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At least 181 records · Page 10Linked to original sources
PubMed1999

Molecular epidemiologic evaluation of transmissibility and virulence of Mycobacterium tuberculosis.

Discovery of genotypic markers associated with increased transmissibility in Mycobacterium tuberculosis would represent an important step in advancing mycobacterial virulence studies. M. tuberculosis strains may be classified into one of three genotypes on the basis of the presence of specific nucleotide substitutions in codon 463 of the katG gene (katG-463) and codon 95 of the gyrA gene (gyrA-95). It has previously been reported that two of these three genotypes are associated with increased IS6110-based clustering, a potential proxy of virulence. We designed a case-control analysis of U.S.-born patients with tuberculosis in San Francisco, Calif., between 1991 and 1997 to investigate associations between katG-463 and gyrA-95 genotypes and epidemiologically determined measures of strain-specific infectivity and pathogenicity and IS6110-based clustering status. We used a new class of molecular probes called molecular beacons to genotype the isolates rapidly. Infectivity was defined as the propensity of isolates to cause tuberculin skin test conversions among named contacts, and pathogenicity was defined as their propensity to cause active disease among named contacts. The molecular beacon assay was a simple and reproducible method for the detection of known single nucleotide polymorphisms in large numbers of clinical M. tuberculosis isolates. The results showed that no genotype of the katG-463- and gyrA-95-based classification system was associated with increased infectivity and pathogenicity or with increased IS6110-based clustering in San Francisco during the study period. We speculate that molecular epidemiologic studies investigating clinically relevant outcomes may contribute to the knowledge of the significance of laboratory-derived virulence factors in the propagation of tuberculosis in human communities.

AIDS-Related Opportunistic Infections↗
PubMed2026

Development of RS1-specific ACMG/AMP variant classification criteria with pilot variant curation.

Gene-based therapies are being developed for retinal diseases, including RS1-related X-linked retinoschisis. Therefore it is essential to determine which variants are pathogenic and which are benign when enrolling patients. The Clinical Genome Resource (ClinGen) X-Linked Inherited Retinal Diseases (XLRD) Variant Curation Expert Panel (VCEP) brings together clinician scientists, molecular biologists, and geneticists to apply their expertise and review the clinical, genetic, population, and functional evidence for variants. American College of Medical Genetics (ACMG) guidelines have been modified for RS1 to develop a highly systematic and conservative framework for evaluating variants. The curation process involves applying 28 different codes, each with 4 strength levels (very strong, strong, moderate, supporting) across different domains of phenotype, population data, computational assessment, functional impact, and segregation. With RS1-specific rules, a total of 54 pilot variants were tested. These included 47 variants in ClinVar. Of these 21 variants were re-classified: 2 likely pathogenic variants and one likely benign were changed to variants of uncertain significance and 4 previously unclassified variants were changed to pathogenic, likely pathogenic and likely benign. Other changes resolved conflicts or multiple classifications.

Humans↗
PubMed1983

Overwhelming pneumonia.

A classification of normal-abnormal hosts and pathogens forms the basis for discussion of the diagnosis and management of pneumonia in the critical care setting. In order to arrive at the appropriate therapy for the unusual as well as the usual causative organisms of pneumonia, individual assessment of the need for invasive procedures must be made. The critical feature, however, is to consider the wide spectrum of possibilities for each individual patient.

Adult↗
PubMed1999

[Immunological bases and classification of allergy].

The task of the immune system consists of destroying foreign structures in order to prevent the invasion of living organisms by pathogens. This destruction often provokes adverse effects defined as hypersensitivity reactions. The classification of hypersensitivity reactions proposed by Gell and Coombs is based on effector mechanisms. Although this framework remains largely used, recent work demonstrated the occurrence of profound similarities between different classes of hypersensitivity reactions. Indeed, all these reactions involve the activation of adhesion mechanisms intended to allow the local recruitment of blood leukocytes and cytokine production. The concept of a separation between two different modes of immune response induced by two different T lymphocyte subpopulations (TH1 and TH2) proved useful in understanding hypersensitivity reactions, although it represents only an approximation. Recent results were an incentive to develop new diagnostic and therapeutic strategies whose usefulness will be evaluated in the near future.

