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[Microbial ecology and the state of the gastrointestinal mucosa in patients with allergic diseases].

Patients with allergic diseases of the skin and the respiratory system were found to have a high rate of disturbances in the microbial ecology of the gastrointestinal tract and the involvement of all its sections into the pathological process. On the mucous membrane of different sections of the digestive tract spiral-like bacteria were detected in a large percentage of cases. The possibility of the fact that the development and maintenance of the allergic process were evidently linked with the detected changes in the microbial ecology and pathomorphological features of the gastrointestinal mucosa could hardly be excluded, which made it necessary to make corrections in the therapeutic process.

Adult↗
PubMed1988

Method for testing the sterility of total nutrient admixtures.

A test for determining the sterility of a total nutrient admixture (TNA) containing equal quantities of 10% fat emulsion (Liposyn II), 8.5% amino acids injection, and 50% dextrose injection using the USP membrane filtration procedure was developed and evaluated. Membrane filter selection was determined by analysis of flow rates, membrane fluid compatibility, bubble point stability, and rinse fluid requirements. Microbial challenges employing five organisms (Bacillus subtilis, Escherichia coli, Candida albicans, Staphylococcus aureus, and Pseudomonas aeruginosa) and both soybean casein digest and fluid thioglycollate media were used to confirm the ability of the test to detect low-level microbial contamination. A polyvinylidene fluoride membrane was determined to be the most appropriate of the membrane types studied because of its superior flow rate and membrane-fluid compatibility. Bubble point testing revealed no detrimental effects on the membrane. The potential problem of haziness caused by retention of the TNA by the membrane with subsequent release in the culture media (which could result in false-positive growth determinations) was diminished by using a sterile 0.1% peptone solution rinse and careful observation techniques. Performance of the sterility test by six hospital pharmacists required an average of 14.2 minutes. Sterility testing of alternate TNAs compounded with Intralipid and Nutralipid was not feasible because of prolonged filtration times. The basic USP membrane filtration procedure for large-volume injections can be used by hospital pharmacists for testing the sterility of TNAs. When fat emulsions are used in compounding, sterility-testing procedures specific to the emulsion product used should be developed and evaluated.

Culture Media↗
PubMed2006

Prokaryotic diversity and metabolically active microbial populations in sediments from an active mud volcano in the Gulf of Mexico.

In this study, ribosomes and genomic DNA were extracted from three sediment depths (0-2, 6-8 and 10-12 cm) to determine the vertical changes in the microbial community composition and identify metabolically active microbial populations in sediments obtained from an active seafloor mud volcano site in the northern Gulf of Mexico. Domain-specific Bacteria and Archaea 16S polymerase chain reaction primers were used to amplify 16S rDNA gene sequences from extracted DNA. Complementary 16S ribosomal DNA (crDNA) was obtained from rRNA extracted from each sediment depth that had been subjected to reverse transcription polymerase chain reaction amplification. Twelve different 16S clone libraries, representing the three sediment depths, were constructed and a total of 154 rDNA (DNA-derived) and 142 crDNA (RNA-derived) Bacteria clones and 134 rDNA and 146 crDNA Archaea clones obtained. Analyses of the 576 clones revealed distinct differences in the composition and patterns of metabolically active microbial phylotypes relative to sediment depth. For example, epsilon-Proteobacteria rDNA clones dominated the 0-2 cm clone library whereas gamma-Proteobacteria dominated the 0-2 cm crDNA library suggesting gamma to be among the most active in situ populations detected at 0-2 cm. Some microbial lineages, although detected at a frequency as high as 9% or greater in the total DNA library (i.e. Actinobacteria, alpha-Proteobacteria), were markedly absent from the RNA-derived libraries suggesting a lack of in situ activity at any depth in the mud volcano sediments. This study is one of the first to report the composition of the microbial assemblages and physiologically active members of archaeal and bacterial populations extant in a Gulf of Mexico submarine mud volcano.

