Salmonella: From Genome to Function
"a valuable resource" (Doodys)
"recommended reading" (Food Sci. Technol. Abstr.)
"indispensable" (Microbiol. Today)
"a wide and exciting range of topics" (Biospektrum)
"great overviews and insights" (ASM Microbe)
Caister Academic Press
Vaccine Research Institute of San Diego, 10835 Road To The Cure, Suite 150, San Diego, CA 92121, USA
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Salmonellae are important pathogens, responsible for an estimated one million deaths and 100 million human infections annually. Their genomes are mosaic puzzles - results of lateral transfer events that occur within a stable genetic background. Extraordinary diversity of host ranges and pathogenicity traits between different strains are the consequence of both specific genome insertions/deletions and minute changes in genome composition. Genomic information decoded from a multitude of different Salmonella strains and new dramatic insights into pathogenic processes emphasize the fact that Salmonella research is currently at a very exciting juncture. In addition to their fascinating resilience in both the environment and eukaryotic hosts, Salmonella prefers tumours over any other location within the human host (by a factor of 1000 or more). This ability could propel Salmonella into future use as a therapeutic delivery agent to control and/or cure cancers.
In this book, internationally acclaimed experts review cutting-edge topics in Salmonella genomics and molecular biology, providing a timely snapshot of the current state of research. Topics include latest approaches to sub-species level classification and phage typing of Salmonella, comparative genomics, the search for genetic determinants for survival of the bacterium in different environments and the evolution of niche specialization by Salmonella. The book also explores the latest genomic information and molecular characterizations of sRNAs and complements of fimbriae, flagella and secreted virulence factors. Moreover, S. Typhi pathogenesis, interactions of the host with intracellular Salmonella and the host's anti-Salmonella immune response are reviewed. The current knowledge on Salmonella biofilm formation and a progress report on using Salmonella as an anti-tumour tool conclude this compendium. Essential reading for all researchers working with Salmonella and related organisms, and recommended reading for other scientists working on bacterial genomics, molecular biology and bacterial molecular and cellular pathogenesis.
"This book contains valuable information on recent research discoveries related to Salmonella. It is a valuable resource for any investigator working in bacterial genetics and pathogenicity." from Doodys
"recommended reading for all scientists working on bacterial genomics, molecular biology and bacterial molecular and cellular pathogenesis." from Food Sci. Technol. Abstr. (2011) 43(5)
"This is a fast-moving field and it is a credit to the editor, contributors and publishers that updates were made as late as July 2010. It is expensive, but indispensable to the serious student of this organism" from Microbiology Today
"The consistently well-written articles cover a wide and exciting range of topics" from Biospektrum (2011) 17: 596.
Table of contents
1 . New approaches in sub-species level Salmonella classification
Burkhard Malorny, Elisabeth Hauser and Ralf Dieckmann
Salmonellae form a complex group of bacteria consisting of two species, 6 subspecies and more than 2,500 serovars (serotypes). Salmonella identification below species level is most often limited to phenotypic typing methods such as biochemical and serological identification, which are costly, time-consuming and do not always reflect the evolution of Salmonella groups. Newer methods for Salmonella typing and subtyping include genome-based methods such as pulsed field gel electrophoresis (PFGE), Multiple Loci VNTR Analysis (MLVA), Multilocus sequence typing (MLST) and (multiplex-) PCR-based methods. In the last years further molecular typing technologies were evaluated for this purpose. This chapter discusses some of these emerging technologies and gives an outlook on future developments with a focus on oligonucleotide microarrays, spectroscopic methods such as MALDI-TOF mass spectrometry and special developments such as bead-based suspension arrays using Luminex technology and DNA sequence-based approaches. We review these new techniques, which promise significant advantages compared to traditional culture-based methods with respect to speed, ease of use, reliability and automation and discuss their advantages and disadvantages.
2 . Typing phages and prophages of Salmonella
Wolfgang Rabsch, Sandra Truepschuch, Daniel Windhorst and Roman G. Gerlach
Most Salmonella strains contain prophages or remnant phages and release them spontaneously. Special bacteriophages were developed and used in phage typing systems for epidemiological work all over the world since 1947 to control salmonellosis. This method provides fast and inexpensive characterization of frequent serovars such as S. Typhimurium or S. Typhi on the sub-serovar level and is especially useful for primary analysis before investigation by other, more expensive molecular techniques such as sequencing. Prophages are themselves not only variable elements in a chromosome but also variable by module exchange within the prophage genome, thus providing a high discriminating power. The availability of several genome sequences of different Salmonella serovars has recently led to the identification of new prophage-like elements. The prophages present in serovars Typhimurium, Enteritidis and Typhi are discussed. Salmonella phages frequently carry foreign DNA, so called morons. These morons are not necessary for phage functions but provide a benefit for the host. A list of some new morons found in different Salmonella serovars is presented. Recently, a monophasic variant of S. Typhimurium mainly belonging to Anderson phage type DT193 has become one of the dominant causes of salmonellosis in Germany and other European countries. These strains with the antigenic formula 4,,12:i:- do not express the 2nd phase flagellum. Investigation of their prophage attachment sites showed that the sites for Gifsy-1, Gifsy-2 and ST64B were occupied by the respective prophages. In about 90% of the monophasic DT193 strains the P22/ST64T attachment site was occupied by a novel 18.4 kb fragment, containing several open reading frames with significant similiarity to phage-related genes.
