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 505 records · Page 28Linked to original sources
PubMed1999

Response to high-pressure, low-temperature treatment in vegetables: determination of survival rates of microbial populations using flow cytometry and detection of peroxidase activity using confocal microscopy.

Application of high hydrostatic pressure (200, 300, 350 and 400 MPa) at 5 degrees C for 30 min to different micro-organisms, including Gram-positive and Gram-negative bacteria, moulds and yeasts, proved to be more effective in inactivating these organisms than treatments at 20 degrees C for 10 min and at 10 degrees C for 20 min. Moulds, yeasts, Gram-negative bacteria and Listeria monocytogenes were most sensitive, and their populations were completely inactivated at pressures between 300 and 350 MPa. The same conditions of pressure, temperature, and time were applied to different vegetables (lettuce, tomato, asparagus, spinach, cauliflower and onion), achieving reductions of from 2-4 log units in both viable mesophiles and moulds and yeasts at pressures of between 300 and 400 MPa. Sensory characteristics were unaltered, especially in asparagus, onion, tomato and cauliflower, though slight browning was observed in cauliflower at 350 MPa. Flow cytometry was applied to certain of the microbial populations used in the above experiment before and after the pressurization treatment. The results were indicative of differing percentage survival rates depending on micro-organism type, with higher survival rates for Gram-positive bacteria, except L. monocytogenes, than in the other test micro-organisms. Growth of survivors was undetectable using the plate count method, suggesting that micro-organisms suffering from pressure stress were metabolically inactive though alive. The pressurization treatments did not inactivate the peroxidase responsible for browning in vegetables. Confocal microscopic examination of epidermal tissue from onion showed that the enzyme had been displaced to the cell interior. Use of low temperatures and moderately long pressurization times yielded improved inactivation of micro-organisms and better sensorial characteristics of the vegetables, and should lower industrial costs.

Aerobiosis↗
PubMed1997

Detection of stable pre-rRNA in toxigenic Pseudo-nitzschia species.

Nucleotide sequence analysis of ribosomal DNA (rDNA) spacer regions is useful for taxonomic comparisons of closely related microorganisms. These regions have been less useful for routine microbial identification and detection, partly because rRNA precursors (pre-rRNAs) in microbial cells are assumed to be too labile to be detectable by high-throughput probe hybridization methods. We characterized the sequence diversity and physiological stability of pre-rRNA in the toxigenic marine diatoms Pseudo-nitzschia australis, P. multiseries, and P. pungens. As with nucleotide sequences of the first internal transcribed spacer (ITS1) reported previously, sequences of ITS2 and the 5' external transcribed spacer (ETS1) exhibited considerable divergence among these species, including large insertions-deletions detectable by PCR-based spacer length analysis. In slot blot hybridization assays on RNA extracted from lysates of Pseudo-nitzschia cells, oligonucleotide probes directed to pre-rRNA spacers generated much stronger signals than did complementary probes directed to the coding strands of the rDNAs, indicating that the pre-rRNA-targeted probes detected multicopy transcripts. A group of probes directed to a discrete 90-base region within the ITS1 pre-rRNA gave no detectable signal, suggesting that this region is degraded early in the rRNA maturation pathway. Other pre-rRNA regions were always detectable and, in marked contrast to prokaryotic systems analyzed in this manner, were stable and abundant in both actively dividing and nondividing cells. Long, multilabeled RNA probes, which would exhibit considerable cross-reactivity if directed to mature rRNA sequences, detected species-specific pre-rRNA sequences from as few as 1,000 cells. Pre-rRNA is a potentially useful molecular target for detecting and identifying Pseudo-nitzschia species and possibly other unicellular eukaryotes as well.

Base Sequence↗
PubMed2001

Potential for milk containing penicillin G or amoxicillin to cause residues in calves.

