Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Pathogen genomics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMed2005

Toward a genome-wide systems biology analysis of host-pathogen interactions in group A Streptococcus.

Genome-wide analysis of microbial pathogens and molecular pathogenesis processes has become an area of considerable activity in the last 5 years. These studies have been made possible by several advances, including completion of the human genome sequence, publication of genome sequences for many human pathogens, development of microarray technology and high-throughput proteomics, and maturation of bioinformatics. Despite these advances, relatively little effort has been expended in the bacterial pathogenesis arena to develop and use integrated research platforms in a systems biology approach to enhance our understanding of disease processes. This review discusses progress made in exploiting an integrated genome-wide research platform to gain new knowledge about how the human bacterial pathogen group A Streptococcus causes disease. Results of these studies have provided many new avenues for basic pathogenesis research and translational research focused on development of an efficacious human vaccine and novel therapeutics. One goal in summarizing this line of study is to bring exciting new findings to the attention of the investigative pathology community. In addition, we hope the review will stimulate investigators to consider using analogous approaches for analysis of the molecular pathogenesis of other microbes.

Computational Biology↗
PubMed2003

First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genome.

A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (pi = 0.72 x 10(-3)) was lower when compared with diploid genotypes (pi = 2.31 x 10(-3)). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet.

Journal Article↗
PubMed2026

A Leucine-Rich Repeat Receptor-Like Protein Associated with a QTL for Septoria Stem Canker in Populus trichocarpa × Populus deltoides Hybrid Poplar.

The fungal plant pathogen Sphaerulina musiva (Ascomycota) causes Septoria stem canker, the most economically damaging disease of Populus plantations in North America, yet the genetic determinants of host resistance remain uncharacterized in hybrid poplar. Using an inoculation experiment with the 52-124 pseudo-backcross family of Populus trichocarpa × Populus deltoides (TD × D) hybrid poplar, a single significant QTL was identified on Chromosome 16 (LOD = 4.93) associated with both stem canker count and disease severity score. Transcriptomic analysis of two resistant and two susceptible genotypes across a 72-hour infection time course identified a single differentially expressed gene within the QTL candidate gene window: Podel.16G125900, a putative leucine-rich repeat receptor-like protein (LRR-RLP) with homology to receptor-like protein 33 in Arabidopsis thaliana. Podel.16G125900 is located 3001 bp (0.019 cM) upstream of the QTL peak and showed a strong infection-induced upregulation in susceptible genotype 852 (log2 fold-change = 20.47) and higher baseline expression in resistant genotypes relative to susceptible genotypes across all infection time points, consistent with a resistance mechanism in which expression level contributes to the degree of resistance conferred. Two P. trichocarpa homologs were not differentially expressed and differ substantially in sequence content, suggesting the resistance function is specific to the resistant P. deltoides lineage. These findings identify Podel.16G125900 as a strong candidate gene underlying quantitative resistance mechanisms modulating Septoria stem canker resistance in the 52-124 family of TD × D hybrid poplar and provide a target for future functional validation and marker-assisted resistance breeding.

Disease Resistance↗
PubMed2005

Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans.

The first known families of tRNA-related short interspersed elements (SINEs) in the oomycetes were identified by exploiting the genomic DNA sequence resources for the potato late blight pathogen, Phytophthora infestans. Fifteen families of tRNA-related SINEs, as well as predicted tRNAs, and other possible RNA polymerase III-transcribed sequences were identified. The size of individual elements ranges from 101 to 392 bp, representing sequences present from low (1) to highly abundant (over 2000) copy number in the P. infestans genome, based on quantitative PCR analysis. Putative short direct repeat sequences (6-14 bp) flanking the elements were also identified for eight of the SINEs. Predicted SINEs were named in a series prefixed infSINE (for infestans-SINE). Two SINEs were apparently present as multimers of tRNA-related units; four copies of a related unit for infSINEr, and two unrelated units for infSINEz. Two SINEs, infSINEh and infSINEi, were typically located within 400 bp of each other. These were also the only two elements identified as being actively transcribed in the mycelial stage of P. infestans by RT-PCR. It is possible that infSINEh and infSINEi represent active retrotransposons in P. infestans. Based on the quantitative PCR estimates of copy number for all of the elements identified, tRNA-related SINEs were estimated to comprise 0.3% of the 250 Mb P. infestans genome. InfSINE-related sequences were found to occur in species throughout the genus Phytophthora. However, seven elements were shown to be exclusive to P. infestans.

