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PubMed1991

[The genetic classification of the Pasteurella pneumotropica complex].

Pasteurella pneumotropica with its biotypes Jawetz and Heyl are the most common bacterial pathogens associated with diseases in rodents. 23 P. pneumotropica biotype Jawetz, biotype Heyl and P. pneumotropica-like rodentia isolates have been investigated phenotypically by characterization of their micromorphology and biochemical fermentation reactions. The taxonomic position within the family Pasteurellaceae has been examined by DNA:DNA hybridisation (optical method). It could be shown that P. pneumotropica biotype Jawetz represents a genus-like cluster containing several species including the V-factor dependent Haemophilus Taxon B and the avian P. pneumotropica-like organism and therefore resembles a new species of the new genus. It is concluded that the biotype Heyl of P. pneumotropica taxonomically remains as a species within the family Pasteurellaceae, however without further relationship to other known genera or genus-like groups.

Animals↗

PubMed1991

[Studies on the classification of thermophilic actinomycetes. IV. Determination of thermophilic Streptomyces hygroscopicus group].

The thermophilic streptomyces hygroscopicus is one of the pathogens of farmer's lung disease. The identified 60 strains of thermophilic streptomyces hygroscopicus coming from the isolates from the haystack, moldy hay and sputa collected from Jiangsu, Hubei province and Shanghai in China. These strains are grown around 50 degrees C and have moist patches on the surface of colonies. It is proved that protease can be extracted from cultured H9-4 strain. This protease is provided with antigen, the farmer's lung disease of rabbit can be induced in animals experiments. On clinical diagnosis the farmer's lung disease can be detected by sera test. From the identification of the 60 thermophilic streptomyces hygroscopicus strains, we found the morphological cultural, physiological characteristics and cell wall composition of H9-4 and T562 well different from description hitherto. So two of them are identified as new species. H9-4 is named as Streptomyces thermoendus sp. nov. and T562 is named as Streptomyces thermobicorno-hygroscopicus sp. nov.

Animals↗

PubMed1995

Genetic differentiation of pathogenic and nonpathogenic strains of Entamoeba histolytica by random amplified polymorphic DNA polymerase chain reaction.

The random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) method was used to compare pathogenic and nonpathogenic strains of Entamoeba histolytica. DNA polymorphisms were detected among the different strains and dendrograms were constructed by PHYLIP and PAUP analyses to study the relationship of the strains. Both analyses resulted in identical results, which indicated that pathogenic strains of E. histolytica are closely related and clearly separated from the nonpathogenic strains. The results of this study agree with classification of the strains based on isoenzyme analyses. This suggests that RAPD-PCR is a valuable method in differentiating between strains of this parasite, and the results are consistent with the concept that pathogenic and nonpathogenic Entamoeba represent two different species.

Animals↗

PubMed2004

The capsalidae (Monogenea: Monopisthocotylea): a review of diversity, classification and phylogeny with a note about species complexes.

The Capsalidae are monogeneans parasitizing 'skin', fins and gills of marine fishes. Some capsalids are pathogenic to cultivated fish and a few have caused epizootic events. It is a cosmopolitan family with broad host associations (elasmobranchs and teleosts, including sturgeons). Approximately 200 capsalid species are placed in nine subfamilies and 44-46 genera, some of which are well known (Benedenia, Capsala, Entobdella, Neobenedenia). Sturgeons host two capsalid species (Nitzschiinae) and 15 species in five genera are reliably reported from elasmobranchs. The combination of ancient (shark, ray, sturgeon) and modem (teleost) host fish lineages indicates that capsalid evolution is likely a blend of coevolution and host-switching, but a family phylogeny has been lacking due to deficient knowledge about homologies. The current phenetic subfamilial classification is discussed in detail using a preliminary phylogeny generated from large subunit ribosomal DNA sequence data from representatives of five subfamilies. Monophyly of the Capsalidae is supported by possession of accessory sclerites. Hypotheses are proposed for the possible radiation of capsalids. A suggestion that Neobenedenia melleni, a pathogenic species atypical due to its broad host-specificity (>100 host teleost species from >30 families in five orders), may be a complex of species is supported from genetic evidence. This may explain peculiarities in biology, taxonomy, host associations and geographic distribution of N. 'melleni' and has implications for fish health. Holistic studies using live and preserved larval and adult capsalid specimens and material for genetic analysis are emphasised to further determine identity, phylogeny and details of biology, especially for pathogenic species.

