Identification of novel staphylococcal virulence genes by in vivo expression technology

We have applied in vivo expression technology (IVET) to the study of staphylococcal virulence. Using a promoter trap that relies on genetic recombination as a reporter of gene expression, we identified 45 staphylococcal genes that are induced during infection in a murine renal abscess model. Of these, only six were known previously; 11 others have homology to known non-staphylococcal genes. The known staphylococcal genes include agrA , part of a key locus regulating numerous virulence products, and a glycerol ester hydrolase, which may enhance staphylococcal survival in abscesses. We constructed 11 strains containing mutations in previously unknown ivi genes. Of these strains, seven were significantly attenuated in virulence compared with the wild-type parent. The mutagenized ivi genes may encode novel staphylococcal virulence factors.     

Temperature-regulated expression of bacterial virulence genes

Virulence gene expression in most bacteria is a highly regulated phenomenon, affected by a variety of parameters including osmolarity, pH, ion concentration, iron levels, growth phase, and population density. Virulence genes are also regulated by temperature, which acts as an 'on-off' switch in a manner distinct from the more general heat-shock response. Here, we review temperature-responsive expression of virulence genes in four diverse pathogens.     

In vivo and ex vivo regulation of bacterial virulence gene expression

Bacteria are remarkably adaptable organisms that are able to survive and multiply in diverse and sometimes hostile environments. Adaptability is determined by the complement of genetic information available to an organism and by the mechanisms that control gene expression. In general, gene products conferring a growth or survival advantage in a particular situation are expressed, while unnecessary or deleterious functions are not. Expression of virulence gene products that allow pathogenic bacteria to multiply on and within host cells and tissues are no exception to this rule. Being of little or no use to the bacterium except during specific stages of the infectious cycle, these accessory factors are nearly always subject to tight and coordinate regulation. As a result of recent advances, we are beginning to appreciate the complexities of the interactions between bacteria and their hosts. The ability to probe virulence gene regulation in vivo has broadened our perspectives on pathogenesis.     

In vivo virulence properties of bacterial cytolethal-distending toxin

Multiple pathogenic Gram-negative bacteria produce cytolethal-distending toxins (CDTs). CDT is typically composed of three subunits: the catalytic subunit CdtB has DNase I-like activity, whereas CdtA and CdtC are binding proteins for delivering CdtB into target cells. Translocation of CdtB to the nucleus induces genotoxic effects on host DNA, triggering DNA repair cascades that lead to cell cycle arrest and eventual cell death. Several lines of evidence indicate that this toxin contributes to the pathogenicity of CDT-producing bacteria in vivo . Helicobacter hepaticus and Campylobacter jejuni CDTs are essential for persistent infection of the gastrointestinal tract and increase the severity of mucosal inflammation or liver disease in susceptible mouse strains. Haemophilus ducreyi CDT may contribute to the pathogenesis of chancroid in rabbits. Recently, H. hepaticus CDT has been shown to play a crucial role in promoting the progression of infectious hepatitis to pre-malignant, dysplastic lesions via activation of a pro-inflammatory NF-κB pathway and increased proliferation of hepatocytes, providing the first evidence that CDT has carcinogenic potential in vivo . Thus, both in vitro and in vivo data indicate that CDT is a bacterial virulence factor.     

Identification and functional analysis of Penicillium digitatum genes putatively involved in virulence towards citrus fruit

The fungus Penicillium digitatum, the causal agent of green mould rot, is the most destructive post‐harvest pathogen of citrus fruit in Mediterranean regions. In order to identify P. digitatum genes up‐regulated during the infection of oranges that may constitute putative virulence factors, we followed a polymerase chain reaction (PCR)‐based suppression subtractive hybridization and cDNA macroarray hybridization approach. The origin of expressed sequence tags (ESTs) was determined by comparison against the available genome sequences of both organisms. Genes coding for fungal proteases and plant cell wall‐degrading enzymes represent the largest categories in the subtracted cDNA library. Northern blot analysis of a selection of P. digitatum genes, including those coding for proteases, cell wall‐related enzymes, redox homoeostasis and detoxification processes, confirmed their up‐regulation at varying time points during the infection process. Agrobacterium tumefaciens‐mediated transformation was used to generate knockout mutants for two genes encoding a pectin lyase (Pnl1) and a naphthalene dioxygenase (Ndo1). Two independent P. digitatum Δndo1 mutants were as virulent as the wild‐type. However, the two Δpnl1 mutants analysed were less virulent than the parental strain or an ectopic transformant. Together, these results provide a significant advance in our understanding of the putative determinants of the virulence mechanisms of P. digitatum.     