Base Sequence↗
PubMed2002

Genomics and the prospects for the discovery of new targets for antibacterial and antifungal agents.

The current increase in the number of microbes resistant to antibacterial or antifungal agents represents a potential crisis in human and veterinary medicine. Some believe that we are entering a post-antibiotic era where most antibiotics no longer will be efficacious. Therefore, it is important that new antibiotics be developed. However, because of the potential for cross-resistance, new targets for the discovery of antibiotics are needed particularly where resistance does not currently exist. The results obtained from the sequencing of genomes from pathogenic bacterial and fungal microbes provide an opportunity to ameliorate this problem. Genomic sequence data can be used to identify new genes that could be used as targets for new antibiotic discoveries. Viable new target genes might represent those that are widely distributed among pathogens or that have homologs and are essential for the viability of the organism. Chemical compounds that attack such targets would be expected to have classical antibiotic activities. Less widely distributed genes still could be valuable targets for narrow spectrum antibiotics. While many of these genes will have known or putative functions based on DNA sequence homology, the most interesting genes are the newly discovered genes with unknown functions. In this paper, it is suggested that novel, non-traditional targets also will be found through the analysis of genome sequences: those that are involved in disease pathogenesis and those that are involved in adaptation and growth in infection sites. The advantage of the non-classical targets is that targeting these sites may not result in the same degree of selective pressure that encourages resistance, and these could have a longer therapeutic life time.

Animals↗
PubMed2003

Small-fragment genomic libraries for the display of putative epitopes from clinically significant pathogens.

Taking advantage of whole genome sequences of bacterial pathogens in many thriving diseases with global impact, we developed a comprehensive screening procedure for the identification of putative vaccine candidate antigens. Importantly, this procedure relies on highly representative small-fragment genomic libraries that are expressed to display frame-selected epitope-size peptides on a bacterial cell surface and to interact directly with carefully selected disease-relevant high-titer sera. Here we describe the generation of small-fragment genomic libraries of Gram-positive and Gram-negative clinically significant pathogens, including Staphylococcus aureus and Staphylococcus epidermidis, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus pneumoniae, Enterococcus faecalis, Helicobacter pylori, Chlamydia pneumoniae, the enterotoxigenic Escherichia coli, and Campylobacter jejuni. Large-scale sequencing revealed that the libraries, which provide an average of 20-fold coverage, were random and, as demonstrated with two S. aureus libraries, highly representative. Consistent with the comprehensive nature of this approach is the identification of epitopes that reside in both annotated and putatively novel open reading frames. The use of these libraries therefore allows for the rapid and direct identification of immunogenic epitopes with no apparent bias or difficulty that often associate with conventional expression methods.

Bacterial Proteins↗
PubMed2006

Towards a universal group B Streptococcus vaccine using multistrain genome analysis.

Genomics has revolutionized the way in which novel vaccine candidates are identified for the development of efficacious vaccines. Reverse vaccinology, whereby all candidates of interest are identified by analysis of a pathogen's genome, enables characterization of many candidates simultaneously. It accelerates the initial steps of vaccine development and greatly increases the chances of obtaining reliable candidates or cocktails thereof. The availability of one or two genome sequences for any given pathogen provides access to strain-specific vaccine candidates but often fails to identify candidates that would confer general protection. The analysis of multiple genomes of group B Streptococcus revealed tremendous diversity and identified candidates that are not shared by all the strains sequenced, but provide general protection when combined.

Drug Design↗
PubMed2003

EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae.

We describe EnteriX, a suite of three web-based visualization tools for graphically portraying alignment information from comparisons among several fixed and user-supplied sequences from related enterobacterial species, anchored on a reference genome (http://bio.cse.psu.edu/). The first visualization, Enteric, displays stacked pairwise alignments between a reference genome and each of the related bacteria, represented schematically as PIPs (Percent Identity Plots). Encoded in the views are large-scale genomic rearrangement events and functional landmarks. The second visualization, Menteric, computes and displays 1 Kb views of nucleotide-level multiple alignments of the sequences, together with annotations of genes, regulatory sites and conserved regions. The third, a Java-based tool named Maj, displays alignment information in two formats, corresponding roughly to the Enteric and Menteric views, and adds zoom-in capabilities. The uses of such tools are diverse, from examining the multiple sequence alignment to infer conserved sites with potential regulatory roles, to scrutinizing the commonalities and differences between the genomes for pathogenicity or phylogenetic studies. The EnteriX suite currently includes >15 enterobacterial genomes, generates views centered on four different anchor genomes and provides support for including user sequences in the alignments.

