have colonized a wide diversity of biological niches, including those as animal, human and plant pathogens. We have collected the publicly available whole genome sequences of Burkholderia spp. to explore the genomic diversity within this genus, and we report here on the comparison of 110 Burkholderia genomes. We have constructed three types of phylogenetic trees, based on different sets of genetic information (16S rRNA genes, multiple locus sequence tags [MLST] and pan-genome sequences), as alternate ways to display taxonomic groupings and evolutionary relationships. We have found, among the more than 35,000 gene families that are represented in the Burkholderia pan-genome, a set of 717 core gene families that are conserved across all the Burkholderia genomes we studied. We have also identified the species-unique core genes for each species. Our findings can be used to find new signature sequences for the rapid and accurate detection of the different Burkholderia species. We have also constructed a BLAST atlas that compares the B. pseudomallei and B. mallei genomes which helps visualize gene homologies and shows the fraction of genes found in common in pair-wise comparison and reveals the duplication of genes within their genomes. The B. mallei genome is known to be significantly smaller in size than that of B. pseudomallei; this is also obvious from our analysis that demonstrates that almost all of the B. mallei proteome is present in B. pseudomallei.
3. Molecular Epidemiology and Population Structure of Clinically Relevant Burkholderia Species
Tom Coenye, Eshwar Mahenthiralingam and John J. LiPuma
The aim of this chapter is to provide a comparative overview of the various 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. 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 is also discussed. In a final section we describe the use of whole genome sequencing and typing as novel approach and illustrate its potential with several examples.
4. Comparative Transcriptomics in Burkholderia
Andrea Sass, Pavel Drevinek and Pam A Sokol
The advance in sequencing technologies and the availablility of whole genome sequences enabled studying the entire transcriptome of organisms, either by microarray analysis or RNA sequencing. Burkholderia species for which such gene expression studies have been performed include B. cenocepacia, B. pseudomallei, B. mallei, B. xenovorans, B. ambifaria, and B. multivorans. This review focusses on findings in the areas of resistance to antibiotics, to biocides and to oxidative stress, iron transport, quorum sensing, mucoidy and host adaptation in these Burkholderia sp., obtained by means of global differential transcriptome analysis.
5. Burkholderia Proteomics: Methodologies, Challenges, and Applications
Isabel Sá-Correia, Sandra C. dos Santos and Andreia Madeira
Complete genome sequencing for a large number of microorganisms has paved the way for large-scale proteomic studies to investigate global protein expression levels, regulation and, and to assist in functional analysis. Although microarray technologies can provide invaluable information on genomic expression, it is also known that mRNA levels often do not correlate directly with protein levels. Proteomics is thus necessary to provide complementary quantitative and functional data to genomic information. In this review we will provide a comparative overview of the various proteomic approaches currently available and give a brief tutorial on the methodology and application of two-dimensional electrophoresis-based expression proteomics. Subsequently, the exploitation of proteomic analyses in studies dedicated to different Burkholderia species with a broad range of objectives will be discussed, based on the relevant scientific literature. These include biomedical research and applications (e.g. elucidation of pathogenic mechanisms and interaction with the host, improvement of diagnostic tools, identification of immunoreactive proteins and candidate vaccine targets) and environmental studies, namely on biodegradation of organic pollutants by Burkholderia strains.
6. Molecular Mechanisms of Virulence in Burkholderia pseudomallei and Burkholderia mallei
Catherine Ong and Patrick Tan
Burkholderia pseudomallei and Burkholderia mallei, causative agents of the diseases melioidosis and glanders, respectively, are two of the deadliest members of the Burkholderia genus. Contained within their large genomes is a sizable number of genes that encode numerous redundant mechanisms involved in virulence. The availability of complete genome sequences of these two species has resulted in targeted characterization of mutiple novel virulence factors. Some of these virulence factors are arguably niche factors, more likely to aid the bacteria to adapt and survive in its environment. The distinct difference in niches of B. pseudomallei and B. mallei allows us to relook at some of these established virulence factors and mechanisms in context of their roles in environmental adaptation and survival. In addition, comparisons with the avirulent environmental saprophyte Burkholderia thailandensis helps to better understand the evolution of mammalian pathogenesis in these two pathogens. This chapter serves to summarize previously established virulence determinants, as well as highlight new and novel factors that have since been discovered post-genome sequencing.
7. Molecular Mechanisms of Burkholderia cepacia Complex Intracellular Survival in Phagocytic Cells
Miguel A. Valvano, Roberto Rosales-Reyes, Crystal L. Schmerk and Hanna Ostapska
Burkholderia cepacia complex (Bcc) species are a group of Gram-negative opportunistic pathogens that chronically infect the airways of cystic fibrosis patients, but they can also infect patients with various types of immunosuppressive disorders. Bcc members are multidrug resistant bacteria that have the ability to persist in the infected host and also elicit robust inflammatory responses. Studies using macrophages, neutrophils and dendritic cells, combined with dramatic advances in the ability to genetically manipulate these microorganisms have contributed to increase our understanding of the molecular mechanisms of virulence in these pathogens and the molecular details of the cell host responses triggering inflammation. This chapter reviews our understanding of the pathogenic mechanisms used by Bcc to establish an intracellular niche in phagocytic cells and modulate host cell responses that ultimately end up in cell death and a proinflammatory response.
