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.

SourceResearch connectionFrom yearThrough year

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

At least 667 records · Page 37Linked to original sources

PubMed2005

Study on some molecular characterization of Babesia orientalis.

The study on buffalo babesiosis indicated that its pathogen was different from other Babesia on many aspects such as morphology, transmission and pathogenicity. Therefore, it was named as a new species-Babesia orientalis. In order to prove the validity of this taxon, molecular taxonomic study on the pathogen was done in this experiment. The complete 18S rRNA gene sequence of B. orientalis was determined by PCR. It was sequenced and blasted. The results indicated that the classification of the parasite belonged to the genus Babesia. The 1700 bp complete sequence was compared with 15 other Babesia sp. available in GenBank. The data were analyzed and a phylogenetic tree was established. The results indicated that the hereditary distance of the parasite was close to that of Babesia sp. from South Africa and Babesia ovis, and the hereditary distance was far from Babesia bigemina and B. bovis.

Animals↗

PubMed1991

Phylogenetic analysis of five medically important Candida species as deduced on the basis of small ribosomal subunit RNA sequences.

The classification of species belonging to the genus Candida Berkhout is problematic. Therefore, we have determined the small ribosomal subunit RNA (srRNA) sequences of the type strains of three human pathogenic Candida species; Candida krusei, C. lusitaniae and C. tropicalis. The srRNA sequences were aligned with published eukaryotic srRNA sequences and evolutionary trees were inferred using a matrix optimization method. An evolutionary tree comprising all available eukaryotic srRNA sequences, including two other pathogenic Candida species, C. albicans and C. glabrata, showed that the yeasts diverge rather late in the course of eukaryote evolution, namely at the same depth as green plants, ciliates and some smaller taxa. The cluster of the higher fungi consists of 10 ascomycetes and ascomycete-like species with the first branches leading to Neurospora crassa, Pneumocystis carinii, Candida lusitaniae and C. krusei, in that order. Next there is a dichotomous divergence leading to a group consisting of Torulaspora delbrueckii, Saccharomyces cerevisiae, C. glabrata and Kluyveromyces lactis and a smaller group comprising C. tropicalis and C. albicans. The divergence pattern obtained on the basis of srRNA sequence data is also compared to various other chemotaxonomic data.

Base Sequence↗

PubMed2026

Phenotypic manifestations and variant reclassification of germline PTEN variants: a nationwide Danish study.

BACKGROUND: Classification of heterozygous germline PTEN variants in patients with, or suspected of having, PTEN hamartoma tumour syndrome (PHTS) remains challenging. Accurate classification is essential as these patients require lifelong cancer surveillance. METHODS: We identified all patients with a PTEN variant previously classified as a variant of uncertain significance (VUS), likely pathogenic (LP) or pathogenic (P), collected clinical data and reclassified all variants using the latest PTEN gene-specific American College of Medical Genetics (ACMG) guidelines. Moreover, genotype-phenotype correlations were assessed. RESULTS: 167 patients from 112 families were enrolled. Eighty-seven unique PTEN variants were identified, including 20 novel variants. After applying the PTEN gene-specific ACMG guidelines, 32 variants (36.8%) were reclassified, resulting in 60 PTEN variants classified as LP/P (69.0%), 18 variants classified as VUS (20.7%), while 9 variants were classified as LB/B (10.3%). Genotype-phenotype correlation was performed among 104 patients with LP/P variants: 51 cancer cases were recorded in 41 patients and a distinct PHTS phenotype was observed in 25% of patients, with macrocephaly being present in 99% of patients with a known head circumference. Twenty-three patients had neurodevelopmental delay and/or autism, and we observed an increased prevalence of missense variants in these patients. CONCLUSION: We identified 87 different PTEN variants, and application of PTEN gene-specific ACMG guidelines led to reclassification of 32 variants (36.8%), underscoring the importance of regular variant reassessment using the most recent gene-specific guidelines, ensuring optimal patient management and surveillance.

