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PubMed1994

[Entamoeba histolytica (Schaudinn 1903) and Entamoeba dispar (E. Brumpt 1925) are 2 different species].

On the basis of epidemiologic and clinical data in humans, and of experimental studies in kittens, E. Brumpt in 1925 showed that Entamoeba histolytica producing quadrinucleate cysts was a complex of 2 species. He differentiated a pathogenic and invasive form, from a non pathogenic and non invasive one that he called Entamoeba dispar. His explanation gained little support until recently, when Sargeaunt reported a study of isoenzyme typing and allow then the classification of amoebae resembling E. histolytica in pathogenic and non pathogenic species. Monoclonal antibodies and PCR have recently been used and have shown to react specifically with the two forms of amoebae. Genetic evidence has also demonstrated that the pathogenic and non pathogenic amoebae represent different species.

Animals↗
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↗
PubMed2005

Gene expression profiling in acute myeloid leukemia.

Over the last decades, significant advances have been made in the knowledge and treatment of acute myeloid leukemia (AML). The WHO has recognized this new information by incorporating into its classification morphologic, immunophenotypic, genetic, and clinical features in an attempt to define biologically and clinically relevant entities. Nevertheless, well-defined cytogenetic subgroups exhibit considerable heterogeneity, and in many AML subtypes the pathogenic event is still not known. A classification system based on the underlying molecular pathogenetic abnormalities would be ideal, but such detailed knowledge is not yet available. Novel approaches in genomics, such as surveying the expression levels of thousands of genes in parallel using DNA microarray technology, open possibilities to further refine the studies on AML. Today, gene expression profiling in AML is becoming well established and has already been proven to be valuable in diagnosing different cytogenetic subtypes, discovering novel AML subclasses, and predicting clinical outcome. Recently, gene expression profiling studies in AML showed a remarkable level of concordance in findings, which may ultimately lead to an increasingly refined molecular taxonomy. While many challenges remain to be overcome, a combination of gene expression profiling with other microarray-based applications, high-throughput mutational analyses and proteomic approaches will not only significantly contribute to the classification and therapeutic decision making of AML, but also give important insights into the true pathobiologic nature of this type of leukemia.

Cytogenetic Analysis↗
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↗
PubMed2005

The treatment of children exposed to pathogens linked to bioterrorism.

Health care providers must understand the following regarding pathogens linked to bioterrorism: (1) the classification and qualities of possible biologic agents; (2) the natural history and management of biologic, chemical and radiologic injuries and exposures; (3) chemical agents that may be used and their properties; (4) different types of radiologic terrorism; (5) decontamination procedures; and (6) availability of antidotes and other therapeutics.

Antitoxins↗
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↗
PubMed2002

Low-grade central nervous system tumors.

Low-grade tumors of the central nervous system constitute 15 to 35% of primary brain tumors. Although this category of tumors encompasses a number of different well-characterized entities, low-grade tumors constitute every tumor not obviously malignant at initial diagnosis. In this brief review, the authors discuss the pathological classification, diagnostic procedures, treatment, and possible pathogenic mechanisms of these tumors. Emphasis is given in the neuroradiological and pathological features of the several entities.

Central Nervous System Neoplasms↗
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↗
PubMed2003

[New fungal classification and their applications in medicine].

Fungi are gaining importance with the increased incidence of invasive, often fatal mycoses, in immunocompromised patients. In addition, the increased number of emerging opportunistic pathogens has prompted interest in studies pertaining to fungal classification. The traditional methods of identification and classification of these microorganisms are based on the morphology of the sexual and asexual reproductive structures. Recently, this system of classification has been shown incongruent with approaches that better establish phylogenetic relationships among these organisms. Novel aspects of fungal reclassification are described as follows: 1) the position of fungi in the historical classification systems, 2) the recognition of their polyphyly, based on comparative studies of nucleic acid sequences and on analysis of descent lines and, 3) the contribution of molecular phylogeny to medical mycology, including identification of mycotic agents, their molecular epidemiology, prevention of infection and methods of diagnosis.

Fungi↗
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↗