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In this article, the most important animal pathogens, which, according to CDC classification, can be used as biological agents, are presented. The means of dissemination and the ways of infection's propagation are reviewed. Typical and the most dangerous signs and symptoms are described, as well as the consequences of these infections.
The present knowledge of the efficiency of antibiotics against bovine mastitis has been reviewed. Criteria for the choice of papers are given, together with tabulated results of treatments with one antibiotic or two. Results are discussed in relation to the time of treatment and the pathogenic agent involved, and a classification of the antibiotics into three groups is proposed: recommended; not advised; not sufficiently studied.
Bioptic investigation of nervous tissue can be made by taking tissue samples of nerves, skin, muscle, rectum, dental pulp and brain. The choice of site for the biopsy depends on the results of previous clinical neurological, neurophysiological and biochemical investigations. Indications are: unexplained peripheral neuropathies, progressive degenerative diseases of the central nervous system and enzymopathies which are principally manifest in the nervous system (neurometabolic diseases). The result of a nerve tissue biopsy usually only leads to classification in a disease group (pathogenic unit) which only becomes diagnostically relevant in conjunction with the clinical data. In biopsies of the brain a virological examination should always be performed in addition to the morphological (light and electron microscopic) and biochemical investigation.
OBJECTIVES: To determine the epidemiologic, clinical and aetiologic features of chronic diarrhoea in patients with human immunodeficiency virus (HIV) infection. METHODS: Between January 1992 and April 1993, all HIV positive patients with chronic diarrhoea were enrolled in a prospective study. There were 46 patients in the study group including 33 (22 homosexuals) in stage C according to the 1993 Centers for Disease Control classification. RESULTS: Thirty-four pathogenic agents were isolated in 26 of the patients (57%). Enterocytozoon bieneusi was the most frequently found pathogen (11 patients, 24%) followed by Cryptosporidium sp (8 patients). Enterocytozoon bieneusi was found in association with other pathogens in 7 patients. All patients with microsporidiosis were in stage C (p = 0.04) and had a longer duration of diarrhoea (19.6 vs 9.8 weeks, p = 0.03), greater weight loss (9.6 vs 2.1 kg, p = 0.0003) and a lower Karnofsky index (48% vs 67%, p = 0.01). Prophylaxy with dapsone or pyrimethamine during the 3 months prior to inclusion had been more frequent (p = 0.04 and p = 0.05 respectively) in patients without microsporidiosis. CONCLUSION: Microsporidiosis should be suspected as a probable cause of chronic diarrhoea in HIV positive patients with a CD4 count < 100/mm3. Multiple infections may be a factor leading to treatment failure. Microsporidiosis seems to be linked to homosexual intercourse.
After an episode of clinical Pasteurella pneumotropica infection was diagnosed in a C57BL/6N mouse, a randomly amplified polymorphic DNA polymerase chain reaction assay (RAPD-PCR) was developed and used to genetically characterize and differentiate 52 field isolates and laboratory reference strains of P. pneumotropica and related bacteria. A survey of rodents in the facility recovered 36 isolates of P. pneumotropica from 30 mice, six isolates from hamsters, and three isolates from rats during the follow-up investigation. Antibiograms and routine bacteriologic evaluations for morphologic and biochemical characteristics on selective media did not substantively aid in the differentiation of these isolates, but the RAPD-PCR revealed four strains of P. pneumotropica in the colony, two of which were confined to rats and hamsters. The RAPD-PCR unambiguously differentiated Heyl and Jawetz biotypes of P. pneumotropica recovered from mice, identified two additional genetic groups for rat and hamster isolates, and clearly distinguished P. pneumotropica from related bacteria. Most field isolates were genetically consistent with the Jawetz biotype of P. pneumotropica. The RAPD-PCR is a fast, sensitive, and efficient method for identifying genetic differences between strains of the P. pneumotropica complex and can contribute substantially in addressing the epidemiology, pathogenesis, and taxonomic classification of this common opportunistic pathogen.
Since choanal atresia may be associated with other cranio-facial malformations, including various degrees of nasal fossa malformation, and be a part of paramedian facial clefts, (as described by Tessier), they can be integrated into the larger group of neurocristopathies. We identified four such cases with combined clinical elements corresponding to Tessier's paramedian facial cleft, including eyelid coloboma, mild to severe choanal and nasal fossa anomalies, ethmoidal hypoplasia and anterior skull base malformation, sometimes with proboscis lateralis. These various malformations are due to abnormality of the olfactive placode and the adjacent mesenchyme. These discoveries incited us to elaborate a conception first of all on the pertinent embryology involved, second, to propose a new classification based on anatomical and pathogenic embryological considerations. And finally, since endonasal laser therapy is particularly dangerous in such cases, to propose the use of transpalatal approach to restore choanal permeability. Pediatric ENT surgeons should pay special attention to any small stigmatism of facial cleft when dealing with children affected by choanal atresia.
Tyrnpanosclerosis continues to be a clinically and pathogenically controversial topic. The options for dealing with it range from a conservative approach using hearing aids to surgery. With a view to justifying our therapeutic criteria, 29 cases of tympanosclerosis, out of a total of 200 surgical operations for otorrhea, were reviewed. An anatormical-surgical classification was established for use in approaching specific therapy for each particular case.
