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PubMed2000

Molecular and phenotypic identification of the yeast pathogen Candida dubliniensis.

Candida dubliniensis is an emerging yeast pathogen generally misclassified as Candida albicans by standard diagnostic procedures. This study examined the efficiency of molecular identification, based on a discriminative PCR test, in a prospective study on the prevalence of C. dubliniensis among 103 oropharyngeal isolates from HIV-infected individuals or transplant recipients, and 30 vaginal isolates. All of the isolates had been classified as C. albicans by standard laboratory procedures. The PCR was evaluated in a blinded fashion against classification achieved by sequencing rDNA. Sequencing results corresponded 100% to the results of the discriminative PCR, indicating the validity of this rapid test. Twenty-one C. dubliniensis isolates were identified, all of them from HIV-infected individuals (prevalence 30%). The internal transcribed spacer regions of the C. dubliniensis isolates were sequenced. Phenotypic features of C. dubliniensis, namely abundant chlamydospore formation, atypical color on CHROMagar, growth defect at 45 degrees C, and colony morphology on Staib agar, were evaluated in a blinded fashion with respect to their discriminative potential, facilitating the design of further epidemiological studies. Carbohydrate assimilation patterns were determined for C. dubliniensis with a novel automated system showing that, in contrast to previous reports, C. dubliniensis is able to utilize D-xylose and trehalose. In evaluating these tests we present a rational approach to identification of the new species and characterization of C. dubliniensis isolates.

AIDS-Related Opportunistic Infections↗
PubMedDate not supplied

Severity of E. coli mastitis is mainly determined by cow factors.

Intramammary infections of dairy cows with Gram-positive bacteria such as Staphylococcus aureus (major cause of mastitis) have received a lot of attention because of their major economic impact on the dairy farm through production losses induced by an increase in somatic cell count. Management strategies, including greater awareness for efficient milking and hygienic measures, have limited the spread of Gram-positive bacteria and resulted in a significant decrease of proportion of S. aureus isolates and subclinical mastitis worldwide. Other organisms such as coliform subspecies and Streptococcus uberis, both environmental bacteria that cause clinical mastitis, have received less attention. Escherichia coli causes inflammation of the mammary gland in dairy cows around parturition and during early lactation with striking local and sometimes severe systemic clinical symptoms. This disease affects many high producing cows in dairy herds and may cause several cases of death per year in the most severe cases. It is well known that bacterial, cow and environmental factors are interdependent and influence mastitis susceptibility. Many studies, executed during the last decade, indicate that the severity of E. coli mastitis is mainly determined by cow factors rather than by E. coli pathogenicity. During E. coli mastitis, the host defense status is a cardinal factor determining the outcome of the disease. Today, we know that the neutrophil is a key factor in the cows' defense against intramammary infection with E. coli. Effective elimination of the pathogen by neutrophils is important for the resolution of infection and the outcome of E. coli mastitis. This review is a compilation of some major findings over the last 15 years concerning mainly host factors that modulate and influence neutrophil function and the mammary inflammatory reaction. The individual chapters address: virulence factors of E. coli strains, how neutrophils kill E. coli, connection between endotoxins, tumor necrosis factor-alpha and nitric oxide, severity classification of E. coli mastitis, lifespan of neutrophils, host factors that influence severity, tissue damage and production loss.

Animals↗
PubMed2006

Risk factors for surgical site infection in a Tanzanian district hospital: a challenge for the traditional National Nosocomial Infections Surveillance system index.

The incidence of surgical site infections (SSIs) was 24% in a district hospital in Tanzania. Wound classification was not an independent risk factor for SSI, indicating that risk scores developed in industrialized countries may require adjustments for nonindustrialized countries. The National Nosocomial Infections Surveillance system score required adjustments to reliably predict SSI, probably to account for improper hygiene and the lack of adjustment for the duration of surgery (defined as the 75th percentile of the duration for each type of operative procedure) to reflect local circumstances. Multidrug-resistant pathogens, such as methicillin-resistant Staphylococcus aureus and gram-negative pathogens expressing broad-spectrum beta-lactamases, have already emerged.

