Identification and characterization of pathogenicity and other genomic islands using base composition analyses

Identification of Candidate Vaccine Antigens In Silico

The identification of immunogenic whole-protein antigens is fundamental to the successful discovery of candidate subunit vaccines and their rapid, effective, and efficient transformation into clinically useful, commercially successful vaccine formulations. In the wider context of the experimental discovery of vaccine antigens, with particular reference to reverse vaccinology, this chapter adumbrates the principal computational approaches currently deployed in the hunt for novel antigens: genome-level prediction of antigens, antigen identification through the use of protein sequence alignment-based approaches, antigen detection through the use of subcellular location prediction, and the use of alignment-independent approaches to antigen discovery. Reference is also made to the recent emergence of various expert systems for protein antigen identification.

Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens

Facultative pathogens have extremely dynamic pan-genomes, to a large extent derived from bacteriophages and other mobile elements. We developed a simple approach to identify phage-derived genomic islands and apply it to show that pathogens from diverse bacterial genera are significantly enriched in clustered phage-derived genes compared with related benign strains. These findings show that genome expansion by integration of prophages containing virulence factors is a major route of evolution of facultative bacterial pathogens.

Integrative analysis of transcriptome and genome indicates two potential genomic islands are associated with pathogenesis of Mycobacterium tuberculosis

Mycobacterium tuberculosis (M.tb) is a successful human pathogen and widely prevalent throughout the world. Genomic islands (GIs) are thought to be related to pathogenicity. In this study, we predicted two potential genomic islands in M.tb genome, respectively named as GI-1 and GI-2. It is indicated that the genes belong to PE_PGRS family in GI-1 and genes involved in sulfolipid-1 (SL-1) synthesis in GI-2 are strongly associated with M.tb pathogenesis. Sequence analysis revealed that the five PGRS genes are more polymorphic than other PGRS members in full virulence M.tb complex strains at significance level 0.01 but not in attenuated strains. Expression analysis of microarrays collected from literatures displayed that GI-1 genes, especially Rv3508 might be correlated with the response to the inhibition of aerobic respiration. Microarray analysis also showed that SL-1 cluster genes are drastically down-expressed in attenuated strains relative to full virulence strains. We speculated that the effect of SL-1 on M.tb pathogenicity could be associated with long-term survival and persistence establishment during infection. Additionally, the gene Rv3508 in GI-1 was under positive selection. Rv3508 may involve the response of M.tb to the inhibition of aerobic respiration by low oxygen or drug PA-824, and it may be a common feature of genes in GI-1. These findings may provide some novel insights into M.tb physiology and pathogenesis.

Computer aided selection of candidate vaccine antigens

Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. It has found disappointingly limited use in the design and discovery of new vaccines, which is an area where proper computational support is generally lacking. Most extant vaccines are not based around isolated epitopes but rather correspond to chemically-treated or attenuated whole pathogens or correspond to individual proteins extract from whole pathogens or correspond to complex carbohydrate. In this chapter we attempt to review what progress there has been in an as-yet-underexplored area of immunoinformatics: the computational discovery of whole protein antigens. The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. We begin our review by placing antigen prediction firmly into context, exploring the role of reverse vaccinology in the design and discovery of vaccines. We also highlight several competing yet ultimately complementary methodological approaches: sub-cellular location prediction, identifying antigens using sequence similarity, and the use of sophisticated statistical approaches for predicting the probability of antigen characteristics. We end by exploring how a systems immunomics approach to the prediction of immunogenicity would prove helpful in the prediction of antigens.

Accurate localization of the integration sites of two genomic islands at single-nucleotide resolution in the genome of Bacillus cereus ATCC 10987

We have identified two genomic islands, that is, BCEGI-1 and BCEGI-2, in the genome of Bacillus cereus ATCC 10987, based on comparative analysis with Bacillus cereus ATCC 14579. Furthermore, by using the cumulative GC profile and performing homology searches between the two genomes, the integration sites of the two genomic islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and D. It is generally believed that unlike the TnsABC+E pathway, the TnsABC+D pathway would only promote vertical transmission to daughter cells. The evidence presented in this paper, however, suggests a role of the TnsABC+D pathway in the horizontal transfer of some genomic islands.

Theoretical methods for identifying important functional genes in bacterial genomes

Some functional genes, such as essential genes, highly expressed genes and horizontally transferred genes, play important roles in the survival and pathogenicity of bacteria. This review attempts to summarize current computational methods in identifying the above functional genes from bacterial genomes, which is of significant importance in exploring the bacterial genomes.