The potential for antibiotic residues in calves from consuming milk containing penicillin G or amoxicillin was investigated. Six calves were fed milk replacer, 6% body weight twice daily, containing 0.293, 2.92, or 5.85 microg of penicillin/ml (ppm) G or 0.25, 1.0, or 2.0 microg of amoxicillin/ml for three consecutive feedings. Urine and blood samples were collected after each feeding. Serum and urine samples were tested with a microbial receptor assay and a microbial growth inhibition assay to indicate potential drug residues. Penicillin G and amoxicillin were detected in the serum and urine of several calves 3 h after drinking spiked milk replacer. Possible violative drug residues in the calves were detected by the microbial growth inhibition assay up to 15 h after drinking spiked milk replacer. Penicillin G, but not amoxicillin, could be detected in urine 24 h after the final feeding of spiked milk replacer. Subsequently, six calves were fed milk replacer containing 11.7 microg of penicillin G/ml (ppm) twice daily, 6% body weight per feeding. Calves were slaughtered 3 h after the final feeding. Mean (+/-SD) concentrations of penicillin G measured by high-pressure liquid chromatography in liver, kidney, muscle, and serum were 0.409 (+/-0.167) microg/g, 0.031 (+/-0.012) microg/g 0.008 (+/-0.002) microg/g, and 0.013 (+/-0.006) mg/ml, respectively. This study indicates that calves fed milk with amoxicillin or penicillin G could possibly have violative residues if slaughtered within 24 h after feeding. Violative drug residues in liver tissue were found in calves slaughtered 3 h after consuming milk replacer containing 11.7 microg of penicillin G/ml (ppm).

Amoxicillin↗
PubMed2001

Detection of lateral gene transfer among microbial genomes.

An increasingly comprehensive assessment is being developed of the extent and potential significance of lateral gene transfer among microbial genomes. Genomic sequences can be identified as being of putatively lateral origin by their unexpected phyletic distribution, atypical sequence composition, differential presence or absence in closely related genomes, or incongruent phylogenetic trees. These complementary approaches sometimes yield inconsistent results. Not only more data but also quantitative models and simulations are needed urgently.

Evolution, Molecular↗
PubMed2001

Detection of catabolic genes in indigenous microbial consortia isolated from a diesel-contaminated soil.

Bioremediation is often used for in situ remediation of petroleum-contaminated sites. The primary focus of this study was on understanding the indigenous microbial community which can survive in contaminated environment and is responsible for the degradation. Diesel. toluene and naphthalene-degrading microbial consortia were isolated from diesel-contaminated soil by growing on selective hydrocarbon substrates. The presence and frequency of the catabolic genes responsible for aromatic hydrocarbon biodegradation (xylE, ndoB) within the isolated consortia were screened using polymerase chain reaction PCR and DNA DNA colony hybridization. The diesel DNA-extract possessed both the xy/E catabolic gene for toluene, and the nah catabolic gene for polynuclear aromatic hydrocarbon degradation. The toluene DNA-extract possessed only the xylE catabolic gene, while the naphthalene DNA-extract only the ndoB gene. Restriction enzyme analysis with HaeIII indicated similar restriction patterns for the xylE gene fragment between toluene DNA-extract and a type strain, Pseudomonas putida ATCC 23973. A substantial proportion (74%) of the colonies from the diesel-consortium possessed the xylE gene, and the ndoB gene (78%), while a minority (29%) of the toluene-consortium harbored the xylE gene. 59% of the colonies from the naphthalene-consortium had the ndoB gene, and did not have the xylE gene. These results indicate that the microbial population has been naturally enriched in organisms carrying genes for aromatic hydrocarbon degradation and that significant aromatic biodegradative potential exists at the site. Characterization of the population genotype constitutes a molecular diagnosis which permits the determination of the catabolic potential of the site to degrade the contaminant present.

Base Sequence↗
PubMed2004

Identification of pathogenic microbial cells and spores by electrochemical detection on a biochip.