3 . Comparison of Salmonella genomes
Ye Feng, Wei-Qiao Liu, Kenneth E. Sanderson, and Shu-Lin Liu
Salmonella contains over 2600 known lineages, each with distinct biological characteristics, including differences in the niche in which they dwell and the nature of diseases they may cause in their hosts. Genomic sequence analysis is beginning to reveal the genetic basis that determines the phenotypic differences among them. Comparison of eight sequenced genomes of Salmonella subgroup I lineages, which infect warm-blooded animals including humans, demonstrates that these pathogens share about 90% of their genes (the "core" genome), with the remaining ca. 10% genes being unique to each of the lineages (the "accessory" genome). Prophages and Salmonella Pathogenicity Islands (SPIs) are the main components of the accessory genome. Insertion of large DNA segments, such as SPI7 in S. Typhi, may disrupt physical balance of the genome between replication origin and terminus and rearrangements of the genome, such as inversions or translocations mediated by homologous sites (rrn operons, prophages, IS200, etc.) may accelerate rebalancing of the genome. Laterally transferred genes are the main driving force in Salmonella evolution and speciation; evidence exists indicating that mismatch repair genes may spontaneously regulate bacterial mutability through allele conversion to facilitate or inhibit incorporation of foreign DNA. Further studies may help elucidate the genetic basis of distinct pathogeneses and host ranges among the Salmonella pathogens.
4 . High-throughput screening to determine the genetic requirements for Salmonella survival under different growth conditions
Mollie Megan Reynolds, Rocio Canals, Michael McClelland and Helene Andrews-Polymenis
Salmonella species are capable of survival in a wide range of niches, both in the environment and in an infected host. Genetic requirements for survival of Salmonella in different niches have traditionally been identified using gene expression and forward genetics. The availability of complete genome sequences, microarray technology, and cost-effective new sequencing capabilities enabled increasingly efficient high-throughput analyses of Salmonella genomes to identify elements that contribute to survival in these niches. In this chapter we describe many of the high-throughput tools that have been developed over the past two decades, and the genetic requirements for Salmonella survival that have been identified using these techniques.
5 . Evolutionary trends associated with niche specialization as modeled by whole genome analysis of egg-contaminating Salmonella enterica serovar Enteritidis
Jean Guard, Devendra Shah, Cesar A. Morales and Doug Call
The mosaic nature of the Salmonella enterica genome facilitates its access to multiple environments. Many large scale genomic events have been described that contribute to the combinatorial complexity of the pathogenic Salmonellae. However, the impact of small scale genetic change occurring at the level of single nucleotide polymorphism (SNP) on the emergence of niche specialization is just now becoming appreciated. This chapter describes concepts behind the evolution that culminated in the remarkable ability of Salmonella enterica serovar Enteritidis to contaminate and survive in the internal content of eggs produced by otherwise healthy hens. Evidence suggests that combinations of SNPs facilitate niche specialization by Salmonella enterica . However, few typing methods incorporate unbiased strategies for their detection. Selection of appropriate biological assays for ranking SNPs and combinations of SNPs for their impact on the ability of Salmonella enterica to propagate outbreaks, pandemics and disease will be a significant challenge to improve the safety of the food supply.
6 . Genomics and Pathogenesis of Salmonella enterica serovars Typhi and Paratyphi A
Kathryn E Holt, Tim T Perkins, Gordon Dougan and Robert A Kingsley
The genomics era has transformed the way that we can study bacterial pathogens. The availability of two complete and 17 draft genomes of S. Typhi has made it possible to study the phylogenetic structure of this pathogen in unparalleled resolution, monitor gene flux, accumulation of pseudogenes, neutral mutations and loci under selective pressure. We describe the molecular basis of Salmonella Typhi pathogenesis, in particular where genomics has contributed to our understanding in the past decade. Potentially important S. Typhi-specific virulence determinants include the Vi polysaccharide capsule, the type IV pilus, and a unique repertoire of fimbria. These may account for key differences in the disease outcome of this pathogen compared with non-typhoidal serotypes. Genome comparison with the closely related serotype S. Paratyphi A identifies a core set of pseudogenes, some of which emerged independently, that may define important features of genome degradation associated with host restriction and pathogenesis of invasive disease. Geo-phylogenetics of S. Typhi constructed from single nucleotide polymorphism data from high throughput draft genome sequences is now being applied to study molecular epidemiology in the field.
