Application of quantitative real-time PCR for rapid identification of Bacteroides fragilis group and related organisms in human wound samples

Our goal was to establish a quantitative real-time PCR (QRT-PCR) method to detect Bacteroides fragilis group and related organisms from clinical specimens. Compared to conventional anaerobic culture, QRT-PCR can provide accurate and more rapid detection and identification of B.?fragilis group and similar species. B.?fragilis group and related organisms are the most frequently isolated anaerobic pathogens from clinical samples. However, culture and phenotypic identification is quite time-consuming. We designed specific primers and probes based on the 16S rRNA gene sequences of Bacteroides caccae, Bacteroides eggerthii, B.?fragilis, Bacteroides ovatus, Bacteroides stercoris, Bacteroides thetaiotaomicron, Bacteroides uniformis, Bacteroides vulgatus, Odoribacter splanchnicus (Bacteroides splanchnicus), Parabacteroides distasonis (Bacteroides distasonis) and Parabacteroides merdae (Bacteroides merdae), and detected these species by means of QRT-PCR in 400 human surgical wound infection samples or closed abscesses. The target bacteria were detected from 31 samples (8%) by culture, but from 132 samples (33%) by QRT-PCR (p-value?相似文献   

The use of alkaline phosphatase-labelled oligonucleotide probes as culture confirmation reagents for the identification of commercially important bacteria

A range of rRNA-targeted alkaline phosphatase-labelled oligonucleotide probes was tested for use as culture confirmation reagents for the rapid identification of micro-organisms. The probes were specific to clinically important bacteria ( Helicobacter pylori and Mycobacterium tuberculosis ), fish and shellfish pathogens ( Renibacterium salmoninarum and Vibrio vulnificus ), food spoilage bacteria ( Listeria spp. and L. monocytogenes ), for bacteria of biotechnological importance ( Streptomyces spp.) and for bacteria associated with the oil industry (Sulphate-reducing bacteria, SRB). A universal bacterial probe and a eukaryotic probe were included in the study as positive and negative controls, respectively. A total of 93 bacterial strains was screened. With the exception of a large number of cross-reactions of the SRB probe (specificity value of 29·4%) and a single cross-reaction of the R. salmoninarum probe (specificity value of 97·7%), dot blot analysis indicated that each probe hybridized 100% specifically to the organisms tested. A simple culture confirmation method was then developed using these probes to enable the identification of bacterial colonies using a simple hybridization procedure.     

Expression of Endogenous RNA C-Type Virus Group-Specific Antigens in Mammalian Cells

Highly sensitive and specific radioimmunoassays are described for quantitation of the intraspecies determinants of several mammalian C-type viral group-specific (gs) antigens. An interspecies (gs-3) immunoassay has been developed which has both the broad reactivity and great sensitivity necessary for detection of C-type viruses where intraspecies gs assays are not available. By using these immunoassays, the expression of endogenous virus-specified gs antigens in mammalian cells of different species has been studied. Whereas mouse gs antigen was clearly detectable in tissue culture cells of several mouse strains, the respective gs antigens of rat, cat, Chinese hamster, woolly monkey, and gibbon ape were not detectable in cells of those species, using assays of comparable sensitivity. Thus, differences exist in the level of endogenous virus expression in cells of different mammalian species.     

The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools

Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.     

Development of real-time PCR assays for rapid detection of Pfiesteria piscicida and related dinoflagellates

Pfiesteria complex species are heterotrophic and mixotrophic dinoflagellates that have been recognized as harmful algal bloom species associated with adverse fish and human health effects along the East Coast of North America, particularly in its largest (Chesapeake Bay in Maryland) and second largest (Albermarle-Pamlico Sound in North Carolina) estuaries. In response to impacts on human health and the economy, monitoring programs to detect the organism have been implemented in affected areas. However, until recently, specific identification of the two toxic species known thus far, Pfiesteria piscicida and P. shumwayae (sp. nov.), required scanning electron microscopy (SEM). SEM is a labor-intensive process in which a small number of cells can be analyzed, posing limitations when the method is applied to environmental estuarine water samples. To overcome these problems, we developed a real-time PCR-based assay that permits rapid and specific identification of these organisms in culture and heterogeneous environmental water samples. Various factors likely to be encountered when assessing environmental samples were addressed, and assay specificity was validated through screening of a comprehensive panel of cultures, including the two recognized Pfiesteria species, morphologically similar species, and a wide range of other estuarine dinoflagellates. Assay sensitivity and sample stability were established for both unpreserved and fixative (acidic Lugol's solution)-preserved samples. The effects of background DNA on organism detection and enumeration were also explored, and based on these results, we conclude that the assay may be utilized to derive quantitative data. This real-time PCR-based method will be useful for many other applications, including adaptation for field-based technology.     