BACKGROUND: Bacillus cereus constitutes a significant cause of acute food poisoning in humans. Despite the recent development of different detection methods, new effective control measures and better diagnostic tools are required for quick and reliable detection of pathogenic micro-organisms. Thus, the objective of this study was to determine a simple method for rapid identification of enterotoxic Bacillus strains. Here, a special attention is given to an electrochemical biosensor since it meets the requirements of minimal size, lower costs and decreased power consumption. RESULTS: A bead-based sandwich hybridization system was employed in conjugation with electric chips for detection of vegetative cells and spores of Bacillus strains based on their toxin-encoding genes. The system consists of a silicon chip based potentiometric cell, and utilizes paramagnetic beads as solid carriers of the DNA probes. The specific signals from 20 amol of bacterial cell or spore DNA were achieved in less than 4 h. The method was also successful when applied directly to unpurified spore and cell extract samples. The assay for the haemolytic enterotoxin genes resulted in reproducible signals from B. cereus and B. thuringiensis while haemolysin-negative B. subtilis strain did not yield any signal. CONCLUSIONS: The sensitivity, convenience and specificity of the system have shown its potential. In this respect an electrochemical detection on a chip enabling a fast characterization and monitoring of pathogens in food is of interest. This system can offer a contribution in the rapid identification of bacteria based on the presence of specific genes without preceding nucleic acid amplification.

Journal Article↗
PubMed2004

An effective method for extracting DNA from contaminated soil due to industrial waste.

Recently, labor accidents caused by toxic gas production such as H2S and CH4 have happened at some waste disposal sites and illegal dumping sites in Japan. The gas production has been known to be end products of bacterial respiration. In order to investigate a microbial flora in industrial waste contaminated soil by a DNA-based detection method, we developed a simple DNA extraction method. The method is based on lysis with sodium dodecyl sulfate (SDS) and a high concentration (4.0 mg/ml) of lysozyme at room temperature. DNA yields increased according to the concentration of lysozyme (0-2 mg/ml), although the cell lysis occurred at comparable efficiency independent of the lysozyme concentration. Interestingly, bovine serum albumin and insulin (4 mg/ml) also contributed high DNA yields. This suggests proteins play an important role at high concentration on a DNA extraction process, presumably by suppressing DNA degradation or adsorption. DNA yields from three contaminated soil samples at 0.3, 1.5 and 3 m in depth by using our method were significantly higher than those extracted by using a widely-used conventional method which did not contain lysozyme. A novel and simple DNA extraction method using high concentration of protein was established for a DNA-based detection method of microbial flora in soil.

Air Pollution↗
PubMed1992

Evaluation of methods for detecting ecological effects from genetically engineered microorganisms and microbial pest control agents in terrestrial systems.

This report summarizes and evaluates research from several laboratories that deals with the detection of ecological effects induced through exposure of microbes or plants to genetically engineered microorganisms (GEMs) and microbial pest control agents (MPCAs). Some 27 potential endpoints for measuring effects have been studied. Perturbations induced by GEMs have been detected in about one-half of these endpoints. Detectable effects have been recorded for over half of the 16 species of bacteria and fungi studied. The effects caused by GEMs and MPCAs include inhibition of beneficial mycorrhizal fungi growing on Douglas fir seedling roots, depression in plant root and shoot growth, inhibition of predatory soil protozoa, accumulation of a toxic metabolite during biodegradation that inhibits soil fungi, increased microbial community respiration due to rapid lignin breakdown in soil, and the displacement of a broad group of gram-negative bacteria that inhabit the root surface of cereal crops. These effects were usually, but not always, of short duration. However, some of the changes were irreversible during the observation time of days, weeks, or in one case, months.

Journal Article↗
PubMed1993

Antigen and antibody assays in the aetiological diagnosis of respiratory infection in children.

