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Results for “pathogenicity classification”

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At least 145 records · Page 8Linked to original sources
PubMed2026

[Genetic and functional characterization of a novel KIT splicing variant in a Chinese three-generation pedigree with piebaldism].

OBJECTIVES: To investigate the genetic etiology of a three-generation pedigree affected with piebaldism. METHODS: Next-generation sequencing and Sanger sequencing were employed to detect and verify gene variants. Bioinformatics tools were used to predict the effects of candidate variants on splicing and protein function. RT-PCR and Sanger sequencing were further performed to validate the impact of the variant on RNA splicing, and homology modeling was applied to predict its effect on the three-dimensional structure of the KIT protein. The pathogenicity of the variant was then classified according to the guidelines of the American College of Medical Genetics and Genomics (ACMG) and the UK Association for Clinical Genomic Science (ACGS). RESULTS: A heterozygous insertion variant near the splice site, c.1990+8_1990+9insTGCACCATTGGAGGTAAA, was identified in the KIT gene in the proband and was found to co-segregate with the phenotype within the family. RT-PCR and cDNA sequencing revealed that this variant led to aberrant splicing during transcription, resulting in a 21 bp in-frame insertion in the mRNA, which encodes an extra 7 amino acids within the tyrosine kinase domain and may thus affect protein function. In silico predictions, together with the experimental findings, supported classification of this variant as likely pathogenic according to relevant variant interpretation guidelines. CONCLUSIONS: The heterozygous splice-site insertion variant KIT:c.1990+8_1990+9insTGCACCATTGGAGGTAAA is the genetic cause of piebaldism in this pedigree.

Genetics diagnosis↗
PubMed1997

The challenge of postoperative infections: does the surgeon make a difference?

Postoperative infections remain a challenge in many surgical procedures despite improved surgical technique and powerful antibiotics. The number of sepsis cases has tripled from 1979 to 1992 due to increased invasive procedures in older and immune-suppressed patients. Increasingly, in recent years, outbreaks of resistant pathogens have been published, provoking the question of how postoperative infections and resistant pathogens should be dealt with. Wound classification and risk stratification were developed to identify patients at risk for postoperative infection. However, other important intrinsic factors of the patient were not included, and further attempts have been made to increase sensitivity and specificity (eg, Study on the Efficacy of Nosocomial Infection Control project, National Nosocomial Infection Surveillance System score); the American Society of Anesthesiologists preoperative assessment score and the operation duration for specific procedures were introduced into the system as risk stratifiers. Advances in immunology have identified new ways in which the surgeon can moderate the immune response (eg, hemorrhage and blood transfusion-induced immune suppression). The increased rate of resistance in enterococci and staphylococci has refocused attention on infection control in surgery. However, there are recent reports from both sides of the Atlantic indicating that guidelines for infection control and antibiotic policy have not become reflected in standard procedures in many hospitals. New antibiotics may be developed, but resistance soon may follow. Sound techniques in surgery, with careful infection control and antibiotic policies, may be the only strategy to prevent further increases in resistance of pathogens in postoperative infections.

Antibiotic Prophylaxis↗
PubMed1981

Early diagnosis and prompt treatment by surgery in Jorge Lobo's disease (keloidal blastomycosis).

In 1931 the Brazilian doctor Jorge Lobo examined a patient from the Amazon Basin who had nodular confluent skin lesions over the lumbosacral region and encountered a new fungus pathogenic for man Paracoccidioides loboi. This classification was based on the morphological aspect of the parasite which was very similar to Paracoccidioides brasiliensis the causative agent of a systemic mycosis Paracoccidioidomycosis or South American Blastomycosis. Other authors use the name Loboa loboi. The final determination of the name must await cultivation of the fungus.

Adult↗
PubMed1988

Infections caused by antibiotic-resistant Corynebacterium group D2.

