PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “microbial detection”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources
PubMed1991

New microbial diagnosis.

Rapid methods for comprehensive nucleic acid analysis are essential for the progress in basic research. In microbial diagnosis nucleic acid analyses are useful for achieving quick, sensitive results with new dimensions of specificity. As to specificity, hybridisation tests are easily constructed for genus or species specific microbial typing or for the detection of genes accounting for pathogenic properties. Modern sequence analysis allows rapid detection of mutations eg., those conferring antiviral resistance. A new level of sensitivity comparable to that of the conventional enrichment culture is obtainable by enzymatic amplification (PCR) of microbial nucleic acids before detection. PCR-technology has proved particularly useful in the diagnosis of microbial infections when the organisms are impossible or tedious to cultivate. For reliable diagnostic use the performance of in vitro amplification requires extreme care to prevent false positive results owing to carry over problems. In conclusion, nucleic acid analyses are expanding the potential for diagnosing microbial infections and may well replace some conventional diagnostic methods.

Bacterial Infections↗
PubMedDate not supplied

[Microbial, enzymatic, and immune biosensors for ecological monitoring and control of biotechnological processes].

Results of the research performed at the Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, on designing immunobiosensors for detection of toxic compounds and microbial cells enzyme-based biosensors for detection of hydrocarbons and alcohols, and microbial biosensors for aromatic compounds, surfactants, and biological oxygen consumption are briefed. Parameters of the mediator electrodes involving microbial cells and data on the properties of microbial biofuel cells--devices based on biosensor principle and representing alternative sources of electric energy--are given.

Alcohols↗
PubMed2005

Environmental microbiology-on-a-chip and its future impacts.

Rapid advances in microfabrication, DNA and protein microarray and microfluidic technologies have enabled the development of fully-integrated, miniaturized systems. These so called 'laboratory-on-a-chip' (LOC) devices perform sample preparation (i.e. concentration, separation and purification) together with biochemical reactions and detection steps in a simple and automated manner. We believe LOC technology for environmental microbiology studies will have immediate impacts on microbial monitoring by achieving detection and identification within minutes at the single-cell level, and on microbial ecology by deepening the understanding of microbial community structure and diversity and correlating these with niche-specific functions within a micro space. In the long run, significant impacts are anticipated on environmental metagenomics and proteomics.

Environmental Microbiology↗
PubMed2004

13CO2 pulse labelling of plants in tandem with stable isotope probing: methodological considerations for examining microbial function in the rhizosphere.

Recently developed 13CO2 pulse labelling and stable isotope probing (SIP) methods offer the potential to track 13C-labelled plant photosynthate into phylogenetic groups of microbial taxa in the rhizosphere, permitting an examination of the link between soil microbial diversity and carbon flow in situ. We tested the feasibility of this approach to detect functional differences in microbial communities utilising recently fixed plant photosynthate in moisture perturbed grassland turfs. Specifically, we addressed two questions: (1) How does moisture perturbation (three treatments; continual wetting, drying, and drying followed by rewetting) affect the assimilation of 13C-labelled exudates carbon into the soil microbial community?; (2) Can 13C deposited in soil from pulse-labelled plants be used to identify microbes utilising plant exudates using SIP methodologies? Net CO2 fluxes showed that prior to 13CO2 pulse labelling, all treatments were photosynthetically active, but differences were observed in night time respiration, indicating moisture treatments had impacted on net CO2 efflux. Measurements of pulse-derived 13C incorporated into soil RNA over 2 months showed that there was only evidence of 13C enrichment in the continuously wetted treatments. However, isotopic values represented only a 0.1-0.2 13C at.% increase over natural abundance levels and were found to be insufficient for the application of RNA-SIP. These findings reveal that in this experimental system, the microbial uptake of labelled carbon from plant exudates is low, and further optimisation of methodologies may be required for application of SIP to natural plant-soil systems where 13C tracer dilution is a consideration.

Carbon Dioxide↗
PubMed2004

Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays.