Genetic Predisposition to Disease↗

PubMed2002

[Bullous pemphigoid, primary biliary cirrhosis and vitiligo: a multiple autoimmune syndrome?].

Bullous pemphigoid is the most frequent autoimmune blistering skin disease. There have been few reports of an association with primary biliary cirrhosis and vitiligo. We report the simultaneous occurrence of bullous pemphigoid and primary biliary cirrhosis in an 86-year-old patient who also suffered from vitiligo. Multiple autoimmune syndrome, proposed by Humbert and Dupond, can be divided into three groups based on preferential associations of autoimmune disorders. The association of bullous pemphigoid, cirrhosis biliary primary and vitiligo has been reported three times in the literature. This association is probably not fortuitous and suggests a pathogenic relationship. This association is not typical of the multiple autoimmune syndrome as defined by Humbert and Dupond but the collection of such observations may contribute to revise the classification of autoimmune disease and provide a better understanding of the pathophysiological mechanisms of autoimmunity.

Adrenal Cortex Hormones↗

PubMed2004

Probing Norwalk-like virus presence in shellfish, using artificial neural networks.

A database was examined using artificial neural network (ANN) models to investigate the efficacy of predicting PCR-identified Norwalk-like virus presence and absence in shellfish. The relative importance of variables in the model and the predictive power obtained by application of ANN modelling methods were compared with previously developed logistic regression models. In addition, two country-specific datasets were analysed separately with ANN models to determine if the relative importance of the input variables was similar for geographically diverse regions. The results of this analysis found that ANN models predicted Norwalk-like virus presence and absence in shellfish with equivalent, and better, precision than logistic regression models. For overall classification performance, ANN modelling had a rate of 93%, vs 75% for the logistic regression. ANN models were able to illuminate the site-specific relationships between indicators and pathogens.

Databases, Factual↗

PubMed2006

Melanocortin 4 receptor mutations in a large cohort of severely obese adults: prevalence, functional classification, genotype-phenotype relationship, and lack of association with binge eating.

CONTEXT: Heterozygous mutations in the melanocortin-4 receptor (MC4R) gene are the most common monogenic form of severe obesity in children. There are conflicting reports regarding the prevalence, nature, and pathogenic effects of MC4R mutations in adults with severe late-onset obesity. OBJECTIVE: Our objective was to determine the prevalence of MC4R mutations in a cohort of severely obese adults and to determine the clinical phenotype and the phenotype-genotype relationship within adult MC4R mutation carriers. DESIGN AND SETTING: We conducted an observational study at a referral center. PATIENTS OR OTHER PARTICIPANTS: Participants included 769 adult patients with body mass index of at least 35 kg/m(2) and 444 nonobese control individuals. INTERVENTIONS: There were no interventions. MAIN OUTCOME MEASURES: We assessed the prevalence of pathogenic MC4R mutations, functional characteristics of the detected mutations, phenotype, and phenotype-genotype relationship within mutation carriers. RESULTS: The global prevalence of obesity-specific MC4R mutations was 2.6%, and the 95% confidence interval (CI(95)) was 1.5-3.7. The prevalence of MC4R mutations was similar in patients developing obesity in childhood (2.83%; CI(95), 0.9-4.8) and in patients with a later onset of the disease (2.35%; CI(95), 0.9-3.8). Adult obese MC4R mutation carriers did not present with binge eating or with any specific clinical phenotype. The severity of the functional alterations of the mutated MC4Rs and in particular the intracellular retention of the receptor correlates both with the severity and the onset of the obesity in the mutation carriers. CONCLUSIONS: Obese adult carriers of functionally relevant MC4R mutations do not specifically present with binge-eating disorder or a history of early-onset obesity. The onset and severity of the obesity in the carriers is related to the functional severity of the MC4R mutations.

