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PubMed1993

[Relationship between nosocomial infection and hospital mortality. Multicenter study].

BACKGROUND: Hospital mortality related to infections acquired in the hospital setting has not been well studied in Spain. We carried out a study of seven hospitals in order to assess and quantify the problem. METHODS: The study period included three months of observations (between November 1, 1989 and January 31, 1990), and data pertaining to all deaths of patients hospitalized for a minimum of 24 hours were collected. The number of people admitted within the study period was 16,025, and the number of deaths registered and included in our study was 488 (3%). The data were obtained from the patient's medical history one week after death as well as from the hospital physicians on the case. In order to quantify the interobserver variability derived from the classification criteria, the simple kappa index was calculated and averaged to form an ordinal scale. RESULTS: 216 (44.3%) of 488 deaths included in our study had no infection, 138 (28%) had an infection no-hospital-associated, and 134 (27%) had nosocomial infection (50-10%--"causally related to death", 59-12%--"contributing to death", and 25-5%--"not related to death"). The lower respiratory tract infections, bacteremias and surgical wound infections were the most related to cause of death. Staphylococcus aureus was the pathogen most frequently associated with the infections found at the time of death. CONCLUSIONS: Those patients admitted with non-fatal diseases made up the greatest percentage (39.9%) of deaths from nosocomial infections. The infection was considered the direct cause of death in 18.8% of these cases, although the differences found had no statistical significance.

Cause of Death↗
PubMed2026

GenProb-PCSM: A Simplified Weighted Germline Score for Prostate Cancer-Specific Mortality.

BACKGROUND: We previously developed a tier-based germline classification using the National Comprehensive Cancer Network (NCCN)-recommended DNA damage repair (DDR) genes and KLK3 I179T to predict prostate cancer (PCa)-specific mortality (PCSM). To provide an easier-to-use single inherited risk score while preserving gene-specific effects, we developed GenProb-PCSM. METHODS: We analyzed 14,644 men with incident PCa from the UK Biobank. The cohort was randomly divided into training (60%) and independent testing (40%) datasets. GenProb-PCSM was developed in the training cohort by integrating pathogenic variants in ten NCCN-recommended DDR genes and the KLK3 I179T variant using gene-specific weights derived from Fine-Gray competing-risk models. Performance was evaluated in the independent testing cohort by discrimination, calibration, and risk stratification. Secondary analyzes evaluated metastatic progression and the composite endpoint of metastatic progression and/or PCSM. RESULTS: Among 14,644 men with incident PCa, 1,581 died from PCa. GenProb-PCSM remained significantly associated with PCSM in the independent testing cohort (HR per SD, 1.18; 95% CI, 1.12-1.24; p&#x2009;<&#x2009;0.001). Using predefined risk thresholds derived from the training cohort, patients in the intermediate- and high-risk groups had significantly increased risks of PCSM compared with the low-risk group (HR 1.49, 95% CI 1.22-1.84; and HR 4.04, 95% CI 2.58-6.33, respectively). GenProb-PCSM also predicted independent metastatic progression and the composite endpoint of metastatic progression and/or PCSM. CONCLUSIONS: GenProb-PCSM transforms complex germline findings into a single inherited risk score for PCSM and metastatic progression. Its simplicity and preservation of gene-specific effects may facilitate clinical implementation of germline prognostic assessment in PCa.

DNA damage repair genes↗
PubMed2000

Clinical consequences of molecular diagnosis in families with mismatch repair gene germline mutations.