A coryneform bacteria known as Corynebacterium group D2 pending definitive taxonomic classification, has emerged as a human pathogen. Although first described 16 years ago, the organism has only recently been implicated in clinical infections. It differs from all previously recognized species of Corynebacterium, and in common with Corynebacterium jeikeium exhibits a broad spectrum of antimicrobial resistance, being sensitive to only vancomycin, teicoplanin and some quinolones. The microorganisms is mainly involved in urinary tract infections, and its strong urease activity seems to play an important role in its pathogenicity. Corynebacterium jeikeium and group D2 are very different from the clinical and microbiological point of view. Corynebacterium group D2, like other coryneform bacteria, may be isolated from healthy skin in hospitalized patients, mainly females, while Corynebacterium jeikeium is more prevalent in males. Microbiologists should be aware that such a slow-growing microorganism may be responsible for clinical infections and should not be overlooked in routine cultures of clinical specimens.

Anti-Bacterial Agents↗
PubMed1990

Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level.

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationship among different serovars of the Mycobacterium avium-M. intracellulare complex as well as to define signature nucleotides characteristic for different serovars. In general, the groups defined by rRNA sequencing reflect the classification obtained with sensitin tests and pathogenicity examinations in chickens. Unique 16S rRNA sequence patterns could be defined for (1) M. avium, (2) M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11, (3) M. intracellulare serovars 12, 13, 14, 15, 17, 19 and 20, (4) M. intracellulare serovar 7 and (5) M. intracellulare serovar 18. Phylogenetically, groups 1 and 2 on one hand and groups 3, 4 and 5 on the other hand each share a common ancestor. M. paratuberculosis was indistinguishable from M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11 by this kind of analysis.

Base Sequence↗
PubMed1975

Clinical aspects of bilateral renal dysplasia in children.

Despite recent attempts to improve classification and to provide data on pathogenic mechanisms, there is a paucity of information concerning the clinical aspects of bilateral renal dysplasia. Therefore, the clinical features and long-term prognosis of eight patients with bilateral renal dysplasia have been evaluated. Three important observations were made, namely (1) a large proportion of patients had an impairment of urinary concentration and acidification, (2) the clinical course was characterized by progressive renal deterioration in patients with bilateral involvement, and (3) four children with renal dysplasia had the clinical features of Laurence-Moon-Biedl syndrome.

Adolescent↗
PubMed1992

A cohort study of coagulase negative staphylococcal mastitis in selected dairy herds in Prince Edward Island.

The epidemiology and importance of coagulase negative staphylococcal (CNS) mastitis in Prince Edward Island had not been documented. To investigate this, a cohort of 84 cows at seven farms were quarter sampled eight times over a lactation, commencing with samples taken prior to drying off in the previous lactation. Thirteen species of CNS were isolated. The quarter prevalence of CNS mastitis varied from 4.8% to 6.4% in the first five months of lactation and increased to 14.2 to 16.6% in the last four months of lactation. The geometric mean somatic cell counts (SCC) for quarters infected with CNS and uninfected quarters were 90 x 10(3) and 64 x 10(3) respectively (difference significant at p > 0.005). The two month new infection risk of CNS was 9.0% while the two month elimination risk was 74.4%. Infection with CNS did not alter the risk of subsequent infection with Staphylococcus aureus. The results from this project support the classification of CNS as a minor pathogen in mastitis control programs.

Animals↗
PubMed1980

[Cephalic neural crests and disorders of craniofacial morphogenesis. Neurocristopathies (author's transl)].

To establish the pathogenicity, and attempt to define a classification of craniofacial malformations is a difficult task, both in animals and humans. Mention is often made of the classification developed by Paul Tessier, which according to this author "is neither based on a theory nor on an embryonic definition. It is the by-product of anatomical findings during clinical examination and operative dissections" (31). The authors propose an embryologic classification of facial malformations, based on disorders of embryonic development of cells derived from the neural crests (NC) of cephalic origin, and constituting the craniofacial ectomesenchyme. The importance of the cephalic NC derivatives in craniofacial morphogenesis is stressed, and the principal malformations of the cephalic shelf outlined, as a function of disorders occurring during the formation of the NC; migrations, proliferation, and differentiation of their derivatives. The main objective of this study was to formulate pathogenetic hypotheses, to propose a classification, and to stimulate interest in further studies in the realm of physiological and pathological craniofacial morphogenesis.

Bone Diseases, Developmental↗
PubMed2019

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants.

