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Progressive external ophthalmoplegia characterized by multiple deletions of mitochondrial DNA: unraveling the pathogenesis of human mitochondrial DNA instability and the initiation of a genetic classification.

Over the last decade, many sporadic and familial cases have been reported with multiple deletions of mitochondrial DNA (mtDNA) in postmitotic tissues. Most patients suffer from progressive external ophthalmoplegia (PEO) and may have a nuclear gene defect that predisposes to the accumulation of mtDNA deletions. Recently, positional cloning has led to the discovery of mutations in four such nuclear genes. Some mutations are dominant and others recessive. In all autosomal mutations, defective mtDNA replication and/or repair are probably responsible for the generation of secondary mtDNA deletions. There are also data suggestive of a prominent pathogenic role for disturbed nucleotide metabolism. We here present a tentative genotype-phenotype correlation. Since clinical presentations are heterogeneous and overlap with different previously described clinical syndromes, we advocate the use of a genetic, instead of a clinical, classification of disorders with multiple mtDNA deletions.

Animals↗

The distinction of pathogenic Vibrio cholerae groups using arbitrarily primed PCR fingerprints.

Pathogenic Vibrio cholerae strains were compared by fingerprinting with arbitrarily primed polymerase chain reaction (AP-PCR). They were O1 classical and El Tor strains and recent non-O1 Bengal strains. Ten oligonucleotides from a total of fifty-two tested gave distinctive patterns, and these strains were separated into four groups. A second technique, amplification of 16S/23S rRNA spacers with a pair of oligonucleotides, was also used. Various bands were obtained, and the result can be treated as an additional fingerprint with a different pattern for each of the groups. The method of AP-PCR fingerprinting is fast and sensitive. A test of the stability of the El Tor patterns was done with a set of strains isolated during the present Brazilian epidemics. Examples of AP-PCRs with non-O1 strains are given. A typing scheme is proposed in which oligo 1 is first used, and depending on the fingerprint obtained, additional oligonucleotides are used to confirm the classification of the strain. It is proposed that the AP-PCR technique be used for epidemiological studies, analysing strains reaching new locations or environmental isolates suspected of being pathogenic. It will be particularly helpful in cases in which traditional methods cannot clearly classify the strain.

DNA Fingerprinting↗

Proteomic survey of the pathogenic Mycoplasma hyopneumoniae strain 7448 and identification of novel post-translationally modified and antigenic proteins.

Mycoplasma hyopneumoniae is an important pathogen for pigs, being the causative agent of enzootic pneumonia. Recently, the genome sequences of three strains, J, 7448 and 232 have been reported. Here, we describe the results of a proteomic analysis, based on two-dimensional gel electrophoresis of soluble protein extracts, immunoblot and mass spectrometry, which was carried out aiming the identification of gene products and antigenic proteins from the M. hyopneumoniae pathogenic strain 7448. A preliminary M. hyopneumoniae proteome map in two pH ranges (3-10 and 4-7) was produced. A total of 31 different coding DNA sequences (CDSs), including three hypothetical ones, were experimentally verified with the identification of the corresponding protein products by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. According to the Clusters of Orthologous Groups (COG) functional classification, the identified proteins were assigned to the groups of metabolism (13), cellular processes (5) and information and storage processing (4). Nine of the identified proteins were not classifiable by COG, including some related to cytoadherence and possibly involved in pathogenicity. Moreover, at least five highly antigenic proteins of M. hyopneumoniae were identified by immunoblots, including four novel ones (a heat shock protein 70, an elongation factor Tu, a pyruvate dehydrogenase E1-beta subunit and the P76 membrane protein). The now available proteome map is expected to serve as a reference for comparative analyses between M. hyopneumoniae pathogenic and non-pathogenic strains, and for methabolic studies based on cells cultured under modified conditions.

Animals↗

Discrimination of Staphylococcus aureus strains from different species of Staphylococcus using Fourier transform infrared (FTIR) spectroscopy.

