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At least 217 records · Page 12Linked to original sources
PubMed2006

Study of bacterial communities in Antarctic coastal waters by a combination of 16S rRNA and 16S rDNA sequencing.

An ecological study on distribution of Antarctic bacterial communities was determined by 16S-based phylogenetic analyses of clone libraries derived from RNA and DNA extracted from two different marine areas and compared between each other. Superficial seawater samples were collected from four stations in Ross Sea, three of them located in Rod Bay and one in Evans Cove; for each station two clone libraries (16S rDNA and 16S rRNA) were prepared and evident divergences between DNA and RNA libraries of each site were obtained. Of all phylotypes 93.6% were found in RNA libraries; in contrast, only 31 phylotypes (70.5%) were retrieved from total microbial community (DNA libraries). DNA and RNA sequences related to gamma-Proteobacteria and Bacteroidetes groups, typical for Antarctic sea-ice bacterial communities, were detected in analysed sites. 16S rDNA and rRNA libraries derived from the two different areas were enriched by picophytoplanktonic 16S sequences of plastid and mitochondrion origins, reflecting that the algal blooms occurred during sampling (Antarctic summer 2003). The finding in Rod Bay libraries of high percentage of DNA clones apparently affiliated with beta-Proteobacteria typical for activated sludges and well water could be explained by the presence of a sewage depuration system at this site. Obtained results clearly demonstrate that combination of 16S rDNA and 16S rRNA gene sequencing is preferred approach to have a more reliable vision on the composition of microbial communities.

Antarctic Regions↗
PubMed2002

Differences between reference laboratories of the European community in their ability to detect Salmonella species.

The ability of national reference laboratories for Salmonella of the European Union member states to detect Salmonella bacteria was tested in four collaborative studies during the period 1995 through 1999. Three different methods were prescribed in the four studies. Capsules containing various numbers of Salmonella Typhimurium or Salmonella Enteritidis were tested. In studies II, III and IV, Salmonella bacteria were isolated in the presence of competitive microorganisms. Significant differences were found between the four studies due to varying levels of difficulty with regard to the level of contamination, the use of serotypes and the presence of competitive organisms. There were also significant differences between the laboratories in the results obtained. Possible reasons for these differences will be further investigated by the European Union Community Reference Laboratory for Salmonella.

Bacterial Typing Techniques↗
PubMed2002

Molecular method to assess the diversity of Burkholderia species in environmental samples.

In spite of the importance of many members of the genus Burkholderia in the soil microbial community, no direct method to assess the diversity of this genus has been developed so far. The aim of this work was the development of soil DNA-based PCR-denaturing gradient gel electrophoresis (DGGE), a powerful tool for studying the diversity of microbial communities, for detection and analysis of the Burkholderia diversity in soil samples. Primers specific for the genus Burkholderia were developed based on the 16S rRNA gene sequence and were evaluated in PCRs performed with genomic DNAs from Burkholderia and non-Burkholderia species as the templates. The primer system used exhibited good specificity and sensitivity for the majority of established species of the genus Burkholderia. DGGE analyses of the PCR products obtained showed that there were sufficient differences in migration behavior to distinguish the majority of the 14 Burkholderia species tested. Sequence analysis of amplicons generated with soil DNA exclusively revealed sequences affiliated with sequences of Burkholderia species, demonstrating that the PCR-DGGE method is suitable for studying the diversity of this genus in natural settings. A PCR-DGGE analysis of the Burkholderia communities in two grassland plots revealed differences in diversity mainly between bulk and rhizosphere soil samples; the communities in the latter samples produced more complex patterns.

Burkholderia↗
PubMed2026

Clinical impact of 16S rRNA RC-PCR NGS on infectious disease management.