8. The Phytopathogenic Burkholderia
Bruna Gonçalves Coutinho, Mayukh Das, Zulma Rocío Suárez-Moreno, Carlos F. Gonzalez and Vittorio Venturi
Historically, species of the genus Burkholderia have been known to be pathogenic to plants, and currently they are known as the ethiological agents of several diseases of a wide variety of plants, causing wilt, rot, blight and canker. This group includes: B. andropogonis, B. caryophilii, B. cepacia, B. cenocepacia, B. gladioli, B. glumae, B. plantarii, B. seminalis and B. rhizoxinica. These species have evolved a spectrum of extracellular factors, including phytotoxins, which allow them to cause disease in a variety of hosts. Some of the species presented here may produce these extracellular factors to obtain nutrients by affecting cell membranes, whereas others are typical vascular pathogens invading plant host by wounding the plant surface. In this chapter we describe the preferred plant hosts of each phytopathogenic Burkholderia species, and their virulence factors, as well as the mechanisms involved in disease development.
9. Molecular Basis for Antibiotic Resistance in the Genus Burkholderia
Silvia Bazzini, Silvia Buroni, Claudia Udine, Maria Rosalia Pasca and Giovanna Riccardi
Bacteria belonging to the Burkholderia cepacia complex (Bcc), as well as other Burkholderia spp. such as Burkholderia pseudomallei and Burkholderia mallei are able to cause infections in humans. Their eradication is difficult due to the high level of intrinsic resistance to several antibiotics, but the efficacy of the antibiotic treatment would likely benefit from a better knowledge on the drug resistance mechanisms. Different resistant mechanisms have been identified in these bacteria, including alteration of drug target site, enzymatic drug inactivation or modification, reduced membrane permeability, and/or activation of efflux systems. To circumvent these mechanisms, a wide range of antimicrobial compounds have been tested and new ones are being discovered in order to improve the clinical approach. Among current therapies, tobramycin, ciprofloxacin, or meropenem/ceftazidime in combination with chloramphenicol, trimethoprim-sulfamethoxazole or aztreonam are mostly recommended.
10. Cell-to-cell Communication and Biofilm Formation of Members of the Genus Burkholderia: A Story of Multilingually Talented Bacteria
Nadine Schmid, Gabriella Pessi, Claudio Aguilar and Leo Eberl
Members of the genus Burkholderia appear to be particularly loquacious. Evidence has accumulated over the past few years that these bacteria are capable of utilizing at least three different chemical languages: N-acyl homoserine lactones, cis-2-unsaturated fatty acids and quinolones. Here we summarize the current knowledge of the underlying molecular architectures of these communication systems and show that they are involved in the control of some highly conserved functions, including the production of extracellular proteolytic enzymes, motility, antifungal activity, expression of virulence factors and biofilm formation. Particular attention is paid to the role of these communication systems in the formation of surface-associated consortia and the genes that are required for the sessile lifestyle of this group of bacteria. The new emerging role of the intracellular secondary messenger cyclic diguanylate (c-di-GMP) in biofilm formation and especially as a downstream regulatory element of the fatty acid signaling cascade is discussed. Finally, given that these communication systems are required for both biofilm formation and pathogenicity, they are suggested to represent highly valuable targets for the development of novel antibacterial drugs.
11. Genomics of Burkholderia Phages
Karlene H. Lynch and Jonathan J. Dennis
Sequenced phages that infect and/or lysogenize strains of Burkholderia pseudomallei, Burkholderia mallei, Burkholderia thailandensis, and the Burkholderia cepacia complex (Bcc) belong to the tailed phage order Caudovirales and families Myoviridae, Podoviridae, and Siphoviridae. Within these families, phages can be classified as part of at least ten distinct genera based on CoreGenes analysis of protein relatedness. Members of these genera show similarity to myoviruses P2, Bcep781, PB1, and BcepMu, podoviruses Bcep22 and BPP-1, and siphoviruses PA73, BcepNazgul, ΦE125, and BcepGomr. Prophage islands have also been identified in the sequenced genomes of B. pseudomallei, B. thailandensis, Burkholderia cenocepacia, and Burkholderia xenovorans, but not B. mallei. Similar to phages infecting other organisms, Burkholderia phage genomes are diverse, unique, and modular. In contrast to many other bacterial pathogens, characterized Burkholderia virulence factors do not appear to be phage-encoded. However, several putative lysogenic conversion genes have been identified that require functional characterization during the development of phage therapy protocols for this genus.
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(EAN: 9781908230355 9781908230973 Subjects: [microbiology] [bacteriology] [molecular microbiology] [genomics] )