Adult↗
PubMedDate not supplied

Potential of bacteriocin-producing lactic acid bacteria for improvements in food safety and quality.

Lactic acid bacteria (LAB) have been used for centuries in the fermentation of a variety of dairy products. The preservative ability of LAB in foods is attributed to the production of anti-microbial metabolites including organic acids and bacteriocins. Bacteriocins generally exert their anti-microbial action by interfering with the cell wall or the membrane of target organisms, either by inhibiting cell wall biosynthesis or causing pore formation, subsequently resulting in death. The incorporation of bacteriocins as a biopreservative ingredient into model food systems has been studied extensively and has been shown to be effective in the control of pathogenic and spoilage microorganisms. However, a more practical and economic option of incorporating bacteriocins into foods can be the direct addition of bacteriocin-producing cultures into food. This paper presents an overview of the potential for using bacteriocin-producing LAB in foods for the improvement of the safety and quality of the final product. It describes the different genera of LAB with potential as biopreservatives, and presents an up-to-date classification system for the bacteriocins they produce. While the problems associated with the use of some bacteriocin-producing cultures in certain foods are elucidated, so also are the situations in which incorporation of the bacteriocin-producer into model food systems have been shown to be very effective.

Bacteria↗
PubMed2006

[Identification and characterization of a Bacillus amyloliquefaciens with high antifungal activity].

Plant disease can cause serious crop losses, and chemical control of disease is costly both to the environment and to the farmer. Some microorganism can produce the substance which has the preventing and exterminating functions to plant pathogens. These substances are valid to plant pathogens with only lower concentration, in addition the substances do not remain in soil and crops without being decomposed. If composization is performed with the microorganism, or the microorganism is mixed into compost, the functional compost having preventing and exterminating action will be made out and that can be more useful to environmental preservation. In order to screen antifungal bacteria for use in biological control, 200 compost samples were taken from different regions in China, over 10 bacterium with clear antifungal activity were isolated from composts, among them, strain Q-12 exhibited the highest antifungal activity which was strongly inhibits the growth of many plant pathogenic fungi such as Fusarium oxysporum and Rhizoctonia solan. According to the characteristics of morphology, physiology and biochemistry tests (API 50 CHB/E system) and the comparison of 16S rDNA sequence, the strain Q-12 was similar to B. subtilis and B. amyloliquefaciens. Some specific genes yyaR, yyaO and tetB, which have previously been shown to be effective for resolving these closely related taxa of the B. subtilis group, were analysed to clarify further the classification of Q-12, and two pairs of primers YyaR _ F/TetB _ R and YyaO _ F/TetB _ R were designed. From the analysis of fingerprints obtained with the two primers, strain Q-12 and B. amyloliquefaciens showed identical genomic fingerprints with primers YyaR _ F/TetB R, indicating their closely genetic relationship, and was identified as B. amyloliquefaciens. In the investigation of the culture condition, growth was carried out in a basal medium and gradually supplemented with the various ingredients to be investigated. The major ingredients being investigated included carbon sources, nitrogen sources and inorganic salts. The optimum medium and culture conditions of the strain all were studied with single factor test. The strain is easy to cultivate, and the optimal antibiotic production condition is growth in a medium (5 g/L glucose, 1 g/L NH4Cl, 0.8 g/L beef extract, 5 g/L MgCl2, pH 6.0) at 33 degrees C for 40 h. A number of Bacillus strains have proven safe over many years as a nonpathogenic species and are consumed in ton quantities in several human food preparations. Strains of Bacillus have several advantages over other biocontrol bacteria in that they are often soil isolates capable of sporulation, easy to cultivate and store, and some strains have been shown to increase yields of various crops.

Antibiosis↗
PubMed1983

[Cefotiam excretion into the bile after radical operation of congenital biliary atresia].