Archaea↗
PubMed1987

Ultrasensitive analysis of microbial fatty acids using gas chromatography with electron capture detection.

Pentafluorobenzyl and pentafluoropropionyl/pentafluorobenzyl esters of bacterial fatty acids were analysed by capillary gas chromatography using both flame ionization and electron capture detection. No differences between the relative peak areas of the various fatty acids were observed as regards the two detectors used except that response of the electron capture dectector to the hydroxy acid derivatives exceeded that to the non-hydroxy acid derivatives by 20%. Use of the described derivatives in combination with electron capture detection yields chromatograms comparable with those obtained by analysis of methyl esters using flame ionization detection but with superior sensitivity.

Bacteria↗
PubMed2002

Comparison of microbial cultivation and a commercial PCR based method for detection of periodontopathogenic species in subgingival plaque samples.

OBJECTIVES: Microbiological laboratory procedures are involved in diagnosis and therapy control of progressive and refractory forms of periodontitis. In recent years techniques have been developed based on the detection of nucleic acids. The purpose of this study was to validate the commercially available micro-Dent(R) test which employs probes for A. actinomycetemcomitans, P. gingivalis, P. intermedia, B. forsythus and T. denticola. METHODS: 122 plaque samples obtained from periodontal pockets with various depths from 33 early onset periodontitis (EOP) patients and 15 periodontally healthy subjects were analysed by cultivation and the microDent(R) kit. RESULTS: Both cultivation and the nucleic acid based assay showed a positive correlation of pocket depth with the frequency and quantity of periodontopathogenic species. T. denticola was found only in pockets > 4 mm in EOP patients. Comparison of the two methods revealed that the microDent(R) kit identified both P. gingivalis and B. forsythus more often than did the cultivation method. CONCLUSIONS: Nucleic acid techniques should replace cultivation methods as gold standard in microbiological diagnosis of progressive periodontitis. The micro-Dent(R) kit can be recommended for microbiological laboratories analysing subgingival plaque samples.

Adolescent↗
PubMed1996

Potential of diagnostic microbiology for treatment and prognosis of dental caries and periodontal diseases.

Most evidence suggests that only a finite number of bacteria are responsible for dental caries and periodontal diseases. This knowledge led to the development of microbial tests which can identify suspected pathogens. Current evaluation of the diagnostic power of microbial tests has shown that they have a low sensitivity and a low prognostic value. Despite these shortcomings, there are valid indications for microbiological-based diagnosis. Salivary microbial tests for the detection of mutans streptococci and lactobacilli may be useful, for example, in young children, oligosialic patients, and orthodontic patients. These tests can be used to monitor the success of chemopreventive measures or compliance with dietary recommendations. Microbial diagnosis, may also be valuable in the treatment of early-onset periodontitis or in subjects who respond poorly to periodontal therapy. The use of microbial tests to monitor the efficacy of chemotherapy or mechanical treatment is of particular interest.

Aggressive Periodontitis↗
PubMed1997

Emerging infections and newly-recognised pathogens.

Clinicians and microbiologists have for many years relied on growth and characterisation of micro-organisms in the laboratory as the major method for their detection and identification, but reliance upon microbial growth in the laboratory has probably significantly limited our ability to recognise important pathogenic micro-organisms. The traditional methods are often slow, non-specific and insensitive, and sometimes discriminate poorly among microbial species and strains. It is now known that the evolutionary ancestry and interrelationships of all living organisms can be reliably inferred from sequences in their genetic material. Highly conserved sequences characterise broad phylogenetic groups and variable sequences allow specific identification. Sequence-based methods combined with DNA amplification methods, such as the polymerase chain reaction (PCR), have led to powerful molecular identification techniques such as consensus nucleic acid amplification and representational difference analysis. These methods allow one to detect and isolate informative gene sequences from occult microbial pathogens in human tissues. Sequence-based methods are often quicker, more sensitive and more specific than traditional methods not only in detecting known microbial pathogens, but also in identifying previously-uncharacterised micro-organisms. Widespread, organised use of these methods will reveal new emerging microbial pathogens, implicate microbes in the aetiology of poorly-understood chronic inflammatory diseases and significantly expand our understanding of microbial diversity.