16S rRNA metagenomics provides a culture-independent method for diagnosing infections with fastidious or uncultivable organisms, guiding targeted therapy, and detecting polymicrobial communities. This study utilizes reverse complement (RC)-PCR next-generation sequencing (NGS) to accurately identify bacterial pathogens from clinical specimens and assess its impact on clinical decision-making, setting it apart from conventional 16S sequencing approaches. A retrospective analysis of an ISO 15189 accredited 16S RC-PCR NGS diagnostic workflow targeting the V1-6 and V9 regions of the 16S rRNA gene was conducted over a 2-year period, including 390 clinical specimens from 316 patients. 16S RC-PCR NGS results were discussed in a multidisciplinary consultation and subsequently reported to the clinic. In total, 1,283 RC-PCR results were analyzed, of which 517 were from clinical specimens, 284 were negative controls, 66 were positive controls, and 416 were from wet lab and bioinformatic pipeline validation. 16S RC-PCR NGS assay detected bacterial taxa in 179/390 (45.9%) of clinical specimens, while 201/390 (51.5%) were negative, and 10/390 (2.6%) yielded uninterpretable results. The specimen types pus, pleural fluid, and heart valves exhibited the highest positivity rate (68% to 70%). Overall, 16S RC-PCR NGS influenced diagnostic decision making in 145/282 (51.4%) clinical cases and guided therapeutic management in 77/282 (27.3%) cases. Results providing definite evidence for either the presence or absence of bacterial infection were considered clinically valuable. Integration of 16S RC-PCR NGS pathogen detection with multidisciplinary consultation markedly improved clinical management, directly impacting diagnosis and treatment of complex clinical cases in a tertiary care setting. The effect was most pronounced in brain abscess patients, where RC-PCR results guided treatment decisions in 9/13 (69.2%) of cases.IMPORTANCETimely and accurate diagnosis is essential for managing serious infections, yet clinicians often face situations where routine laboratory tests do not provide clear answers. This study demonstrates that next-generation sequencing (NGS) of the bacterial 16S rRNA gene can decisively resolve these uncertainties. By revealing whether bacteria are present in clinical specimens, this approach influenced clinical reasoning and supported treatment decisions across a variety of challenging cases. 16S reverse-complement PCR was especially powerful for brain abscesses and infections where the causative microorganism was unclear, providing clarity that directly improved patient care. These findings show that integrating advanced sequencing with expert clinical interpretation can enhance the management of complex infections and support more confident, evidence-based therapy.

Humans↗
PubMed1989

Detecting early breast cancer. Experience in a community hospital.

The successful development and implementation of a mammography program at one community hospital is described. A substantial reduction in the size of breast mammography to change the diagnosis and treatment of breast cancer in one community hospital. As the vast majority of American women receive their medical care in community facilities, the more widespread development and implementation of community hospital-based mammography programs for early breast cancer detection has the potential to significantly improve survival rates for patients in whom these early lesions are found. Substantial improvement in the rate of early breast cancer detection can be achieved by community radiologists whether in private hospital or office-based practices.

Breast Neoplasms↗
PubMed2026

Re-emerging Marburg virus disease in Africa: spillover ecology, geographic expansion, and surveillance vulnerabilities.

Marburg virus disease (MVD) is re-emerging across Africa as a high-consequence zoonosis shaped by expanding ecological suitability, repeated spillover, and uneven surveillance capacity. This review synthesizes current evidence on the ecological, epidemiological, and operational determinants of contemporary Marburg virus (MARV) emergence. We conceptualize MVD as an ecological-emergence system produced by interactions among reservoir-host biology, environmental change, human exposure, health-system readiness, and mobility, rather than as a series of isolated outbreaks. Recent detections in multiple African regions indicate wider enzootic circulation than previously recognized and support repeated, reservoir-associated introductions from distributed ecological foci. Spillover risk is heightened where mining, land-use change, agricultural encroachment, settlement growth, climate-sensitive habitat disruption, and population movement increase contact with Egyptian rousette bats (Rousettus aegyptiacus) and contaminated roost environments. Following primary spillover, diagnostic delays, fragmented surveillance, limited laboratory decentralization, healthcare-associated transmission, and mobility-linked exposure can enable outbreak amplification and delayed recognition. Serological findings further suggest possible "shadow epidemiology," with unrecognized or mild MARV infections occurring outside confirmed outbreak chains. Critical preparedness gaps persist in ecological risk mapping, longitudinal reservoir surveillance, decentralized molecular diagnostics, genomic sequencing, data integration, and cross-border early warning. Future preparedness should move beyond reactive containment toward integrated One Health approach combining predictive ecological surveillance, rapid community-level detection, real-time genomics, infection prevention, risk communication, and regional coordination to identify spillover early and prevent human transmission.