Adult↗

PubMed1993

Classification and diagnosis of periodontal diseases.

The classic periodontal diseases are gingivitis and periodontitis; there are, however, numerous and distinct types of both of these diseases. These types of diseases are distinguished by age of onset, clinical appearance, rate of disease progression, pathogenic microbial flora and systemic influences. Determining the type of periodontal disease a patient has requires a proper medical and dental history, a thorough periodontal examination and recording, and possible additional tests such as identification of subgingival flora and medical laboratory tests. Specific periodontal diagnosis will lead to more rational and efficient patient management.

Gingivitis↗

PubMedDate not supplied

Phylogenetic relationship of equine Actinobacillus species and distribution of RTX toxin genes among clusters.

Equine Actinobacillus species were analysed phylogenetically by 16S rRNA gene (rrs) sequencing focusing on the species Actinobacillus equuli, which has recently been subdivided into the non-haemolytic A. equuli subsp. equuli and the haemolytic A. equuli subsp. haemolyticus. In parallel we determined the profile for RTX toxin genes of the sample of strains by PCR testing for the presence of the A. equuli haemolysin gene aqx, and the toxin genes apxI, apxII, apxIII and apxIV, which are known in porcine pathogens such as Actinobacillus pleuropneumoniae and Actinobacillus suis. The rrs-based phylogenetic analysis revealed two distinct subclusters containing both A. equuli subsp. equuli and A. equuli subsp. haemolyticus distributed through both subclusters with no correlation to taxonomic classification. Within one of the rrs-based subclusters containing the A. equuli subsp. equuli type strain, clustered as well the porcine Actinobacillus suis strains. This latter is known to be also phenotypically closely related to A. equuli. The toxin gene analysis revealed that all A. equuli subsp. haemolyticus strains from both rrs subclusters specifically contained the aqx gene while the A. suis strains harboured the genes apxI and apxII. The aqx gene was found to be specific for A. equuli subsp. haemolyticus, since A. equuli subsp. equuli contained no aqx nor any of the other RTX genes tested. The specificity of aqx for the haemolytic equine A. equuli and ApxI and ApxII for the porcine A. suis indicates a role of these RTX toxins in host species predilection of the two closely related species of bacterial pathogens and allows PCR based diagnostic differentiation of the two.

Actinobacillus↗

PubMed1997

Comparative sensitivity of 13 species of pathogenic bacteria to seven chemical germicides.

BACKGROUND: The relative resistance of diverse human bacterial pathogens to commonly used germicidal agents has not been established. METHODS: We measured by titration the survival of thirteen different bacteria after exposure to glutaraldehyde, formaldehyde, hydrogen peroxide, peracetic acid, cupric ascorbate, sodium hypochlorite, or phenol. RESULTS: Our comparative experiments allowed classification of the organisms' survival into four groups: (a) Pseudomonas aeruginosa and Staphylococcus aureus showed the most resistance, (b) Clostridium perfringens, Salmonella typhimurium, Staphylococcus epidermidis, and Escherichia coli O157:H7 showed intermediate resistance, (c) Listeria monocytogenes, Shigella sonnei, and Vibrio parahaemolyticus survived some treatments with chemical agents only in the presence of protecting protein (serum albumin), and (d) Vibrio cholerae, Vibrio vulnificus, Bacillus cereus, and Yersinia enterocolitica did not survive any of the treatments applied. CONCLUSION: We found species that more frequently survived exposure to germicidal agents were also those most commonly reported in association with hospital infections. Our findings suggest that resistance to disinfectants may be more important than pathogenicity in determining the relative prominence of an organism as an agent responsible for nosocomial infections.

Bacteria↗

PubMed2006

Eosinophilic mucus chronic rhinosinusitis: clinical subgroups or a homogeneous pathogenic entity?