Staphylococcus aureus is a widespread opportunistic pathogen that can cause food-borne illness and is sometimes associated with raw milk and raw milk cheese products. The traditional taxonomic procedures for classification of staphylococcal species are time consuming and often several tests are required. FTIR spectroscopy offers a rapid method for the discrimination and identification of S. aureus strains isolated from raw milk and raw milk cheeses. FTIR spectroscopy was used to discriminate S. aureus from other species of Staphylococcus. This was achieved by using a model composed of 39 species and subspecies of Staphylococcus. The model was validated using a set of spectra of strains isolated from raw milk and different varieties of French raw milk cheese. S. aureus was successfully discriminated from the other species of Staphylococcus and all the strains of S. aureus isolated from raw milk and different varieties of French raw milk cheese were also successfully identified as such. These results demonstrated that FTIR spectroscopy is a rapid (results obtained within 24 h starting from a pure strain or a single colony) and robust method for the identification of S. aureus isolates of dairy origin and food-borne origin in general.

Animals↗

Simultaneous assessment of antigen-stimulated cytokine production and memory subset composition of memory CD8 T cells.

The functional identification of antigen-specific CD8 T cell populations is critical to understanding host responses to infection by intracellular pathogens. Furthermore, assessing the properties of protective memory CD8 T cell populations generated by immunization is necessary in the rational design of vaccines. Recently, a classification scheme was proposed in which memory CD8 T cells were divided into one of two distinct subsets, based on CD62L expression, that have different functional properties and protective capacities. Intracellular cytokine staining functionally identifies antigen-specific CD8 T cell populations after short in vitro stimulation with cognate peptide. This short stimulation, however, results in the cleavage of CD62L from the cell surface of antigen-specific CD8 T cells and precludes distinguishing CD62L(hi)- and CD62L(lo)-expressing memory cell subsets within this population. Here, we describe a method of preserving CD62L expression by the antigen-specific CD8 T cell population during coculture with antigen. This methodology allows for the identification and functional assessment of antigen-specific memory CD8 T cell populations, while simultaneously characterizing the memory subset composition of that population. Using this method, we directly identify differences in IL-2 production capacity by CD62L(hi)- and CD62L(lo)-expressing antigen-specific memory CD8 T cell populations.

Adoptive Transfer↗

Rheumatologic manifestations of diabetes mellitus.

Diabetes mellitus has been linked to disorders of bones and joints, including neuroarthropathy, limited joint mobility, and hyperostosis. Some of the relations have known pathogenic mechanisms, but most are based on epidemiologic findings. This article reviews the associations between diabetes mellitus and its putative rheumatologic manifestations, and proposes a classification composed of four categories: consequences of diabetic complications, consequences of metabolic derangements inherent to diabetes, syndromes that may share etiologic mechanisms with microvascular disease, and probable associations. This approach may facilitate a clearer understanding of the musculoskeletal conditions that are prevalent in patients with diabetes mellitus.

Diabetic Nephropathies↗

Pancreatic cancer biology and genetics.

Pancreatic ductal adenocarcinoma is an aggressive and devastating disease, which is characterized by invasiveness, rapid progression and profound resistance to treatment. Advances in pathological classification and cancer genetics have improved our descriptive understanding of this disease; however, important aspects of pancreatic cancer biology remain poorly understood. What is the pathogenic role of specific gene mutations? What is the cell of origin? And how does the stroma contribute to tumorigenesis? A better understanding of pancreatic cancer biology should lead the way to more effective treatments.

Adenocarcinoma↗

Bacteriological quality control in a human milk bank.

The best nutrient for newborn babies is breast milk and preferably provided via breast feeding. Pooled human milk must be used when the babies' own mother's milk is not available. Very often pooled milk is pasteurised. Recent studies, however, suggest avoidance of any sterilisation procedures in view of the decreased nutritional value and loss of anti-infective benefits associated with heating of human milk. In this study a quality control system of banked human milk based on the recent literature is presented. The purpose of systematic bacteriological monitoring is to separate those milk samples contaminated with pathogenic bacteria from the bulk of the collected milk which has only light contamination with likely nonpathogenic skin bacteria. According to our new standards of classification, over 60 per cent of the collected milk proved to be sufficiently free of bacteria to be fed unheated to pre-term infants. Most of the remainder could be fed unheated to full-term infants and less than 10 per cent had to be pasteurised.