We previously reported the identification of homologous cDNA clones derived from a pathogenic isolate and a nonpathogenic isolate of Entamoeba histolytica, which had been designated cEh-P1 and cEh-NP1, respectively. Sequence analysis of both clones had revealed 10% nucleic acid substitutions, which were dispersed over the entire sequence. This genetic difference had been found to be conserved between all four pathogenic and all five nonpathogenic laboratory strains of E. histolytica tested. On the basis of nucleic acid substitutions, we have now developed a sensitive assay to distinguish pathogenic from nonpathogenic forms of E. histolytica by using fresh clinical isolates. Comparing the sequence of cEh-P1 and cEh-NP1, we identified a 482-bp segment that contained identical 5' and 3' ends but differed in internal cleavage sites for restriction endonucleases. By using oligonucleotide primers corresponding to the 5' and 3' ends of this segment, the corresponding gene was amplified by the polymerase chain reaction. Endonuclease digestion of the amplified DNA yielded restriction fragments that are characteristic for pathogenic and nonpathogenic forms. This assay allows the detection and classification of fewer than 10 amoebae within a few hours. The differentiation of 48 isolates into pathogenic and nonpathogenic strains by using this method corresponded to the clinical status of the infected individuals and to the classification obtained by isoenzyme determination. The results further support the concept that pathogenic and nonpathogenic strains of E. histolytica constitute distinct subspecies.
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In this paper, we propose to use probabilistic neural networks (PNNs) for classification of bacterial growth/no-growth data and modeling the probability of growth. The PNN approach combines both Bayes theorem of conditional probability and Parzen's method for estimating the probability density functions of the random variables. Unlike other neural network training paradigms, PNNs are characterized by high training speed and their ability to produce confidence levels for their classification decision. As a practical application of the proposed approach, PNNs were investigated for their ability in classification of growth/no-growth state of a pathogenic Escherichia coli R31 in response to temperature and water activity. A comparison with the most frequently used traditional statistical method based on logistic regression and multilayer feedforward artificial neural network (MFANN) trained by error backpropagation was also carried out. The PNN-based models were found to outperform linear and nonlinear logistic regression and MFANN in both the classification accuracy and ease by which PNN-based models are developed.
The genus Acanthamoeba includes pathogenic and nonpathogenic strains of amebas with unclear taxonomic and evolutionary relationships. To explore these relationships further, we have examined mitochondrial DNA fragment patterns obtained for 15 Acanthamoeba strains by use of five restriction endonucleases. The mitochondrial DNA molecules were circular, averaging 41.6 +/- 1.5 kilobase pairs. Fragments resulting from endonuclease digestion of the DNA were separated by agarose gel electrophoresis. Ten distinct families of electrophoretic patterns (digestion phenotypes) were observed. Seven phenotypes were found for seven strains considered nonpathogenic or of unknown pathogenicity. Three phenotypes were associated with pathogenic strains. One of these phenotypes included a single pathogenic strain, a second included one pathogen and one strain of unknown pathogenicity, and the third included five pathogenic strains. The latter five were of widespread geographic origin and previously were assigned to two different species. The results suggest that extensive nucleotide sequence diversity occurs among strains from a single species of Acanthamoeba, but that subgroups of strains with similar sequences also occur. Thus, restriction enzyme analysis can identify clusters of strains and may be a useful approach to classification in the genus. Improvements in classification should help clarify relationships among pathogenic and non-pathogenic strains.
The identification and discrimination of 2 closely related and morphologically similar species of Gyrodactylus, G. salaris and G. thymalli, were assessed using the statistical classification methodologies Linear Discriminant Analysis (LDA) and k-Nearest Neighbours (KNN). These statistical methods were applied to morphometric measurements made on the gyrodactylid attachment hooks. The mean estimated classification percentages of correctly identifying each species were 98.1% (LDA) and 97.9% (KNN) for G. salaris and 99.9% (LDA) and 73.2% (KNN) for G. thymalli. The analysis was expanded to include another 2 closely related species and the new classification efficiencies were 94.6% (LDA) and 98.% (KNN) for G. salaris; 98.2% (LDA) and 72.6% (KNN) for G. thymalli; 86.7% (LDA) and 91.8% (KNN) for G. derjavini; and 76.5% (LDA) and 77.7% (KNN) for G. truttae. The higher correct classification scores of G. salaris and G. thymalli by the LDA classifier in the 2-species analysis over the 4-species analysis suggested the development of a 2-stage classifier. The mean estimated correct classification scores were 99.97% (LDA) and 99.99% (KNN) for the G. salaris-G. thymalli pairing and 99.4% (LDA) and 99.92% (KNN) for the G. derjavini-G. truttae pairing. Assessment of the 2-stage classifier using only marginal hook data was very good with classification efficiencies of 100% (LDA) and 99.6% (KNN) for the G. salaris G. thymalli pairing and 97.2% (LDA) and 99.2% (KNN) for the G. derjavini-G. truttae pairing. Paired species were then discriminated individually in the second stage of the classifier using data from the full set of hooks. These analyses demonstrate that using the methods of LDA and KNN statistical classification, the discrimination of closely related and pathogenic species of Gyrodactylus may be achieved using data derived from light microscope studies.
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MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score. RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest. AVAILABILITY AND IMPLEMENTATION: Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.
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.
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.
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.
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.