Adult↗
PubMed1999

Coagulase-negative staphylococci and mammary gland infections in cows.

Coagulase-negative staphylococci (CNS) are the most frequently isolated bacteria from bovine mammary gland milk samples. The objective of this study was to determine the type of inflammation evoked by CNS in the mammary gland of cows during their first lactation. Twenty-four Israeli-Holstein heifers in their first lactation were tested for bacteriological status, somatic cell count (SCC) and differential leucocyte count in milk 60-120 days postparturition and every 50-60 days after until drying off. Following the first testing, the 96 quarters of the 24 heifers were classified as follows: 69.8% as no bacterial growth (NBG), 27.1% infected with CNS and 3.1% infected with Staphylococcus aureus. During lactation, 84.5% quarters had no change in their classification, 6.2% were newly infected with other pathogens, 3.1% were classified as self-cured and in 6.2% sporadic bacteria were isolated. Among the CNS, S. intermedius, S. chromogenes and S. haemolyticus were the most frequently isolated. Milk from CNS-infected quarters had significantly higher SCC than milk from NBG quarters. An analysis of the leucocyte pattern in milk from CNS vs. NBG quarters revealed a significant increase in polymorphonuclears and a significant decrease in the percentage of total lymphocytes and lymphocytes bearing CD4+ or CD8+. The high percentage of CNS-infected quarters that remained unchanged in their bacterial status during the first lactation, indicates that those CNS have the ability to elude the immune system and persist in the mammary gland for a long time. The persisting infection, resulting to some extent from an increase of SCC by some CNS strains, suggests that in the near future control steps will have to be taken into consideration, in order to enhance the improvement of milk quality.

Animals↗
PubMed2000

Evidence for mating of the "asexual" yeast Candida albicans in a mammalian host.

Since its classification nearly 80 years ago, the human pathogen Candida albicans has been designated as an asexual yeast. In this report, we describe the construction of C. albicans strains that were subtly altered at the mating-type-like (MTL) locus, a cluster of genes that resembles the mating-type loci of other fungi. These derivatives were capable of mating after inoculation into a mammalian host. C. albicans is a diploid organism, but most of the mating products isolated from a mouse host were tetrasomic for the two chromosomes that could be rigorously monitored and, overall, exhibited substantially higher than 2n DNA content. These observations demonstrated that C. albicans can recombine sexually.

Animals↗
PubMed1983

Virulence and phenotypic characterization of Yersinia enterocolitica isolated from humans in the United States.

Yersinia enterocolitica was recently reclassified into Yersinia enterocolitica sensu stricto and three additional species. With this new classification, it was of interest to reexamine pathogenicity previously ascribed to Y. enterocolitica. All available clinical isolates of Y. enterocolitica sent to the Centers for Disease Control from 1970 through 1980 were selected for characterization and comparison. One-hundred such strains had been submitted, from 21 states. Most (85%) were biotype 1, and O:8 was the most common of the 24 serotypes encountered. All strains were examined by several virulence assays. Two strains caused conjunctivitis in guinea pigs, 7 were lethal for mice, 54 invaded HEp2 cells, 18 produced a heat-stable enterotoxin, 9 were calcium dependent, 20 autoagglutinated, and 34 had a distinctive colonial morphology at 37 degrees C. Ten isolates of each of the new species that had previously been grouped with Y. enterocolitica (Y. kristensenii, Y. intermedia, and Y. frederiksenii) were characterized and were generally negative in all assays. This study points out pathogenicity differences among Yersinia species, confirms the complex nature of virulence in Y. enterocolitica, and confirms that no single current assay correlates with virulence in Y. enterocolitica.

Agglutination↗
PubMed1999

Cerebral systems in the pathogenesis of endogenous psychoses. 1974.