Animals↗
PubMedDate not supplied

[Risk factors for multiple intestinal parasites in an indigenous community of the State of Pernambuco, Brazil].

An investigation into the ethno-epidemiological profile of the Pankararu indigenous group in the State of Pernambuco, Brazil, identified multiple intestinal parasites in nearly all members of the community. To detect possible environmental risk factors, we used the data base from a previous survey to test relations between daily living conditions (housing, sanitation, water supply and treatment, and garbage disposal) and the number of different parasite species found in the same household. The sample consisted of 84 families from the original sample of 112. Selection was based on the number of stool tests performed in the family. The mean number of parasite species was 5.0 per family, for a mean family size of 6.1 members. This number was greater for wattle-and-daub houses (mean 6.0 parasite species vs. 4.9 for brick houses; p < 0.03) and when water used in the household was not treated (mean 5.1 parasite species, vs. 4.5 for treated water; p < 0.05). Other household characteristics and hygienic habits did not significantly influence this number. We concluded that multiple intestinal parasitism in the Pernambuco Pankararu community is frequent, to the point of being the rule, and that it relates essentially to water source and treatment.

Adolescent↗
PubMed2001

Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns.

Bacterial diversity in unimproved and improved grassland soils was assessed by PCR amplification of bacterial 16S ribosomal DNA (rDNA) from directly extracted soil DNA, followed by sequencing of ~45 16S rDNA clones from each of three unimproved and three improved grassland samples (A. E. McCaig, L. A. Glover, and J. I. Prosser, Appl. Environ. Microbiol. 65:1721-1730, 1999) or by denaturing gradient gel electrophoresis (DGGE) of total amplification products. Semi-improved grassland soils were analyzed only by DGGE. No differences between communities were detected by calculation of diversity indices and similarity coefficients for clone data (possibly due to poor coverage). Differences were not observed between the diversities of individual unimproved and improved grassland DGGE profiles, although considerable spatial variation was observed among triplicate samples. Semi-improved grassland samples, however, were less diverse than the other grassland samples and had much lower within-group variation. DGGE banding profiles obtained from triplicate samples pooled prior to analysis indicated that there was less evenness in improved soils, suggesting that selection for specific bacterial groups occurred. Analysis of DGGE profiles by canonical variate analysis but not by principal-coordinate analysis, using unweighted data (considering only the presence and absence of bands) and weighted data (considering the relative intensity of each band), demonstrated that there were clear differences between grasslands, and the results were not affected by weighting of data. This study demonstrated that quantitative analysis of data obtained by community profiling methods, such as DGGE, can reveal differences between complex microbial communities.

Bacteria↗
PubMed2006

Rapid HIV testing at home: does it solve a problem or create one?