Twelve infants having undergone extrahepatic cholangiojejunostomy (SURUGA'S procedure II) after portal hepaticojejunostomy as a radical operation for congenital biliary atresia received prophylactic cefotiam (CTM) against biliary tract infection, 50 mg/kg by intravenous drip in 1 hour, followed by serial determinations of bile and serum CTM levels. The patients were evaluated as to degree of CTM excretion into the bile, by classification into 4 groups according to success or failure in establishing the anastomosis, bile outflow and persistence of jaundice. Patients with an established anastomosis, satisfactory bile flow and no longer jaundice showed high biliary antibiotic concentrations whereas lower biliary antibiotic levels were seen in those with failure in anastomosis, poor bile flow and persistent jaundice. In both cases, nevertheless, the antibiotic concentration in bile sufficiently exceeded the MIC80 values of CTM against principal bacterial pathogens causative of biliary tract infections, thus demonstrating clinical significance of the use of CTM for this purpose. The antibiotic excretion into the bile improved with normalization of liver function in an infant displaying satisfactory bile outflow from an early postoperative stage. The bile and serum CTM assay data obtained by the agar well method showed a high degree of correlation with those by high performance liquid chromatography.

Bacterial Infections↗
PubMed1977

[Protothecosis in cattle. Report of a case (author's transl)].

A brief review of the classification of the genus Prototheca is followed by a report on a case of protothecosis in cattle. A pure culture of Prototheca was isolated from the milk of the affected quarter. Despite the fact that the alga showed some sensitivity of nystatin in vitro, the mastitis failed to disappear on treatment with this agent. In the discussion, the incidence of Prototheca infection in man and animals and the appearance of infections with this facultatively pathogenic alga are reviewed.

Animals↗
PubMedDate not supplied

Case report of multiple myeloma and hypothyroidism in primary biliary cirrhosis.

A 71-year-old female with primary biliary cirrhosis, multiple myeloma and hypothyroidism is reported. The liver biopsy showed stage II-III histologic damage according to Scheuer's classification and the multiple myeloma was IgG-lambda type, stage II-A at the time of diagnosis. Another three cases of primary biliary cirrhosis associated with multiple myeloma were found in the literature. As a group, the four cases had mild or moderate liver damage, extensive bone lesions and three of four cases had multiple myeloma IgG-lambda type. Although this association could be incidental, there is evidence that implies a pathogenic relationship. This information is summarized in this report.

Aged↗
PubMed1998

Extracellular proteolytic enzymes of filamentous fungi.

This review involves generalized data on extracellular proteases of filamentous fungi. General characteristics of secreted proteases and their classification are considered. Analysis of the data available revealed that fungi secrete only serine, aspartyl, and metalloproteases. Nothing is known about secretion of cysteine proteases; some available data do not have clear experimental evidence. Physicochemical and kinetic properties of the most typical extracellular proteases of different classes and families are discussed in detail. Special attention is focused in the review on regulation of synthesis of extracellular proteases and participation of the secreted proteases of pathogenic fungi in the infection process in animals, insects, or plants.

Aspartic Acid Endopeptidases↗
PubMedDate not supplied

Nonsevere community-acquired pneumonia: correlation between cause and severity or comorbidity.

BACKGROUND: Community-acquired pneumonia frequently constitutes a nonsevere infection manageable at home. However, for these low-risk episodes, the epidemiological features have not been carefully analyzed. OBJECTIVES: To determine the cause of nonsevere community-acquired pneumonia and to investigate if a correlation exists between cause and severity or comorbidity. METHODS: During a 3-year period, all patients with nonsevere community-acquired pneumonia, according to the Pneumonia Patient Outcome Research Team prognostic classification (patients in groups 1-3), were included in the study. Causes were investigated through the following procedures: cultures of blood, sputum, and pleural fluid; serologic tests; and polymerase chain reaction methods to detect Streptococcus pneumoniae DNA in whole blood or Mycoplasma pneumoniae and Chlamydia pneumoniae DNA in throat swab specimens. RESULTS: Of 317 initially included patients, 247 were eligible for the study. A microbial diagnosis was obtained in 162 patients (66%), and the main pathogens detected were S pneumoniae (69 patients [28%]), M pneumoniae (40 patients [16%]), and C pneumoniae (28 patients [11%]). For the 58 patients in prognostic group 1, M pneumoniae was the most prevalent cause, and atypical microorganisms constituted 40 (69%) of the isolated agents. In contrast, for patients in prognostic groups 2 and 3, S pneumoniae was the leading agent, and a significant reduction of M pneumoniae cases and a greater presence of other more uncommon pathogens were observed. The existence of comorbid conditions was not a determining factor for particular causes. CONCLUSIONS: Among low-risk patients with community-acquired pneumonia, there was a certain correlation between severity and cause. In contrast, the existence of a comorbidity did not have a predictive causative value.

