Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “pathogenicity classification”

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 1,153 records · Page 64Linked to original sources
PubMed2005

DNA vaccines for aquacultured fish.

Deoxyribonucleic acid (DNA) vaccination is based on the administration of the gene encoding the vaccine antigen, rather than the antigen itself. Subsequent expression of the antigen by cells in the vaccinated hosts triggers the host immune system. Among the many experimental DNA vaccines tested in various animal species as well as in humans, the vaccines against rhabdovirus diseases in fish have given some of the most promising results. A single intramuscular (IM) injection of microgram amounts of DNA induces rapid and long-lasting protection in farmed salmonids against economically important viruses such as infectious haematopoietic necrosis virus (IHNV) and viral haemorrhagic septicaemia virus (VHSV). DNA vaccines against other types of fish pathogens, however, have so far had limited success. The most efficient delivery route at present is IM injection, and suitable delivery strategies for mass vaccination of small fish have yet to be developed. In terms of safety, no adverse effects in the vaccinated fish have been observed to date. As DNA vaccination is a relatively new technology, various theoretical and long-term safety issues related to the environment and the consumer remain to be fully addressed, although inherently the risks should not be any greater than with the commercial fish vaccines that are currently used. Present classification systems lack clarity in distinguishing DNA-vaccinated animals from genetically modified organisms (GMOs), which could raise issues in terms of licensing and public acceptance of the technology. The potential benefits of DNA vaccines for farmed fish include improved animal welfare, reduced environmental impacts of aquaculture activities, increased food quality and quantity, and more sustainable production. Testing under commercial production conditions has recently been initiated in Canada and Denmark.

Animal Welfare↗
PubMed2005

Deciphering data anomalies in BioSense.

INTRODUCTION: Since June 2004, CDC's BioIntelligence Center has monitored daily nationwide syndromic data by using the BioSense surveillance application. OBJECTIVES: The BioSense application has been monitored by a team of full-time CDC analysts. This report examines their role in identifying and deciphering data anomalies. It also discusses the limitations of the current surveillance application, lessons learned, and potential next steps to improve national syndromic surveillance methodology. METHODS: Data on clinical diagnoses (International Classification of Diseases, Ninth Revision, Clinical Modifications [ICD-9-CM]) and medical procedures (CPT codes) are provided by Department of Veterans Affairs and Department of Defense ambulatory-care clinics; data on select sales of over-the-counter health-care products are provided by participating retail pharmacies; and data on laboratory tests ordered are provided by Laboratory Corporation of America, Inc. All data are filtered to exclude information irrelevant to syndromic surveillance. RESULTS: During June-November 2004, of the approximately 160 data anomalies examined, no events involving disease outbreaks or deliberate exposure to a pathogen were detected. Data anomalies were detected by using a combination of statistical algorithms and analytical visualization features. The anomalies primarily reflected unusual changes in either daily data volume or in types of clinical diagnoses and procedures. This report describes steps taken in routine monitoring, including 1) detecting data anomalies, 2) estimating geographic and temporal scope of the anomalies, 3) gathering supplemental facts, 4) comparing data from multiple data sources, 5) developing hypotheses, and 6) ruling out or validating the existence of an actual event. To be useful for early detection, these steps must be completed quickly (i.e., in hours or days). Anomalies described are attributable to multiple causes, including miscoded data, effects of retail sales promotions, and smaller but explainable signals. CONCLUSION: BioSense requires an empirical learning curve to make the best use of the public health data it contains. This process can be made more effective by continued improvements to the user interface and collective input from local public health partners.

Bioterrorism↗
PubMed1980

Taxonomy and clinical significance of Actinomycetaceae and Propionibacteriaceae.