7 . The small RNAs of Salmonella
Sridhar Javayel, Kai Papenfort and Jörg Vogel
To date, close to one hundred distinct small noncoding RNAs (sRNAs) have been identified in Salmonella by a variety of biocomputational or wet-lab approaches including RNA sequencing. The function of more than twenty of these sRNAs is known from studies in Salmonella itself or can be inferred from conserved homologs in E. coli Many of these sRNAs act in conjunction with the RNA-chaperone Hfq to post-transcriptionally repress or activate trans-encoded target genes, but cis-antisense RNAs and regulators of protein activity are also abundantly present. In addition to a large number of sRNAs conserved in other enteric bacteria, Salmonella also expresses a set of sRNAs specific to this genus. Interestingly, such regulators have been shown to control the expression of conserved genes encoded on the "core" Salmonella genome. Conversely, conserved sRNA can act as regulators of recently acquired Salmonella-specific genes, indicating significant cross-talk of conserved and horizontally acquired elements at the RNA level. The present chapter covers strategies for the identification of sRNAs as well as their characterized functional roles in Salmonella.
8 . Fimbrial signature arrangements in Salmonella
Sean-Paul Nuccio, Nicholas R. Thomson, Maria C. Fookes and Andreas J. Bäumler
The complement of fimbrial operons held within a genome represents one of the key differentiating features of the sequenced Salmonella serovars and one of the single largest sources of genetic diversity. Generically described as filamentous non-flagellar surface appendages, fimbriae (also known as pili) typically imbue an adhesive trait to the cells expressing them. While much is known about the general biology of fimbrial assembly mechanisms, the role of these structures in Salmonella pathogenesis remains poorly characterized. Here we present fimbrial operon data gathered from the seventeen completed Salmonella genome sequences and discuss its implications in Salmonella pathogenesis and dissemination.
9 . New insights into the role and formation of flagella in Salmonella
Rasika M. Harshey
The flagellum of Salmonella enterica serovar Typhimurium is the best studied of all flagellar systems. The major function of the flagellum is to enable swimming and chemotaxis in liquid media, and swarming on surfaces. New structural information, along with biochemical, physicochemical and genetic analyses has greatly accelerated our understanding of the self-assembly of this highly sophisticated nano-machine. The study of swarming motility is a relatively new field, but has begun to reveal new roles for the flagellum, new functions for motility genes and new regulatory circuits that control the decision between motility and sessility. Morphological and functional similarities between flagella and needle complexes, discovery of partial flagellar structures that likely function in export rather than motility, and a rapidly accumulating genome database are gradually illuminating the evolutionary origins of the flagellum.
10 . Salmonella secreted virulence factors
Fred Heffron, George Niemann, Hyunjin Yoon, Afshan Kidwai, Roslyn Brown, Jason McDermott, Richard Smith and Joshua Adkins
Research in the past twenty years has shown that Salmonella precisely manipulates their host by hierarchical secretion of virulence factors (effectors). More than 40 secreted virulence factors have been identified in Salmonella, but the function and mammalian targets of only a few are known. Effectors are directed to specific sub-cellular compartments and mammalian targets, and they mediate a diverse array of activities. Thus, the first half of this review focuses upon our understanding of effector mechanisms and their roles during infection. However, the known effector repertoire is incomplete and the second half of this review places an emphasis on discovery. Computer analysis identified common secretion motifs and predicted that as many as 300 additional proteins may be secreted by Salmonella. In fact, mass spectrometry analysis identified a more complete secretome and found many novel, uncharacterized effector proteins. Several effectors identified in this study were small proteins of only 30-100 amino acids in length, suggesting that they are not enzymes but agonists or antagonists of specific host factors. One surprise from the mass spectrometry analysis was the identification of proteins that are secreted to mammalian cells via outer membrane vesicles. Complete characterization of the bewildering array of secreted proteins will take many years.
