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Application of flow cytometry to studies of pathogenic free-living amoebae.

Species of small, free-living amoebae of the genera Naegleria and Acanthamoeba can cause fatal amoebic meningoencephalitis. Previous investigations have shown that pathogenic amoebae are associated with thermally altered water. Flow cytometric techniques for identifying species of pathogenic and nonpathogenic amoebae from such water have been developed, using immunofluorescence and fluorescein-bound concanavalin A. Flow cytometry is accomplished with a cytofluorograph, in which cells are dispersed in a suspended carrier liquid and passed in front of a focused argon ion laser beam. Cells are then distinguished by the degree of scattered light (size) or fluorescence. Flow cytometry techniques have proven efficient for environmental samples, as indicated by the identification of pathogenic Naegleria fowleri and nonpathogenic Naegleri gruberi and Acanthamoeba castellanii isolated from the Savannah River Plant in South Carolina. Cytofluorographic analysis of environmental samples has several advantages over the current methods of isolation and classification of free-living amoebae. With this system, it is possible to rapidly identify species and quantitate mixtures of pathogenic amoebae in environmental samples. Cytofluorographic analysis of amoebic isolates reduces the time presently required to screen environmental sites for pathogenic amoebae. The cytofluorograph permits detection and species identification of nonthermophilic Naegleria spp. and Acanthamoeba spp. that could not easily be isolated for species identification by conventional methods. Other advantages of flow cytometry over fluorescent microscopy include a high degree of statistical precision due to the large numbers measured, high immunofluorescent titers, and elimination of subjectivity and fluorescence fading.

Agglutination Tests↗

Pathology of human immunodeficiency virus infection: infectious conditions.

Infection with the human immunodeficiency virus (HIV) and the subsequent derangement of host immunity place affected patients at risk for secondary infections. Some of the secondary pathogens occur with such frequency or are so rare in the non-immunosuppressed population that they have become part of the Centers for Disease Control and Prevention (CDC) classification for HIV/acquired immune deficiency syndrome (AIDS). Other infectious agents not yet included in the CDC definition are being reported in the HIV-infected population with increased frequency. General observations of the degree of immunosuppression associated with specific secondary infections have been useful in developing classification systems for HIV disease such as that of the CDC. However, the specific alterations in host immunity that promote infection with specific secondary pathogens are generally unknown. Geographic differences in the types and frequency of secondary infections also have been reported. Variation in strains of HIV, effect of malnutrition, lack of appropriate medical treatment, prevalence of virulent infectious diseases, and epidemiologic differences are possible contributing factors. Some infections that seemed likely to be closely associated with HIV infection have not occurred more frequently in HIV-infected patients. This review summarizes the histopathology of infectious conditions in the current CDC classification and highlights some conditions seen in HIV-infected individuals that are not currently HIV/AIDS-defining infections, yet may be seen by practicing pathologists.

AIDS-Related Opportunistic Infections↗

Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage.

MOTIVATION: Discovery of host and pathogen genes expressed at the plant-pathogen interface often requires the construction of mixed libraries that contain sequences from both genomes. Sequence identification requires high-throughput and reliable classification of genome origin. When using single-pass cDNA sequences difficulties arise from the short sequence length, the lack of sufficient taxonomically relevant sequence data in public databases and ambiguous sequence homology between plant and pathogen genes. RESULTS: A novel method is described, which is independent of the availability of homologous genes and relies on subtle differences in codon usage between plant and fungal genes. We used support vector machines (SVMs) to identify the probable origin of sequences. SVMs were compared to several other machine learning techniques and to a probabilistic algorithm (PF-IND) for expressed sequence tag (EST) classification also based on codon bias differences. Our software (Eclat) has achieved a classification accuracy of 93.1% on a test set of 3217 EST sequences from Hordeum vulgare and Blumeria graminis, which is a significant improvement compared to PF-IND (prediction accuracy of 81.2% on the same test set). EST sequences with at least 50 nt of coding sequence can be classified using Eclat with high confidence. Eclat allows training of classifiers for any host-pathogen combination for which there are sufficient classified training sequences. AVAILABILITY: Eclat is freely available on the Internet (http://mips.gsf.de/proj/est) or on request as a standalone version. CONTACT: friedel@informatik.uni-muenchen.de.

Algorithms↗

Hendra and Nipah viruses: different and dangerous.