The U.S. Food and Drug Administration (FDA) is considering approval of an over-the-counter, rapid HIV test for home use. To date, testimony presented before the FDA has been overwhelmingly supportive. Advocates have argued enthusiastically that there is value in empowering individuals to manage their HIV risks and have suggested that the availability of a rapid home HIV test will dramatically increase rates of disease detection in communities that have proven difficult to reach and to link to appropriate care. The authors offer a more cautious perspective. According to what is already known about the market demand for over-the-counter HIV testing kits, their costs, and the performance of rapid HIV tests in that market, the authors do not anticipate that the rapid home test will have a profound impact either on the HIV public health crisis or on the populations in greatest need. Home HIV testing will attract a predominantly affluent clientele, composed disproportionately of HIV-uninfected new couples and "worried well" persons, as well as very recently infected persons with undetectable disease. The authors illustrate how testing in these populations may have the perverse effect of increasing both false-positive and false-negative results. A poorly functioning home HIV test may thereby undermine confidence in the reliability of HIV testing more generally and weaken critical efforts to expand HIV detection and linkage to lifesaving care for the estimated 300,000 U.S. citizens with unidentified HIV infection.

Costs and Cost Analysis↗
PubMed2004

Analysis of bacterial diversity in river biofilms using 16S rDNA PCR-DGGE: methodological settings and fingerprints interpretation.

Reliability of bacterial diversity assessment using polymerase chain reaction (PCR) denaturing gradient gel electrophoresis (DGGE) analysis of 16S rDNA fragments was evaluated for a particular complex microbial assemblage: river epilithic biofilm. By comparing 3 routine protocols on replicates of one river biofilm sample, we found that common DNA extraction procedures gave comparable diversity (from 28.0 to 30.7 bands detected) and community composition (> 75% of homology) despite differences in the total amount of extracted DNA (from 0.9 to 4.2 microg). Therefore methodological improvements only concerned electrophoretic separation of DNA fragments (range of denaturing gradient from 35% to 70% and migration time=18h) and standardisation of DNA amounts used (PCR-template=50 ng, gel loading=700 ng). Using such a standardised methodology we found a good reproducibility of all steps of the procedure. When an Escherichia coli strain was introduced as a contaminant in a biofilm sample, we were able to recover ribotypes from the strain. As concerns fields sampling, a satisfactory repeatability of banding patterns from neighbouring pebbles (sampling point) allowed discriminating between the biofilm intrasite variability (various points from a cross-profile). These trials confirmed that PCR-DGGE is suitable to assess a reliable genetic fingerprint of epilithic biofilms in the river. Phylogenetic analysis of 40 partial sequences of 16S rDNA from DGGE gels of two sets of river biofilms samples proved evidences for the retrieval of DNA fragments related to phototroph Eukarya. However, in both cases plastidial 16S rDNA represented less than 25% of the analysed operational taxonomic units. Taking into account that Cyanobacteria, as members of the Bacteria, were also detected, sequence analysis of relevant bands from the pattern is required to target "bacteria", i.e. the functional group of prokaryotic microorganisms to which one commonly refers as a key component in sustaining the nutrient turnover.

Bacteria↗
PubMed1997

Detection of mild dementia in community surveys. Is it possible to increase the accuracy of our diagnostic instruments?

OBJECTIVE: To investigate the accuracy of cognitive tests and clinical dementia diagnosis in distinguishing between mildly demented and nondemented subjects. DESIGN: Three-year longitudinal follow-up of a community-based cohort sample. Using the Diagnostic and Statistical Manual of Mental Disorders, Third Edition, Revised as criterion variable, subjects were classified as demented and nondemented based on the results of cognitive test performance at time 1. These subjects were then examined prospectively for development of dementia at time 2. PARTICIPANTS: The sample consisted of 63 mildly demented (Mini-Mental State Examination score > 18 < 24) and 398 nondemented subjects at time 1. At follow-up, due to death and refusal of participation, the sample consisted of 108 demented and 217 nondemented subjects. RESULTS: The group of subjects who were considered to be demented according to the results of the cognitive tests and nondemented by the clinical diagnosis at time 1 had a higher incidence of dementia at time 2 than did the subjects who were considered to be nondemented according to both cognitive tests and clinical diagnosis. Among the incident dementia cases, subjects considered to be demented according to the cognitive tests but nondemented by the clinical diagnosis performed at a lower level on most cognitive tests were older, had less education, and consisted of more women than did the group of subjects who were considered to be demented by the clinical diagnosis and nondemented by the cognitive tests at time 1. CONCLUSIONS: A combination of cognitive tests, especially tasks assessing episodic memory, can detect many subjects in a preclinical state of dementia who could be missed in the clinical diagnostic procedure due to subjects' relatively high age, low education, and female sex. However, cognitive tests also may miss a sizable proportion of prevalent dementia cases due to possible insensitivity to the same demographic variables. These findings indicate the need of integration between clinical and cognitive data to increase the accuracy in detecting dementia in an early phase.