Conventional culture for water quality assessment: is there a future?

Conventional culture for the detection, enumeration and identification of micro-organisms has been the traditional tool of the microbiologist. It is, however, time-consuming and labour-intensive and confirmed results often require several days of analysis. Culture may not grow the organisms being sought and for enumeration may only detect a small proportion of the total population. However, it does have the advantage of being simple to use and relatively inexpensive. It is also a direct means of assessing cell viability. Novel fluorogenic dyes and fluorgenic and chromogenic substrates have overcome some of these problems by providing a means of rapid and specific detection and enumeration whilst removing the need for subculture and confirmation tests. Immunological tests such as ELISA have significantly reduced analysis time by providing specific target organism detection. Molecular techniques have removed the need for culture. Improvements in sensitivity, and removal of the inhibitory nature of sample matrices, have allowed analysts to detect low levels of micro-organisms but the questions of viability and comparability with cultural techniques still remain. Are we about to see a change of culture in water quality assessment, or can cultural techniques be developed that reduce analysis time to a few hours and can rapid methods be used for detecting the presence and viability of organisms?     

Immunoassay of infectious agents

Immunoassays have evolved for a broad range of applications since the pioneering work of Yalow and Berson who developed the first competitive radioimmunoassay (RIA) for human insulin in 1959. Immunoassay detection of specific antigens and host-produced antibodies directed against such antigens consitutes one of the most widely used and successful methods for diagnosing infectious diseases (IDs). The number and variety of new assay systems that are continually being developed reflect the increasing demand for immunoassays possessing greater sensitivity, speed, and ease of use. This trend has been driven, in part, by the need for improved immunodiagnostic systems to perform rapid testing and counter emerging IDs and biothreat (BT) agents. Another factor driving this trend is the need to integrate immunoassays with more sensitive nucleic acid-based methods for a comprehensive approach. Here we examine the development of immunoassays, some of the key formats used for the detection and identification of BT/ID agents, and the application of these technologies under different scenarios.     

Purification and immunochemical study of Plasmodium falciparum exoantigens

Plasmodium falciparum, in in vitro culture, elaborated many antigens including soluble exoantigens that are released into the culture medium. Anionic and cationic methods of isolating these antigens offer a great potential for large scale purification from medium that is rich in proteins but contains relatively low concentrations of P. falciparum specific antigens. These exoantigens have cationic and anionic dependent elution profiles (pI between 3.7 and 4.8). Five apparent molecular weight entities (58, 80, 145, 200, and 290 kdaltons) have been determined by GEDELISA. Susceptibility to lipase and to a proteolytic enzyme confirmed the proteinaceous nature of the antigens. They were isolated from 4 strains of different geographic origin, indicating their ubiquitous nature. The analogy of these exoantigens to circulating antigens in patients with acute malaria and their potential usefulness in immunodiagnosis and immunoprophylaxis are discussed.     

Fanconi's anemia: what have we learned from the genes so far?

Fanconi's anemia (FA) is a rare genetic disorder affecting children at an early age; patients suffer from progressive bone marrow failure and, in many cases, from congenital malformations. As cells from FA patients have an increased sensitivity to DNA-crosslinking agents, FA has been included among the group of DNA repair disorders. However, identification of a specific DNA repair defect in FA has not been firmly established. None the less, this cellular phenotype has allowed the classification of FA patients into eight complementation groups defining eight possible FA genes. Two of these genes have now been cloned and, although they have raised more questions than they have answered, are facilitating the identification of cellular processes implicated in the pathophysiology of FA, and the design of new therapies.     