Hendra virus and Nipah virus are highly pathogenic paramyxoviruses that have recently emerged from flying foxes to cause serious disease outbreaks in humans and livestock in Australia, Malaysia, Singapore and Bangladesh. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses. These features led to their classification into the new genus Henipavirus within the family Paramyxoviridae and to their designation as Biosafety Level 4 pathogens. This review provides an overview of henipaviruses and the types of infection they cause, and describes how studies on the structure and function of henipavirus proteins expressed from cloned genes have provided insights into the unique biological properties of these emerging human pathogens.

Animals↗

Crystal structures of Nipah and Hendra virus fusion core proteins.

The Nipah and Hendra viruses are highly pathogenic paramyxoviruses that recently emerged from flying foxes to cause serious disease outbreaks in humans and livestock in Australia, Malaysia, Singapore and Bangladesh. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses. These characteristics have led to their classification into the new genus Henpavirus within the family Paramyxoviridae and to their designation as Biosafety Level 4 pathogens. The fusion protein, an enveloped glycoprotein essential for viral entry, belongs to the family of class I fusion proteins and is characterized by the presence of two heptad repeat (HR) regions, HR1 and HR2. These two regions associate to form a fusion-active hairpin conformation that juxtaposes the viral and cellular membranes to facilitate membrane fusion and enable subsequent viral entry. The Hendra and Nipah virus fusion core proteins were crystallized and their structures determined to 2.2 A resolution. The Nipah and Hendra fusion core structures are six-helix bundles with three HR2 helices packed against the hydrophobic grooves on the surface of a central coiled coil formed by three parallel HR1 helices in an oblique antiparallel manner. Because of the high level of conservation in core regions, it is proposed that the Nipah and Hendra virus fusion cores can provide a model for membrane fusion in all paramyxoviruses. The relatively deep grooves on the surface of the central coiled coil represent a good target site for drug discovery strategies aimed at inhibiting viral entry by blocking hairpin formation.

Amino Acid Sequence↗

Serological classification and epitope specificity of Proteus penneri S29 lipopolysaccharide.

INTRODUCTION: Gram-negative bacteria of genus Proteus are common human intestinal and urinary tract pathogens. In the genus Proteus there are four clinically important named species: P. mirabilis, P. vulgaris, P. penneri, and P. hauseri, and three unnamed Proteus genomospecies: 4, 5, and 6. The clinical significance of P. penneri, described in 1982 as a new species, is poorly documented. The aim of this work is serological characterization and classification of a ceftriaxone-susceptible P. penneri S29 strain isolated from a 34-year-old patient with postneurosurgical meningitis. In this characterization we will also include a ceftriaxonresistant strain, P. penneri R15, isolated from the same patient after 12 days' treatment with ceftriaxon and other antibiotics. MATERIAL/METHODS: Rabbit polyclonal O-antisera were obtained against these two strains and purified and lipopolysaccharides (LPS) were extracted from the bacterial mass of the P. penneri S29 and R15 strains. In the serological investigations the following tests were used: enzyme immunosorbent assay (EIA), passive immunohemolysis (PIH), inhibition of these tests, absorption of rabbit O-antisera with the respective LPS, and repeated PIH, SDS/PAGE, and Western blot techniques. RESULTS: The serological studies of the LPS extracted from both P. penneri strains showed the identity of both preparations of O-polysaccharides from LPS. In P. penneri S29 O-antiserum, four different types of antibodies were described and characterized. CONCLUSIONS: Both investigated P. penneri S29 and R15 strains were classified to the Proteus O31ab serogroup.

Adult↗

[Problems of food hygiene with carriers of microorganisms and permanent excretors].

To appraise the significance of chronic excretors and carriers for the development of "food poisoning", the analysis must also include the food. First of all, the question arises as to whether foods only have a vector function or whether an increase in the bacterial count is an important prerequisite for the elicitation of human disease. When pure intoxication pathogens are not involved, this question arises in connection with the minimum infectious dose. A classification of the most important causative organisms of bacterial foodborne infections and intoxications is presented in the light of these considerations. If foods only have a vector function, hygiene measures are automatically concentrated on excretors in order to prevent the bacteria from passing into foods. When this is not the case (as in the vast majority of human foodborne infections and intoxications of bacterial origin), two strategies can be successfully applied. First of all, precautions must be taken to rule out bacterial contamination. On the other hand, an increase in the bacterial count, i.e. proliferation of the pathogens in the food must be prevented by appropriate measures. The interacting factors are described. The example of salmonellae is cited to illustrate the routes of contamination from excretors (humans and animals) to foods ready for consumption and possible hygiene measures.