Humans↗
PubMed2005

Microbial incorporation of 13C-labeled acetate at the field scale: detection of microbes responsible for reduction of U(VI).

A field-scale acetate amendment experiment was performed in a contaminated aquifer at Old Rifle, CO to stimulate in situ microbial reduction of U(VI) in groundwater. To evaluate the microorganisms responsible for microbial uranium reduction during the experiment, 13C-labeled acetate was introduced into well bores via bio-traps containing porous activated carbon beads (Bio-Sep). Incorporation of the 13C from labeled acetate into cellular DNA and phospholipid fatty acid (PLFA) biomarkers was analyzed in parallel with geochemical parameters. An enrichment of active sigma-proteobacteria was demonstrated in downgradient monitoring wells: Geobacter dominated in wells closer to the acetate injection gallery, while various sulfate reducers were prominent in different downgradient wells. These results were consistent with the geochemical evidence of Fe(III), U(VI), and SO(4)2- reduction. PLFA profiling of bio-traps suspended in the monitoring wells also showed the incorporation of 13C into bacterial cellular lipids. Community composition of downgradient monitoring wells based on quinone and PLFA profiling was in general agreement with the 13C-DNA result. The direct application of 13C label to biosystems, coupled with DNA and PLFA analysis,

Acetates↗
PubMed2004

A rapid and automated fiber optic-based biosensor assay for the detection of Salmonella in spent irrigation water used in the sprouting of sprout seeds.

Recent outbreaks of foodborne illness have been linked to the consumption of contaminated sprouts. The spent irrigation water used to irrigate sprouts can carry many microorganisms, including pathogenic strains of Escherichia coli and Salmonella enterica. These pathogens are believed to originate from the seeds. The U.S. Food and Drug Administration recommends that sprout producers conduct microbiological testing of spent irrigation water from each production lot at least 48 h after seeds have germinated. Microbial analysis for the detection of Salmonella is labor-intensive and takes days to complete. A rapid and automated fiber-optic biosensor assay for the detection of Salmonella in sprout rinse water was developed in this study. Alfalfa seeds contaminated with various concentrations of Salmonella Typhimurium were sprouted. The spent irrigation water was assayed 67 h after alfalfa seed germination with the RAPTOR (Research International, Monroe, Wash.), an automated fiber optic-based detector. Salmonella Typhimurium could be positively identified in spent irrigation water when seeds were contaminated with 50 CFU/g. Viable Salmonella Typhimurium cells were also recovered from the waveguides after the assay. This biosensor assay system has the potential to be directly connected to water lines within the sprout-processing facility and to operate automatically, requiring manual labor only for preventative maintenance. Therefore, the presence of Salmonella Typhimurium in spent irrigation water could be continuously and rapidly detected 3 to 5 days before the completion of the sprouting process.

Biosensing Techniques↗
PubMed2004

Electronic noses and disease diagnostics.

Rapid developments in sensor technology have facilitated the production of devices--known as electronic noses--that can detect and discriminate the production profiles of volatile compounds from microbial infections in situ. Such qualitative and semi-quantitative approaches could have a significant role in the early diagnosis and detection of microbial diseases. Using artificial intelligence and web-based knowledge systems, electronic noses might also have a valuable role in monitoring disease epidemiology.

Biosensing Techniques↗
PubMed1977

New blood culture medium.