Finland↗

Human papillomavirus biology and cervical neoplasia: implications for diagnostic criteria and testing.

Human papillomaviruses are necessary for the development of cervical neoplasia. Progress in our understanding of the epithelial biology of this common pathogen has greatly influenced current concepts of cervical carcinogenesis. This understanding has provided a framework for understanding the biologic basis of many diagnostic criteria. Furthermore, classification schemes, diagnostic testing, and clinical management have been modified and clarified in light of this knowledge.

Biomarkers↗

[Surgical treatment of gastrointestinal stromal tumors: personal cases].

Surgical management of gastrointestinal stromal tumors: our experience. Gastrointestinal stromal tumors (GIST) are rare neoplasm even if they are the most common mesenchimal malignancies of the gastrointestinal tract. GIST have long been a source of confusion and controversy, in particular to define their pathological classification, preoperative diagnosis, management strategies, and prognosis. A radical resection of the tumor is often possible and always recommended. Recent studies have identified its principal pathogenic defect. An effective adjuvant therapy treatment (STI571) have been found for advanced and metastatic GIST.

Antineoplastic Agents↗

[Molecular nature of renal tumours of adults].

Significant progress has been achieved recently in the cytogenetic and molecular research of the kidney parenchymal tumors which incidence has been steadily increasing in the developed countries. Renal cancer is an important clinical problem, still without effective therapy. The accuracy of current diagnosis, prognosis of the disease and the effectiveness of the treatment are limited by the poor understanding of its cytogenetic and molecular pathogenic mechanisms. In this review we summarize up to date cytogenetic alterations and gene expression profiles of the most important tumor genes, focusing at the classification of parenchyma tumors of adult patients.

Cytogenetics↗

[Current chemotherapy in urinary tract infection].

Because of the many newly developed chemotherapeutics it is often hard to choose the most suitable substance for treatment of urinary tract infection (UTI). Substances for first-line oral treatment are the benzylpyrimidine/sulphonamide combinations, amino-penicillins, fluoroquinolones and cephalosporins. In severe infections any of these can be given i.v., as can amino-glycosides or the combination of imipenem and cilastin. It is easier to decide which substance to give before urine culture results are available if the local resistance patterns to the typical pathogens are known. Particular care is mandatory for risk groups such as children, pregnant women, immunocompromised patients and those with renal insufficiency. Before treatment clinical classification of UTI is necessary. In acute uncomplicated cystitis oral antibiotics should be given either as single-shot therapy or over 3 days. In acute uncomplicated pyelonephritis therapy should last for 7 days or until 3 days after fever is gone. If enteral absorption is not guaranteed or in complicated cases of UTI, intravenous drugs should be used for 10-14 days until fever is gone or the complicating factor has been corrected.

Administration, Oral↗

Immunization with bacterial antigens: infections with streptococci and related organisms.

Streptococcal infections of fish have been reported from various parts of the world, including the Far East, the United States, South Africa, Australia, Israel and Europe. Classification of Gram-positive cocci (DNA-DNA hybridization studies coupled with 165 sequencing) has shown that at least five different defined species are pathogenic to fish, e.g. Streptococcus iniae (syn. S. shilot), Streptococcus difficile, Lactococcus garvieae (syn. Enterococcus seriolicida), Lactococcus piscium and Vagococcus salmoninarum. "Streptococcosis" of fish should therefore be regarded as a complex of similar diseases caused by different genera and species of Gram-positive cocci, each capable of inducing CNS damage, as well as various degrees of multisystem organ involvement. Panophthalmitis ("pop-eye") and meningitis/meningoencephalitis are the sole findings in trout infected by S. iniae and in tilapines infected by S. difficile. In contrast, L. garvieae-infected trout bear a systemic hyperacute infection with diffuse haemorrhages. Therapeutic measures are generally ineffective. Development of vaccines is therefore essential to control these diseases. In our studies, trout were vaccinated intraperitoneally with whole-cell formalin-inactivated S. iniae and L. garvieae and tilapines with whole-cell formalin-inactivated and acellular S. difficile extract. Under laboratory conditions, S. difficile-vaccinated tilapines were protected against a challenge of 100 LD50s. Protection was correlated with the development of specific agglutinins. Western blot analysis supported the hypothesis that only a few proteins act as protective antigens. S. iniae autovaccines were effective in preventing the disease in rainbow trout in Israel. Under field conditions, fish vaccinated at 50 g were protected for over four months. The qualitative analysis of the humoral response indicated that specific antibodies are directed against a few protein moieties. The fact that passive transfer of antibodies protected fish from experimental infection suggests that the basic mechanism of protection is antibody mediated. L. garvieae autovaccines developed for Italian trout farming were found to elicit a response similar to that of S. iniae. Despite the high virulence of L. garvieae (LD50 of 6 x 10(1) CFU/fish, compared with 3 x 10(4) CFU/fish of S. iniae), the protection against the experimentally induced disease lasted for five months under laboratory conditions, with survival rates of 80-90%. A single injection of the vaccine (0.1 ml/fish) resulted in specific antibody production detectable for six months. In the field, protection rates of 70-80% were obtained for a period of three months, in fish of 200-300 g reared at water temperatures of 18-21 degrees C.