Mental process imply a harmonious functioning of psychic systems, assembled into larger units, psychic spheres (Table 1). Their neurophysiological representatives are brain systems of areas and pathways (Figs 1-4). Under functional and/or organic disturbances these systems originate the leading mental symptoms (Table 2) characterizing the diverse endogenous psychoses: hence, the latter's distinctive patterns. Accordingly, understanding and classification of psychoses should rest on the pathogenic dynamisms, not on clinical description. This is why Kleist's and Leonhard's conceptions of the endogenous psychoses surpass any other to exist. Kleist stands among the founders of psychiatry, by describing the "degeneration psychoses" and many single psychoses, as well as redefining, isolating and clarifying the progressive ones, later on renamed as schizophrenias (Table 3). Such pathogenic criterion may also be useful to define mental conditions other than psychoses, as hysteria, neuroses and psychopathic inferiority (Tables 4 and 5). One should consider here, besides the psychic systems and spheres involved, the way they were caught and the corresponding developmental phase. In Kleist's "degeneration psychoses"--cyclic or episodic (Table 6) the systems and spheres are disturbed by functional transient processes due to latent dispositions, while his and Leonhard's schizophrenias (Table 7) show a rather progressive, deteriorating course. The nature of the disorder is itself genetically determined, as is either its confinement to one sphere or its spreading out. The spread out pattern, while exceptional in schizophrenia, represents a rule for the "degeneration psychoses", in discussant's mind. Both groups may have symptoms alike by involvement of the same sphere (Table 8), but proper diagnosis is reached by taking pathogenesis into consideration.

Brain Diseases↗
PubMed1984

Pathogenic mechanisms in osteochondrodysplasias.

UNLABELLED: We performed histochemical, immunohistochemical, electron-microscopic, and microchemical studies on cartilage growth plates from sixty-eight patients with nineteen different forms of human osteochondrodysplasia. Cartilage biopsies were obtained during orthopaedic procedures. Postmortem specimens were obtained within a short time after death. The combined morphological and biochemical studies revealed specific abnormalities suggestive of a particular biochemical defect in several chondrodysplasias. In pseudoachondroplasia, non-collagenous protein accumulated in the rough endoplasmic reticulum of chondrocytes and a proteoglycan species that normally is present in the extracellular matrix was not detected by gel electrophoresis. The accumulated material was stained with antibodies against the core protein of proteoglycan. This strongly suggested that in this syndrome an abnormal core protein of a proteoglycan species is not properly transferred to the Golgi system. In Kniest syndrome, intracytoplasmic accumulation of metachromatic material, dilatation of rough endoplasmic reticulum, and an abnormal gel-electrophoretic pattern of cartilage proteoglycans suggested an abnormality of cartilage proteoglycan metabolism. Abnormalities that probably are related to degradative lysosomal processes of proteoglycans in chondrocytes were found in spondylometaphyseal dysplasia of the Kozlowski type. An abnormal organization of type-II collagen was found in fibrochondrogenesis. In diastrophic dysplasia, an abnormal organization of collagen was found in areas of interterritorial matrix and around many degenerated cells, but also in the lacunae of cells without ultrastructural signs of degeneration. The segment-long-spacing form of collagen prepared from cartilage of three patients with diastrophic dysplasia showed an abnormal cross-striation pattern in a portion between bands 42 and 45, corresponding to the position of the alpha 1(II) cyanogen-bromide-derived 10,5 peptide. This suggested that in this syndrome there is a structural alteration of the type-II collagen molecule. There was an accumulation of intracellular lipid in pyknodysostosis and in hypochondrogenesis, and of glycoproteins in several atypical cases of spondyloepiphyseal dysplasia. In a pair of twins with an atypical form of spondyloepiphyseal dysplasia, the presence of many multinucleated chondrocytes suggested a primary impairment of cell division. CLINICAL RELEVANCE: A knowledge of the pathogenic mechanisms in osteochondrodysplasias might improve the classification; aid in diagnosis, prognosis, and genetic counseling; and contribute to the understanding of normal endochondral growth.(ABSTRACT TRUNCATED AT 400 WORDS)

Achondroplasia↗
PubMed1999

[Taxonomy of genus Malassezia: progress and problems].