Adult↗
PubMed2005

Serotyping and evaluation of the virulence in mice of Streptococcus suis strains isolated from diseased pigs.

A total of 110 strains of Streptococcus suis, isolated from diseased pigs in Brazil were serotyped and analyzed for virulence. Serotyping of the strains resulted in the following classification: 42 strains of serotype 2 (38.2%), 10 strains of serotype 14 (9.1%), seven strains of serotype 9 (6.4%), three strains each of serotype 7 and 11 (2.7%), two strains each of serotype 1 and 8 (1.8%) and one strain each of serotypes 1/2, 3, 5, 6 and 10 (0.9%). Cross reactions among serotypes 1, 14 and 7 were observed in 21 strains (19.1%). Only 41.9% of the strains were lethal for mice using the pathogenicity test.

Animals↗
PubMedDate not supplied

Mycoplasma hominis: historical outline and taxonomy.

Although known as a separate group of organisms since 1898, the isolation in 1937 of a human genital mycoplasma represented the first observation of the association of this group of organisms with humans, a discovery that provided the impetus for extensive investigations of the interactions of mycoplasmas with the human host. These studies showed that mycoplasmas were frequent inhabitants of the mucous membranes of the urogenital and upper respiratory tracts. In early studies of human mycoplasmas, they were not speciated but were assigned to this group of organisms almost exclusively on the basis of cultural characteristics. However, differentiation between groups of human genital and oral mycoplasmas based on cultural, morphologic, biochemical, and serologic properties was achieved in 1953. A few years later formal proposals for the establishment of three human species of Mycoplasma (including Mycoplasma hominis) were made, along with suggestions for a new classification and nomenclature of the mycoplasmas. Serologic, genetic, and other data clearly show that M. hominis does constitute a relatively heterogeneous group of organisms. However, although this heterogeneity has practical implications for identification of isolates of M. hominis and for demonstration of antibodies to M. hominis, further studies are necessary to justify formal recognition of a taxonomic subdivision of M. hominis into distinct serovars. Investigations of the role of M. hominis as a potential human pathogen date back to the very first years of its discovery.(ABSTRACT TRUNCATED AT 250 WORDS)

Bacteriology↗
PubMed1996

[ANCA-associated forms of vasculitis].

Among the various types of primary systemic vasculitides, which were recently newly classified (Chapel Hill Classification, 1994), in two forms of small vessel vasculitis, i.e. in Wegener's granulomatosis and in microscopic polyangiitis, the diagnostic utility of anti-neutrophil cytoplasmic antibodies (ANCA) is now well established. In most cases of Wegener's granulomatosis and microscopic polyangiitis the target antigens of these autoantibodies are proteinase 3 (c-ANCA) or myeloperoxidase (p-ANCA), respectively. Both of these autoantibodies are probably not only diagnostic tools but also contribute to the pathogenic mechanisms causing the vascular damage. In Wegener's granulomatosis and in microscopic polyangiitis the upper and lower respiratory tract and the kidneys are preferentially affected. The lesions of Wegener's granulomatosis show an extremely wide morphologic spectrum. In the oropharynx, nasal sinuses, trachea, and large bronchi, they appear for the most part as ulcerations in which a granulomatous response may or may not be evident. Thus in the absence of granulomas, especially in small biopsy material, the diagnosis of Wegener's granulomatosis should by no means be excluded. In the kidneys a focal and segmental necrotizing glomerulonephritis, often associated with crescent formation, is the typical lesion in Wegener's granulomatosis and in microscopic polyangiitis, as well. Histologically, this glomerulonephritis does not differ from the forms also seen in Schoenlein-Henoch disease, in Goodpasture's syndrome and in some cases of systemic lupus erythematosus, but in Wegener's granulomatosis and in microscopic polyangiitis immune glomerular deposits are uncommon. In fact, by analysis of our biopsy material, these "pauci immune" type of necrotizing glomerulonephritis account for nearly 70%. In the past, Wegener's granulomatosis was usually fatal within 5 months of diagnosis. After introduction of the combined therapy with steroids and cyclophosphamide the prognosis improved considerably. Nevertheless, a further improvement is necessary. This could be reached, without any doubt, by an earlier detection of the disease.