In spite of considerable advances during the last years, classification and identification of Actinomycetaceae and Propionibacteriaceae still present major problems. Uncertainties about the systematic position and taxonomic status of several genera and species, the lack of reliable distinguishing characteristics or use of inadequately adapted techniques of investigation interfere with both micribiological and clinical research and also with routine work in the diagnostic laboratory. Nevertheless, besides actinomycosis, an etiologically well defined suppurative infection, several other diseases and lesions such as lacrimal canaliculitis, caries and periodontal disease, inflammation following use of intrauterine pessaries, various types of abscess, septicaemia, and acne vulgaris have been attributed to the direct or indirect pathogenic effects of fermentative actinomycetes, propionibacteria, or eubacteria. Many questions concerning their individual pathogenicity and their pathomechanisms still remain to be answered, however.

Acne Vulgaris↗
PubMed2005

Expressed sequence tag analysis of the soybean rust pathogen Phakopsora pachyrhizi.

Soybean rust is caused by the obligate fungal pathogen Phakopsora pachyrhizi Sydow. A unidirectional cDNA library was constructed using mRNA isolated from germinating P. pachyrhizi urediniospores to identify genes expressed at this physiological stage. Single pass sequence analysis of 908 clones revealed 488 unique expressed sequence tags (ESTs, unigenes) of which 107 appeared as multiple copies. BLASTX analysis identified 189 unigenes with significant similarities (Evalue<10(-5)) to sequences deposited in the NCBI non-redundant protein database. A search against the NCBI dbEST using the BLASTN algorithm revealed 32 ESTs with high or moderate similarities to plant and fungal sequences. Using the Expressed Gene Anatomy Classification, 31.7% of these ESTs were involved in primary metabolism, 14.3% in gene/protein expression, 7.4% in cell structure and growth, 6.9% in cell division, 4.8% in cell signaling/cell communication, and 4.8% in cell/organism defense. Approximately 29.6% of the identities were to hypothetical proteins and proteins with unknown function.

Basidiomycota↗
PubMed2005

Hemolytic uremic syndrome; pathogenesis, treatment, and outcome.

PURPOSE OF REVIEW: The hemolytic uremic syndrome (HUS) is the most common cause of acute renal failure in infants and young children, and is a substantial cause of acute mortality and chronic morbidity. It is therefore relevant and appropriate that pediatricians remain familiar with the various subsets of the disease including its classification, management, and outcome. RECENT FINDINGS: This review will focus on recent information relative to epidemiology, pathogenesis, treatment, and outcome. It will include some of the newer associations between HUS and a variety of infections, including, but not limited to E. coli 0157:H7 (Shiga toxin-mediated) HUS, as well as the ever-increasing number of associations between HUS and a variety of drugs. It will review some of the newer therapies for the more common subsets, but will acknowledge that choosing evidence-based therapies is often limited by our incomplete understanding of the various pathogenic cascades, and that with the possible exception of Shiga toxin-mediated HUS(D+HUS), long-term outcome information is often limited by small numbers and limited follow-up. SUMMARY: This review should provide a framework for making the proper diagnosis, implementing appropriate treatment, and advising the family about anticipated outcome.

Bone Marrow Transplantation↗
PubMed1993

Comparative study of the activity and lingering effect of topical antifungals.

We present a combined method of culturing pathogenic dermatophytes and yeasts on human stratum corneum. Topical marketed antifungals are applied in vivo, and the stratum corneum is removed by cyanoacrylate skin surface strippings. After inoculation of the test organism, the extent of fungal growth is measured, indicating by comparison with controls the level of inhibitory effect of the antifungal. Other samples of stratum corneum collected at different time intervals after the arrest of antimicrobial treatment are used to evaluate the lingering effect of the drug. The combination of the data gained by these approaches close to the in vivo situation is used to introduce a classification of antifungals.

Administration, Topical↗
PubMed2003

Relationship of SARS-CoV to other pathogenic RNA viruses explored by tetranucleotide usage profiling.