Hereditary nonpolyposis colorectal cancer (HNPCC), clinically defined by the Amsterdam criteria, is associated with mismatch repair gene germline mutations. This study was performed to evaluate the efficiency of combined clinical and molecular diagnostics in identifying carriers of a mutated gene in families meeting criteria of the Bethesda guidelines and to examine the influence of molecular diagnosis on clinical decision-making in carriers and noncarriers. Seventy-two patients meeting criteria of the Bethesda guidelines were tested for microsatellite instabilities (MSI). MSI-H tumors were found in 38 (52.8%) index patients. Complete sequencing of hMLH1 and hMSH2 in 38 MSI-H patients and of hMSH6 in one of these patients revealed 15 pathogenic germline mutations, including three novel mutations, and three novel unclassified germline variants. Twelve of the 15 pathogenic mutations were found in patients fulfilling the Amsterdam I/II criteria. Surgical and genetic counseling was offered to the affected families; as a result of molecular diagnosis in the 15 families, 26 index patients and affected carriers and 8 asymptomatic carriers of a mutated mismatch repair gene were included in the surveillance program, and 26 noncarriers were excluded from this program. Although germline mutations are detected in only 20.8% of patients fulfilling criteria of the Bethesda guidelines, family history and MSI-H tumor classification are both strong indicators for germline mutations in hMSH2, hMLH1, and hMSH6 genes, resulting in a 51.9% mutation detection rate. Identification of individual mutation status allows clear-cut decisions on whether or not inclusion in surveillance programs is indicated.

Adaptor Proteins, Signal Transducing↗
PubMed1996

Intracellular survival of Brucella abortus, Mycobacterium bovis BCG, Salmonella dublin, and Salmonella typhimurium in macrophages from cattle genetically resistant to Brucella abortus.

Peripheral blood monocyte-derived macrophages were obtained from a herd of cows selected, bred, and confirmed as resistant or susceptible by in vivo challenge of Brucella abortus Strain 2308. The ability to control in vitro intracellular bacterial replication of B. abortus Strain 2308, Mycobacterium bovis Bacillus Calmette-Guerin (BCG) Montreal Strain 9003, Salmonella dublin Strain 5631, and Salmonella typhimurium Strain 14028 was evaluated in a bactericidal assay. The macrophages from resistant cattle were significantly superior (P < 0.05) in controlling intracellular growth of B. abortus, M. bovis BCG, S. dublin but not of S, typhimurium than macrophages from susceptible animals. Controls of all four pathogens correlated strongly with each other in resistant or susceptible macrophages. Data from resistant cattle had a tighter grouping than that of susceptible cattle, while data from susceptible cattle overlapped considerably with data from resistant animals. Therefore, this assay was considered a phenotypic marker of the resistant trait. For each bacterial species a percent bacterial survival value was used as a cut-off point to designate animals as resistant or susceptible. These data were compared with the in vivo challenged resistant or susceptible classification by using the Chi-square analyses. A cut-off point of 70 percent bacterial survival for B. abortus designated 14 cattle as susceptible and seven as resistant and this correlated 100 percent with the number of animals designated as to the relevant category by in vivo challenge. A value of 65 percent bacterial survival for M. bovis BCG, and 100 percent bacterial survival for S. dublin correlated highly with actual numbers of animals designated as susceptible or resistant.

Animals↗
PubMed1992

Onchocerca volvulus DNA probe classification correlates with epidemiologic patterns of blindness.

Onchocerciasis, or river blindness, results from infection with Onchocerca volvulus. The parasite is endemic to West Africa, in both rain forest and savanna bioclimes. Several lines of evidence suggest that different strains of the parasite exist in the rain forest and savanna. Furthermore, epidemiologic evidence indicates that ocular onchocerciasis is most severe in savanna regions. This has led to the hypothesis that there is a strain association with ocular pathology. To test this hypothesis, parasites from villages in which severe and mild onchocerciasis were endemic were classified with two strain-specific DNA probes. A strong correlation (P less than .001) was found between disease severity and probe recognition, supporting the hypothesis that pathogenicity is strain related. The results suggest that pFS-1 and pSS-1BT may be used to predict the pathogenic potential of parasite populations throughout much of West Africa.

Africa, Western↗
PubMed2003

Detection of septicemia in chicken livers by spectroscopy,.