Variant interpretation in the era of massively parallel sequencing is challenging. Although many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here, we present the Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE), a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in variant call format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4000 pediatric cancer patients and serves as a repository for the expert-reviewed results. PeCanPIE was originally developed for pediatric cancer but can be easily extended for use for nonpediatric cancers and noncancer genetic diseases. Although PeCanPIE's web-based interface was designed to be accessible to non-bioinformaticians, its back-end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.

Child↗
PubMed1982

Fatty acid composition of mycobacterial lipids as an index of pathogenicity.

Five species of Mycobacterium were analyzed for the fatty acid composition of total and neutral lipids and of individual classes of phosphatides. The methyl esters of fatty acids were analyzed using the technique of gas liquid chromatography. It was found that myristic, palmitic, palmitoleic, and tuberculostearic acids were the major fatty acids present in all of the lipid components of these strains of tubercle bacilli. The ratio of unsaturated to saturated fatty acids is lowest in the most pathogenic strain, indicating a progressive increase in this ratio, and the highest ratio is represented by a saprophytic strain. An avian pathogenic organism falls in the center of this classification among the examined strains of mycobacteria. These results indicate that the ratio of unsaturated to saturated fatty acids of lipids can be used to determine and establish the pathogenic species of mycobacteria.

Animals↗
PubMed1977

[Classification of acute bacterial enteropathies].

The first part considers pathogenic microorganisms (Vibrio cholerae and parahaemolytic vibrio, Clostridium welchii, enteropathogenic E. coli, Shigella, Salmonella, other enterobacteria and pseudomonas. Yersinia, simply enterotoxic Staphylococcus and that producing acute enteritis) and the process of infection (formation of a surface link without endocellular penetration with elaboration of hexotoxins, formation of a surface link with subsequent intracellular penetration, submucosa penetration). The second part discusses Salmonellae on the basis of personal experience. Particular attention is paid to current aspects of Salmonella microbiological pathomorphosis, the various isolated serotypes in relation to carriers or patients, biochemical atypias of Salmonellae strains, present-day aspects of resistance to chemoantibiotic treatment and the transfer of Salmonella Wien resistances.

Bacterial Infections↗
PubMed1996

Demonstration of antigenic and genotypic variation in Orientia tsutsugamushi which were isolated in Japan, and their classification into type and subtype.

A total of 40 strains of Orientia tsutsugamushi (34 isolates from patients and trombiculid mites in Japan, and 6 prototype strains of antigenic variants) were examined for classification based on the reactivities with type-specific monoclonal antibodies in indirect immunofluorescence tests, and on the restriction fragment length polymorphism of a polymerase chain reaction (PCR)-amplified 56-kilodalton type-specific antigenic protein gene. By these methods, several antigenic and genotypic variants were found among the strains, and these variants were classified into types and further into subtypes. These results suggest that there are many variants in O. tsutsugamushi, and the methods used here seem to be useful for the systematic classification of the numerous variants. A strain which may be a new type distinguishable from those identified previously was also found in this study. Furthermore, variety in the degree of pathogenicity in mice related to type and/or subtype classification were observed.

Animals↗
PubMed1995

Practical approach to the management of prostatitis.

The management of prostatitis remains a frustrating problem for the clinical urologist. The various disease processes are poorly understood, the clinical presentation is extremely variable, the definitive diagnosis is difficult, and treatment is dismal. A sound clinical approach to the diagnosis and treatment of the various prostatitis syndromes by clarifying the etiology, rationalizing the classification, and describing a practical plan for diagnosis and a common sense approach to treatment is presented in this article. A combination of dysfunctional voiding and intraprostatic reflux of urine (sterile or infected) is the underlying pathogenic mechanism. Prostatodynia should be dropped from the classification of the prostatitis syndromes and should be relegated to the role of the most important differential diagnosis. Physicians who have abandoned the standard three-glass test of Meares and Stamey should consider the Pre- and Post-Massage Test (PPMT) for the diagnosis of prostatitis. An understanding of the pathogenic and etiologic mechanisms along with an appreciation of the importance of correct diagnosis at first presentation combined with a knowledge of the latest treatment studies will lead to improved management and treatment of patients with prostatitis.