The diagnostic efficacy of two methods--demonstration of seroconversion in paired sera and detection of antigen in clinical specimens--was evaluated in 183 children with respiratory syncytial, parainfluenza or adenoviral, or pneumococcal respiratory tract infection. Viral infection was diagnosed in 46 (37%) of the 125 cases by antigen assay alone, in 36 (29%) by antibody assay alone and in 43 (34%) by both methods. In respiratory syncytial viral infections, antigen assays were more often positive than antibody assays; 80% of the cases were antigen positive and 63% solely antigen positive. In parainfluenza and adenoviral infections, antigen assays were not as useful; a positive result was seen in 59% and 44% of cases, respectively. Pneumococcal infection was diagnosed in 25 (30%) of the 84 cases by antigen assay alone, in 54 (64%) by antibody assay alone and in only 5 (6%) by both methods. Thus nearly all pneumococcal infections were diagnosed by only one method. The efficacy of antigen and antibody assay was clearly dependent on the age of the patients. In infants less than six months of age, nearly all (27 (90%)) of the 30 infections were diagnosed by antigen detection; 25 solely by antigen detection. In older patients, antigen and antibody assays supplemented each other. We conclude that antigen detection should be used as the primary method for the diagnosis of viral or pneumococcal respiratory tract infection. In infants, antigen detection is the only reliable method of microbial diagnosis. In addition, antigen detection is the method of rapid microbial diagnosis. In pneumococcal infections, the sensitivities of antigen detection methods are not sufficient; this is an important area for further research.

Adolescent↗
PubMed2026

Seqwin: ultrafast identification of signature sequences in microbial genomes.

MOTIVATION: Polymerase chain reaction (PCR) enables rapid, cost-effective diagnostics but requires prior identification of genomic regions that allow sensitive and specific detection of target microbial groups, herein referred to as microbial signature sequences. We introduce Seqwin, an open-source framework designed to automate microbial genome signature discovery. Tens of thousands of microbial genomes are now available for a single species, limiting the application of existing manual and automated approaches for identifying signatures. Modern approaches that are capable of leveraging all available microbial genomes will ensure sensitive and accurate DNA signature identification and enable robust pathogen detection for clinical, environmental, and public health applications. RESULTS: Seqwin builds weighted pan-genome minimizer graphs and uses a traversal algorithm to identify signature sequences that occur frequently in target genomes but remain rare in non-targets. Unlike earlier tools that depend on strict presence or absence of sequences, Seqwin accommodates natural sequence variation and scales to very large genome collections. When applied to genomes from C. difficile, M. tuberculosis, and S. enterica, Seqwin recovered more high-quality signatures than alternative methods with lower computational burden. Seqwin's analysis of nearly 15 000 S. enterica genomes yielded over 200 candidate signatures in three minutes. Seqwin provides an open-source solution for the long-standing need for scalable microbial signature discovery and diagnostic assay design. AVAILABILITY AND IMPLEMENTATION: Seqwin is available on GitHub (https://github.com/treangenlab/Seqwin) and can be installed via Bioconda (https://bioconda.github.io/recipes/seqwin/README.html). Benchmarking datasets, outputs, and scripts are available on Zenodo (https://doi.org/10.5281/zenodo.19874011).

Software↗
PubMed2006

Capillary isoelectric focusing of proteins and microorganisms in dynamically modified fused silica with UV detection.

We suggest a method for the reproducible and efficient capillary isoelectric focusing of proteins and microorganisms in the pH gradient 3-10. The method involves the segmental injection of the simple ampholytes, the solution of the selected electrolytes, and the sample mixture of bioanalytes and carrier ampholytes to the fused silica capillaries dynamically modified by poly(ethylene glycol), PEG 4000, which is added to the catholyte, the anolyte and injected solutions. In order to receive the reproducible results, the capillaries were rinsed by the mixture of acetone/ethanol between analyses. For the tracing of the pH gradients the low-molecular-mass pI markers were used. The simple proteins and the mixed cultures of microorganisms, Saccharomyces cerevisiae CCM 8191, Escherichia coli CCM 3954, Candida albicans CCM 8180, Candida parapsilosis, Candida krusei, Staphylococcus aureus, Streptococcus agalactiae CCM 6187, Enterococcus faecalis CCM 4224, Staphylococcus epidermidis CCM 4418 and Stenotrophomonas maltophilia, were focused and separated by the method suggested. The minimum detectable number of microbial cells was 5x10(2) to 1x10(3) with on-column UV detection at 280 nm.