Computer Graphics↗
PubMed2006

Genome-sequence analysis of the pathogenic H5N1 avian influenza A virus isolated in China in 2004.

Analysis of the sequences of the genome of the avian influenza A/chicken/Hubei/327/2004 (H5N1) virus, isolated from a poultry farm during the outbreak of avian influenza (AI) in Hubei Province, central China, in the spring of 2004, revealed that the hemagglutinin (HA) gene of the virus was genetically similar to those of the H5 highly pathogenic avian influenza virus (HPAI). Notably, the neuraminidase gene of the virus had a 20-amino acid deletion in the stalk region and a 5-amino acid deletion in the NS gene which belonged to allele B. Furthermore, the internal genes (PB2, PA, NP, M2) of the A/chicken/Hubei/327/2004 virus with the particular amino acid residues were more closely related to H5N1 viruses of 2000-2003 isolated in Hong Kong and the AIV of Thailand and Vietnam in 2004, but less likely to evolve from the viruses of Hong Kong 1997. Finally, our results demonstrated that the influenza A/chicken/Hubei/327/2004 (H5N1) virus was similar to those of the AI viruses isolated from Hong Kong (2000-2003), Vietnam, and Thailand rather than the viruses from the 1997 lineage of Hong Kong and with closest genetic relatives to the influenza A/Chicken/Hong Kong/61.9/02 (H5N1) virus. These data suggest that the influenza A/chicken/Hubei/327/2004 (H5N1) virus which circulated in central China derived its internal gene from a virus similar to the influenza A/Chicken/Hong Kong/61.9/02 (H5N1) virus.

Amino Acid Sequence↗
PubMed1997

Versatile insertion plasmids for targeted genome manipulations in bacteria: isolation, deletion, and rescue of the pathogenicity island LEE of the Escherichia coli O157:H7 genome.

A system of versatile insertion plasmids was constructed that permits efficient delivery of the target sites of an ultra-rare-cutting endonuclease and the recombinase FLP into preselected sites of the bacterial genome. With the help of this system, the pathogenicity island LEE of the Escherichia coli O157:H7 genome was excised and isolated in vitro, deleted in vivo, rescued as a plasmid, and transferred into another strain.

Base Sequence↗
PubMed2002

Novel targets for the future development of antibacterial agents.

Recent advances in DNA sequencing technology have made it possible to elucidate the entire genomes of pathogenic bacteria, and advancements in bioinformatic tools have driven comparative studies of these genome sequences. These evaluations are dramatically increasing our ability to make valid considerations of the limitations and advantages of particular targets based on their predicted spectrum and selectivity. In addition, developments in gene knockout technologies amenable to pathogenic organisms have enabled new genes and gene products critical to bacterial growth and pathogenicity to be uncovered at an unprecedented rate. Specific target examples in the areas of cell wall biosynthesis, aromatic amino acid biosynthesis, cell division, two component signal transduction, fatty acid biosynthesis, isopreniod biosynthesis and tRNA synthetases illustrate how aspects of the above capabilities are impacting on the discovery and characterization of novel antibacterial targets. An example of a novel inhibitor of bacterial fatty acid biosynthesis discovered from high throughput screening processes is described, along with its subsequent chemical optimization. Furthermore, the application and importance of technologies for tracking the mode of antibacterial action of these novel inhibitors is discussed.

Animals↗
PubMed2002

[A method for estimating penetrance of pathogenic mutations in a mitochondrial genome].

Variation in the manifestation age is typical of many mitochondrial diseases. The estimation of penetrance of pathogenic mutations causing such diseases is usually conducted on samples of individuals whose age exceeds the maximum age of the disease manifestation. In the case of rare diseases, samples of sufficient size sometimes cannot be formed. In this study, we propose a method for estimating penetrance involving individuals of any age. The efficiency of the method is demonstrated using Leber hereditary optic neuropathy as an example. It is shown that the method provides an unbiased estimate of penetrance and considerably reduces the error of this estimate in comparison with a sample including individuals whose age exceeds the maximum age of disease manifestation.