To effectively monitor biodegrading populations, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the 2,402 known genes and pathways involved in biodegradation and metal resistance. This array contained 1,662 unique and group-specific probes with <85% similarity to their nontarget sequences. Based on artificial probes, our results showed that under hybridization conditions of 50 degrees C and 50% formamide, the 50-mer microarray hybridization can differentiate sequences having <88% similarity. Specificity tests with representative pure cultures indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. The detection limit was approximately 5 to 10 ng of genomic DNA in the absence of background DNA and 50 to 100 ng of pure-culture genomic DNA in the presence of background DNA or 1.3 x 10(7) cells in the presence of background RNA. Strong linear relationships between the signal intensity and the target DNA and RNA were observed (r(2) = 0.95 to 0.99). Application of this type of microarray to analyze naphthalene-amended enrichment and soil microcosms demonstrated that microflora changed differently depending on the incubation conditions. While the naphthalene-degrading genes from Rhodococcus-type microorganisms were dominant in naphthalene-degrading enrichments, the genes involved in naphthalene (and polyaromatic hydrocarbon and nitrotoluene) degradation from gram-negative microorganisms, such as Ralstonia, Comamonas, and Burkholderia, were most abundant in the soil microcosms. In contrast to general conceptions, naphthalene-degrading genes from Pseudomonas were not detected, although Pseudomonas is widely known as a model microorganism for studying naphthalene degradation. The real-time PCR analysis with four representative genes showed that the microarray-based quantification was very consistent with real-time PCR (r(2) = 0.74). In addition, application of the arrays to both polyaromatic-hydrocarbon- and benzene-toluene-ethylbenzene-xylene-contaminated and uncontaminated soils indicated that the developed microarrays appeared to be useful for profiling differences in microbial community structures. Our results indicate that this technology has potential as a specific, sensitive, and quantitative tool in revealing a comprehensive picture of the compositions of biodegradation genes and the microbial community in contaminated environments, although more work is needed to improve detection sensitivity.

Bacteria↗
PubMed2002

Bacteria-degraders as the base of an amperometric biosensor for detection of anionic surfactants.

Several strains belonging to genera Pseudomonas and Achromobacter and characterized by the ability to degrade anionic surfactants were tested as potential bases of microbial biosensors for surfactant detection. For each strain the substrate specificity and stability of sensor signals were studied. The total amount of the substrates tested (including carbohydrates, alcohols, aromatics, organic acids, etc.) was equal to 60; the maximal signals were observed towards the anionic surfactants. The lower limit of detection for sodium dodecyl sulfate used as a model surfactant was in the field of 1 microM for all the strains. The created microbial biosensor model can extend the practical possibilities for rapid evaluation of surfactants in water media.

Alcaligenes↗
PubMed2002

Detection of genes with atypical nucleotide sequence in microbial genomes.

Along the gene, nucleotides in various codon positions tend to exert a slight but observable influence on the nucleotide choice at neighboring positions. Such context biases are different in different organisms and can be used as genomic signatures. In this paper, we will focus specifically on the dinucleotide composed of a third codon position nucleotide and its succeeding first position nucleotide. Using the 16 possible dinucleotide combinations, we calculate how well individual genes conform to the observed mean dinucleotide frequencies of an entire genome, forming a distance measure for each gene. It is found that genes from different genomes can be separated with a high degree of accuracy, according to these distance values. In particular, we address the problem of recent horizontal gene transfer, and how imported genes may be evaluated by their poor assimilation to the host's context biases. By concentrating on the third- and succeeding first position nucleotides, we eliminate most spurious contributions from codon usage and amino-acid requirements, focusing mainly on mutational effects. Since imported genes are expected to converge only gradually to genomic signatures, it is possible to question whether a gene present in only one of two closely related organisms has been imported into one organism or deleted in the other. Striking correlations between the proposed distance measure and poor homology are observed when Escherichia coli genes are compared to Salmonella typhi, indicating that sets of outlier genes in E. coli may contain a high number of genes that have been imported into E. coli, and not deleted in S. typhi.

Bacteria↗
PubMed2005

Amperometric detection of the bacterial metabolic regulation with a microbial array chip.

A microbial array chip with collagen gel spots entrapping living bacterial cells has been applied to investigate the metabolic regulation in Paracoccus denitrificans. Scanning electrochemical microscopy (SECM) was used to monitor the ferrocyanide production that reflects the electron flow in the respiratory chain located within the internal membrane of P. denitrificans. The ferrocyanide production from P. denitrificans largely depends on the types of the carbon source (glucose or lactate), suggesting that the electron flow rate in the respiratory chain depends on the activity of the metabolic pathway located up-stream of the respiratory chain. More importantly, it was found that the enzymes affecting glucose catabolic reactions were significantly up-regulated in cultures with a nutrient agar medium containing D-(+)-glucose as a sole carbon source. Enzyme assays using crude extracts of P. denitrificans were carried out to identify the enzymes expressed at a higher level in cultures supplemented with D-(+)-glucose. It was confirmed that the pyruvate kinase and enzymes of the overall Entner-Doudoroff pathway were highly induced in cultures containing D-(+)-glucose.