A growth medium with a specific oxidation-reduction potential containing peptone, dextrose, sodium succinate, sodium lactate, gelatin, sodium bicarbonate and blue tetrazolium, an indicator dye, in a tris(hydroxymethyl)aminomethane buffer was used to detect the presence of microorganisms in blood. The procedure involved the introduction of blood (and bacteria) into the growth medium with the dye in its colorless state. As the bacteria grew, they converted the dye to a visible blue color (formazan) with their reductases. The growth medium served as its own contamination control, since microbial growth and be detected by a color change before it was used for blood culture. The experiments described herein demonstrate that the composition of this medium (with the dye) provides a unique system that is able to make a reliable and rapid detection of both gram-positive and gram-negative microorganisms and yeasts (Candida albicans) commonly associated with bacteremia.

Bacteria↗
PubMed2003

Microbial and sensory quality of marinated and irradiated chicken.

Chicken legs were subjected to two pretreatments (packaged in air or marinated in natural plant extracts and then packaged in air) followed by irradiation (0, 3, or 5 kGy). The control and irradiated chicken legs were stored at 4 degrees C and underwent microbial analysis (mesophilic aerobic plate counts and Salmonella detection) and sensory evaluation at predetermined intervals. Microbial analysis indicated that irradiation had a significant effect (P < or = 0.05) on the mesophilic aerobic plate counts of the poultry. For each treatment, the bacterial growth decreased with an increase of irradiation dose. The marinade had an additive effect with irradiation in reducing bacterial growth and controlling proliferation during storage at 4 +/- 1 degree C. No Salmonella was observed until day 12 in marinated chicken irradiated at 3 kGy and for all experiments with chicken legs stored under air or marinated at 5 kGy. However, Salmonella was found in chicken legs irradiated at 3 kGy in air and in nonirradiated samples. The sensory evaluation indicated a significant (P < or = 0.05) difference in odor and flavor intensities between the irradiated chicken at 5 kGy and the control. No significant difference was found (P > 0.05) between the marinated chicken irradiated at 5 kGy and the control.

Animals↗
PubMed1993

Microbial DNA challenge studies of variable number tandem repeat (VNTR) probes used for DNA profiling analysis.

DNA probes commonly used for forensic DNA profiling analysis were hybridized to Hinfl digested DNA isolated from various common microbial species. Extended exposures to light sensitive film failed to detect any DNA fragments of a microbial origin following hybridizations to radio-labeled DNA insert single-locus probes (SLPs) and nonisotopically labeled oligonucleotide SLPs.

DNA Fingerprinting↗
PubMed2000

Profile of subgingival microbiota in children with mixed dentition.

A diversity of microbial species has been detected in children's oral flora at an early age. To investigate the composition of the subgingival microbiota of different groups of teeth in children with mixed dentition, 40 systemically healthy children, aged 7-8 years, randomly chosen, were examined. Subgingival plaque samples were taken from the mesiobuccal sites of 21, 41, 16 and 36 permanent teeth and 53, 73, 64 and 84 deciduous teeth. The samples were cultured for bacterial isolation anaerobically and in 10% CO2 plus air using selective and nonselective media. Forty-five different microbial species were isolated from both permanent and deciduous teeth. Streptococcus sanguis (79-70%), Streptococcus mitis (66-65%), Prevotella melaninogenica (51-57%), Eikenella corrodens (51-52%), Capnocytophaga gingivalis (46-34%), Capnocytophaga ochracea (45-45%), Actinomyces naeslundii (39-60%) and Prevotella intermedia (42-35%) were among the most frequently detected species in permanent and deciduous teeth respectively. Several suspected periodontal pathogens, such as Porphyromonas gingivalis, Prevotella loescheii, Campylobacter gracilis, Bacteroides forsythus, Campylobacter concisus, Peptostreptococcus micros and Selenomonas sputigena, albeit less frequently detected, were present in the microbiota of these children. The bacterial species Streptococcus constellatus, Peptostreptococcus micros, Pseudoramibacter alactolyticus, E. corrodens and Fusobacterium nucleatum were associated with non-bleeding permanent and deciduous teeth whereas Streptococcus intermedius, C. concisus, P. intermedia and P. loescheii were associated with bleeding.