Age Factors↗
PubMed2002

Novel targets for the future development of antibacterial agents.

Recent advances in DNA sequencing technology have made it possible to elucidate the entire genomes of pathogenic bacteria, and advancements in bioinformatic tools have driven comparative studies of these genome sequences. These evaluations are dramatically increasing our ability to make valid considerations of the limitations and advantages of particular targets based on their predicted spectrum and selectivity. In addition, developments in gene knockout technologies amenable to pathogenic organisms have enabled new genes and gene products critical to bacterial growth and pathogenicity to be uncovered at an unprecedented rate. Specific target examples in the areas of cell wall biosynthesis, aromatic amino acid biosynthesis, cell division, two component signal transduction, fatty acid biosynthesis, isopreniod biosynthesis and tRNA synthetases illustrate how aspects of the above capabilities are impacting on the discovery and characterization of novel antibacterial targets. An example of a novel inhibitor of bacterial fatty acid biosynthesis discovered from high throughput screening processes is described, along with its subsequent chemical optimization. Furthermore, the application and importance of technologies for tracking the mode of antibacterial action of these novel inhibitors is discussed.

Anti-Bacterial Agents↗
PubMed2002

Pathogen inactivation of blood components: current status and introduction of an approach using riboflavin as a photosensitizer.

Riboflavin is a naturally occurring compound and an essential human nutrient. Studies in the 1960s and 70s showed that it could be effective, when exposed to visible or UV light, in inactivating viruses and bacteria. This suggested to us that it could act as a photosensitizer useful in the inactivation of pathogens found in blood products, because of its nucleic acid specificity and its limited tendency toward indiscriminate oxidation. The riboflavin molecule is a planar, conjugated ring structure with a sugar side chain that confers water solubility. The planar portion is capable of intercalating between the bases of DNA or RNA. Light activated riboflavin oxidizes guanine in nucleic acids, preventing replication of the pathogen's genome. Gambro BCT is developing processes using riboflavin and light to inactivate pathogens in plasma, platelet, and red cell products. We call these Pathogen Eradication Technology (PET) processes. Riboflavin is non-toxic; it must be present in the body for good health. The photo-byproducts formed in the PET processes are lumichrome and protein adducts. The photodegradation of riboflavin in the body is clearly shown by the decrease in its concentration in neonates who are treated with intense visible light to break down circulating bilirubin, which their immature livers cannot yet handle. A definitive lookback study showed no difference in cancer rates between the 55,000 children receiving this therapy in Denmark from 1977 through 1989 and nonirradiated controls. Gambro BCT is developing specific riboflavin-based PET processes for platelet concentrates, fresh frozen plasma, and packed red blood cells. In each, the process is being optimized to achieve high levels of inactivation of specific pathogens, while maintaining acceptable levels of product quality and activity. Extra- and intracellular HIV, BVDV (a model for HCV), and pseudorabies virus (a herpes virus) have been used to guide process development and validation. We have demonstrated 4 to 7 log10 reductions in the titers of these viruses, when they are spiked into blood products and irradiated in the presence of riboflavin. Porcine parvovirus, a tight-capsid, nonenveloped virus is more resistant, a finding in all experimental inactivation approaches. A range of bacteria implicated in platelet and red cell transfusion injuries and deaths, including S. aureus, E. coli, K. pneumoniae, and Y. enterocolitica, are being used to validate antibacterial efficacy. The PET platelet process involves the addition of riboflavin to platelets in plasma, illumination of the product, storage of the product and transfusion without further manipulation. The lack of toxicity of the treatment byproducts permits this ease of use. Quality of the platelets throughout storage has been assessed by pH, PO2, lactate, hypotonic shock response, morphology, glucose, and GMP-140 expression. In vitro function is well maintained. The levels seen are within the range of those reported in commonly transfused products. Radiolabeled transfusion studies of treated platelets have been carried out in primates to determine a preliminary measure of their in-vivo circulation. The in vivo recoveries and survivals of treated and control platelets did not differ. This work suggests that an endogenous photosensitizer, riboflavin, which has an extremely good safety profile, can inactivate high levels of a broad range of viruses and bacteria in platelet concentrates, fresh frozen plasma, and in red blood cells, preserving the activity and functionality of the components. Planned animal and clinical studies are expected to solidify this suggestion into a well-characterized process which can be safely and readily applied to reduce the risks of transfusion transmitted disease.