To establish a procedure for differentiating normal chickens from chickens with septicemia/toxemia (septox) by machine inspection under the Hazard Analysis and Critical Control Point-Based Inspection Models Project, spectral measurements of 300 chicken livers, of which half were normal and half were condemned due to septox conditions, were collected and analyzed. Neural network classification of the spectral data after principal component analysis (PCA) indicated that normal and septox livers were correctly differentiated by spectroscopy at a rate of 96%. Analysis of the data established 100% correlation between the spectroscopic identification and the subset of samples, both normal and septox, that were histopathologically diagnosed. In an attempt to establish the microbiological etiology of the diseased livers, isolates from 30 livers indicated that the poultry carcasses were contaminated mostly with coliforms present in the environment, hindering the isolation of pathogenic microorganisms. Therefore, to establish the cause of diseased livers, a strictly aseptic environment and procedure for sample collection is required.

Animals↗
PubMed2000

Infectivity, transmission and 16S rRNA sequencing of a rickettsia, Coxiella cheraxi sp. nov., from the freshwater crayfish Cherax quadricarinatus.

A rickettsia-like organism isolated from infected, farm-reared Cherax quadricarinatus was cultured in the yolk sac of developing chicken eggs, but could not be cultured in 3 continuous cell lines, bluegill fry (BF-2), fathead minnow (FHM), and Spodoptera frugiperda (Sf-9). The organism was confirmed by fulfilling Koch's postulates as the aetiological agent of mortalities amongst C. quadricarinatus. When C. quadricarinatus was inoculated with the organism, mortality was 100% at 28 degrees C and 80% at an ambient temperature of 24 degrees C. Horizontal transmission with food and via the waterborne route was demonstrated, but mortalities were lower at 30 and 10% respectively over a 4 wk period. The 16S rRNA sequence of 1325 base pairs of the Gram-negative, obligate intracellular organism was 95.6% homologous to Coxiella burnetii. Of 18 species compared to this rickettsia, the next most closely related bacterium was Legionella pneumophila at 86.7%. The suggested classification of this organism is Order Rickettsiales, family Rickettsiaceae, tribe Rickettsieae, within the genus Coxiella. We suggest it should be named Coxiella cheraxi sp. nov.

Animals↗
PubMed2004

Web-accessible proteome databases for microbial research.

The analysis of proteomes of biological organisms represents a major challenge of the post-genome era. Classical proteomics combines two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) for the identification of proteins. Novel technologies such as isotope coded affinity tag (ICAT)-liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations. The vast amount and diverse types of proteomic data require adequate web-accessible computational and database technologies for storage, integration, dissemination, analysis and visualization. A proteome database system (http://www.mpiib-berlin.mpg.de/2D-PAGE) for microbial research has been constructed which integrates 2-DE/MS, ICAT-LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources. The two-dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification. The ICAT-LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs. H37Rv. By formulating complex queries within a functional protein classification database "FUNC_CLASS" for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways. The use of the R language in the database architecture allows high-level data analysis and visualization to be performed "on-the-fly". The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data. The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. Currently, the database system includes proteome information for six strains of microorganisms.

Bacterial Proteins↗
PubMed1996

Human pathogeneic fungi and their close nonpathogenic relatives.

In order to understand the relationships between human pathogenic fungi and their close, nonpathogenic relatives, we compared small-subunit ribosomal DNA sequences among four closely related pathogens, Histoplasma capsulatum, Blastomyces dermatitidis, Trichophyton rubrum, and Coccidioides immitis, and seven nonpathogenic fungi expected on morphological grounds to be their nearest relatives. We sequenced small-subunit RNA genes from these fungi and used both genetic distance and parsimony algorithms to evaluate their evolutionary relationships to the pathogens. We show that the pathogens are not a monophyletic group, but rather are interspersed among nonpathogenic fungi; thus it is likely that pathogenicity has arisen multiple times within this group. The saprobic fungi Chrysosporium parvum and Uncinocarpus reesii are the closest known relatives of the highly pathogenic Blastomyces dermatitidis and Coccidioides immitis, respectively, and thus may be considered primary candidates for model systems for researchers studying these fungi. The branching order suggests that the conidium (asexual spore) types aleurioconidia and arthroconidia do not define monophyletic groups and may be less distinct than their names suggest. Fungi with a complete life cycle are shown to have closest relatives that lack a known sexual cycle. Such analyses offer a means by which the sexual and asexual fungi could be integrated into a single classification system.