Computational bacterial genome-wide analysis of phylogenetic profiles reveals potential virulence genes of Streptococcus agalactiae

The phylogenetic profile of a gene is a reflection of its evolutionary history and can be defined as the differential presence or absence of a gene in a set of reference genomes. It has been employed to facilitate the prediction of gene functions. However, the hypothesis that the application of this concept can also facilitate the discovery of bacterial virulence factors has not been fully examined. In this paper, we test this hypothesis and report a computational pipeline designed to identify previously unknown bacterial virulence genes using group B streptococcus (GBS) as an example. Phylogenetic profiles of all GBS genes across 467 bacterial reference genomes were determined by candidate-against-all BLAST searches,which were then used to identify candidate virulence genes by machine learning models. Evaluation experiments with known GBS virulence genes suggested good functional and model consistency in cross-validation analyses (areas under ROC curve, 0.80 and 0.98 respectively). Inspection of the top-10 genes in each of the 15 virulence functional groups revealed at least 15 (of 119) homologous genes implicated in virulence in other human pathogens but previously unrecognized as potential virulence genes in GBS. Among these highly-ranked genes, many encode hypothetical proteins with possible roles in GBS virulence. Thus, our approach has led to the identification of a set of genes potentially affecting the virulence potential of GBS, which are potential candidates for further in vitro and in vivo investigations. This computational pipeline can also be extended to in silico analysis of virulence determinants of other bacterial pathogens.     

Identification and phylogenetic analysis of heme synthesis genes in trypanosomatids and their bacterial endosymbionts

It has been known for decades that some insect-infecting trypanosomatids can survive in culture without heme supplementation while others cannot, and that this capability is associated with the presence of a betaproteobacterial endosymbiont in the flagellate's cytoplasm. However, the specific mechanisms involved in this process remained obscure. In this work, we sequence and phylogenetically analyze the heme pathway genes from the symbionts and from their hosts, as well as from a number of heme synthesis-deficient Kinetoplastida. Our results show that the enzymes responsible for synthesis of heme are encoded on the symbiont genomes and produced in close cooperation with the flagellate host. Our evidence suggests that this synergistic relationship is the end result of a history of extensive gene loss and multiple lateral gene transfer events in different branches of the phylogeny of the Trypanosomatidae.     

Identification of endothelial genes up-regulated in vivo

We have used microarrays to identify genes that are selectively expressed in endothelial cells in vivo. Analysis of freshly isolated endothelial cells from the lungs and kidneys reveals that 350 out of the 10,000 genes represented on the microarrays were expressed at higher levels than by the corresponding parenchymal cells. Thirteen of these genes were identified both in the lung and kidney screens from a subset of about 5000 genes. Many of these genes are known to be specifically expressed in endothelial cells, but about 200 genes were potentially novel endothelial genes. The preferential endothelial expression of a selected group of these genes was confirmed by quantitative polymerase chain reaction or in situ mRNA hybridization. Comparison of the genes expressed in lung and kidney endothelia revealed numerous differences. Notably, genes encoding components of an ephrin signaling pathway were highly expressed in lung endothelial cells. In summary, the genes we have identified represent potentially new pan-endothelial and tissue-specific endothelial markers.     

Molecular analysis of spv virulence genes of the salmonella virulence plasmids

Genes on an 8 kb region common to the virulence plasmids of several serovars of Salmonella are sufficient to replace the entire plasmid in enabling systemic infection in animal models. This virulence region encompasses five genes which previously have been designated with different names from each investigating laboratory. A common nomenclature has been devised for the five genes, i.e. spv for s almonella p lasmid v irulence. The first gene, spvR, encodes a positive activator for the following four genes, spvABCD. DNA sequence analysis of the spv genes from Salmonella typhimurium. Salmonella dublin, and Salmonella choleraesuis demonstrated extremely high conservation of the DNA and amino acid sequences. The spv genes are induced at stationary phase and in carbon-poor media, and optimal expression is dependent on the katF locus. The cirulence functions of the spv genes are not known, but these genes may increase the growth rate of salmonellae in host cells and affect the interaction of salmonellae with the host immune system.     

Identification of disulfide bond isomerase substrates reveals bacterial virulence factors

Bacterial pathogens are exposed to toxic molecules inside the host and require efficient systems to form and maintain correct disulfide bonds for protein stability and function. The intracellular pathogen Francisella tularensis encodes a disulfide bond formation protein ortholog, DsbA, which previously was reported to be required for infection of macrophages and mice. However, the molecular mechanisms by which F. tularensis DsbA contributes to virulence are unknown. Here, we demonstrate that F. tularensis DsbA is a bifunctional protein that oxidizes and, more importantly, isomerizes complex disulfide connectivity in substrates. A single amino acid in the conserved cis‐proline loop of the DsbA thioredoxin domain was shown to modulate both isomerase activity and F. tularensis virulence. Trapping experiments in F. tularensis identified over 50 F. tularensis DsbA substrates, including outer membrane proteins, virulence factors, and many hypothetical proteins. Six of these hypothetical proteins were randomly selected and deleted, revealing two novel proteins, FTL_1548 and FTL_1709, which are required for F. tularensis virulence. We propose that the extreme virulence of F. tularensis is partially due to the bifunctional nature of DsbA, that many of the newly identified substrates are required for virulence, and that the development of future DsbA inhibitors could have broad anti‐bacterial implications.     

Reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans

Although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. The advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. In this work we determined presence/absence patterns of [Formula: see text] different virulence-related genes among more than [Formula: see text] finished bacterial genomes from both human pathogenic and non-pathogenic strains, belonging to different taxonomic groups (i.e: Actinobacteria, Gammaproteobacteria, Firmicutes, etc.). An accuracy of 95% using a cross-fold validation scheme with in-fold feature selection is obtained when classifying human pathogens and non-pathogens. A reduced subset of highly informative genes ([Formula: see text]) is presented and applied to an external validation set. The statistical model was implemented in the BacFier v1.0 software (freely available at [Formula: see text]), that displays not only the prediction (pathogen/non-pathogen) and an associated probability for pathogenicity, but also the presence/absence vector for the analyzed genes, so it is possible to decipher the subset of virulence genes responsible for the classification on the analyzed genome. Furthermore, we discuss the biological relevance for bacterial pathogenesis of the core set of genes, corresponding to eight functional categories, all with evident and documented association with the phenotypes of interest. Also, we analyze which functional categories of virulence genes were more distinctive for pathogenicity in each taxonomic group, which seems to be a completely new kind of information and could lead to important evolutionary conclusions.     

Transcriptional analysis of antibiotic resistance and virulence genes in multiresistant hospital-acquired MRSA

The staphylococcal chromosome cassette mec cannot solely explain the multiresistance phenotype or the relatively mild virulence profile of hospital-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA). This study reports that several multiresistant HA-MRSA strains differently expressed genes that may support antibiotic resistance, modify the bacterial surface and influence the pathogenic process. Genes encoding efflux pumps (norA, arsB, emrB) and the macrolide resistance gene ermA were found to be commonly expressed by HA-MRSA strains, but not in the archetypal MRSA strain COL. At equivalent cell density, the agr system was considerably less activated in all MRSA strains (including COL) in comparison with a prototypic antibiotic-susceptible strain. These results are in contrast to those observed in recent community-acquired MRSA isolates and may partly explain how multiresistant HA-MRSA persist in the hospital setting.     

Stress-inducible bacterial proteins and virulence

Different species of pathogenic bacteria, including Salmonella, Neisseria, Listeria and Francisella have been used to demonstrate relationship between the synthesis of stressor induced proteins by cells and the phenotypic manifestation of their virulence. The impact of such external factors as high temperature, low pH, osmolarity, substrate limitation, the content of active forms of oxygen, etc. is accompanied by the synthesis of different stressor induced proteins playing a complex role. Under unfavorable environmental conditions the synthesis of these proteins ensures the survival of the infective agents. Under conditions of a macroorganism synthesis of some stressor induced proteins promotes the survival of infective agents and their resistance to the action of humoral and cell-mediated protective factors of the host. As is known, the expression of virulence genes is not constitutive. The expression of these genes greatly depends on environmental conditions and its induction is determined by extra- or intracellular location of the infective agent. Several systems of the regulation of bacterial pathogenicity factors have been described that are relatively not numerous, conservative and respond to external signals. The relevance of a number of stressor induced proteins of bacteria to virulence associated factors is discussed.     

鲫源迟缓爱德华氏菌的分离鉴定及其毒力基因的检测

【目的】探明上海某养殖场的异育银鲫(Carassius auratus gibelio)发生死亡的病因,研究致病菌分类地位和毒力基因携带情况。【方法】通过病原菌的筛查和回感试验,确定发病原因,对16S rRNA基因、gyrB和rpoB管家基因测序,建立病原菌系统进化树,结合API-32E细菌鉴定系统对菌株的生理生化进行鉴定,综合判定致病菌的种类及其分类地位;根据已报道的7个毒力基因fimA、citC、gadB、mukF、katB、esrB和sodB序列,设计引物进行PCR扩增,研究病原菌毒力基因携带情况。【结果】致病菌GY15是导致异育银鲫发病的原因,GY15的16S rRNA、gyrB和rpoB基因与已报道的迟缓爱德华氏菌(Edwardsiella tarda)相似性在99%以上,构建系统进化树和API鉴定确定该菌株为E.tarda,腹腔注射回感可导致异育银鲫死亡,半致死浓度(LD_(50))为4.26×105 CFU/m L;已报道的7种毒力基因在该致病菌中均能被检测到;药敏试验结果显示,该菌对恩诺沙星、氟苯尼考和氧氟沙星等15种药物敏感,对新霉素、四环素和复方新诺明等18种药物表现为耐药。【结论】首次报道E.tarda可感染异育银鲫,它对异育银鲫的养殖造成威胁。