BACKGROUND: Eosinophilic mucus chronic rhinosinusitis (EMCRS) can be subclassified using the criteria of detection of fungi in eosinophilic mucus and systemic fungal allergy. Allergic fungal sinusitis (AFS), a subgroup of EMCRS characterized by the presence of fungal allergy, is proposed to be an immunoglobulin (Ig)E-driven disease, distinct from other EMCRS subgroups. However, our recent studies cast doubt on the central pathogenic role of allergy in AFS. The purpose of this study was to examine the clinical features of EMCRS patients from the different subcategories to determine the relevance of this classification system. METHOD: The demographic, clinical, and immunologic characteristics of the EMCRS subgroups were examined prospectively and compared with three control groups: healthy volunteers, allergic rhinitis with fungal allergy, and chronic rhinosinusitis without eosinophilic mucus. RESULTS: EMCRS patients with allergy were younger than those without. There was no significant difference in clinicopathologic parameters between EMCRS subgroups. As a single group, EMCRS had a more severe sinus disease compared with chronic rhinosinusitis patients. CONCLUSIONS: AFS was not clinically distinct from other subgroups of EMCRS. However, eosinophilic mucus may mark a more severe and distinct form of sinus disease.

Adult↗

PubMed2007

Assessment and treatment of pulmonary arterial hypertension: an Australian perspective in 2006.

Pulmonary arterial hypertension is a group of diseases which forms a small subset of those with elevated pulmonary artery pressure (pulmonary hypertension). The recent development of selective pulmonary vasodilator has lead to a substantial resurgence of interest in what have been previously regarded as rare and incurable diseases. This review aims to describe the spectrum of pulmonary vascular diseases, the evolving understanding as to pathogenesis, the evolving evidence of efficacy for drug therapies, trying to put this into a contemporary Australian context. Several key pathogenic pathways may be involved: prostacycline, Nitric Oxide-cGMP-phosphodiesterase 5 and endothelin- all of which are exploited for therapeutic benefit by newly available drug therapies. A recently modified classification system reasserts the importance of precise diagnosis. The cardinal symptom of exertional dyspnea warrants careful evaluation in an attempt to prevent (frequently occurring) substantial delay in diagnosis. Echocardiogram is the cornerstone of screening for pulmonary arterial hypertension; however, a detailed evaluation including a carefully performed right heart catheterisation with sufficient data to allow calculation of pulmonary vascular resistance is key to accurate diagnosis. These new approaches to therapy are already substantially improving quality of life and prognosis.

Adolescent↗

PubMed2003

Application and refinement of the WHO risk framework for recreational waters in Sydney, Australia.

Local adaptation of the World Health Organisation (WHO) Farnham approach to managing pathogen risk in recreational waters was readily achieved given the extensive microbiological beach data for Sydney, and a clear understanding of applying the 'Annapolis Protocol' sanitary survey component to beach classification. Daily enterococci counts were predicted by rainfall (>10 mm in 24 h or >5 mm over 4-5 days), or by wind direction/speed, sunlight and tide during dry periods. Quantitative microbial risk assessment models (maximum risk exponential model for gastroenteritis and adenovirus exponential model for respiratory illness) fitted the United Kingdom epidemiological data and show potential for use. Flexibility in interpreting what is important for local conditions is essential, illustrated by replacing the general descriptions in the Farnham report with more ridged values for stormwater-impacted beaches. Hence, a user-friendly format for bather risk management, based on key environmental predictors of faecal pollution (such as rainfall, wind direction and tide) should largely replace the need for regular and costly microbiological testing; providing risk estimates in real time and allowing immediate control measures, such as signage or temporary beach closures. Ongoing testing resources should be directed to understanding the source(s) of faecal contamination, comparing enterococci/enteric virus survival under warm Australian conditions and spot checks for recalibration of environmental factors.

Calibration↗

PubMedDate not supplied

[Netilmicin in the treatment of bacterial respiratory tract infections].