Electrochemistry↗
PubMed1995

Extraction and purification of microbial DNA from petroleum-contaminated soils and detection of low numbers of toluene, octane and pesticide degraders by multiplex polymerase chain reaction and Southern analysis.

We investigated the use of multiplex polymerase chain reaction (PCR) techniques coupled with Southern analysis to detect xenobiotic-degrading organisms that had been added to three soils. Two soils highly contaminated with petroleum hydrocarbons and a less contaminated control soil were amended with tenfold dilutions of Pseudomonas putida mt-2 (pWW0), P. oleovorans (OCT), and Alcaligenes eutrophus JMP134 (pJP4), or, for controls, phosphate buffer alone. Total DNA was then isolated from the soils and purified using a sequential precipitation and dissolution purification procedure. This DNA was subjected to multiplex polymerase chain reaction (PCR) using primers that amplify regions of xylM (PCR product = 631 bp), alkB (546 bp) and tfdA (710 bp), which are found on pWW0, OCT and pJP4, respectively. The sizes of the amplified DNA fragments were designed to permit simultaneous amplification and detection of the target genes. Ethidium bromide-stained gels of the initial PCR reaction indicated detectable amplification of between 10(0) to 10(6) cells per gram soil, depending on the soil and the target gene. Southern analysis of the PCR amplified DNA improved detection limits to between 1 and 10 cells of each target species per gram of soil, and confirmed the identity of the PCR products. For some samples that were initially resistant to PCR, dilution of the environmental DNA resulted in positive PCR results. This treatment presumably overcame the inhibition of the PCR by diluting coextracted contaminants in the environmental DNA. A second PCR on an aliquot (1 microL) of the first reaction increased the ethidium bromide-based detection limits for one of the soils to six cells per gram of soil; it did not increase the detection limits for the other soils. Therefore, the DNA extraction procedure and multiplex PCR permitted the simultaneous detection of three types of biodegradative cells, at a lower detection limit of approximately 10 cells per gram of highly contaminated, organic soil. However, due to kinetic limitations of multiplex PCR, the amplified signals did not follow a close dose response to the numbers of added target cells.

Alcaligenes↗
PubMed2004

SARS: an emerging global microbial threat.

In March 2003, the Institute of Medicine published an update to its 1992 landmark report on emerging infections. The new report, Microbial Threats to Health: Emergence, Detection, and Response, describes the current spectrum of global microbial threats, factors affecting their emergence or resurgence, and measures that should be undertaken to effectively address them. Coincident with this publication came increasing reports of severe atypical pneumonia of unknown etiology among persons in southeast Asia. This new disease, designated severe acute respiratory syndrome (SARS), spread globally in a matter of weeks, infecting primarily close contacts of index patients (e.g., household members and healthcare workers caring for index patients) but also resulting in community transmission in some areas. An unprecedented worldwide collaborative effort was undertaken to determine the cause of the illness and implement prevention measures. A previously unrecognized coronavirus was identified as the causative agent, and health officials throughout the world struggled to implement measures to contain its spread, including isolation of suspect SARS cases and quarantine of exposed persons. The emergence of SARS is a timely reminder of the need to expect the unexpected and to ensure strong national and global public health partnerships when preparing for and responding to infectious diseases. Effectively addressing the threat of SARS will require enhanced global infectious disease surveillance, the development of rapid diagnostics, new therapies, and vaccines, implementation of aggressive evidence-based infection control strategies, and effective communication.

Animals↗
PubMed2004

The potent in vitro antioxidant ellagitannins from pomegranate juice are metabolised into bioavailable but poor antioxidant hydroxy-6H-dibenzopyran-6-one derivatives by the colonic microflora of healthy humans.