The genus Malassezia is composed of lipophilic basidiomycetous yeasts which were recently shown to consist of seven species, one lipid-independent species, M. pachydermatis and six lipid-dependent species, M. furfur, M. sympodialis, M. globosa, M. obtusa, M. restricta and M. slooffiae. Based on this classification, we will be able to analyze pathogenicity or relationship between Malassezia-related diseases and each species.

Malassezia↗
PubMed1993

Periodontal diseases in young individuals.

The prevalence and severity of periodontal diseases in young people are significant. Recent progress in understanding the etiology and pathogenesis of periodontal diseases in this group of patients has allowed significant improvement in periodontal classifications. Actinobacillus actinomycetemcomitans characteristically is the major pathogen involved; black-pigmented anaerobic rods and other organisms can also be important. Treatment of periodontitis should focus on meticulous plaque control and eradication of periodontal pathogens, possibly by means of systemic or topical antimicrobial therapies.

Adolescent↗
PubMed1996

[Proposal of a new topographic classification of mandibular fractures].

There has been a certain amount of confusion in publications concerning fractures of the mandible due to the lack of consensus on classification. Starting with the embryological, anatomic, biomechanical, pathogenic and epidemiological features of these fractures, we propose a new terminology and a new distribution of the units and subunits of the mandible in traumatology. The main point is to incorporate the angle subunit into the ramus unit.

Adult↗
PubMed1991

Protein pI alteration related to strain variation of infectious bronchitis virus, an avian Coronavirus.

Viral proteins of two strains of infectious bronchitis virus (IBV), which have different tissue trophism and serology, were separated on the basis of their isoelectric points (pI). The viruses have four structural proteins; the protein of greatest serological importance is found at the peplomer tip. The viral structural proteins separated by isoelectric focusing were identified by comparison to SDS-PAGE separations. Three protein bands were identical in pI and one protein band showed a difference in pI between strains. When the renatured viral proteins were Western blotted and reacted with strain-specific antiserum, antigen-antibody complexing was seen only at points corresponding to the strain-specific variant bands. For IBV strain Mass-41, antigen-antibody complexing occurred at a pI of 6.8, and, for IBV strain Ark-99, at 7.2. No cross reaction of antisera was observed for either strain. Since tissue affinities are a function of the viral peplomer-mediated attachment of virus to cells and are often directly related to pathogenicity, it appears that altered pathogenicity of strains of IBV may be detected by alteration of pI of the proteins. Classification by pI of proteins of at least the smaller viruses allows untypeable, highly pathogenic or persistent strains of these viruses to be characterized on the basis of variant proteins.

Antibodies, Viral↗
PubMed2025

Distinct rates of VUS reclassification are observed when subclassifying VUS by evidence level.

PURPOSE: Genetic testing commonly yields a plethora of variants of uncertain significance (VUS) that can lead to ongoing uncertainty for patients and their caregivers. Although all VUS hold uncertainty, some VUS have more evidence in support of pathogenicity, whereas others have more evidence of a benign role. Sharing these nuances can help guide the investment in follow-up clinical and research investigations and may, at times, influence medical decision making despite appreciated uncertainty. METHODS: Four clinical laboratories have been subclassifying VUS to help prioritize investigation and guide reporting decisions. Each laboratory developed a distinct approach for how these subclasses are used in their laboratories and, in some cases, displayed on reports. We examined the composition of each laboratory's VUS subclasses and the likelihood variants from each subclass were reclassified toward pathogenic or benign. RESULTS: We found that variants in the lowest subclass of VUS were never reclassified as likely pathogenic or pathogenic, whereas those in the highest subclass were much more likely to be reclassified as pathogenic or likely pathogenic. CONCLUSION: Given that forthcoming professional guidance in variant classification will advise the use of VUS subclasses, the experience of our laboratories in using VUS subclasses can inform future practices.