Bacteria↗
PubMedDate not supplied

Fast antimicrobial screen test (FAST): improved screen test for detecting antimicrobial residues in meat tissue.

The Fast Antimicrobial Screen Test (FAST) is a simple and quick screening test developed to detect antibiotic and sulfonamide residues in food animal carcasses in slaughter establishments. This microbial inhibition test detects antimicrobials that are allowed to be used in food animals. It has the ability to detect these antimicrobials at or above the allowable limit in carcass kidney fluids in 6 h. Laboratory evaluations show that the lower limit of detection (LLD) of FAST and the Calf Antibiotic and Sulfa Test (CAST) for antibiotics tested was the same, but the LLD for sulfonamides of FAST was lower than the LLD of CAST. Compared with the Swab Test on Premises (STOP) developed in 1977, the LLD's of FAST for both antibiotics and sulfonamides were significantly better. Under field conditions, the sensitivity of FAST and CAST to antibiotic and sulfonamide residues in animal kidneys was not significantly different, but the time required by FAST was significantly lower than CAST (6 versus 18 h). Compared with the STOP, the sensitivity and the range of detection by FAST for all antimicrobials were significantly higher and the testing time was lower (18 versus 6 h).

Animals↗
PubMed1984

Comparative differential dark-field microscopy of subgingival bacteria from tooth surfaces with recent evidence of recurring periodontitis and from nonaffected surfaces.

Ninety-two subjects with a history of treatment for chronic periodontitis were monitored on a regular basis for an average period of 10.7 months. During this monitoring period, in spite of their participation in a preventive maintenance program, 19 subjects out of 92 showed evidence of significantly increased probing depth (greater than or equal to 3 mm from base line measurements) on at least one tooth surface, or approximately 1% of the dental units at risk in this population. A comparison of differential microscopic counts of subgingival bacteria from the affected tooth surfaces with a pooled sample of 6 other surfaces with the greatest probing depth, in the same mouth, taken at the same appointment, revealed no significant differences between proportions of coccoid cells, spirochetes, motile rods or other cell types. These findings suggest that disease recurrence, as measured by a comparatively rapid increase in probing depth, might be accounted for on the basis of the following hypotheses: an alteration in the host response without a detectable change in the composition of the subgingival microbiota, a qualitative change in the microbial flora not detectable by a microscopic assay, relatively brief episodes of disease activity which may be accompanied by brief, transient, qualitative changes in the local microbiota that cannot be readily detected by biannual examinations.

Bacteria↗
PubMedDate not supplied

Pharmaceutical container/closure integrity. II: The relationship between microbial ingress and helium leak rates in rubber-stoppered glass vials.

Helium leak rate measurements were quantitatively correlated to the probability of microbial ingress for rubber-stoppered glass vials subjected to immersion challenge. Standard 10-mL tubing glass vials were modified by inserting micropipettes of various sizes (0.1 to 10 microns nominal diameter) into a side wall hole and securing them with epoxy. Butyl rubber closures and aluminum crimps were used to seal the vials. The test units were sealed in a helium-filled glove bag, then the absolute helium leak rates were determined. The test units were disassembled, filled with media, resealed, and autoclaved. The test units were thermally treated to eliminate airlocks within the micropipette lumen and establish a liquid path between microbial challenge media and the test units' contents. Microbial challenge was performed by immersing the test units in a 35 degrees C bath containing magnesium ion and 8 to 10 logs of viable P. diminuta and E. coli for 24 hours. The test units were then incubated at 35 degrees C for an additional 13 days. Microbial ingress was detected by turbidity and plating on blood agar. The elimination of airlocks was confirmed by the presence of magnesium ions in the vial contents by atomic absorption spectrometry. A total of 288 vials were subjected to microbial challenge testing. Those test units whose contents failed to show detectable magnesium ions were eliminated from further analysis. At large leak rates, the probability of microbial ingress approached 100% and at very low leak rates microbial ingress rates were 0%. A dramatic increase in microbial failure occurred in the leak rate region 10(-4.5) to 10(-3) std cc/sec, which roughly corresponded to leak diameters ranging from 0.4 to 2 microns. Below a leak rate of 10(-4.5) std cc/sec the microbial failure rate was < 10%. The critical leak rate in our studies, i.e. the value below which microbial ingress cannot occur because the leak is too small, was observed to be between 10(-5) and 10(-5.8) std cc/sec, which corresponds to an approximate leak diameter of 0.2-0.3 micron.