Desulfovibrionales-related bacteria in a paper mill environment as detected with molecular techniques and culture

The aim of the present study was to evaluate the suitability of a nested PCR-DGGE (denaturing gradient gel electrophoresis) method for the detection of Desulfovibrionales-related sulfate-reducing bacteria (SRB) from paper mill samples. The samples were also analyzed with culturing. SRB cause/enhance industrial problems, namely creation of foul-smelling gases (hydrogen sulfide) and biological corrosion, and so far there has not been a simple method to study these bacteria in paper mill laboratories. In our study, culturing was able to detect Desulfovibrionales-related bacteria from two different white waters, two different brokes, pulp, clay, and slime. Out of the isolated Desulfovibrionales, 23 enrichment cultures were further characterized with Desulfovibrionales-selective PCR-DGGE. An identical Desulfovibrio species sequence was found from paper machine I (broke I, slime, and pulp) and from paper machine II (broke II and white water II), suggesting an in-house contamination with the same strain. Desulfovibrionales-selective PCR-DGGE was also performed from DNA templates extracted directly from the paper mill samples. The DGGE profiles derived from the samples without prior enrichment were more diverse and the sequenced amplicons proved to belong to the Desulfovibrionales order. Moreover, molecular techniques were able to detect Desulfovibrionales-related bacteria from calcium carbonate samples whereas culture did not. Altogether, the nested PCR-DGGE method used in this study was suitable for the detection of Desulfovibrionales-related SRB directly from different paper mill samples and it could be used for the rapid identification of SRB-contaminated industrial sites and, when combined with sequencing, for tracing of the contamination routes.     

The effect of ethanol on cell wall antigens ofSaccharomyces cerevisiae and specific isolation of high ethanol producing strains of this yeast,making use of a serological technique

Generally, natural isolates of high ethanol producingSaccharomyces cerevisiae obtained by screening are used in alcoholic industries. The methods involved in their isolation and identification are elaborate. Antigenic analysis using antibodies raised against wholeSaccharomyces cells indicated species specificity of cell wall surface thermostable antigens. By affinity purification, the specific antibodies could be obtained and used for specific isolation ofS. cerevisiae. Antigenic studies using antibodies raised against isolated cell walls of fermentatively grownS. cerevisiae indicated the occurrence of thermolabile antigens common toSaccharomyces species. Higher concentrations of these antigens could be detected in thoseS. cerevisiae that had the ability for high ethanol production. The concentrations of these cell wall common antigens increased with increasing culture age and ethanol accumulation in culture broths. In younger yeast cells, the concentration could be increased by growing the cells in a medium containing added ethanol. Using dilutions of cross absorbed antibody specific for common antigens and Ouchterlony test, high ethanol producingS. cerevisiae could be identified.     

Development of Real-Time PCR Assays for Rapid Detection of Pfiesteria piscicida and Related Dinoflagellates

Pfiesteria complex species are heterotrophic and mixotrophic dinoflagellates that have been recognized as harmful algal bloom species associated with adverse fish and human health effects along the East Coast of North America, particularly in its largest (Chesapeake Bay in Maryland) and second largest (Albermarle-Pamlico Sound in North Carolina) estuaries. In response to impacts on human health and the economy, monitoring programs to detect the organism have been implemented in affected areas. However, until recently, specific identification of the two toxic species known thus far, Pfiesteria piscicida and P. shumwayae (sp. nov.), required scanning electron microscopy (SEM). SEM is a labor-intensive process in which a small number of cells can be analyzed, posing limitations when the method is applied to environmental estuarine water samples. To overcome these problems, we developed a real-time PCR-based assay that permits rapid and specific identification of these organisms in culture and heterogeneous environmental water samples. Various factors likely to be encountered when assessing environmental samples were addressed, and assay specificity was validated through screening of a comprehensive panel of cultures, including the two recognized Pfiesteria species, morphologically similar species, and a wide range of other estuarine dinoflagellates. Assay sensitivity and sample stability were established for both unpreserved and fixative (acidic Lugol's solution)-preserved samples. The effects of background DNA on organism detection and enumeration were also explored, and based on these results, we conclude that the assay may be utilized to derive quantitative data. This real-time PCR-based method will be useful for many other applications, including adaptation for field-based technology.     

Mercury methylation independent of the acetyl-coenzyme A pathway in sulfate-reducing bacteria

