Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “pathogen identification”

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 1,225 records · Page 68Linked to original sources
PubMed2003

Identification of essential genes in the human fungal pathogen Aspergillus fumigatus by transposon mutagenesis.

The opportunistic pathogen Aspergillus fumigatus is the most frequent cause of deadly airborne fungal infections in developed countries. In order to identify novel antifungal-drug targets, we investigated the genome of A. fumigatus for genes that are necessary for efficient fungal growth. An artificial A. fumigatus diploid strain with one copy of an engineered impala160 transposon from Fusarium oxysporum integrated into its genome was used to generate a library of diploid strains by random in vivo transposon mutagenesis. Among 2,386 heterozygous diploid strains screened by parasexual genetics, 1.2% had a copy of the transposable element integrated into a locus essential for A. fumigatus growth. Comparison of genomic sequences flanking impala160 in these mutants with that of the genome of A. fumigatus allowed the characterization of 20 previously uncharacterized A. fumigatus genes. Among these, homologues of genes essential for Saccharomyces cerevisiae growth have been identified, as well as genes that do not have homologues in other fungal species. These results confirm that heterologous transposition using the transposable element impala is a powerful tool for functional genomics in ascomycota, and they pave the way for defining the complete set of essential genes in A. fumigatus, the first step toward target-based development of new antifungal drugs.

Antifungal Agents↗
PubMed2000

Identification and phylogenetic relationship of the most common pathogenic Candida species inferred from mitochondrial cytochrome b gene sequences.

We sequenced a 396-bp region of the mitochondrial cytochrome b gene of the most common clinically important Candida species: Candida albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. lusitaniae. The recently described species of Candida, C. dubliniensis, associated with mucosal candidiasis in human immunodeficiency virus-infected individuals, was also included. Two to five strains of each species were examined. Some species represented intraspecies variation, which was not more than 1.8% (DNA). However, interspecies variations were more than 10 and 7%, respectively, for DNA and amino acid sequences. Multiple alignments of nucleotide and deduced amino acid sequences revealed species-specific nucleotides and amino acids. Nucleotide- and amino acid-based phylogenetic trees were constructed and are discussed. Using the database, it is possible to identify presumptive Candida species within a working day.

Amino Acid Sequence↗
PubMed2001

Rapid identification of dimorphic and yeast-like fungal pathogens using specific DNA probes.

Specific oligonucleotide probes were developed to identify medically important fungi that display yeast-like morphology in vivo. Universal fungal primers ITS1 and ITS4, directed to the conserved regions of ribosomal DNA, were used to amplify DNA from Histoplasma capsulatum, Blastomyces dermatitidis, Coccidioides immitis, Paracoccidioides brasiliensis, Penicillium marneffei, Sporothrix schenckii, Cryptococcus neoformans, five Candida species, and Pneumocystis carinii. Specific oligonucleotide probes to identify these fungi, as well as a probe to detect all dimorphic, systemic pathogens, were developed. PCR amplicons were detected colorimetrically in an enzyme immunoassay format. The dimorphic probe hybridized with DNA from H. capsulatum, B. dermatitidis, C. immitis, P. brasiliensis, and P. marneffei but not with DNA from nondimorphic fungi. Specific probes for H. capsulatum, B. dermatitidis, C. immitis, P. brasiliensis, P. marneffei, S. schenckii, C. neoformans, and P. carinii hybridized with homologous but not heterologous DNA. Minor cross-reactivity was observed for the B. dermititidis probe used against C. immitis DNA and for the H. capsulatum probe used against Candida albicans DNA. However, the C. immitis probe did not cross-react with B. dermititidis DNA, nor did the dimorphic probe hybridize with C. albicans DNA. Therefore, these fungi could be differentiated by a process of elimination. In conclusion, probes developed to yeast-like pathogens were found to be highly specific and should prove to be useful in differentiating these organisms in the clinical setting.

Genes, rRNA↗
PubMed2004

Identification of antigenic proteins of a Theileria species pathogenic for small ruminants in China recognized by antisera of infected animals.

The antigenic proteins of the piroplasm stage of Theileria species (China), the causative agent of theilerosis of small ruminants in China, were analyzed by Western blot, revealing several specific immunoreactive proteins of different predicted molecular weights. Furthermore, sera from Theileria species (China)-infected animals were probed for reactivity with the TaSP protein of T. annulata, for which a homologue has been described in Theileria species (China). Affinity chromatography demonstrated the presence of TaSP-reactive antibodies, and the majority of the sera showed reactivity with this protein both in Western blots and in ELISA. The identified parasite antigens and TaSP will be assessed for their suitability for developing diagnostic methods as well as evaluated for their capacity to stimulated host immune competent cells.