A LuxRI-family regulatory system controls excision and transfer of the Mesorhizobium loti strain R7A symbiosis island by activating expression of two conserved hypothetical genes

The symbiosis island ICEMlSym(R7A) of Mesorhizobium loti R7A is an integrative and conjugative element (ICE) that carries genes required for a nitrogen-fixing symbiosis with Lotus species. ICEMlSym(R7A) encodes homologues (TraR, TraI1 and TraI2) of proteins that regulate plasmid transfer by quorum sensing in rhizobia and agrobacteria. Introduction of traR cloned on a plasmid induced excision of ICEMlSym(R7A) in all cells, a 1000-fold increase in the production of 3-oxo-C6-homoserine lactone (3-oxo-C6-HSL) and a 40-fold increase in conjugative transfer. These effects were dependent on traI1 but not traI2. Induction of expression from the traI1 and traI2 promoters required the presence of plasmid-borne traR and either traI1 or 100 pM 3-oxo-C6-HSL, suggesting that traR expression or TraR activity is repressed in wild-type cells by a mechanism that can be overcome by additional copies of traR. The traI2 gene formed an operon with hypothetical genes msi172 and msi171 that were essential for ICEMlSym(R7A) excision and transfer. Our data suggest that derepressed TraR in conjunction with TraI1-synthesized 3-oxo-C6-HSL regulates excision and transfer of ICEMlSym(R7A) through expression of msi172 and msi171. Homologues of msi172 and msi171 were present on putative ICEs in several alpha-proteobacteria, indicating a conserved role in ICE excision and transfer.

M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island

BACKGROUND

The increasing number of completely sequenced bacterial genomes allows comparing their architecture and genetic makeup. Such new information highlights the crucial role of lateral genetic exchanges in bacterial evolution and speciation.

RESULTS

Here we analyzed the twelve sequenced genomes of Streptococcus pyogenes by a naïve approach that examines the preferential nucleotide usage along the chromosome, namely the usage of G versus C (GC-skew) and T versus A (TA-skew). The cumulative GC-skew plot presented an inverted V-shape composed of two symmetrical linear segments, where the minimum and maximum corresponded to the origin and terminus of DNA replication. In contrast, the cumulative TA-skew presented a V-shape, which segments were interrupted by several steep slopes regions (SSRs), indicative of a different nucleotide composition bias. Each S. pyogenes genome contained up to nine individual SSRs, encompassing all described strain-specific prophages. In addition, each genome contained a similar unique non-phage SSR, the core of which consisted of 31 highly homologous genes. This core includes the M-protein, other mga-related factors and other virulence genes, totaling ten intrinsic virulence genes. In addition to a high content in virulence-related genes and to a peculiar nucleotide bias, this SSR, which is 47 kb-long in a M1GAS strain, harbors direct repeats and a tRNA gene, suggesting a mobile element. Moreover, its complete absence in a M-protein negative group A Streptococcus natural isolate demonstrates that it could be spontaneously lost, but in vitro deletion experiments indicates that its excision occurred at very low rate. The stability of this SSR, combined to its presence in all sequenced S. pyogenes sequenced genome, suggests that it results from an ancient acquisition.

CONCLUSION

Thus, this non-phagic SSR is compatible with a pathogenicity island, acquired before S. pyogenes speciation. Its potential excision might bear relevance for vaccine development, because vaccines targeting M-protein might select for M-protein-negative variants that still carry other virulence determinants.

Antibiotherapy and pathogenesis of uncomplicated UTI: difficult relationships

In a time when conventional antibiotics are becoming increasingly less effective for treatment of infections, the relationship between bacteria and antimicrobial resistance is becoming more and more complicated. This paper provides a current review of studies reported in the literature pertaining to the antibiotherapy of human urinary tract infections (UTI), in a way that helps the reader direct a bibliographic search and develop an integrated perspective of the subject. Highlights are given to (bio)pathogenesis of uncomplicated cystitis. Features associated with the antibiotherapy of UTI such as development of resistance are presented in the text systematically. This review discusses recent advances in the understanding of how the predominant uropathogen Escherichia coli interacts with its host and leads to infection; so one can understand some of the reasons behind antibiotherapy failures.

Genome content determination in methicillin-resistant Staphylococcus aureus

Staphylococcus aureus is a major pathogen responsible for both nosocomial and community-acquired infections. While the first S. aureus isolates displaying resistance to methicillin were reported in the early 1960s, endemic strains of methicillin-resistant S. aureus (MRSA) carrying multiple resistance determinants only became a worldwide nosocomial problem in the early 1980s, carrying a threefold attributable cost and a threefold excess length of hospital stay when compared with methicillin-susceptible S. aureus bacteremia. Recent efforts in the field of high-throughput sequencing resulted in the release of several MRSA genome sequences enabling the development of massively parallel tools to study clinical isolates of MRSA at the organism scale. Microarrays covering whole genomes and high-throughput sequencing devices are the two main techniques currently utilizable for whole-genome characterization. These tools not only provide information for the development of genotyping assays but also allow evaluation of potential virulence of the strains, by enumerating genetic-encoded resistance markers and toxin content. This appears particularly attractive for understanding the epidemiology of MRSA and the relationship between genome content on one side and virulence potential or epidemicity on the other side. In addition, sequence information is mandatory for the development of molecular tests allowing the rapid identification, genotyping and characterization of clinical isolates.