Animals↗

PubMed1998

Comparison of Randomly Amplified Polymorphic DNA with Amplified Fragment Length Polymorphism To Assess Genetic Diversity and Genetic Relatedness within Genospecies III of Pseudomonas syringae.

Recently, DNA pairing analyses showed that Pseudomonas syringae pv. tomato and related pathovars, including P. syringae pv. maculicola, form a genomic species (Pseudomonas tomato) (L. Gardan, H. L. Shafik, and P. A. D. Grimont, p. 445-448, in K. Rudolph, T. J. Burr, J. W. Mansfield, D. Stead, A. Vivian, and J. von Kietzell, ed., Pseudomonas syringae Pathovars and Related Pathogens, 1997). The genetic diversity of 23 strains belonging to this genomic species and 4 outgroup strains was analyzed with randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphic (AFLP) techniques. Simple boiling of P. syringae cells was suitable for subsequent DNA amplification to obtain reliable patterns in RAPD and AFLP analyses. In general, the grouping of P. syringae strains by both analysis techniques corresponded well with the classification obtained from an RFLP analysis of ribosomal DNA operons, DNA pairing studies, and an analysis of pathogenicity data. However, two strains of P. syringae pv. maculicola produced distinct DNA patterns compared to the DNA patterns of other P. syringae pv. maculicola strains; these patterns led us to assume that horizontal transfer of DNA could occur between bacterial populations. Both techniques used in this study have high discriminating power because strains of P. syringae pv. tomato and P. syringae pv. maculicola which were indistinguishable by other techniques, including pathogenicity tests on tomato, were separated into two groups by both RAPD and AFLP analyses. In addition, data analysis showed that the AFLP method was more efficient for assessing intrapathovar diversity than RAPD analysis and allowed clear delineation between intraspecific and interspecific genetic distances, suggesting that it could be an alternative to DNA pairing studies. However, it was not possible to distinguish the two races of P. syringae pv. tomato on the basis of an analysis of the data provided by either the AFLP or RAPD technique.

Journal Article↗

PubMed1975

Identification of Chromobacterium violaceum: pigmented and non-pigmented strains.

The classification and, therefore, identification of Chromobacterium violaceum has been based upon its ability to produce a violet pigment. Although the organism may yield non-pigmented variants when subcultured on artificial media, the isolation of non-pigmented strains from pathological tissues or from nature had not been reported. With a method established for the identification of C. violaceum regardless of violet pigmentation, non-pigmented strains were isolated from nature. The presence of non-pigmented strains of C. violaceum in nature is of significance to taxonomy and clinical bacteriology. Pigmentation cannot be held as an essential characteristic of the definition of the genus Chromobacterium and gives credence to the suspicion of Sneath (1960, 1966) that the genus is not a natural one. Non-pigmented strains may have been isolated from clinical material but wrongly identified as belonging to other genera of non-pigmented Gram-negative bacilli and regarded as not being pathogenic.

Animal Diseases↗

PubMed1999

Relationships among seminal culture, seminal white blood cells, and the percentage of primary sperm abnormalities in bulls evaluated prior to the breeding season.

Semen samples from 100 beef breed bulls were evaluated for sperm morphology (phased contrast microscopy), seminal white blood cells, and the presence of potential reproductive pathogens. Eligibility required visualization of the glans penis throughout semen collection. Based on clinical spermiograms, bulls were grouped into normal, marginal, or unsatisfactory morphology classifications. The 3 experimental groups were similar in age and scrotal circumference and differed significantly in the percentage of primary sperm abnormalities. Most semen samples (94%) contained one or more potential reproductive pathogens (Hemophilus somnus. Mycoplasma bovigenitalium, Arcanobacterium pyogenes and Ureaplasma diversum). No significant relationship could be demonstrated between primary abnormalities and the assigned culture score. Our experimental results suggest that clinicians should interpret clinical semen culture results with great care. No significant relationship could be demonstrated between primary abnormalities and assigned white blood cell (WBC) score, although, only 1% of the samples was scored >5 WBC per high power field. The use of seminal WBC score may be valid adjunct to routine semen evaluation when that threshold is the basis for clinical decisions.

Actinomycetaceae↗

PubMed1992

Subgingival distribution of periodontal pathogenic microorganisms in adult periodontitis.