Animals↗
PubMed1998

Identification of carbohydrates on the surface membrane of pathogenic and nonpathogenic piscine haemoflagellates, Cryptobia salmositica, C. bullocki and C. catostomi (Kinetoplastida).

Carbohydrates and protein glycoconjugates on the cell membranes of Cryptobia salmositica, C. bullocki and C. catostomi were analyzed using 13 highly purified lectins (unlabelled or digoxigenin/biotin labelled). No agglutinations were observed with C. salmositica, C. bullocki and C. catostomi using lectin TPA (Tetragonolobus purpureas agglutinin, for alpha-L-fucose). C. salmositica was agglutinated by 3 of 12 lectins [Con A, for alpha-man and alpha-D-glc; PSA, for alpha-man; PWM, for (glcNAc)3], while C. bullocki was agglutinated by 8 lectins and C. catostomi was agglutinated by 10 lectins. Glycoconjugate analysis with digoxigenin or biotin labelled lectins showed a species-specific staining pattern in pathogenic and nonpathogenic Cryptobia spp. The nonpathogenic C. catostomi had the strongest reaction. These results indicate that the surface carbohydrate residues and glycoconjugate compositions on Cryptobia spp. are different between species they may be related to the virulence of the parasite.

Agglutination↗
PubMed2000

Identification of glycosomes and metabolic end products in pathogenic and nonpathogenic strains of Cryptobia salmositica (Kinetoplastida: Bodonidae).

Whole cell lysates of pathogenic and nonpathogenic strains of Cryptobia salmositica were subjected to subcellular fractionation using differential and isopycnic centrifugation in sucrose. The glycolytic enzymes hexokinase, fructose-1,6-biphosphate aldolase, triosephosphate isomerase, glucosephosphate isomerase and glyceraldehyde-3-phosphate-dehydrogenase and the peroxisomal enzyme catalase were associated with a microbody that had a buoyant density in sucrose of 1.21 g cm-3. Lactate dehydrogenase was detected in whole cell lysates, but not in purified organelles. A microbody with a positive reaction for catalase was detected in electron microscope sections of the pathogenic and nonpathogenic strains. These catalase-containing microbodies fused with lipid bodies and vacuoles, arose by division from pre-existing microbodies and expelled their contents into the cytoplasm of the cell. Both strains also modified the catalase content in their microbodies. Under aerobic conditions, they metabolized glucose to pyruvate and lactate. We conclude that part of the glycolytic pathway in C. salmositica is compartmentalized in a microbody called the glycosome.

Aerobiosis↗
PubMed2005

From single cell gene-based diagnostics to diagnostic genomics: current applications and future perspectives.

Molecular diagnostics is a branch of clinical diagnostics that uses primarily DNA or RNA as a biomarker for clinical testing. It combines various gene-based amplification technologies with highly sophisticated detection methods for the clinical diagnosis of a vast variety of diseases including infectious diseases, cancer, and inherited diseases. The principal application of gene-based amplification technology is to identify pathogen or gene-specific nucleic acid sequences that are used as surrogate markers for the identification of either infectious pathogens or alteration of disease-related genes. There are generally three classes of gene-based amplification technologies: target-based, e.g., PCR; probe-based, e.g., LCR; and signal-based, e.g., bDNA. Real-time detection of PCR allows us to quantify amplified amplicons with a broad dynamic range and it offers a unique way to detect genetic mutations. Other technologies such as immuno-PCR and bio-barcode assay (BCA) combine different amplification tactics offering extreme detection sensitivity ranging from femtogram (10(-15)) to zeptogram (10(-21)). Even though quantum dots technology is in its infant stage, its potential to further increase diagnostic sensitivity and specificity is likely beyond our current imagination. Future diagnostic technologies include the use of genomic and proteomic approaches especially in pure cell types or even in the single-cell level, which open up endless new possibilities for gene-based diagnostics at entirely different levels. In this article, principles of various current gene-based amplification and detection technologies along with their clinical applications are discussed. New technologies that could potentially be used in future gene-based diagnosis are introduced.

Genetics, Medical↗
PubMed2003

Genome sequencing and comparative genomics of tropical disease pathogens.