Base Sequence↗
PubMed2004

[Classification and microbiology of osteomyelitis].

The clinical presentation of osteomyelitis is multifarious. Therefore, patients are diagnosed and treated by various specialists with many different concepts of optimal management. Originally, only the acute and the chronic presentations were differentiated. The classification of Waldvogel, which is based on pathogenetic mechanisms, is more sophisticated. Diabetic foot is classified according to Wagner, who takes into account the continuous progression from sore to ulcer to osteomyelitis to gangrene. The staging according to Cierny-Mader is the most useful for the therapeutic management by surgeons. The spectrum of microorganisms is variable according to the type of osteomyelitis, epidemiology, age of the patient, co-morbidity, microbiological technique (culture, PCR), and duration of the infection. S. aureus is the leading pathogen in each type of osteomyelitis. Over the past 20 years, antimicrobial resistance has become an increasing problem. In case of osteomyelitis, standard susceptibility testing can be inaccurate. In case of device-related infection or in any type of chronic osteomyelitis, antimicrobial agents must be efficacious on stationary-phase and adhering microorganisms. Microbiologic culture and susceptibility testing should always be performed, in order to optimize the antimicrobial therapy.

Anti-Bacterial Agents↗
PubMed2003

Phylogeny of sheep and goat Theileria and Babesia parasites.

The phylogenetic relationship of Theileria and Babesia species infecting sheep and goats on the basis of their 18S RNA gene structure was addressed in the present study. For this purpose, the complete sequences of the small ribosomal RNA genes of a panel of sheep and goat piroplasm isolates, including T. lestoquardi, T. ovis, T. separata, B. ovis, B. motasi, B. crassa and several novel species, were sequenced and compared. The classification based on the established phylogenetic tree corresponded with traditional systematics and revealed that sheep/goat piroplasm species are of polyphyletic origin. The independent evolution of almost all sheep/goat piroplasms suggests that speciation may have occurred after transfer of the piroplasm-transmitting tick from a primal wild ruminant host to domestic sheep and goats. In accordance with recent reports, our study confirms the existence of at least two additional sheep/goat piroplasm species, designated Theileria sp. 1 (China) and Theileria sp. 2 (China). The recently reported pathogenic sheep/goat Theileria sp. 1 (China) seems to be identical with a Theileria sp. isolated from Japanese serow. Furthermore, our results suggest that T. ovis represents a single species.

Animals↗
PubMed2006

Cefepime pharmacodynamics in patients with extended spectrum beta-lactamase (ESBL) and non-ESBL infections.