The association between specific plaque microorganisms and periodontal diseases has been the subject of much recent interest due to its potential importance in the diagnosis and classification of these diseases. In order to optimize microbiological tests in periodontal therapy, it is important to know how many subgingival plaque samples must be assayed from a single patient in order to ascertain infection with a periodontal pathogen. To answer this question the present study assessed the distribution of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Bacteroides forsythus, and Prevotella intermedia in multiple subgingival plaque samples. The samples were quantitatively assessed for specific bacteria by indirect immunofluorescence, a technique previously found to correlate well with cultural assessment of these same organisms. Subgingival plaque from the mesial pockets/sulci of all teeth except third molars was sampled in 12 patients with adult periodontitis, 22 to 28 sites/patient for a total of 315 samples. These patients demonstrated an average mesial probing depth and loss of attachment of 3.7 +/- 1.2 mm and 3.1 +/- 1.5 mm, respectively (mean +/- SD). P. gingivalis, P. intermedia, and B. forsythus were demonstrated in one or more sites from all patients, while A. actinomycetemcomitans was found in one or more sites in 8 of 12 patients. The proportion of positive sites per subject varied, but it was, on average, similar for the 3 black-pigmented organisms and ranged from 44% to 54%. In contrast, A. actinomycetemcomitans was identified, on average, in only 11.4% of the sites in these same patients.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed1979

An examination of the possibilities of preventive therapy in arteriolar retinopathies.

The identification of certain chronic vascular retinopathies has been marked by a search for their classification. Such proper classification has therapeutic implications. The similarities of these retinopathies are based on a shared pathogenic process, initiated by diminished arteriolar perfusion pressure, as the result of varied causes but leading to somewhat nonspecific capillary and reactive stages. On the basis of such a pathogenesis, various possible prophylactic and therapeutic measures and their organizational requirements are significant. These measures are directed to the correction of a blood perfusion pressure defect and to leaking capillaries and new vessels. Prophylactic and therapeutic exercises will be required for various chronic arteriolar capillaropathies, although the experience with one disease may be applicable to the others. Senile macular disciform degeneration provides the factors necessary for a therapeutic trial.

Arterioles↗

PubMed2026

Matching genomic evidence to claims about Mycobacterium avium subsp. paratuberculosis: Host association, host adaptation, mechanism, and virulence.

Whole-genome sequencing (WGS) permits high-resolution comparison of Mycobacterium avium subsp. paratuberculosis (MAP) isolates and pangenome analysis. Combined with animal-movement data, WGS can support transmission inference, but resolution alone does not establish the biological meaning of genomic variation. This focused narrative review applies a two-dimensional framework to purposively selected MAP studies, separating claim targets from support profiles. Claim targets include lineage identity, host-source or lineage characterization, host association, transmission, candidate genomic features, measured bacterial or host-cell phenotypes, natural-host infection fitness, disease or damage, shedding, and control outcomes. Depending on the claim, evidence operations may include characterization, context-aware comparative inference, direct endpoint ascertainment, and controlled feature perturbation; these are non-ordinal and may co-occur. On-target attribution, independent replication, and transportability are reported separately. The claim, not the study, is the unit of assessment. Typing markers support isolate or lineage discrimination, whereas phylogenomics supports evolutionary inference; neither alone establishes host adaptation. Pangenome comparisons and microbial genome-wide association studies nominate candidate features rather than establish adaptation. Cell-envelope and iron-associated studies support specified biochemical, transcriptional, or physiological phenotypes under defined conditions, while macrophage and calf models support only the endpoints measured. Annotated sequence variation alone nominates pathogenicity hypotheses. Across the illustrative studies selected here, MAP genomics most directly supported lineage classification, candidate discovery, measured bacterial phenotypes, bounded transmission inference, and natural-host infection-fitness claims. Claims about adaptation, mechanism, virulence, or control require endpoints and comparisons matched to the stated claim and model; feature-specific causal claims additionally require evidence linking the bacterial feature to the measured endpoint.

Claim boundaries↗

PubMed2003

Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of Arabidopsis responding to pathogen infection.

A major task in computational analysis of mRNA expression profiles is definition of relationships among profiles on the basis of similarities among them. This is generally achieved by pattern recognition in the distribution of data points representing each profile in a high-dimensional space. Some drawbacks of commonly used pattern recognition algorithms stem from their use of a globally linear space and/or limited degrees of freedom. A pattern recognition method called Local Context Finder (LCF) is described here. LCF uses nonlinear dimensionality reduction for pattern recognition. Then it builds a network of profiles based on the nonlinear dimensionality reduction results. LCF was used to analyze mRNA expression profiles of the plant host Arabidopsis interacting with the bacterial pathogen Pseudomonas syringae. In one case, LCF revealed two dimensions essential to explain the effects of the NahG transgene and the ndr1 mutation on resistant and susceptible responses. In another case, plant mutants deficient in responses to pathogen infection were classified on the basis of LCF analysis of their profiles. The classification by LCF was consistent with the results of biological characterization of the mutants. Thus, LCF is a powerful method for extracting information from expression profile data.