Netilmicin - a semisynthetic aminoglycoside - was administered to 33 patients with the acute or chronic lower respiratory tract or pulmonary infections in a daily dose of 5 mg/kg body weight for 10 days. A principle criterium of patients classification to netilmicin therapy were sensitive bacterial strains either in sputum or in BAL liquid. A significant clinical improvement was noted in 88% of the treated patients. However, elimination of pathogens from the sputum was achieved only in 52% of these patients. No improvement was observed in 4% of the treated patients. No adverse reactions were noted. Netilmicin proved safe and effective antibacterial agent in patients with respiratory infections.

Adult↗

PubMed1987

[Severe and extensive algodystrophies and malignant tumors. Apropos of 4 cases].

The authors report on 4 cases of particularly severe and extensive reflex neurovascular dystrophy, whose clinical course was marked by the onset of a malignant tumor, without any sign of improvement in the reflex neurovascular dystrophy, despite various therapeutic regimens, until the patient's death from malignancy. At this time, the authors compiled a total of 63 case reports (4 of which were reported) and have proposed a classification to differentiate 4 types of disorders in combination according to whether there is a very probable, probable, or possible link or whether the combination is strictly a coincidence. The pathogenic mechanism remains a mystery, when a link is observed; but it never corresponds to criteria to describe a paraneoplastic disorder. Finally, the authors insist on the practical value of detecting this combination, even if due to chance: in order to systematically detect cancer in the presence of any reflex neurovascular dystrophy, and especially to be conscious of a possible reflex neurovascular dystrophy, besides possible metastatic lesions, in the presence of osteoarticular pain present in a patient with cancer. Such a diagnosis, although difficult to realize, has great prognostic and therapeutic interest.

Aged↗

PubMed2005

Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species.

Extracellular proteins of bacterial pathogens play a crucial role in the infection of the host. Here we present the first comprehensive validation of the secretory subproteome of the Gram positive pathogen Listeria monocytogenes using predictive bioinformatic and experimental proteomic approaches. The previous original signal peptide (SP) prediction (Glaser et al., Science 2001, 294, 849-852) has been greatly improved by an in-depth analysis using seven different bioinformatic tools. Subsequent careful classification of the resulting data gives a probability dependent annotation of 121 putatively secreted proteins of which 45 are novel. Complementary proteomic analysis using both two-dimensional gel electrophoresis/matrix assisted laser desorption/ionization mass spectrometry and high performance liquid chromatography/electrospray ionization-mass spectrometry has identified 105 proteins in the culture supernatant of L. monocytogenes. Among these, we were able to detect all the currently known virulence factors with an SP showing the importance of this subproteome and demonstrating the reliability of the techniques used. The comparison between the L. monocytogenes wildtype and the nonpathogenic species Listeria innocua was performed to reveal proteins probably involved in pathogenicity and/or the adaptation to their respective lifestyles. In addition to the eight known virulence factors, all of which have no orthologous genes in L. innocua, eight additional proteins have been identified that exhibit the typical key feature defining the known listerial virulence factors. Further significant differences between the two species are evident in the group of cell wall and secretory proteins that warrant further study. Our investigation clearly demonstrates that the major difference between the pathogenic and nonpathogenic species, noted in the comparative genome analysis, manifests itself strongest in the secretome.

Bacterial Proteins↗

PubMed2001

Natural anti-FcepsilonRIalpha autoantibodies isolated from healthy donors and chronic idiopathic urticaria patients reveal a restricted repertoire and autoreactivity on human basophils.