Anti-Glomerular Basement Membrane Disease↗
PubMed1982

Classification of Corynebacterium species from axillary skin by numerical analysis of electrophoretic protein patterns.

The genus Corynebacterium, defined by the presence of mesodiaminopimelic acid, arabinose and corynomycolic acids in the cell wall, contains a very diverse group of organisms according to the results of numerical analysis of protein patterns; 13 groups were distinguished in this study. Strains isolated from axillary skin and hair included representatives of several groups but many strains were placed in groups 1 and 6A. Neither of these groups contained any reference strains and may constitute hitherto undescribed species. The reference strains of C. diphtheriae formed a coherent group not closely related to any non-pathogenic Corynebacterium species.

Axilla↗
PubMed2026

Reinforcement learning-based dynamic ensemble for missense variant effect prediction and tiered prioritization of VUS.

BACKGROUND: Accurate classification of missense variants remains a challenging task despite major advances in genomics. Numerous computational models have been developed to assist in variant classification, but often require repeated integration and benchmarking efforts. Ensemble methods have been proposed to overcome the limitations of single predictors, but mostly rely on fixed, predefined weights that constrain their ability to capture interactions among predictive signals. METHODS: We present GenixRL, a dynamic ensemble framework that reformulates model fusion as a reinforcement learning optimization problem. GenixRL uses a Q-learning agent to learn a policy that dynamically weights the probabilistic outputs of complementary predictors, including BayesDel (addAF and noAF), ClinPred, and MetaRNN. Replacing static weighting with policy learning allows GenixRL to adaptively identify optimal weightings and substantially improve classification accuracy. RESULTS: In benchmark evaluation against 25 state-of-the-art predictors, GenixRL achieved an AUROC of 0.9644 on an independent ClinVar dataset. On saturation genome editing assays for BRCA1 and BRCA2, GenixRL achieved the best performance and ranked highest on 14 of 17 clinically significant genes in a zero-shot evaluation. Applied to uncertain and conflicting ClinVar variants, GenixRL enabled tiered, evidence-based prioritization of hundreds of thousands of variants as likely pathogenic or pathogenic with high confidence, supported by orthogonal population evidence from gnomAD. CONCLUSION: GenixRL advances pathogenicity prediction for missense variants and provides an adaptive ensemble that sorts variants of uncertain significance into tiered candidates for expert curation and functional validation.

Mutation, Missense↗
PubMed1975

Survival of human enteric and other sewage microorganisms under simulated deep-sea conditions.