Drug Contamination↗
PubMed2004

The time-related changes of antimicrobial resistance patterns and predominant bacterial profiles of burn wounds and body flora of burned patients.

To examine the bacterial isolates from the burn patients and to compare the antibiograms of the predominant bacteria isolated from 51 patients who were hospitalized at least 3 weeks or more over a period of 7 months, a prospective study was undertaken. Periodic swabs were taken from burn wound, nasal, axillary, inguinal, and umbilical region of the patients on admission and on 7th, 14th, and 21st days of hospitalization. Mean hospital stay was 36.5 days. A total of 1098 microbial isolates were detected during the study period. Coagulase-negative staphylococci (CNS, 63.0%) and Staphylococcus aureus (19.7%) were the most prevalent isolates in admission cultures. During the next weeks, these bacteria were superceded by mainly Pseudomonas aeruginosa. Between admission and 21st day, the rates of methicillin resistance of staphylococci strains increased steadily. There was no vancomycin resistance in any staphylococci strains, although nine of the S. aureus isolates (2.7%) were resistant to teicoplanin. There were no strains producing inducible beta lactamase (IBL) among P. aeruginosa strains. One extended-spectrum beta-lactamase (ESBL)-producing strain was recovered on admission, although strains producing IBL and ESBL were detected at rates of 79.6 and 57.1%, respectively, on the 21st day. The nature of microbial wound colonization, flora changes, and antimicrobial sensitivity profiles should be taken into consideration in using empirical antimicrobial therapy of burned patients.

Adolescent↗
PubMed2006

Direct infusion electrospray ionization mass spectra of crude cell extracts for microbial characterizations: influence of solvent conditions on the detection of proteins.

Direct infusion electrospray ionization mass spectrometry (DIES-MS) of crude bacterial extracts is a rapid method that can be used to characterize microbial cells. Phospholipids, metabolites, and proteins can be detected rapidly with minimal sample preparation. However, several factors influence the detection of signals in such high-throughput analyses. We studied the influence of solvent conditions, including the organic content and pH of the solvent, on the extraction and subsequent detection of signals in DIES-MS, with a view to improving the detection of protein signals. Unfractionated cell extracts from three strains of the Gram-negative Escherichia coli (including one encoding a recombinant green fluorescence protein), and the Gram-positive Bacillus sphaericus and B. subtilis were investigated. Both pH and the organic content of the solvent were found to influence the spectral information as observed from principal component analysis of the spectral data. A polar solvent with higher organic content resulted in the extraction of phospholipids that overtly dominate the spectral information. Decreasing the organic content of the extraction solvent resulted in the improved detection of protein peaks. Altering the pH of the extraction solvent resulted in different protein profiles from the same bacterium, as observed after spectral deconvolution. In addition, the protein profiles were also different when using different organic solvents. Spectral deconvolution showed several protein peaks that had mass-based homology with those in protein databases for the (sequenced) organisms studied. These results suggest that a combination of solvent conditions can be used to generate protein profiles rapidly that when combined can provide additional valuable proteomic information.

Bacillus↗
PubMedDate not supplied

[Evolution of microbial flora and organic matter in bottled mineral water].

A 15-week survey was carried out by the authors in order to detect the total microbial count and the quantity of organic matter in mineral waters bottled in dark glass containers and stored at room temperature. Two different and significant increases were registered at the 2nd and 11th week respectively. A relation between microbial count and organic matter was observed during the period examined.

English Abstract↗