Animals↗

A framework for automated scalable designation of viral pathogen lineages from genomic data.

Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.

Animals↗

WHO and ADA criteria for the diagnosis of diabetes mellitus in relation to body mass index. Insulin sensitivity and secretion in resulting subcategories of glucose tolerance.

OBJECTIVE: To determine the influence of body mass index (BMI) on agreement between the American Diabetes Association (ADA) and the new World Health Organization diagnostic criteria for the diagnosis of diabetes mellitus and to investigate the metabolic profile of the resulting subcategories. DESIGN: Cross-sectional study SUBJECTS: A total of 3018 subjects with no previous history of diabetes and fasting glucose <7.8 mmol/l, with a wide range of BMIs. MEASUREMENTS: (1) Prevalence of impaired glucose regulation (IGR) and diabetes (DM) according to ADA and WHO diagnostic criteria; (2) basal and post-load insulin sensitivity and secretion, calculated on the basis of data derived from an oral glucose tolerance test (OGTT). RESULTS: The diagnosis according to the two classifications was concordant in 2490 subjects, discordant in 528 (452 were identified as impaired glucose tolerance (IGT) and 76 as DM only by means of OGTT). The disagreement increased with increasing BMI, being as high as 25.3% in subjects with BMI > or = 35 kg/m(2). Subjects with isolated fasting hyperglycaemia were mainly characterised by reduced insulin sensitivity and secretion in the basal state, but normal first-phase insulin secretion and moderately reduced insulin sensitivity after glucose challenge. Subjects with isolated 2 h hyperglycaemia were mainly characterised by normal basal insulin secretion and by a marked insulin resistance associated with a blunted first-phase insulin secretion after the glucose load. CONCLUSIONS: The disagreement between ADA and WHO classifications is particularly relevant in obesity, making OGTT mandatory in these subjects. Different pathogenic mechanisms are involved in isolated fasting or post-load hyperglycaemia, possibly related to a different site of insulin resistance (hepatic vs peripheral), and/or to a different disregulation of insulin secretion (basal vs post-load). A correct identification of the underlying mechanism(s) is the rationale for future studies to detect the effectiveness of different pharmacological or behavioural approaches.

Adolescent↗

Pathophysiology and treatment of idiopathic hypercalciuria.

Nearly 50 years after its initial description by Dr. F. Albright, the term idiopathic hypercalciuria (IH) is still in use. The exact mechanism of hypercalciuria is still unknown despite extensive pathophysiologic investigations; recent advances represent the focus of this review. A precise definition of true IH is proposed, taking into account the various nutritional conditions influencing calcium excretion. The potential pathogenic mechanisms are discussed, and the limits of the classical Pak's pathophysiological classification are recalled. The evidence supporting the role of an increased intestinal calcium absorption, a defect in renal tubular calcium reabsorption, or an increased bone loss as a primary mechanism in IH are successively examined. Since overall available human data indicates that all three mechanisms may be found in IH, the hypothesis that a broader disorder encompassing all these various abnormalities may be involved in IH is discussed. Three global hypotheses to account for IH physiopathology are examined: a diffuse defect in fatty acid content of cell membranes, an increased expression of the vitamin D receptor of the 25(OH) vitamin D 1 alpha-hydroxylase, or of the calcium sensor receptor and a monocyte disease. Finally, the available clinical data justifying the therapeutic approaches are reviewed, and guidelines for dietary recommendations regarding calcium and also animal protein, sodium chloride, alcohol, carbohydrate, phosphate, and potassium intakes are proposed, and drug therapy indications are discussed.

Bone Diseases, Metabolic↗

Occurrence of two superoxide dismutases in Aeromonas hydrophila: molecular cloning and differential expression of the sodA and sodB genes.