Bacterial Infections↗
PubMed2026

Expansion of the allelic and phenotypic spectrum of MED25-related developmental disorder: novel compound heterozygous variants with structural domain implications.

MED25-related developmental disorder (Basel-Vanagaite-Smirin-Yosef syndrome) is a rare autosomal recessive disorder, defined by severe neurodevelopmental delay, corpus callosum abnormalities, ocular involvement, epilepsy, and marked facial appearance. MED25 pathogenic variants interfere with the functioning of the Mediator complex, which is responsible for RNA polymerase II transcription. We report a 9-year-old girl who presents with significant global developmental delay, agenesis of the corpus callosum, congenital cataracts, epilepsy, hypotonia, musculoskeletal abnormalities, and typical craniofacial features. Trio-based whole-exome sequencing revealed compound heterozygous variants in MED25: a maternally transmitted truncating variant (c.1366 C > T; p.Gln456*) and a paternally inherited missense variant (c.430 C > T; p.Leu144Phe). The new classification of the missense variant as potentially pathogenic is supported by a systematic ACMG re-evaluation supported by segregation analysis, phenotypic specificity, computational prediction, and structural localization in the MED25 Activator Interaction Domain (ACID). Comparative phenotypic analyses show strong agreement with reported cases but add more data to fine-tune clinical spectrum. This article broadens the allelic and phenotypic spectrum of MED25-related developmental disorder and highlights the need for comprehensive evaluation across molecular, structural, and phenotypic pathways to elucidate variant signature in rare genetic disease models correctly.

Humans↗
PubMed1990

[Pathogens and pathogenesis of dermatophytoses].

The principles of taxonomic and systematic classification of dermatophytes are described with an emphasis on the relevance of teleomorphic forms. Special attention is given to their relation to dimorphic fungi and the formation of arthroconidia as a parasitic growth form. The main factors contributing to pathogenicity of dermatophytes are explained, including enzymes (especially keratinases), allergens and leukotaxins. Genetic predisposition and the unspecific (serum factors, polymorphoneutrophilic granulocytes) and specific immunological mechanisms of host defence are differentiated and critically evaluated.

Arthrodermataceae↗
PubMed1992

Streptococcus milleri group: renewed interest in an elusive pathogen.

The following review examines the bacteriological characteristics, epidemiology, pathogenicity and antimicrobial susceptibility of the "Streptococcus milleri group". "Streptococcus milleri group" is a term for a large group of streptococci which includes Streptococcus intermedius, Streptococcus constellatus and Streptococcus anginosus. Usually considered commensals, these organisms are often associated with various pyogenic infections including cardiac, abdominal, skin and central nervous system infections. Organisms of the "Streptococcus milleri group" are often unrecognized pathogens due to the lack of uniformity in classifications and difficulties in microbiological identification. Penicillin G, cephalosporins, clindamycin and vancomycin all possess activity against these streptococci. Use of agents with poor activity may promote infections with "Streptococcus milleri group" and allow it to exhibit its pathogenicity. An understanding of these organisms may aid in their recognition and proper treatment.

Animals↗
PubMed1999

Multiple system atrophy.

MSA is a complex disorder, with regard to its pathology and cause as well as its clinical diagnosis and treatment. Although a number of clinical treatments may improve quality of life for these patients, given the widespread pathology present, symptomatic treatment, particularly that involving neurotransmitter replacement, is likely to remain difficult. Truly effective treatment for these patients is likely to depend on an understanding of the underlying pathogenic mechanisms and methods to halt or reverse disease progression. A firm understanding of the classification of these disorders is the first step to understanding the relevant pathogenic mechanisms. The finding of intracytoplasmic glial inclusion bodies provides a compelling piece of evidence that SND, OPCA, and SDS do, in fact, belong to one nosologic entity. These inclusions do not seem to be present in familial cases of OPCA; thus, they may provide a means to improve diagnostic specificity as well as sensitivity. With the ability to define clearly the entity of MSA, an understanding of the pathophysiology can be developed along with other degenerative neurologic diseases, including Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, and Huntington's disease.

Brain↗