Aged↗
PubMed2005

Novel approach to quantitative detection of specific rRNA in a microbial community, using catalytic DNA.

We developed a novel method for the quantitative detection of the 16S rRNA of a specific bacterial species in the microbial community by using deoxyribozyme (DNAzyme), which possesses the catalytic function to cleave RNA in a sequence-specific manner. A mixture of heterogeneous 16S rRNA containing the target 16S rRNA was incubated with a species-specific DNAzyme. The cleaved target 16S rRNA was separated from the intact 16S rRNA by electrophoresis, and then their amounts were compared for the quantitative detection of target 16S rRNA. This method was used to determine the abundance of the 16S rRNA of a filamentous bacterium, Sphaerotilus natans, in activated sludge, which is a microbial mixture used in wastewater treatment systems. The result indicated that this DNAzyme-based approach would be applicable to actual microbial communities.

Base Sequence↗
PubMed1998

Multiple analysis of a foodborne outbreak caused by infant formula contaminated by an atypical Salmonella virchow strain.

An outbreak of food poisoning involving most autonomous Spanish communities was detected in the first half of 1994. The causative food was infant formula milk contaminated by lactose-fermenting Salmonella virchow. It was not possible to isolate the causative strain from the manufacturer's facilities. During the same period of time, there was a significant increase in lactose-non-fermenting Salmonella virchow strains compared with the same period in previous years. Simultaneously, lactose-non-fermenting strains were recovered from clinical samples from children and from some milk samples that were involved in the outbreak. Therefore, it was speculated that the outbreak might be more extensive than initially thought. The following epidemiological markers were used for typing the Salmonella virchow strains involved in the outbreak: (i) phage typing: (ii) ribotyping, using a set of 20 different endonucleases: and (iii) pulsed-field gel electrophoresis, using three different endonucleases. The most useful markers for this serotype were phage typing and pulsed-field gel electrophoresis, since ribotyping was not able to distinguish all strains tested. The results obtained revealed that the outbreak was caused by at least two strains: one presenting phage type 4-4a and pulsed-field patterns A1 or A2 and L+ or L-, and another presenting phage type 2 and pulsed-field patterns A1 or A2 and L+ or L-. The results indicate that the outbreak was more extensive than initially thought and that the Virchow serotype is very clonal in Spain.

Animals↗
PubMedDate not supplied

Immunology and the confocal microscope.

The techniques of classical epifluorescence microscopy are already widely used by the immunological community to detect antigens at the cellular level. Coupled with the use of specific inhibitors that affect diverse intracellular events, these techniques have provided valuable information on the mechanisms involved in antigen presentation. The same biological samples can now be examined by confocal microscopy, which has a higher resolution than conventional microscopy and allows one to analyse quantitatively single cross-sections of the sample. The confocal microscope is therefore especially well-suited for studies on intracellular membrane traffic, cell-to-cell interactions, and the distribution of particular antigens and their co-localization with other intracellular markers. This review describes the technique of confocal microscopy and the goals of sample preparation, along with several detailed protocols for fixing and permeabilizing cells and mounting them on microscope slides. Representative examples are cited from studies on the endocytosis of surface receptors, the distribution of adhesion and major histocompatibility complex (MHC) molecules, and the interaction of an intracellular parasite with MHC molecules of the host cell.