Aeromonas spp., considered as emerging opportunistic pathogens, belong to the family Vibrionaceae. Among the criteria currently used for their classification is the presence of a single FeSOD (iron-containing superoxide dismutase), which distinguishes them from Enterobacteriacea. In this paper the cloning of the sodA and sodB genes encoding two different SODs in Aeromonas hydrophila ATCC 7966 is reported. The sodB gene encoded an FeSOD (196 amino acids, 21.5 kDa), was constitutively expressed and showed 75% homology with the E. coli FeSOD. The sodA gene encoded a protein of 206 amino acids (22.5 kDa) with MnSOD (manganese-containing SOD) activity and showed 55% homology with the Escherichia coli MnSOD. The MnSOD of A. hydrophila was detected only during the stationary phase of growth under high aeration or when induced by lack of iron. Nevertheless, paraquat had no detectable effect on its production. The amino-terminal part of the Mn-containing protein contained a putative signal sequence which could permit a periplasmic localization.

Aeromonas↗

Review: hepatitis delta.

The causative agent of hepatitis delta virus (HDV) is the most unusual of all causative agents for all hepatitis viruses. Current knowledge of the molecular biology of HDV strengthens its proposed classification within the satellites, a family of subviral agents, some of which are pathogens of higher plants. Hepatitis delta virus is the only virus in the satellite family known to infect animal species, with hepatitis D having affected more than 10 million people worldwide who are also infected with its helper virus, HBV. Recently, the world map for hepatitis D appears somewhat modified, with decreasing HDV prevalence in certain areas and some new foci of HDV endemicity. Despite changing HDV prevalence, hepatitis. D, particularly the chronic form, is still an important health problem worldwide in terms of morbidity and mortality (mainly due to chronic liver disease, including hepatocellular carcinoma). Molecular studies have greatly advanced our understanding of the life cycle of HDV and of the function of its proteins. The new molecular information is of clinical relevance, with implications for the pathogenesis of liver damage, the diagnosis of HDV infection, for the natural course of the disease and, potentially, for therapy. Sensitive assays for HDV-RNA by polymerase chain reaction and sequencing techniques have clarified the patterns of HDV transmission and have confirmed the existence of unusual clinical forms of the virus and their relationship to replicative levels and genotypes of HDV. Prevention and treatment of hepatitis D are still in their infancy. However, liver transplantation for delta cirrhosis has proven far more successful than in any other viral form of cirrhosis, with few reinfections of the grafted liver, and has given important information on HDV biology and the pathogenesis of liver damage.

Animals↗

High frequency of HLA-DQB1*0301 allele in patients with pure ocular cicatricial pemphigoid.

Two factors, is classification and its immunogenetics, may have contributed to an incomplete understanding of the pathogenic mechanism in the disease group commonly termed 'cicatricial pemphigoid'. We have previously demonstrated that pure ocular cicatricial pemphigoid (OCP) is a unique clinical and immunopathological entity. In an effort to better define the immunogenetic characteristics for patients with pure OCP, we performed HLA typing for the class II MHC gene HLA-DQB1*0301 allele, by amplifying genomic DNA extracted from patients with polymerase chain reaction, followed by hybridization with a sequence-specific oligonucleotide probe on dot-blotted and Southern-blotted amplified DNA samples. Ninety percent (9/10) of patients with pure OCP had the DQB1*0301 allele, in contrast to 52% (17/33) of normal individuals who had the DQB1*0301 allele. The high frequency of the HLA-DQB1*0301 allele in patients with pure OCP may point to a distinct immunogenetic pattern and possibly a distinct pathomechanism for the disease.

Alleles↗

Treatment of atypical mycobacterial disease.

The most common disease patterns produced by atypical mycobacteria are pulmonary disease, cervical lymphadenitis, and infection of soft tissue, bones, and joints. The treatment of disease due to atypical mycobacteria can be confusing unless one clearly differentiates the organisms according to clinical characteristics and response to various chemotherapeutic agents. For this reason, we have attempted to simplify the task by proposing a new classification system. The organisms that might be isolated from human material are divided into the following three classes: nonpathogens; those that are easy to treat with standard mycobacterial therapy; and finally, those that are difficult to treat with standard mycobacterial therapy and require other approaches. This new system of classification should help the clinician in dealing with these organisms. Because even the pathogens may sometimes appear as a contaminant in human material, including sputum, one must document that these organisms are associated with disease prior to instituting therapy.

Drug Resistance, Microbial↗

[Blastocystis hominis: in search of a disease, a misunderstood organism].