Arabidopsis↗

PubMed2005

Classifying noisy protein sequence data: a case study of immunoglobulin light chains.

SUMMARY: The classification of protein sequences obtained from patients with various immunoglobulin-related conformational diseases may provide insight into structural correlates of pathogenicity. However, clinical data are very sparse and, in the case of antibody-related proteins, the collected sequences have large variability with only a small subset of variations relevant to the protein pathogenicity (function). On this basis, these sequences represent a model system for development of strategies to recognize the small subset of function-determining variations among the much larger number of primary structure diversifications introduced during evolution. Under such conditions, most protein classification algorithms have limited accuracy. To address this problem, we propose a support vector machine (SVM)-based classifier that combines sequence and 3D structural averaging information. Each amino acid in the sequence is represented by a set of six physicochemical properties: hydrophobicity, hydrophilicity, volume, surface area, bulkiness and refractivity. Each position in the sequence is described by the properties of the amino acid at that position and the properties of its neighbors in 3D space or in the sequence. A structure template is selected to determine neighbors in 3D space and a window size is used to determine the neighbors in the sequence. The test data consist of 209 proteins of human antibody immunoglobulin light chains, each represented by aligned sequences of 120 amino acids. The methodology is applied to the classification of protein sequences collected from patients with and without amyloidosis, and indicates that the proposed modified classifiers are more robust to sequence variability than standard SVM classifiers, improving classification error between 5 and 25% and sensitivity between 9 and 17%. The classification results might also suggest possible mechanisms for the propensity of immunoglobulin light chains to amyloid formation.

Algorithms↗

PubMedDate not supplied

Human microsporidiosis and AIDS.

Several protozoan parasites of the phylum Microspora, previously only rarely recognized in humans, are being detected with increasing frequency in patients with AIDS. These protozoa are small obligate intracellular parasites of the intestine, liver, muscles, cornea, and several other tissues. They are difficult to detect because they stain poorly, often evoke little or no tissue response, and require electron-microscopic methods for classification. Although there are no human isolates, serologic evidence in humans (using an animal pathogen [Encephalitozoon cuniculi] as the antigen) suggests that clinically silent infections may occur in humans, as they do in mice, rabbits, dogs, foxes, squirrel monkeys, and birds. Experiments in mice suggest that patients with impaired T cell functions may be vulnerable to clinical disease caused by these parasites. There is no known treatment.

Acquired Immunodeficiency Syndrome↗

PubMed1999

THE EVOLUTION OF ASEXUAL FUNGI: Reproduction, Speciation and Classification.

Phylogenetic and population genetic methods that compare nucleic acid variation are being used to identify species and populations of pathogenic fungi and determine how they reproduce in nature. These studies show that asexual or sexual reproductive morphology does not necessarily correlate with clonal or recombining reproductive behavior, and that fungi with all types of reproductive morphologies and behaviors can be accommodated by a phylogenetic species concept. Although approximately one fifth of described fungi have been thought to be asexual and clonal, recent studies have shown that they are also recombining. Whether a particular pathogen reproduces clonally or by recombination depends on factors relating to its biology and its distribution in space and time. Knowing the identity of species and populations and their reproductive modes, while taking a broad view of pathogen behavior in space and time, should enhance the ability of pathologists to control pathogens and even predict their behavior.

Journal Article↗

PubMed2022

Profiling Genome-Wide DNA Methylation in Children with Autism Spectrum Disorder and in Children with Fragile X Syndrome.