Animals↗

Use of the espZ gene encoded in the locus of enterocyte effacement for molecular typing of shiga toxin-producing Escherichia coli.

Infections with Shiga toxin-producing Escherichia coli (STEC) result in frequent cases of sporadic and outbreak-associated enteric bacterial disease in humans. Classification of STEC is by stx genotype (encoding the Shiga toxins), O and H antigen serotype, and seropathotype (subgroupings based upon the clinical relevance and virulence-related genotypes of individual serotypes). The espZ gene is encoded in the locus of enterocyte effacement (LEE) pathogenicity island responsible for the attaching and effacing (A/E) lesions caused by various E. coli pathogens (but not limited to STEC), and this individual gene ( approximately 300 bp) has previously been identified as hypervariable among these A/E pathogens. Sequence analysis of the espZ locus encoded by additional STEC serotypes and strains (including O26:H11, O121:H19, O111:NM, O145:NM, O165:H25, O121:NM, O157:NM, O157:H7, and O5:NM) indicated that distinct sequence variants exist which correlate to subgroups among these serotypes. Allelic discrimination at the espZ locus was achieved using Light Upon eXtension real-time PCR and by liquid microsphere suspension arrays. The allele subtype of espZ did not correlate with STEC seropathotype classification; however, a correlation with the allele type of the LEE-encoded intimin (eae) gene was supported, and these sequence variations were conserved among individual serotypes. The study focused on the characterization of three clinically significant seropathotypes of LEE-positive STEC, and we have used the observed genetic variation at a pathogen-specific locus for detection and subtyping of STEC.

Bacterial Typing Techniques↗

Community-acquired pneumonia in adolescents.

Community acquired pneumonia (CAP) is defined as pneumonia acquired outside of the hospital setting. Extensive studies of CAP in adolescents that characterize the true incidence of various etiologic pathogens are not available. However, Streptococcus pneumoniae, Mycoplasma pneumoniae, and Chlamydia pneumoniae appear to be the most frequently encountered pathogens. These organisms often cause CAP in adults as well; other infections are noted as well, including Legionella. "Atypical pneumonia" refers to pneumonia not presenting with the usual clinical picture of pneumococcal infection (which includes high fever, productive cough, chills, and other "classic" features). The term is frequently used in adolescents with CAP. However, this classification may not help in individual patients, who often show a high degree of variability in the clinical presentation of pneumonia; also it does not always predict microbial cause. There is currently a trend away from the concept of atypical pneumonia syndrome and more discussion of atypical pathogens as commonly causes of CAP. This article reviews recent literature on CAP with special emphasis on its diagnosis and management in adolescent patients.

Adolescent↗

Use of elution marker for the intratypic characterization of poliovirus strains.