BACKGROUND: The antiatherogenic activity of pomegranate juice has been attributed to its antioxidant polyphenols. The most potent in vitro antioxidant polyphenol from this juice is the ellagitannin punicalagin. However, the bioavailability of ellagitannins, including punicalagin, has not been previously described in humans. AIM OF THE STUDY: The present work aims to evaluate, in healthy humans, the bioavailability and metabolism of pomegranate juice ellagitannins, to assess their effect on several blood parameters (including cardiovascular risk disease markers) and to compare the antioxidant activity of punicalagin with that of the in vivo generated metabolites. DESIGN: Six healthy subjects (four men and two women) consumed 1 L of pomegranate juice daily (5.58 g/L polyphenols, including 4.37 g/L punicalagin isomers) for 5 days. The polyphenols and the in vivo generated metabolites were measured by HPLC-DAD-MS-MS. Fourteen haematological and twenty serobiochemical parameters including LDL, HDL and VLDL as well as cholesterol and triglycerides in each lipoprotein were evaluated. In vitro antioxidant activity of plasma (ABTS and FRAP assays) and urine (ABTS and DPPH) were determined. RESULTS: Neither punicalagin nor ellagic acid present in the juice were detected in both plasma and urine. Three microbial ellagitannin-derived metabolites were detected: 3,8-dihydroxy-6H-dibenzo[b,d]pyran-6-one glucuronide, an unidentified aglycone (tentatively, trihydroxy-6H-dibenzo[b,d]pyran-6-one) and hydroxy-6-H-dibenzo[b,d]pyran-6-one glucuronide. These metabolites could reach up to 18.6 microM in plasma, although a large inter-individual variability was observed. In urine, the same metabolites and their corresponding aglycones became evident after 1 day of juice consumption. Total urine excretion of metabolites ranged from 0.7 to 52.7% regarding the ingested punicalagin. No relevant effect was observed on any blood parameter. The metabolites did not show significant antioxidant activity compared to punicalagin from pomegranate juice. CONCLUSIONS: The potential systemic biological effects of pomegranate juice ingestion should be attributed to the colonic microflora metabolites rather than to the polyphenols present in the juice.

Adult↗
PubMed2001

Microbial community analysis in the denitrification process of saline-wastewater by denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA and the cultivation method.

The metallurgic wastewater generated from the processes of recovering precious metals from industrial wastes contains high concentrations of nitrogen compounds and salts. Biological nitrogen removal from this wastewater was attempted using a circulating bioreactor system equipped with an anaerobic packed bed or an anaerobic fluidized bed. The denitrification capability of the system with the anaerobic packed bed was more stable than that of the system with the anaerobic fluidized bed. The NOx removal rate of the anaerobic packed bed was as high as 97%. Microbial community analysis by denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA (rDNA) fragments and the cultivation method revealed that the community diversity varied in accordance with wastewater composition such as the level of salinity and so on. Phylogenetic analysis suggested that the taxonomic affiliation of the dominant species in the anaerobic reactors was to the gamma-Proteobacteria including Halomonadaceae species. The PCR-DGGE method as a non-cultivation method was found to be a powerful tool for analysis of the microbial community, because the cultivation method could detect only a fraction of the microbial species present in these systems. The genetic diversity of the isolated bacteria belonging to the gamma-Proteobacteria which reduced both nitrate and nitrite in the anaerobic packed bed was higher than that of the bacteria in the anaerobic fluidized bed. This suggested that a genetically diverse microbial community stabilized the denitrifying performance in the anaerobic packed bed.

Journal Article↗
PubMed2003

Volatile metabolites from indoor molds grown on media containing wood constituents.

Since volatile mold metabolites are used for the detection of mold growth in buildings, it was interesting to determine whether different indoor mold species show different affinity for the major components of wood, a common building material. Growth and volatile metabolites were studied when Aspergillus versicolor, Penicillium chrysogenum, and P. palitans were grown on laboratory substrates containing the major wood constituents cellulose, xylan and lignin. Microbial volatile organic compounds (MVOCs) were characterized by thermal desorption/gas chromatography/mass spectroscopy. Growth and volatile metabolites varied considerably and there appeared to be complementary substrate specificities for P. chrysogenum, and P. palitans grown on cellulose and xylan. The failure of A. versicolor to produce characteristic MVOCs when grown on media containing wood constituents suggests that systems using volatile metabolites to detect microbial growth in buildings may be fundamentally unreliable for the detection of this species.

Air Pollution, Indoor↗
PubMed1997

Application of triphenyltetrazolium chloride in microbial limit test in pharmaceuticals and cosmetics. Multiple- tube method for yeasts detection.

The triphenyltetrazolium chloride (TTC) was studied as a means to detect yeasts growth in liquid medium, aiming its application to microbial limit test using Multiple-tube method, for testing pharmaceuticals or cosmetics samples with opacity. The results from most probable number (MPN) using TTC and sub-culture techniques obtained from the tests of simulated samples, spiked with Candida albicans and Sacharomyces cerevisiae, showed to be equivalents.