The sequencing of eukaryotic genomes has lagged behind sequencing of organisms in the other domains of life, archae and bacteria, primarily due to their greater size and complexity. With recent advances in high-throughput technologies such as robotics and improved computational resources, the number of eukaryotic genome sequencing projects has increased significantly. Among these are a number of sequencing projects of tropical pathogens of medical and veterinary importance, many of which are responsible for causing widespread morbidity and mortality in peoples of developing countries. Uncovering the complete gene complement of these organisms is proving to be of immense value in the development of novel methods of parasite control, such as antiparasitic drugs and vaccines, as well as the development of new diagnostic tools. Combining pathogen genome sequences with the host and vector genome sequences is promising to be a robust method for the identification of host-pathogen interactions. Finally, comparative sequencing of related species, especially of organisms used as model systems in the study of the disease, is beginning to realize its potential in the identification of genes, and the evolutionary forces that shape the genes, that are involved in evasion of the host immune response.

Animals↗
PubMed1980

The clinical significance, taxonomy and special methodological problems of the pathogenic clostridia.

The clinical significance of clostridia is much greater than is generally recognized. The organisms are a major cause of septic abortion, Clostridium perfringens being the most important single organism. This species is also the principle agent in food-poisoning. Clostridium botulinum is considered to be one of the main causes of the sudden death syndrome in infants. As clostridia are universally distributed in nature and the human body, the isolation of an organism of this group from the human body is significant only if it can be linked with pathological changes. In the case of histotoxic disease, a direct gramstained smear from the lesion is of paramount importance, since the pathogens are always present in large numbers. Generally, a few simple procedures and tests ensure the rapid isolation and identification of the main pathogenic clostridia. C. perfringens, by far the most important species, may be identified by its ability to produce lecithinase on egg yolk-glucose agar and stormy clot in litmus milk. However, strain identification of this microorganism is much more complicated.

Anaerobiosis↗
PubMedDate not supplied

Evaluation of the pediatric Septi-Chek blood culture system.

The pediatric Septi-Chek blood culture system is a biphasic system that uses a 20-ml bottle of brain-heart infusion broth. We compared this system with a supplemented peptone broth tube (Vacutainer) for the recovery of aerobic organisms from blood cultures obtained from patients in a pediatric hospital. Blood specimens for culture were drawn into transport tubes containing sodium polyanetholsulfonate (SPS), and equal volumes were allocated into a Septi-Chek bottle and a Vacutainer tube which was vented for the first day of incubation. A total of 4828 blood culture sets was included, from which 243 probable pathogens were recovered, including 211 in the Septi-Chek system and 204 from the Vacutainer Tube. There were no significant differences in the recovery of individual pathogens. The mean time to initial detection of pathogens was comparable in the two systems, but the mean time to growth on solid media for pathogens recovered in both systems was shorter with Septi-Chek (37.2 hr compared with 45.5 hr, p less than 0.001). The pediatric Septi-Chek system is comparable with a vented Vacutainer tube for the recovery of aerobic pathogens, and its use facilitates the early identification and susceptibility testing of bloodstream pathogens.

Bacteremia↗
PubMed2003

CD8 T cell immunome analysis of Listeria monocytogenes.

The identification of T cell epitopes is crucial for the understanding of the host response during infections with pathogenic microorganisms. Generally, the identification of relevant T cell responses is based on the analysis of T cell lines propagated in vitro. We used an ex vivo approach for the analysis of the CD8 T cell response against Listeria monocytogenes that is based upon the fractionation of naturally processed antigenic peptides and subsequent analysis with T cells in an enzyme-linked immunospot (ELISPOT) assay. Our data indicate that the direct ex vivo ELISPOT analysis of peptides extracted from infected tissues represents a versatile and potent test system for the analysis of the CD8 T cell immunome of microorganisms that furthermore requires neither the knowledge of the microbial genome nor of the specificity of responding T cells.

Animals↗
PubMed2003

Genes to genetic immunization: identification of bacterial vaccine candidates.

Pathogenic bacteria still represent a major threat to human health worldwide and the need for new vaccines is great. Virulence factors, particularly surface-located molecules, often make good vaccine targets because they are essential for access to their niche within the host. The advent of whole-genome sequencing of bacterial pathogens has revolutionized the methods by which these organisms are studied and provides us with the possibility of identifying potential targets for vaccines by sequence scanning alone. Other developments in molecular biology, such as whole genome expression and mass mutagenesis, are also contributing to the identification of potential vaccine targets. In this chapter, we review approaches that exploit whole genome sequence data to identify potential virulence determinants and vaccine antigens.