11 . The intracellular lifestyle of Salmonella enterica and novel approaches to understand the adaptation to life within the Salmonella-containing vacuole
Roopa Rajashekar and Michael Hensel
Salmonella enterica is a facultative intracellular pathogen that resides in a unique membrane-bound compartment, referred to as Salmonella-containing vacuole or SCV. Within the SCV, Salmonella is able to survive the antimicrobial activities of phagocytic cells and can rapidly multiply in a variety of host cells. Intracellular life of Salmonella is dependent on a large number of virulence traits, but the function of the type III secretion system (T3SS) encoded by Salmonella Pathogenicity Island 2 (SPI2) is of central importance. Although more than 20 effector proteins have been identified as translocated by the SPI2-T3SS, the molecular function and contribution to intracellular live is only known for a few of these proteins. Intracellular Salmonella modify basic functions of the host cell such as the structure of the microtubule cytoskeleton and induce a massive reorganization of vesicular transport and the endosomal system. Unique phenomena are the SPI2-dependent induction of extensive tubular membrane aggregations of endosomal or Golgi-derived vesicles. The SCV itself has features of a novel organelle and the fate of this compartment is controlled by the pathogen. Previous observations indicated that the SCV is arrested in the state of late endosomal compartment, but recent studies using advanced ultrastructural analyses and live cell studies indicate a complex and highly dynamic interaction of the intracellular Salmonella and their host cells.
12 . Anti-Salmonella immunity: Highlighting new research in vaccines, mucosal immunology and systemic disease
Jennifer L. Bishop, Ellen T. Arena, Kenneth W. Harder and B. Brett Finlay
Enteric fever and non-typhoidal salmonelloses (NTS) are caused by a wide variety of Salmonella enterica serovars and are a serious health threat throughout the world. Immunity to systemic typhoid and NTS requires intricate crosstalk between both innate and adaptive immune cells spanning multiple organ systems. The development of a number of new mouse and in vitro culture models suitable for studying gastroenteritis has highlighted the complexity of mucosal responses and shown how a diverse subset of cells interact within the intestinal architecture to elicit anti-Salmonella immunity. These include specific dendritic cell subsets, natural killer cells and TH17 skewed T helper cells and the repertoire of cytokines they produce, including IL-17, IL-23, IL-22 and IL-15. Furthermore, the importance of commensal microflora has been stressed in various Salmonella models, and new research has shown the various effects of prebiotics, probiotics and antibiotics on Salmonella pathogenesis. Systemic immune responses are also more explicitly understood, as the location and phenotype of cells harboring intracellular bacteria become more defined. This chapter will review these recent advances and how they are being translated into new therapies and vaccine studies in the human population.
13 . Salmonella Biofilms: From food to human disease
Robert W. Crawford, Geoffrey Gonzalez-Escobedo and John S. Gunn
Bacterial biofilms are increasingly implicated as burdens to food and public safety. Over the past few decades, we have learned that this sessile environment provides diverse species of bacteria selective advantages in natural, medical, and industrial ecosystems, as well as resistance to commonly administered antibiotics and protection from host immune responses during chronic infection of humans and animals. Salmonella spp. are food-borne pathogens that remain a critical health concern in impoverished and industrialized nations. In the laboratory, salmonellae have been shown to form biofilms on a variety of surfaces. These Salmonella spp. biofilms have been found to contaminate plant and animal food sources to cause human disease upon consumption, and/or to enhance salmonellae colonization of and persistence at sites of infection.
14 . Salmonella as the paradigm for bacterial therapy of cancer: A progress report
Robert M. Hoffman
For over 300 years it has been observed that cancer patients who became infected with bacteria sometimes experienced spontaneous remission of their cancer. Recently, there have been attempts to develop cancer treatments by using tumor-targeting bacteria. Anaerobic microorganisms, such as Clostridium,
that preferentially grow in necrotic tumor areas have mostly been used. However, the resulting tumor killing was, at best, limited. Salmonella
was originally developed as an antitumor agent by attenuating the bacteria with multiple mutations, including auxotrophs. These multiple auxotrophs appeared to direct the bacteria to the metastatic areas of tumors where more nutrients are available. We have developed a more effective bacterial cancer therapy strategy by targeting viable tumor tissue with Salmonella enterica
serovar Typhimurium containing only two auxotrophic mutations. These auxotrophs grow in viable as well as necrotic areas of tumors. However, the auxotrophy severely restricts growth of these bacteria in normal tissue, making this a safe treatment. The S
. Typhimurium A1-R mutant, which is auxotrophic for leucine and arginine and had been selected for high antitumor virulence, was effective as monotherapy against human prostate and breast tumors that had been orthotopically implanted in nude mice. The approach described here, where bacterial monotherapy effectively treats primary and metastatic tumors, is a significant improvement over previous bacterial tumor-therapy strategies that require combination with toxic chemotherapy. Exploitation of the tumor-killing capability of Salmonella
has great potential for a new paradigm of cancer therapy.
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(EAN: 9781904455738 9781912530748 Subjects: [bacteriology] [microbiology] [medical microbiology] [molecular microbiology] [genomics] )