BACKGROUND: The exact origin of the cause of the Severe Acute Respiratory Syndrome (SARS) is still an open question. The genomic sequence relationship of SARS-CoV with 30 different single-stranded RNA (ssRNA) viruses of various families was studied using two non-standard approaches. Both approaches began with the vectorial profiling of the tetra-nucleotide usage pattern V for each virus. In approach one, a distance measure of a vector V, based on correlation coefficient was devised to construct a relationship tree by the neighbor-joining algorithm. In approach two, a multivariate factor analysis was performed to derive the embedded tetra-nucleotide usage patterns. These patterns were subsequently used to classify the selected viruses. RESULTS: Both approaches yielded relationship outcomes that are consistent with the known virus classification. They also indicated that the genome of RNA viruses from the same family conform to a specific pattern of word usage. Based on the correlation of the overall tetra-nucleotide usage patterns, the Transmissible Gastroenteritis Virus (TGV) and the Feline CoronaVirus (FCoV) are closest to SARS-CoV. Surprisingly also, the RNA viruses that do not go through a DNA stage displayed a remarkable discrimination against the CpG and UpA di-nucleotide (z = -77.31, -52.48 respectively) and selection for UpG and CpA (z = 65.79,49.99 respectively). Potential factors influencing these biases are discussed. CONCLUSION: The study of genomic word usage is a powerful method to classify RNA viruses. The congruence of the relationship outcomes with the known classification indicates that there exist phylogenetic signals in the tetra-nucleotide usage patterns, that is most prominent in the replicase open reading frames.

Algorithms↗
PubMed2004

Blastocystis hominis as a cause of hypoalbuminemia and anasarca.

The protozoan Blastocystis hominis has been considered nonpathogenic, but this classification has come under scrutiny in light of reports in the medical literature indicating it could be the cause of intestinal disorders and, in one case, hypoalbuminemia. Reported here is a severe case of infection with B. hominis that caused acute gastroenteritis with prolonged diarrhea, hypoalbuminemia and anasarca. The diagnosis was based on the parasitological finding, since no other pathological evidence was found. The patient responded favorably to treatment with metronidazole for 10 days. This case supports the idea that B. hominis should be considered as a cause of opportunistic infection in debilitated patients despite the controversy surrounding its pathogenicity.

Animals↗
PubMed1991

Identification of epitope(s) on the internal virion proteins of rinderpest virus which are absent from peste des petits ruminants virus.

Monoclonal antibodies (MAb) raised against the RBOK vaccine strain of rinderpest virus were characterized by radio-immunoprecipitation (RIPA) and in the indirect ELISA using measles (MV), distemper (CDV), rinderpest (RPV) and peste des petits ruminants viruses (PPRV). Those found to be specific for the matrix (M) protein and the nucleocapsid (N) protein could be classified into different groups on the basis of the anti-morbillivirus MAb classification scheme; a number of these MAb showed a selective recognition of RPV, measles virus and distemper virus, or of different isolates of rinderpest virus, demonstrating that greater inter-isolate variation occurs than was apparent from analyses using polyclonal antisera. One group of anti-F protein MAb (group F1) reacted with all isolates of both RPV and PPRV. A second group of anti-N protein MAb (group N1/A) reacted with all RPV isolates, but not with the PPRV isolates. Furthermore, these group N1/A antibodies reacted strongly with RPV isolates which were upon original isolation of high pathogenicity, but had a weaker reaction against the isolates of this virus which were of low pathogenicity. Thus, MAb against RPV, in particular those against the N protein offered a potential superior to that of molecular analyses for "isolate fingerprinting", the differentiation of RPV from PPRV and the discrimination between rinderpest viruses which had been, upon isolation, of either high or low pathogenicity.

Animals↗
PubMed1999

Use of RAPD (random amplified polymorphic DNA) to analyse genetic diversity of dematiaceous fungal pathogens.

Thirteen strains of chromoblastomycosis and phaeohyphomycosis etiologic agent fungi were obtained from different geographical origins. These strains were genotypically compared by means of the RAPD (Random Amplified Polymorphic DNA) technique. The data generated showed a high degree of polymorphism between distinct species and a low polymorphism between strains of the same species. The results generated by these tests were subjected to a numerical taxonomy analysis, using the unweighted pair-group method. A phenogram was constructed for the set of strains studied. Based on its structure, we concluded that genotypical data provide enough information to us to use the unweighted pair-group method to cluster the strains in accordance to their respective species. The phenogram grouped in a single branch the strains of Fonsecaea pedrosoi and F. compacta species, indicating a great similarity between these fungi, and suggesting that the classification as distinct species may not be appropriate for these species of the genus Fonsecaea.