Elution marker was used for intratypic characterization of poliovirus strains with Al(OH)3 gel as adsorbent. The virion suspensions to be tested were partially purified by chromatography and labelled with 32P. In the labelled preparations of wild virus strains practically all radioactivity was found in virus-specific bond, whereas in those of the vaccine strains and isolates of vaccine origin a considerable, but variable, proportion of the activity was bound to residual cell components. For this reason, the EC50 value (i.e. the phosphate molarity corresponding to the 50% adsorption equilibrium of virions), for the vaccine and vaccine-like strains showed a wide scattering. The activity bound to cell components was removable from the gel with 0.005 M phosphate buffer, whereas the elution maxima for all the poliovirus strains examined so far were over 0.02 M. The elution marker was calculated for 25 type-2 and 30 type-3 strains, all isolated during or soon after vaccination periods from cases suspect of poliomyelitis, both with and without taking into account the cell-bound activity. In the latter case, the EC50 values agreed with that for the corresponding reference vaccine strain much better than in the former; furthermore, the type-2 reference vaccine strain and the type-2 isolates, indistinguishable from the wild reference strain by the original method, could easily be differentiated on the basis of the corrected EC50 value. The possibility that the lack of an appreciable proportion of cell-bound radioactivity may reflect the pathogenicity of poliovirus strains is discussed.

Adsorption↗

Molecular phylogenetic studies on Theileria parasites based on small subunit ribosomal RNA gene sequences.

Classification of Theileria parasites of south-east Asian countries is still ambiguous due to the lack of basic studies, especially their molecular genetic information. In this study, we included 6 known species and 14 unclassified Theileria parasite isolates: Theileria annulata, Theileria parva, Theileria taurotragi, Theileria sergenti, Theileria buffeli, Theileria types Sable, Theileria types A, B, B1, B2, C, D, E, F, G, G1, Theileria type Medan (Indonesia), Theileria type Ipoh (Malaysia) and Theileria type Thong Song (Thailand). Small subunit ribosomal RNA (srRNA) nucleotide sequence data were collected by PCR, cloning and dideoxy sequencing. The srRNA nucleotide sequences were aligned and analyzed by distance methods, maximum parsimony algorithms and maximum likelihood methods to construct phylogenetic trees. Bootstrap analysis was used to test the strength of the different phylogenetic reconstructions. The data indicated that all of the tree-building methods gave very similar results. This study identified two groups of Theileria, the pathogenic and benign groups, which are strongly supported by bootstrap analysis. The analysis also indicated that three subgroups (A, B and C) were generated within the benign Theileria group whereas the classification of Theileria type D and Thong Song is questionable. However, more basic information such as life cycle differences, vectors, modes of transmission, virulent and genetic/sexual compatability is essential for clearer taxonomic definition of the benign Theileria parasites.

Animals↗

Rapid detection and differentiation of Gram-negative and Gram-positive pathogenic bacteria in urine using TaqMan probe.

Urinary tract infection has been shown to be quite complicated and often difficult to diagnose and treat. For appropriate diagnosis, it is very important to find the correct Gram stain classification as soon as possible, especially in severe cases where there is a possibility of severe sepsis developing. In order to solve this problem, we developed a new method to detect a Gram stain of bacteria obtained from 1 ml of urine from urinary tract infection patients using a consensus real-time PCR protocol with a TaqMan probe that allows detection of spiked bacterial 16S DNA from urine. We extracted DNA of 55 urine samples obtained from patients with complicated urinary tract infection and at the same time performed urine culture testing. After DNA extraction, they were subjected to real-time PCR using a TaqMan discrimination system. Sixteen kinds of bacteria were cultured from the urine culture testing. Of these bacteria, eight were classified as Gram-positive bacteria and the other eight were classified as Gram-negative bacteria. Of the 55 samples, the TaqMan technique result showed 27 samples that were classified as Gram-negative bacteria; 11 samples that were Gram-positive, 10 that included both Gram-negative and -positive bacteria, and 7 that showed no amplification. The classifications of all samples corresponded exactly to those determined by urine culture testing. The present genotyping method of real-time PCR using a TaqMan discrimination system could be applied to the rapid detection of Gram-positive or -negative bacteria in urine of urinary tract infection patients. This assay can differentiate those species tested, but whether the presence of other (untested) bacteria could lead to misinterpretation is unknown. For further investigation, it is important to test other (untested) bacteria in the near future.

Gram-Negative Bacteria↗