The survival of pure cultures of Escherichia coli, Streptococcus faecalis, Clostridium perfringens, and Vibrio parahaemolyticus under simulated deep-sea conditions of low temperature (4 C), seawater, and hydrostatic pressures ranging from 1 to 1,000 atm was determined over a period exceeding 300 h. The viability of E. coli and total aerobic bacteria in seawater-diluted raw sewage subjected to these deep-sea conditions was also measured. There was a greater survival of both E. coli and S. faecalis at 250 and 500 atm than at 1 atm at 4 C. S. faecalis was quite insensitive to 1,000 atm, whereas with E. coli there was a 10-fold die-off per 50-h exposure to 1,000 atm. In contrast, V. parahaemolyticus and C. perfringens were quite sensitive to pressures exceeding 250 atm, and with both of these species there was a total loss of viability of approximately 10(8) cells per ml within 100 h at 1,000 arm and within 200 h at 500 atm. The viability of the naturally occurring fecal coliforms in sewage exposed to moderate pressures at 4 C was found to be similar to the survival patterns demonstrated with pure cultures of E. coli. The total numbers of aerobic bacteria in these sewage samples, however, stabilized at 500 and 1,000 atm after 100 h, and at 1 and 250 atm there was significant growth of sewage-associated bacteria, which apparently utilized the organic compounds in the seawater-diluted sewage samples. A preliminary classification of some of these bacteria indicated that approximately 90% (160 isolates) of the organisms that survived over a 400-h exposure to 500 and 1,000 atm were Arthrobacter/Corynebacterium species, and the representative organisms capable of growing at 1 and 250 atm in seawater at 4 C were gram-positive cellulose digesters and an unidentified gram-negative coccus. The significance of these results with respect to the contamination of the deep ocean with human pathogens and the possibility of sewage-associated microorganisms growing and competing with indigenous marine microbial flora in situ is discussed.

Arthrobacter↗
PubMed2006

Microarray-based identification of antigenic variants of foot-and-mouth disease virus: a bioinformatics quality assessment.

BACKGROUND: The evolution of viral quasispecies can influence viral pathogenesis and the response to antiviral treatments. Mutant clouds in infected organisms represent the first stage in the genetic and antigenic diversification of RNA viruses, such as foot and mouth disease virus (FMDV), an important animal pathogen. Antigenic variants of FMDV have been classically diagnosed by immunological or RT-PCR-based methods. DNA microarrays are becoming increasingly useful for the analysis of gene expression and single nucleotide polymorphisms (SNPs). Recently, a FMDV microarray was described to detect simultaneously the seven FMDV serotypes. These results encourage the development of new oligonucleotide microarrays to probe the fine genetic and antigenic composition of FMDV for diagnosis, vaccine design, and to gain insight into the molecular epidemiology of this pathogen. RESULTS: A FMDV microarray was designed and optimized to detect SNPs at a major antigenic site of the virus. A screening of point mutants of the genomic region encoding antigenic site A of FMDV C-S8c1 was achieved. The hybridization pattern of a mutant includes specific positive and negative signals as well as crosshybridization signals, which are of different intensity depending on the thermodynamic stability of each probe-target pair. Moreover, an array bioinformatic classification method was developed to evaluate the hybridization signals. This statistical analysis shows that the procedure allows a very accurate classification per variant genome. CONCLUSION: A specific approach based on a microarray platform aimed at distinguishing point mutants within an important determinant of antigenicity and host cell tropism, namely the G-H loop of capsid protein VP1, was developed. The procedure is of general applicability as a test for specificity and discriminatory power of microarray-based diagnostic procedures using multiple oligonucleotide probes.

Animals↗
PubMed2007

Expression profiling in granulomatous lung disease.

Granulomatous lung diseases, such as sarcoidosis, hypersensitivity pneumonitis, Wegener's granulomatosis, and chronic beryllium disease, along with granulomatous diseases of known infectious etiologies, such as tuberculosis, are major causes of morbidity and mortality throughout the world. Clinical manifestations of these diseases are highly heterogeneous, and the determinants of disease susceptibility and clinical course (e.g., resolution vs. chronic, progressive fibrosis) are largely unknown. The underlying pathogenic mechanisms of these diseases also remain poorly understood. Within this context, these diseases have been approached using genomic and proteomic technologies to allow us to identify patterns of gene/protein expression that track with clinical disease or to identify new pathways involved in disease pathogenesis. The results from these initial studies highlight the potential for these "-omics" approaches to reveal novel insights into the pathogenesis of granulomatous lung disease and provide new tools to improve diagnosis, clinical classification, course prediction, and response to therapy. Realizing this potential will require collaboration among multidisciplinary groups with expertise in the respective technologies, bioinformatics, and clinical medicine for these complex diseases.

Gene Expression Profiling↗