Chromoblastomycosis↗
PubMed2003

Human rhinoviruses.

Human rhinoviruses are the most important causative agents of upper respiratory infections and are also implicated in more severe clinical entities. Although often present, very little is known about human rhinoviruses. Molecular methods have been used in the classification of this large group of viruses into two separate clades. In addition, one known serotype was found to be a member of enterovirus group D. Laboratory diagnosis of human rhinovirus infection is based on reverse transcription polymerase chain reaction methods or the more tedious virus culture but a rapid "bedside" method is unavailable. Anti-rhinoviral therapy has been under extensive study over the past few decades but symptomatic treatment of the common cold is still the only useful approach in clinical use. More data on circulating human rhinovirus strains would facilitate both detection and treatment of these common pathogens.

Acute Disease↗
PubMed1990

Prepubertal periodontitis: a review of diagnostic criteria, pathogenesis, and differential diagnosis.

This paper reviews the literature on prepubertal periodontitis (PP) according to the definition and the classification of PP by Page. The generalized form of PP (G-PP) defined by Page was identified as the oral manifestation of a systemic disease called leukocyte adhesion deficiency (LAD) and thus the pathogenesis is known at the molecular level. On the other hand, the localized form of PP (L-PP) is a disease defined by clinical criteria and its pathogenesis is not known at the molecular level. The reported prevalence of L-PP differs widely in reports, according to the methodology and population studied. However, it seems to be at least 0.84% or greater. Potential periodontal pathogens that have been associated with L-PP include the following bacteria: Actinobacillus actinomycetemcomitans (A.a.), Bacteroides intermedius, Bacteroides gingivalis, Capnocytophaga sputigena, and Eikenella corrodens. Suggested contributing factors have included PMN or monocyte chemotactic defects and cementum defects. There is no unique pattern of bone loss in L-PP; however, there may be a type of periodontitis that affects all deciduous teeth, in the absence of LAD. L-PP may lead to localized juvenile periodontitis (LJP) or generalized juvenile periodontitis (GJP). Histiocytosis X, hypophosphatasia and mild forms of blood dyscrasias may have minimal or no clinical signs and symptoms except for alveolar bone loss. Therefore diseases known to be associated with alveolar bone loss must be definitively excluded in prepubertal children until the pathogenesis of L-PP at the cellular and molecular levels is understood and L-PP can be definitively diagnosed either as a distinct disease entity or entities.

Adolescent↗
PubMed2000

Collagens, the basic proteins of the human body.

Collagens are structural elements of many tissues in the human body. The family of collagens can be divided into fibrillar and non-fibrillar collagens. The criterion of the classification is the structure of these proteins. Mutations in the genes encoding collagens cause a variety of human diseases that include osteogenesis imperfecta, some forms of osteoporosis, chondrodysplasias, some types of Ehlers-Danlos syndrome, arterial and intracranial aneurysms, epidermolysis bullosa and the renal disease known as Alport syndrome. The detection of mutations is important both scientifically and clinically. Defining the molecular defects underlying a disorder helps in the understanding of not only the properties of the mutated protein but also the function of the normal protein. Even though many mutations in the genes encoding collagens have been described, the pathogenic consequences of some of the mutations are not fully understood. The important rationale for mutation detection is the clinical use of molecular diagnostics in genetic counselling and differential diagnosis.

Journal Article↗
PubMed1980

Group B streptococcus-comparison of Streptococcus agalactiae isolated from humans and cows in the Republic of South Africa.