Candida albicans↗
PubMed2004

The potential of next-generation microbiological diagnostics to improve bioterrorism detection speed.

Emerging, rapid, multivalent, microbial diagnostic technologies can produce results in hours, as contrasted to the standard methods that require at least the better part of a week. Used in bioterrorism surveillance in medical settings, the new biodetectors could significantly reduce the time between a covert attack and its detection. By how much is determined by the intensity of sampling. If used to screen all patients reporting flu-like symptoms to their doctors, this basic level of "front-line" sampling would reduce life-threatening medical floundering and missteps and give responders 3-5 days of warning that they otherwise would not have had. Being miniaturized and amenable to mass production, these devices could reduce the cost of screening to a fraction of current costs and so it is tempting to imagine their use in more intensive bioterrorism screening programs aimed at the apparently healthy population, programs that could detect a covert attack even before the victims felt ill. This article examines the tradeoffs between surveillance effort and probability of detection for such programs. Dual-use deployment, where the biodetector provides some medically useful information in addition to bioterrorism surveillance, is discussed.

Bioterrorism↗
PubMed1980

Selective nonroutine microbial surveillance of in-use hospital nebulizers by aerosol entrapment and direct sampling analyses of solutions in reservoirs.

Effluent aerosols and liquid reservoir samples from 255 in-use hospital nebulization devices were analyzed by Aero-Test samplers (Olympic Corp.) and direct dilution procedures (0.1-, 0.01-, and 0.001-ml plated samples). Thirty-five percent (89 of 255) of the in-use hospital reservoir samples were positive by direct dilution, and 24% (61 of 255) were positive by Aero- Test samplers. Acinetobacter calcoaceticus var. anitratus was found either alone or in association with Pseudomonas spp. in 50% of all the contaminated in-use reservoirs. This indicates a high endemicity for Acinetobacter in the environment studied. Viable microbes in the reservoirs of contaminated nebulizers ranged from as few as 20 to >2 x 10(5) colony-forming units/ml. Microbial contamination at moderate to heavy levels (1 x 10(4) to >2 x 10(5)) was regularly detected by both procedures. Microbial densities of 10(3) colony-forming units/ml and less in contaminated reservoirs often were negative in the Aero- Test but positive by direct dilution techniques. These hospital-based results were similar to laboratory data obtained with sterile nebulizers intentionally contaminated in graduated densities with either Staphylococcus aureus or Pseudomonas aeruginosa. Sensitivity of the Aero- Test system was best when >/=10(4) colony-forming units/ml were present in the reservoirs of operating nebulizers. The manufacturer suggests that five or less colonies appearing after sampling on Aero- Test plates upon 48-h incubation does not indicate contamination of the reservoir. Our data show that even a single colony, particularly if it is typical, water-associated, gram-negative bacterial species, may well indicate low levels of reservoir contamination. Both the Aero- Test and direct dilution methods indicated the need for more rigorous management of the in-use respiratory therapy equipment in the hospital surveyed. These studies demonstrate the value of selective nonroutine surveillance for identifying potential or actual contamination problems of in-use nebulizing equipment, particularly when recommended care guidelines are not followed due to choice or unawareness. Ameliorative-corrective measures, which included routine 24-h substitution of old units with new sterile units, were initiated as a result of this surveillance program.

Acinetobacter↗
PubMedDate not supplied

Identification of beta-lactam antibiotics in tissue samples containing unknown microbial inhibitors.

Antibiotic residues in animal tissues can be detected by various screening tests based on microbial inhibition. In the 7-plate assay used by the U.S. Department of Agriculture's Food Safety and Inspection Service (FSIS), penicillinase is incorporated into all but one plate to distinguish beta-lactam antibiotics from other types. However, beta-lactams such as cloxacillin and the cephalosporins are resistant to degradation by penicillinase. They may not be identified as beta-lactams by this procedure, and thus, they may be identified as unidentified microbial inhibitors (UMIs). However, these penicillinase-resistant compounds can be degraded by other beta-lactamases. The present study describes an improved screening protocol to identify beta-lactam antibiotics classified as UMIs. A multiresidue liquid chromatographic procedure based on a method for determining beta-lactams in milk was also used to identify and quantitate residues. The 2 methods were tested with 24 tissue FSIS samples classified as containing UMIs. Of these, 3 contained penicillin G, including one at a violative level, and 5 contained a metabolite of ceftiofur. The others were negative for beta-lactam antibiotics.

Animals↗