Blastocystis hominis is a micro-organism which remains somewhat mysterious. Having defined its present position in the classification of Protozoa, the authors describe its ultrastructure and morphology. Its epidemiology and pathogenicity are discussed in the light of experimental studies and human clinical data, especially in AIDS patients. Metronidazole seems to be the most active drug against this organism, but extreme caution must be exerted when the possible pathogenic property of B. hominis is discussed.

Animals↗

[Role of Staphylococcus epidermidis in outer eye infections].

Coagulase-negative staphylococci (CNS) from 57 patients with outer eye infections and healthy control eyes were isolated according to the Schleifer and Cloos classification and the sensitivity to antibiotics of the isolated CNS was examined. The pathogenicity of CNS in rabbit cornea was studied by direct inoculation of CNS. The results showed that of 57 strains of CNS, 25 strains (43.9%) belonged to S. epidermidis, 22 (38.6%) belonged to non-detectable strains, 4 (7%) belonged to S. capitis, 3 (5.3%) belonged to S. hominis and 2 (3.5%) belonged to S. saprophyticus. Furthermore these CNS were resistant to aminoglycoside and machloride antibiotics which are commonly used as eye drops for ocular infectious diseases. Control rabbit corneas inoculated with CNS almost became clear within 24 hours. Therefore, it was suggested that ocular CNS infections can occur in immunologically compromised host patients.

Adolescent↗

In silico prediction method for plant Nucleotide-binding leucine-rich repeat- and pathogen effector interactions.

Plant Nucleotide-binding leucine-rich repeat (NLR) proteins play a crucial role in effector recognition and activation of Effector triggered immunity following pathogen infection. Genome sequencing advancements have led to the identification of a myriad of NLRs in numerous agriculturally important plant species. However, deciphering which NLRs recognize specific pathogen effectors remains challenging. Predicting NLR-effector interactions in silico will provide a more targeted approach for experimental validation, critical for elucidating function, and advancing our understanding of NLR-triggered immunity. In this study, NLR-effector protein complex structures were predicted using AlphaFold2-Multimer for all experimentally validated NLR-effector interactions reported in literature. Binding affinities- and energies were predicted using 97 machine learning models from Area-Affinity. We show that AlphaFold2-Multimer predicted structures have acceptable accuracy and can be used to investigate NLR-effector interactions in silico. Binding affinities for 58 NLR-effector complexes ranged between -8.5 and -10.6 log(K), and binding energies between -11.8 and -14.4&#x2009;kcal/mol-1, depending on the Area-Affinity model used. For 2427 "forced" NLR-effector complexes, these estimates showed larger variability, enabling identification of novel NLR-effector interactions with 99% accuracy using an Ensemble machine learning model. The narrow range of binding energies- and affinities for "true" interactions suggest a specific change in Gibbs free energy, and thus conformational change, is required for NLR activation. This is the first study to provide a method for predicting NLR-effector interactions, applicable to all pathosystems. Finally, the NLR-Effector Interaction Classification (NEIC) resource can streamline research efforts by identifying NLRs important for plant-pathogen resistance, advancing our understanding of plant immunity.

Plant Proteins↗

Molecular phylogeny of the plant pathogenic genus Botrytis and the evolution of host specificity.

The cosmopolitan genus Botrytis contains 22 recognized species and one hybrid. The current classification is largely based on morphological characters and, to a minor extent, on physiology and host range. In this study, a classification of the genus was constructed based on DNA sequence data of three nuclear protein-coding genes (RPB2, G3PDH, and HSP60) and compared with the traditional classification. Sexual reproduction and the host range, important fitness traits, were traced in the tree and used for the identification of major evolutionary events during speciation. The phylogenetic analysis corroborated the classical species delineation. In addition, the hybrid status of B. allii (B. byssoidea x B. aclada) was confirmed. Both individual gene trees and combined trees show that the genus Botrytis can be divided into two clades, radiating after the separation of Botrytis from other Sclerotiniaceae genera. Clade 1 contains four species that all colonize exclusively eudicot hosts, whereas clade 2 contains 18 species that are pathogenic on either eudicot (3) or monocot (15) hosts. A comparison of Botrytis and angiosperm phylogenies shows that cospeciation of pathogens and their hosts have not occurred during their respective evolution. Rather, we propose that host shifts have occurred during Botrytis speciation, possibly by the acquisition of novel pathogenicity factors. Loss of sexual reproduction has occurred at least three times and is supposed to be a consequence of negative selection.

Base Sequence↗