The serological and biochemical characteristics of 100 strains of Streptococcus agalactiae isolated from quarter mild of dairy cows and of 107 strains cultured from various sites of human patients, were determined and compared. All the isolates were CAMP-phenomenon and Na-hippurate positive, aesulin negative, fell into Lancefield's Group B and could be placed into one of the 6 recognised serotypes. No human isolates fell into type R but for the rest all the other types were represented in the series of bovine and human cultures. In order of frequency, the human isolates were of type III, II, Ib, X and Ia and the bovine of type II, X, III, Ia, Ib and R. Of the human and bovine cultures respectively, 34 and 96% altered litmus milk, 30 and 100% were sensitive to bacitracin, 32 and 4% were pathogenic to mice, 82 and 93% reduced the ultimate pH of glucose broth to 4,2-4,8, 36 and 100% fermented lactose, 93 and 99% salicin and 94 and 79% trehalose. Concerning the combination of lactose/salicin fermentation, 35 and 95% of bovine and human isolates were , 0 and 5% were , 59 and 0% were -/=nd 7 and 0% were -/-. Data are summarised in 5 tables and discussed against the background of reports from other countries. It appears that a proportion of the human infections concern organisms likely to have been derived from bovine sources, either directly or indirectly. Definite classification of South African GBS into either human or animal strains does not seem possible. It is concluded that it would be more correct to refer to the source of an isolate instead of inferring that because the organism was primarily cultured from, say human resources, it is necessarily a human "strain'.

Adolescent↗
PubMed2004

Changes in stone composition according to age and gender of patients: a multivariate epidemiological approach.

Urinary stone incidence and composition have changed markedly over the past half-century in industrialized countries, in parallel with profound changes in living standards and dietary habits, with a dramatic increase in the incidence of calcium oxalate stones. However, studies evaluating the influence of age and gender on the distribution of the various types of urinary calculi are scarce. We report the results of a study based on 27,980 calculi (from 19,442 males and 8,538 females) analyzed by infrared spectroscopy between 1976 and 2001. The relationships between age and sex and stone composition were investigated using a multivariate approach, based on correspondence factor analysis (CFA). We found a male predominance for calcium oxalate and uric acid, a female preponderance for calcium phosphate and struvite stones, and an increasing prevalence of uric acid stones with age in both genders. CFA was able to reconstruct in blind the age curve from stone composition. The first two axes of the multidimensional classification, which correspond to age, included 86.9% of the total variance, indicating that age was the main factor involved in stone type. Superimposition of age classes and stone components showed a strong relationship between age and whewellite, weddellite, brushite, carbapatite, octacalcium phosphate and uric acid, while other substances (whitlockite, amorphous carbonated calcium phosphate, struvite, proteins, mucopolysaccharides, triglycerides or ammonium urate) appeared weakly related to age. In addition, CFA suggests the role of common lithogenic factors between weddellite, carbapatite and brushite, which clustered in the same area, whereas the various crystalline forms of phosphate stones segregated into two different clusters, suggesting distinct pathogenic factors. In conclusion, this study provides a picture of the present epidemiology of urinary stones in France. CFA helped to confirm: (1) an etiopathogenic distinction between weddellite and whewellite, (2) etiopathogenic associations between chemical compounds, which were only suspected on a clinical basis, and (3) suggested yet unrecognized associations, especially with respect to the heterogeneous group of phosphate stones.

Adolescent↗
PubMed1999

An automated comparative analysis of 17 complete microbial genomes.

MOTIVATION: As sequenced genomes become larger and sequencing becomes faster, there is a need to develop accurate automated genome comparison techniques and databases to facilitate derivation of genome functionality; identification of enzymes, putative operons and metabolic pathways; and to derive phylogenetic classification of microbes. RESULTS: This paper extends an automated pair-wise genome comparison technique (Bansal et al., Math. Model. Sci. Comput., 9, 1-23, 1998, Bansal and Bork, in First International Workshop of Declarative Languages, Springer, pp. 275-289, 1999) used to identify orthologs and gene groups to derive orthologous genes in a group of genomes and to identify genes with conserved functionality. Seventeen microbial genomes archived at ftp://ncbi.nlm.nih.gov/genbank/genomes have been compared using the automated technique. Data related to orthologs, gene groups, gene duplication, gene fusion, orthologs with conserved functionality, and genes specifically orthologous to Escherichia coli and pathogens has been presented and analyzed. AVAILABILITY: A prototype database is available at ftp://www.mcs.kent.edu/arvind/intellibio / orthos.html. The software is free for academic research under an academic license. The detailed database for every microbial genome in NCBI is commercially available through intellibio software and consultancy corporation (Web site: http://www.mcs.kent.edu/årvind/intellibio . html). CONTACT: arvind@mcs.kent.edu.