OBJECTIVE: This study was designed to compare cefepime exposures with microbiological outcomes in ESBL and non-ESBL infections and determine the pharmacodynamic profiles associated with successful outcome. METHODS: Cefepime pharmacodynamic exposures of unbound drug [time above MIC (fT>MIC), minimal concentration over MIC (fC(min)/MIC), and area under the curve over MIC (fAUC/MIC)] for 18 patients with ESBL and non-ESBL infections were determined by using a published population pharmacokinetic model. Classification and regression tree analysis was used to identify pharmacodynamic breakpoints that predicted eradication. A 5000-patient Monte Carlo Simulation was conducted to estimate the probability of target attainment for the goal pharmacodynamic exposures. RESULTS: Eradication was 80% when fT>MIC was 50% compared with 0% when T>MIC was less than 50% (p<0.05). The median fC(min)/MIC ratio for ESBL group was statistically lower than that for the non-ESBL group (1.54 versus 138, p<0.001). Regardless of ESBL production, all pathogens were eradicated when fC(min)/MIC>7.6 and only 33.3% were eradicated when fC(min)/MIC< or =7.6 (p<0.05). Pharmacodynamic exposures of 50% fT>MIC and fAUC/MIC>1654 were also predictive of eradication. While conventional dosage regimens of 2g q 12h and q 8h failed to achieve adequate target attainment, 4 g continuous infusion and 2g q 6-8h prolonged infusion could attain more than 90% of target attainment at the MIC of 2 microg/ml for the breakpoint of fCmin/MIC=7.6. CONCLUSION: Microbiological eradication in patients receiving cefepime was best predicted by fCmin/MIC ratio greater than 7.6 regardless of the presence of an ESBL. Continuous or prolonged infusion regimens provided the greatest probability of attaining this exposure.

Aged↗
PubMed1992

Two ascomycete classes based on fruiting-body characters and ribosomal DNA sequence.

Traditional fruiting body-based classification of ascomycetes has been under attack for 2 decades. Fruiting-body types can converge, and few researchers now assume that either the closed fruiting bodies (cleistothecia) characterizing the class Plectomycetes or the flask-shaped fruiting bodies (perithecia) characterizing the class Pyrenomycetes are stable, unifying characters. Unless we identify characters uniting major ascomycete groups, orders of ascomycetes remain narrowly defined, and supraordinal classification is impossible. We sequenced both strands of 18s rDNA from nine ascomycete fungi, adding three sequences from GenBank into our analysis. The phylogeny, inferred from 162 informative sites in 1,700 bp of DNA sequence data and using yeast as an outgroup, divided the fungi into two groups correlating well both with fruiting-body type and with the traditional classes Plectomycetes and Pyrenomycetes. Each group received strong statistical support. Genera producing cleistothecia, such as Talaromyces (with a Penicillium asexual state) and the human pathogen Ajellomyces capsulatus (causing histoplasmosis), fall within the plectomycete group. Plectomycetes also includes Eremascus albus and the bee pathogen Ascosphaera apis, although both lack typical fruiting bodies. The Dutch elm disease fungus groups with pyrenomycetes such as Neurospora, in spite of its confusing mixture of class-level characters.

Ascomycota↗
PubMed1998

Variation in flagellin genes and proteins of Burkholderia cepacia.

The majority of isolates of Burkholderia cepacia, an important opportunistic pathogen associated with cystic fibrosis, can be classified into two types on the basis of flagellin protein size. Electron microscopic analysis indicates that the flagella of strains with the larger flagellin type (type I) are wider in diameter. Flagellin genes representative of both types were cloned and sequenced to design oligonucleotide primers for PCR amplification of the central variable domain of B. cepacia flagellin genes. PCR-restriction fragment length polymorphism analysis of amplified B. cepacia flagellin gene products from 16 strains enabled flagellin type classification on the basis of product size and revealed considerable differences in sequence, indicating that the flagellin gene is a useful biomarker for epidemiological and phylogenetic studies of this organism.

Amino Acid Sequence↗
PubMed2002

Digital image analysis system for the quantification of infiltrates and cell adhesion molecules in inflammatory cardiomyopathy.