The role of autoantibodies against the alpha-subunit of the human high-affinity IgE receptor (FcepsilonRIalpha) in the pathogenesis of chronic idiopathic urticaria (CIU) is controversial. We have shown that these antibodies are widespread, apparently non-pathogenic and belong to the natural antibody repertoire. To clarify this controversy, we constructed antibody libraries from both healthy donors and CIU patients with active disease. Here we describe the first three high affinity IgM anti-FcepsilonRIalphaautoantibodies isolated from normal and urticaria libraries. Sequence analysis revealed germline VH in both cases paired with a slightly mutated VL, thus supporting their classification as natural antibodies. Strikingly, one major IgM clone was present in both CIU patients and normal donors. The anti-FcepsilonRIalpha autoantibodies recognize FcepsilonRIalpha on cells, but are non-anaphylactogenic on blood basophils, except when IgE is removed from the receptor. Based on their functional activities we propose a concept of "conditional autoimmunity" where natural anti-FcepsilonRIalphaautoantibodies can become pathogenic dependent on the state of occupancy of the FcepsilonRIalpha by its natural ligand IgE.

Animals↗

PubMed2026

Core genome and whole genome multi-locus sequence typing of Cronobacter isolates.

UNLABELLED: Cronobacter species, especially C. sakazakii and C. malonaticus, are opportunistic pathogens that are linked to severe infections in infants with high case fatality rates. In this study, we investigated whole genome sequencing (WGS) analysis approaches, specifically 7-gene multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) to subtype Cronobacter isolates. We analyzed a comprehensive set of 743 Cronobacter isolates derived from clinical, food, and environmental sources. We also evaluated high-quality single nucleotide polymorphism (hqSNP), cgMLST, and wgMLST to cluster epidemiologically related and differentiate sporadic C. sakazakii isolates. Our results indicate that both cgMLST and wgMLST accurately identify closely related isolates and are consistent with epidemiological findings. The allele-based analyses were also comparable with hqSNP analyses, the current gold standard. Our workflow also outputs 7-gene MLST allele calls, Cronobacter sequence types, and clonal complexes, which may be useful for historic comparisons during outbreak investigations. Following the recent classification of Cronobacter infections as nationally notifiable in the United States, our findings demonstrate the efficacy of WGS-based approaches within the PulseNet framework to improve outbreak detection and response strategies for Cronobacter. IMPORTANCE: Cronobacter species, specifically C. sakazakii and C. malonaticus, are opportunistic pathogens linked to severe infections in infants with high case fatality rates. This study highlights the critical importance of advanced molecular techniques in public health surveillance, using whole genome sequencing (WGS) methodologies such as multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST). The validation of these WGS-based approaches within the PulseNet framework is timely, especially following the recent classification of Cronobacter infections as nationally notifiable in the United States. WGS methods not only enhance outbreak detection but can also inform public health guidance aimed at preventing infections and reducing mortality in vulnerable populations, especially infants. Our research supports implementation of cgMLST as a standardized approach for routine PulseNet surveillance of Cronobacter, with wgMLST and hqSNP analyses providing additional discriminatory power for outbreak investigations and high resolution phylogenetic analysis.

Multilocus Sequence Typing↗

PubMed2000

Molecular and biochemical classification of plant-derived food allergens.

Molecular biology and biochemical techniques have significantly advanced the knowledge of allergens derived from plant foods. Surprisingly, many of the known plant food allergens are homologous to pathogenesis-related proteins (PRs), proteins that are induced by pathogens, wounding, or certain environmental stresses. PRs have been classified into 14 families. Examples of allergens homologous to PRs include chitinases (PR-3 family) from avocado, banana, and chestnut; antifungal proteins such as the thaumatin-like proteins (PR-5) from cherry and apple; proteins homologous to the major birch pollen allergen Bet v 1 (PR-10) from vegetables and fruits; and lipid transfer proteins (PR-14) from fruits and cereals. Allergens other than PR homologs can be allotted to other well-known protein families such as inhibitors of alpha-amylases and trypsin from cereal seeds, profilins from fruits and vegetables, seed storage proteins from nuts and mustard seeds, and proteases from fruits. As more clinical data and structural information on allergenic molecules becomes available, we may finally be able to answer what characteristics of a molecule are responsible for its allergenicity.

Allergens↗