Algorithms↗
PubMed2000

Human immunodeficiency virus type 2 (HIV-2) in Portugal: clinical spectrum, circulating subtypes, virus isolation, and plasma viral load.

The human immunodeficiency virus type 2 (HIV-2) is responsible for 4. 5% of AIDS cases in Portugal. Six HIV-2 subtypes have been described so far, subtype A being proposed as more pathogenic than the rest. The relationship between the clinical status and levels of both cellular and plasma HIV-2 viraemia is not well known, nor their modifications under antiretroviral therapy. Thirty-two consecutive HIV-2 infected persons (17 men, 15 women) attending two different hospitals in Lisbon in 1997 were enrolled prospectively in the study. All but 4 individuals most likely acquired the infection through heterosexual contact. More than half of the study population was of African origin, mainly from Guinea-Bissau. Eleven (34.4%) patients had developed clinical manifestations included within the B or C groups of the CDC classification system for HIV infection, with the rest being asymptomatic. Half of the population was undergoing antiretroviral treatment at the time of the study. HIV-2 subtypes were investigated using a new Nef-based restriction fragment length polymorphism (RFLP) method that allows differentiation of the main two variants, A and B. Plasma viral load was quantified using a new quantitative competitive reverse transcriptase polymerase chain reaction (QcRT-PCR) procedure as well as the Amp-RT assay. Virus isolation was attempted from peripheral blood mononuclear cells. All but one person carried HIV-2 subtype A. Plasma viraemia examined by QcRT-PCR was measurable in 15 (50%) of 30 subjects, yielding in all instances values below 20,000 HIV-2 RNA copies per ml. Plasma RT activity could be detected in only 10 (33%) of 30 subjects, a rate much lower than that seen in HIV-1 infection. Virus was isolated from 16 (53.3%) of 30 patients. A significant correlation was found between CD4+ counts, clinical status, rate of virus isolation, and plasma viral load by both QcRT-PCR and Amp-RT. In conclusion, HIV-2 subtype A is the predominant variant circulating in Portugal among both natives and immigrants. A lower cellular and plasma viral load with respect to HIV-1 was seen in persons without immunosuppression, from whom the rate of virus recovery was extremely low.

Female↗
PubMed2006

A phloem-enriched cDNA library from Ricinus: insights into phloem function.

The aim of this study was to identify genes that are expressed in the phloem. Increased knowledge of phloem regulation will contribute to our understanding of its many roles, from transport of solutes to information about interactions with pathogens. A cDNA library constructed from phloem-enriched sap exuding from cut Ricinus communis (L.) hypocotyls was sequenced. To assess contamination from other tissues, two libraries were constructed: one using the first 15 min of exudation and the other from sap collected after 120 min of exudation had elapsed. Of 1012 clones sequenced, 158 unique transcripts were identified. The presence of marker molecules such as profilin, the low occurrence of chloroplast-related mRNAs, and the sieve element localization of constituent mRNA using in situ hybridization were consistent with a phloem origin of the sap. Functional analysis of the cDNAs revealed classifications including ribosomal function, interaction with the environment, transport, DNA/RNA binding, and protein turnover. An analysis of the closest Arabidopsis thaliana (L.) homologue for each clone indicated that genes involved in cell localization, protein synthesis, tissue localization, organ localization, organ differentiation, and cell fate were represented at twice the level occurring in the whole Arabidopsis genome. The transcripts found in this phloem-enriched library are discussed in the context of phloem function and the relationship between the companion cell and sieve element.

Amino Acids↗