Blood Cells↗
PubMed2001

[Current concepts on the pathogenicity of phytopathogenic bacteria].

What are the molecular determinants that make a bacterium a plant pathogen? In the last 10-20 years, important progress has been made in answering this question. In the early 20th century soon after the discovery of infectious diseases, the first studies of pathogenicity were undertaken. These early studies relied mostly on biochemistry and led to the discovery of several major pathogenicity determinants, such as toxins and hydrolytic enzymes which govern the production of major disease symptoms. From these pioneering studies, a simplistic view of pathogenicity arose. It was thought that only a few functions were sufficient to transform a bacterium into a pathogen. This view rapidly changed when modern techniques of molecular genetics were applied to analyse pathogenicity. Modern analyses of pathogenicity determinants took advantage of the relatively simple organization of the haploid genome of pathogenic bacteria. By creating non-pathogenic mutants, a large number of genes governing bacterium-host interactions were identified. These genes are required either for host colonization or for the production of symptoms. Even though the role of motility and chemotaxis in these processes is still unclear, it is clear that a strong attachment of Agrobacterium to plant cells is a prerequisite for efficient plant transformation and disease. Other important pathogenicity factors identified with a molecular genetic approach include hydrolytic enzymes such as pectinases and cellulases which not only provide nutrients to the bacteria but also facilitate pathogen invasion into host tissues. The precise role of exopolysaccharide in pathogenicity is still under discussion, however it is has been established that it is crucial for the induction of wilt symptoms caused by Ralstonia solanacearum. Trafficking of effector proteins from the invading bacterium into the host cell emerged recently as a new central concept. In plant pathogenic bacteria, protein translocation takes place through the so-called 'type II secretion machinery' encoded by hrp genes in the bacterium. These genes are present in representatives of all the major groups of Gram negative plant pathogenic bacteria except Agrobacterium. Most of these genes have counterparts in pathogens of mammals (including those of human) and they also play a central role in pathogenicity. Additionally, recent evidence suggests that a 'type IV secretion machinery' injects bacterial proteins into host cells. This machinery, originally found to be involved in the transfer of t-DNA from Agrobacterium into plant cells, was recently shown to translocate pathogenicity proteins in pathogens of mammals such as Helicobacter pylori and Brucella. Discovery of the trafficking of proteins from the pathogen into host cells revolutionized our conception of pathogenicity. First, it rather unexpectedly established the conservation of basic pathogenicity strategies in plant and animal pathogens. Second, this discovery changes our ideas about the overall strategy (or mechanism) of pathogenicity, although we still think the end result is exploitation of host cell nutritive components. Rather than killing the host cell from outside, we envision a more subtle approach in which pathogens inject effector proteins into the host cell to effect a change in host cell biology advantageous to the pathogen. Identification of the effector proteins, of their function and of the corresponding molecular targets in the host is a new challenge which will contribute to the conception of new strategies to control diseases.

Bacteria↗
PubMed2006

ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.

ASAP is a comprehensive web-based system for community genome annotation and analysis. ASAP is being used for a large-scale effort to augment and curate annotations for genomes of enterobacterial pathogens and for additional genome sequences. New tools, such as the genome alignment program Mauve, have been incorporated into ASAP in order to improve display and analysis of related genomes. Recent improvements to the database and challenges for future development of the system are discussed. ASAP is available on the web at https://asap.ahabs.wisc.edu/asap/logon.php.

Databases, Nucleic Acid↗
PubMed2002

From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways.

Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD, coaD, and ribF), are discussed in detail.

Anti-Bacterial Agents↗
PubMed2001

Delivering novel targets and antibiotics from genomics.

Recent advances in DNA sequencing technology have made it possible to elucidate the sequences of the entire genomes of pathogenic bacteria and concomitant advancements in bioinformatic tools have driven comparative studies of these genome sequences. These evaluations are significantly increasing our ability to make valid considerations of the limitations and advantages of particular targets based on their predicted spectrum and selectivity. In addition, developments in gene-essentiality technologies amenable to pathogenic organisms liave enabled new genes and gene products critical to bacterial growth and pathogenicity to be uncovered at an unprecedented rate. This review will describe how aspects of the above capabilities are impacting the discovery and characterization of known and novel antibacterial targets using specific examples taken from a variety of important, diverse bacterial processes.

Anti-Bacterial Agents↗