Animals↗
PubMed2003

Rapid detection of human pathogenic orthobunyaviruses.

Modern detection and identification tools can help to provide answers to urgent questions about the incidence, prevalence, and epidemiology of currently emerging diseases. We developed highly sensitive one-step TaqMan reverse transcription-PCR assays with sensitivities ranging from 10(4) to 10(1) molecules for 11 human pathogens of the orthobunyaviruses. We compared the performances of these assays on three currently available cyclers (ABI-PRISM 7700, LightCycler, and SmartCycler). The assay for Oropouche virus (OROV) was tested using sera collected from days 1 to 5 after onset of OROV disease and was found to be greatly superior to an established nested PCR system. A mean copy number of 1.31 x 10(7) OROV RNA/ml of serum was detected. Diagnostic RNA detection can be used as early as day 1 after onset of OROV disease. The use of a mobile SmartCycler and a hands-on time of less than 3 h could help to intensify outbreak surveillance and control, especially in field studies.

Animals↗
PubMed2005

Advances on cyclin-dependent kinases (CDKs) as novel targets for antiviral drugs.

Although targeting viral proteins has lead to many successful antiviral drugs, these antivirals have certain limitations. They rapidly select for resistance, tend to be active against only a few related viruses and the proteins of a pathogen must be characterized before such drugs can be developed. Consequently, a long period is required from the identification of a new pathogen to the development of relevant antivirals, a major concern for emerging diseases. Cellular proteins are now considered as potential targets for antivirals. Drugs that target cellular proteins required for several viral functions might not easily select for drug-resistance. They may also be active against a variety of unrelated viruses, which commonly require the same cellular proteins, and against viral strains resistant to conventional antiviral drugs. These antivirals could be promptly tested against emerging viruses because even distantly related viruses commonly require the same cellular proteins. Cellular cyclin-dependent kinases (CDKs) are required for replication of many viruses and specific pharmacological CDK inhibitors (PCIs) are proving to have surprisingly few negative side effects in clinical trials (against cancer). PCIs inhibit replication of wild-type and multi-drug resistant strains of HIV, HSV-1, HSV-2, HCMV, EBV and VZV. Two PCIs, roscovitine and flavopiridol, were recently proven active in a mouse model of HIV-induced nephropathy. Because the antiviral mechanisms of PCIs require no viral proteins, mutations in viral genes may not easily overcome inhibition by these drugs. In fact, no PCI-resistant viral mutant has been reported. PCIs are scheduled to enter clinical trials as antivirals in 2005.

Animals↗
PubMed1990

Characterization of potentially pathogenic free-living amoebae in sewage samples of Calcutta, India.

1. It is widely accepted that foul or polluted environments are the principal sources of potentially pathogenic species of free-living amoebae. The present paper is the first report of occurrence of potentially pathogenic free-living amoebae in sewage samples of Calcutta, India. 2. We describe the occurrence, isolation, specific identification and comparative mouse pathogenicity test of two pathogenic amoebae, viz., Naegleria fowleri (N. aerobia) Carter, 1970, causing human meningoencephalitis and Acanthamoeba castellanii Douglas, 1930, causing granulomatous amoebic encephalitis, and one non-pathogenic amoeba, viz., A. astronyxis Ray and Hayes, 1959, in sewage samples of Calcutta, India. 3. The existence of both pathogenic and non-pathogenic amoebae living side by side is of considerable epidemiological relevance.

Acanthamoeba↗
PubMedDate not supplied

[Probable aerodiffusion of pathogens in the vicinity of an oxidation basin belonging to a purification plant].

The Authors intent was to study the convenience of exposing selective media for identification of finely atomized pathogenic bacteria such as Staphylococcus aureus, in the proximity of oxidation basins of the mechanical surface aeration-type purification plants, and also to assess the percentage of pathogenic elements spread throughout the air. The Authors consider the use of elective or selective media for the isolation of bacteria in the air hardly important and useful. But since the dishes exposed in the vicinity of the liquid sewage oxidation basin have revealed the presence of polluting aerosols, it would seem convenient to provide for an in-depth study on the mechanism governing the spreading of aerosol particles throughout the air, in relation to the estimate of the meteorological and climatic parameters of the area and to a survey of the persons therein exposed.

Air Microbiology↗