Humans↗
PubMedDate not supplied

Subgenus systematics of Acanthamoeba: four nuclear 18S rDNA sequence types.

Classification of Acanthamoeba at the subgenus level has been problematic, but increasing reports of Acanthamoeba as an opportunistic human pathogen have generated an interest in finding a more consistent basis for classification. Thus, we are developing a classification scheme based on RNA gene sequences. This first report is based on analysis of complete sequences of nuclear small ribosomal subunit RNA genes (Rns) from 18 strains. Sequence variation was localized in 12 highly variable regions. Four distinct sequence types were identified based on parsimony and distance analyses. Three were obtained from single strains: Type T1 from Acanthamoeba castellanii V006, T2 from Acanthamoeba palestinensis Reich, and T3 from Acanthamoeba griffini S-7. T4, the fourth sequence type, included 15 isolates classified as A. castellanii, Acanthamoeba polyphaga, Acanthamoeba rhysodes or Acanthamoeba sp., and included all 10 Acanthamoeba keratitis isolates. Interstrain sequence differences within T4 were 0%-4.3%, whereas differences among sequence types were 6%-12%. Branching orders obtained by parsimony and distance analyses were inconsistent with the current classification of T4 strains and provided further evidence of a need to reevaluate criteria for classification in this genus. Based on this report and others in preparation, we propose that Rns sequence types provide the consistent quantititive basis for classification that is needed.

Acanthamoeba↗
PubMed1985

Classification and pathogenesis of vulvovaginal candidiasis.

Although candidiasis of the female genital tract is one of the most common of the vaginitides, it is a poorly understood disease entity. Vulvovaginal candidiasis is a monoetiologic disease, but the pathways by which pathogenic expression is attained are sufficiently divergent to constitute a classification schema that influences therapy. For selection of appropriate therapy, the following three broad categories are proposed: (1) primary candidiasis, (2) antibiotic-induced candidiasis, and (3) systemically induced candidiasis.

Anti-Bacterial Agents↗
PubMed1980

Persistent hog cholera infection detected during virulence typing of 135 field isolates.

During the hog cholera (HC) eradication program in the United States, 135 field isolates were characterized by inoculation into specific-pathogen-free pigs. This gave origin to the classification of 61 (45%) as high virulent, 37 (27%) as low virulent, 29 (22%) as avirulent or immunizing, and 8 (6%) as capable of causing persistent infection. The persistent infections caused by the eight isolates were of long durtion, lasting in one instance to 152 days. The persistently infected pigs remained relatively free of clinical signs of HC but had high concentrations of HC virus (HCV) in their blood. When 6 of these pigs were given a second inoculation (with the virulent Ames strain of HCV), 2 died while the health status of 4 remained unchanged.

Animals↗
PubMed2025

NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.

MOTIVATION: Oncoviruses, pathogens known to cause or increase the risk of cancer, include both common viruses such as human papillomaviruses and rarer pathogens such as human T-lymphotropic viruses. Computational methods for detecting viral DNA from data acquired by modern DNA sequencing technologies have enabled studies of the association between oncoviruses and cancers. Those studies are rendered particularly challenging when multiple species of oncovirus are present in a tumor sample. In such scenarios, merely detecting the presence of a sequencing read of viral origin is insufficiently informative-instead, a more precise characterization of the viral content in the sample is required. RESULTS: We address this need with NextVir, to our knowledge the first multi-class viral classification framework that adapts genomic foundation models to detecting and classifying sequencing reads of oncoviral origin. Specifically, NextVir explores several foundation models-DNABERT-S, Nucelotide Transformer, and HyenaDNA-and efficiently fine-tunes them to enable accurate identification of the sequencing reads' origin. The results demonstrate superior performance of the proposed framework over existing deep learning methods and suggest downstream potential for foundational models in genomics.

Humans↗