Autism spectrum disorder (ASD) is an early onset, developmental disorder whose genetic cause is heterogeneous and complex. In total, 70% of ASD cases are due to an unknown etiology. Among the monogenic causes of ASD, fragile X syndrome (FXS) accounts for 2-4% of ASD cases, and 60% of individuals with FXS present with ASD. Epigenetic changes, specifically DNA methylation, which modulates gene expression levels, play a significant role in the pathogenesis of both disorders. Thus, in this study, using the Human Methylation EPIC Bead Chip, we examined the global DNA methylation profiles of biological samples derived from 57 age-matched male participants (2-6 years old), including 23 subjects with ASD, 23 subjects with FXS with ASD (FXSA) and 11 typical developing (TD) children. After controlling for technical variation and white blood cell composition, using the conservatory threshold of the false discovery rate (FDR ≤ 0.05), in the three comparison groups, TD vs. AD, TD vs. FXSA and ASD vs. FXSA, we identified 156, 79 and 3100 differentially methylated sites (DMS), and 14, 13 and 263 differential methylation regions (DMRs). Interestingly, several genes differentially methylated among the three groups were among those listed in the SFARI Gene database, including the PAK2, GTF2I and FOXP1 genes important for brain development. Further, enrichment analyses identified pathways involved in several functions, including synaptic plasticity. Our preliminary study identified a significant role of altered DNA methylation in the pathology of ASD and FXS, suggesting that the characterization of a DNA methylation signature may help to unravel the pathogenicity of FXS and ASD and may help the development of an improved diagnostic classification of children with ASD and FXSA. In addition, it may pave the way for developing therapeutic interventions that could reverse the altered methylome profile in children with neurodevelopmental disorders.

Child↗

PubMedDate not supplied

[Morphological, clinical and therapeutic characteristics of Cyclospora cayetanensis].

In the last years Cyclospora sp. has been increasingly associated to human intestinal diseases. The first studies have been reported to this parasite as a Cyanobacterium-like body, large Cryptosporidium or coccidian-like body. The ultrastructural characteristic and the "in vitro" sporulation have revealed the existence of oocyst constituted for two sporocysts with two sporozoites per sporocyst. This evidence has allowed its classification as a coccidian within the genus Cyclospora and its designation as a new pathogen species in humans, Cyclospora cayetanensis. Recently phylogenetic analysis based on rDNA sequences suggested that Cyclospora sp. was closely related to the Eimeria genus. The identification, morphological characteristics, clinical evaluation and chemotherapy of the human intestinal disease associated to Cyclospora sp. are commented in the present paper.

Animals↗

PubMed1993

Safe biotechnology (5). Recommendations for safe work with animal and human cell cultures concerning potential human pathogens.

The benefits of using animal or human cell cultures have been clearly demonstrated in diagnostic and therapeutic research and in their application for manufacturing. Cell cultures serve as a tools for the production of vaccines, receptors, enzymes, monoclonal antibodies and recombinant DNA-derived proteins. They represent an integral part of drug development for which corresponding facilities, equipment and manufacturing processes are required. Although the cells themselves offer no particular risk to workers in laboratories and production areas or to the environment, the cell cultures may be contaminated with viruses, mycoplasma, bacteria, yeast and fungi or might contain endogenous viruses. The containment level for animal and human cells is therefore determined by the risk class of these agents. The history of animal and human cell cultures has proved that they can be handled safely. The recommendations in this publication concern the safe handling of cell cultures (tissue explants, primary cell cultures) and permanent cell lines of animal and human origin. A classification system of safety precautions has been elaborated according to the potential for contamination with the pathogenic agents involved.

Animal Population Groups↗

PubMed2005

Genomics in myeloid leukemias: an array of possibilities.

Myeloid leukemias are clonal hematopoietic stem cell disorders characterized either by proliferation of one or more of the myeloid lineages (chronic myelogenous leukemia) or by clonal expansion of myeloid blasts (acute myeloid leukemia). Over the past several years our knowledge of these hematologic malignancies has increased tremendously. The result is a classification that incorporates morphologic, immunophenotypic, genetic and clinical features in an attempt to define biologically and clinically relevant entities. Nevertheless, in many tumor subtypes the pathogenic event is still unknown. Furthermore, well-defined leukemia subgroups exhibit considerable heterogeneity, arousing the suspicion that several molecularly distinct subtypes might exist within the same cytogenetic category. Therefore, an ideal classification system would ultimately be based on the underlying molecular pathogenesis, but such knowledge is not yet available. However, by surveying the expression levels of thousands of genes in parallel, DNA microarrays have recently contributed to an increasingly refined molecular taxonomy of myeloid disorders. This powerful technology is becoming well established and has been used to diagnosis cancer and predict clinical outcome, to discover novel tumor subclasses, to gain insights into pathogenesis, and to identify new therapeutic targets. While many challenges remain ahead, genomic technologies have already demonstrated tremendous potential. We expect whole genome approaches will significantly contribute to a better understanding of the pathogenesis and result in a refined molecular classification of myeloid leukemias.

Gene Expression Profiling↗