BACKGROUND: We attempted to develop a digital image analysis (DIA) system for endomyocardial biopsies (EMBs) to reliably quantify a) biopsy quality, b) immunohistochemically-marked infiltrates, and c) cell adhesion molecules (CAMs) in relation to net heart area (HA) for the semi-automated diagnosis of inflammatory cardiomyopathy (InfCM). MATERIAL/METHODS: 140 EMBs from dilated cardiomyopathy (DCM) patients and 14 autopsy heart samples (controls) were immunostained for T-lymphocytes (CD2, CD3, CD4, CD8), beta(2)-integrin+ infiltrates (CD18, LFA-1, Mac-1) and CAMs (immunoglobulin superfamily: ICAM-1, HLA class I, HLA DR, VCAM-1, CD58; selectins: CD62E and CD62P; and the beta(1)-integrin chain CD29). EMB quality was assessed visually on a three-point scale. Infiltrates were quantified visually (per hpf) and by DIA (per mm2 HA). CAM expression was evaluated semiquantitatively and by DIA (area fraction [AF]: stained area relative to HA). RESULTS: DIA-evaluated HA correlated significantly with the visual assessment of EMB quality. The visual evaluation of both infiltrates and CAMs correlated significantly with the respective DIA-based quantification. DIA-quantified CAM-AF and infiltrates were discriminated by the CAM classification (CAMs+: n=87; 62%) compared to controls. DIA-quantified CAM immunoreactivity correlated significantly with the DIA-quantified counter-receptor+ infiltrates. DIA evaluation of biopsy quality, infiltrates, and CAMs was devoid of inter- and intraobserver variability. CONCLUSIONS: The DIA system presented here enables standardized and observer-independent assessment of EMB quality and intramyocardial inflammation (density of infiltrates and CAM expression) in DCM biopsies related to HA. Our data confirm that endothelial CAM count and counter-receptor+ immunocompetent infiltration are interdependent pathogenic and diagnostic hallmarks of InfCM.

Adult↗
PubMed2004

[Multifactor analysis in prediction of outcome for ischemic stroke with combined cardiac symptomatology].

Basing on the results of multiple classifications of 70 clinical, paraclinical and anamnestic signs of ischemic stroke with combined cardiac symptomatology, the models predicting clinical outcome in acute period of the disease and an original scale of numerical score have been worked out. It is mathematically proved that the severity of ischemic stroke with combined cardiac symptomatology, scoring 75 and above, inevitably results in progression of fatal outcome. A group of unfavorable clinical predictors was singled out. The periods with high rate of fatal outcome within exacerbation of ischemic stroke and pathogenic types of stroke were studied. It is first-ever shown that a role of cardiac and neurological symptoms in predicting fatal outcome depends on ischemic stroke severity. A relation between the probable fatal outcome and dynamics of severity of stroke with combined cardiac symptomatology within the first 3 days of the disease was also revealed for the first time.

Adult↗
PubMed1993

Increased expression of CD25 and adhesion molecules on peripheral blood lymphocytes of patients with Wegener's granulomatosis (WG) and ANCA positive vasculitides.

Peripheral blood lymphocytes of 29 c-ANCA positive WG patients fulfilling the ACR classification criteria were examined for the expression of various leukocyte surface molecules by dual marker cytofluorometry (FACStar, Becton Dickinson). Activation markers such as CD25, HLA-DR, CD29 and adhesion molecules (ICAM-1 and LFA-3) were clearly elevated in this group in comparison to 40 healthy volunteers. Similar results were obtained for p-ANCA positives vasculitides (n = 13) and, unexpectedly, also for patients suffering from cholesteatoma, a chronic, bacterial infection of the middle ear (n = 21). The results are discussed in view of a pathogenic model for WG and vasculitic disorders.

Adult↗
PubMed2004

Intracellular bacterial communities of uropathogenic Escherichia coli in urinary tract pathogenesis.

Urinary tract infections in young, healthy women frequently recur, despite their traditional classification as acute infections. Conventional wisdom dictates that uropathogens causing recurrent infections in such individuals come from the fecal or vaginal flora, in the same manner as the initial infection. However, recent studies of uropathogenic Escherichia coli have found that it can carry out a complex developmental program within the superficial epithelial cells of the mouse bladder, forming intracellular bacterial communities with many biofilm-like properties. These intracellular biofilms allow the bacteria to outlast a strong host immune response to establish a dormant reservoir of pathogens inside the bladder cells. Re-emergence of bacteria from this reservoir might be the source of recurrent infection.

Animals↗