Allergy and Immunology↗
PubMed2005

Application of 16S rDNA-PCR amplification and DGGE fingerprinting for detection of shift in microbial community diversity in Cu-, Zn-, and Cd-contaminated paddy soils.

Seven soils were sampled from farmland at different distances (0.01-5 km) from a copper and zinc smelter. The total contents of heavy metals in these soils ranged from 46 to 4895 mg Cu kg-1, 96 to 1133 mg Zn kg-1, and 6.9 to 28.8 mg Cd kg-1, respectively. The available fractions were highly correlated with total contents of the metals. In order to assess the impact of combined contamination of heavy metals on soil bacterial communities, denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR) amplicons of 16S rDNA sequence of bacteria in soil was used. Bacterial community structure was affected to some extent by heavy metals. The number of DGGE bands in soils increased with increasing distance from the copper and zinc smelter. Clustering analysis of the DGGE profiles showed that bacteria in the seven soils belonged to three clusters. Bacterial communities in three soils sampled at 0.01-0.60 km from the smelter belonged to one cluster, and those in three soils sampled at 0.8-1.2 km from the smelter belong to another cluster. Bacterial community in soil farthest from the smelter belonged to a single cluster. This study demonstrated that heavy metal contamination decreased both biomass and diversity of bacterial community in the soil.

Cadmium↗
PubMed2006

Detecting changes in insect herbivore communities along a pollution gradient.

The forests surrounding the urban areas of the Los Angeles basin are impacted by ozone and nitrogen pollutants arising from urban areas. We examined changes in the herbivore communities of three prominent plant species (ponderosa pine, California black oak and bracken fern) at six sites along an air pollution gradient. Insects were extracted from foliage samples collected in spring, as foliage reached full expansion. Community differences were evaluated using total herbivore abundance, richness, Shannon-Weiner diversity, and discriminant function analysis. Even without conspicuous changes in total numbers, diversity or richness of herbivores, herbivore groups showed patterns of change that followed the air pollution gradient that were apparent through discriminant function analysis. For bracken fern and oak, chewing insects were more dominant at high pollution sites. Oak herbivore communities showed the strongest effect. These changes in herbivore communities may affect nutrient cycling in forest systems.

Air Pollution↗
PubMed2006

Microbial activity in an acid resin deposit: biodegradation potential and ecotoxicology in an extremely acidic hydrocarbon contamination.

Acid resins are residues produced in a recycling process for used oils that was in use in the forties and fifties of the last century. The resin-like material is highly contaminated with mineral oil hydrocarbons, extremely acidic and co-contaminated with substituted and aromatic hydrocarbons, and heavy metals. To determine the potential for microbial biodegradation the acid resin deposit and its surroundings were screened for microbial activity by soil respiration measurements. No microbial activity was found in the core deposit. However, biodegradation of hydrocarbons was possible in zones with a lower degree of contamination surrounding the deposit. An extreme acidophilic microbial community was detected close to the core deposit. With a simple ecotoxicological approach it could be shown that the pure acid resin that formed the major part of the core deposit, was toxic to the indigenous microflora due to its extremely low pH of 0-1.

Biodegradation, Environmental↗
PubMed2004

Identification of culturable bacteria present in haemodialysis water and fluid.

Water used to prepare haemodialysis fluid is not sterile, and its microbiological control is important for the prevention of haemodialysis-associated illness. Bacterial populations inhabiting a distribution system for haemodialysis water were studied over an 18-month period. 203 planktonic bacteria isolated on R2A medium were identified by restriction analysis and sequencing of 16S rRNA gene. A diverse bacterial community was detected, containing predominantly Gram-negative members of the Alphaproteobacteria and Betaproteobacteria, as well as representatives of the genus Mycobacterium. Ecological and clinical consequences are discussed: bacteria from the genera Novosphingobium, Pseudomonas and Sphingomonas have been described in the build-up of biofilms, and others like Acinetobacter, Mycobacterium or Brevibacterium may represent a health risk to patients under haemodialysis treatment.

Bacteria↗