Actinomyces↗
PubMed2026

Microbial signal profiles and organism-level concordance between plasma metagenomic sequencing and blood culture in suspected bloodstream infection.

Plasma metagenomic next-generation sequencing (mNGS) and blood culture detect different components of the microbial signal and frequently produce discordant organism reports. We characterized microbial signal class, report-derived burden, organism-level concordance, and independent clinical attribution in a retrospective, single-center, episode-level cohort. Among 329 episodes with evaluable plasma mNGS reports, 315 had blood culture performed; 232 were mNGS positive/culture negative and 53 were positive by both methods. In the 232 discordant episodes, the recorded routine-care diagnosis classified 124 as bloodstream infection (BSI) and 108 as non-BSI. Nonviral signals were present in 78.2% and 42.6%, respectively (P&#x2009;<&#x2009;0.001), and median maximum report-derived sequence counts were 98.5 and 11.5 (P&#x2009;<&#x2009;0.001). Two laboratory physicians then independently reviewed source records using structured criteria while masked to the recorded BSI label and mNGS organism and sequence-count information. Initial agreement for the five-category BSI assessment was 97.6% (Cohen's kappa, 0.960). Within the mNGS-positive/culture-negative subgroup, adjudicated BSI likelihood showed a modest ordinal association with report burden (Spearman rho&#x2009;=&#x2009;0.190; P&#x2009;=&#x2009;0.004), while mNGS organisms were considered supported in 1 episode, plausible in 158, unlikely or contaminant in 72, and unresolved in 1. Among 53 dual-positive episodes, 33 (62.3%) shared at least one species, but only 5 (9.4%) had complete species-set concordance. Plasma mNGS and blood culture therefore frequently generated non-equivalent organism sets. Signal class and report burden contributed graded contextual evidence, but organism-level attribution required clinical review and orthogonal microbiology rather than binary positivity alone.

Humans↗
PubMed2003

Market analysis of biosensors for food safety.

This paper is presented as an overview of the pathogen detection industry. The review includes pathogen detection markets and their prospects for the future. Potential markets include the medical, military, food, and environmental industries. Those industries combined have a market size of $563 million for pathogen detecting biosensors and are expected to grow at a compounded annual growth rate of 4.5%. The food market is further segmented into different food product industries. The overall food-pathogen testing market is expected to grow to $192 million and 34 million tests by 2005. The trend in pathogen testing emphasizes the need to commercialize biosensors for the food safety industry as legislation creates new standards for microbial monitoring. With quicker detection time and reusable features, biosensors will be important to those interested in real time diagnostics of disease causing pathogens. As the world becomes more concerned with safe food and water supply, the demand for rapid detecting biosensors will only increase.

Biological Assay↗
PubMed1975

BL-P1654: a bacteriostatic penicillin?

In tube dilution studies, large discrepancies between inhibitory and bactericidal concentrations of BL-P1654 against Pseudomonas were observed. To explain these discrepancies which were not observed with carbenicillin, the kinetics of bacterial killing by these two penicillins were evaluated and compared. The kinetics of bacterial killing by both antimicrobial agents were characteristic of a penicillin, with killing initiating simultaneously with growth. Kill curves revealed the presence of a small number of cells resistant to BL-P1654 which were not detectable macroscopically. Studies on microbial resistance also showed the presence of a small but consistent number of cells resistant to BL-P1654 over a broad range of concentrations above its minimal inhibitory concentration. This pattern of resistance was not observed with carbenicillin. Thus, the discrepancies between inhibitory and bactericidal concentrations of BL-P1654 were not due to any unusual bacteriostatic activity but rather due to a small number of resistant cells whose presence could be detected only by sensitive subculturing techniques.

Carbenicillin↗