Sulfate-reducing bacteria (SRB) in anoxic waters and sediments are the major producers of methylmercury in aquatic systems. Although a considerable amount of work has addressed the environmental factors that control methylmercury formation and the conditions that control bioavailability of inorganic mercury to SRB, little work has been undertaken analyzing the biochemical mechanism of methylmercury production. The acetyl-coenzyme A (CoA) pathway has been implicated as being key to mercury methylation in one SRB strain, Desulfovibrio desulfuricans LS, but this result has not been extended to other SRB species. To probe whether the acetyl-CoA pathway is the controlling biochemical process for methylmercury production in SRB, five incomplete-oxidizing SRB strains and two Desulfobacter strains that do not use the acetyl-CoA pathway for major carbon metabolism were assayed for methylmercury formation and acetyl-CoA pathway enzyme activities. Three of the SRB strains were also incubated with chloroform to inhibit the acetyl-CoA pathway. So far, all species that have been found to have acetyl-CoA activity are complete oxidizers that require the acetyl-CoA pathway for basic metabolism, as well as methylate mercury. Chloroform inhibits Hg methylation in these species either by blocking the methylating enzyme or by indirect effects on metabolism and growth. However, we have identified four incomplete-oxidizing strains that clearly do not utilize the acetyl-CoA pathway either for metabolism or mercury methylation (as confirmed by the absence of chloroform inhibition). Hg methylation is thus independent of the acetyl-CoA pathway and may not require vitamin B(12) in some and perhaps many incomplete-oxidizing SRB strains.     

Antigenic similarity among Anabaena azollae separated from different species of Azolla

Direct fluorescent antibody (FA) reaction results of 5 FAs against symbiotic Anabaena azollae indicated that all the A. azollae freshly separated from 32 specimens of Azolla collected worldwide (belonging to 6 different species) shared identical and highly specific antigens. None of these FAs exhibited cross-reaction with any of the free-living blue-green algae tested. FA absorption results confirmed these results and also indicate the existence of cross-reactive antigens between Azolla leaves and the surfaces of A. azollae. Antibodies made against free-living A. azollae did not cross-react with any of the symbiotic A. azollae indicating either: (i) these isolates are not true isolates, or (ii) their antigenic properties were altered during isolation and culturing. Such possibilities and their implications are discussed.     

Research on marine actinobacteria in India

Marine actinobacteriology is one of the major emerging areas of research in tropics. Marine actinobacteria occur on the sediments and in water and also other biomass (mangrove) and substrates (animal). These organisms are gaining importance not only for their taxonomic and ecological perspectives, but also for their unique metabolites and enzymes. Many earlier studies on these organisms were confined only to the temperate regions. In tropical environment, investigations on them have gained importance only in the last two decades. So far, from the Indian peninsula, 41 species of actinobacteria belonging to 8 genera have been recorded. The genus, Streptomyces of marine origin has been more frequently recorded. Of 9 maritime states of India, only 4 have been extensively covered for the study of marine actinobacteria. Most of the studies conducted pertain to isolation, identification and maintenance of these organisms in different culture media. Further, attention has been focused on studying their antagonistic properties against different pathogens. Their biotechnological potentials are yet to be fully explored.     

Identification of Actinomyces israelii and Actinomyces naeslundii by Fluorescent-Antibody and Agar-Gel Diffusion Techniques

This study was an attempt to develop a fluorescent-antibody (FA) test to differentiate Actinomyces israelii and A. naeslundii as an aid in their laboratory identification. Two strains of A. israelii (X522 and A601) and two strains of A. naeslundii (X454 and X600), which had received intensive study by several investigators, were used for the immunization of rabbits. Working titers, based on tests with antigens prepared from the homologous strains and from well-established heterologous strains, were determined for each labeled antibody preparation. These conjugates and their normal serum control conjugates were used separately to stain 85 cultures of Actinomyes species and 23 strains of other species that might be confused with them. Acetone-precipitated soluble antigens from these same strains were tested with different antisera in the agar-gel diffusion test. Results showed that A. israelii (X522 and A601) and A. naeslundii (X454 and X600) labeled antiglobulins, when used at their working titers, stained most strains of their homologous species. Agar-gel diffusion results showed general agreement with those of the FA tests. The two tests appear to be equal in sensitivity, but the FA test is more specific, since several cross-reactions were noted with the agar-gel diffusion test whereas no cross-reactions were obtained with the FA reagents. Agar-gel and FA studies suggest that at least two serotypes of A. israelii may be associated with human disease. Although the majority of strains tested in this study appear to belong to a common serotype, "serotype 1," two strains of an apparent second serotype, "serotype 2," were encountered. FA staining of tissue impression smears from experimentally infected mice was successful when a counterstain, Evans Blue dye, was used.     

Mercury Methylation Independent of the Acetyl-Coenzyme A Pathway in Sulfate-Reducing Bacteria

Sulfate-reducing bacteria (SRB) in anoxic waters and sediments are the major producers of methylmercury in aquatic systems. Although a considerable amount of work has addressed the environmental factors that control methylmercury formation and the conditions that control bioavailability of inorganic mercury to SRB, little work has been undertaken analyzing the biochemical mechanism of methylmercury production. The acetyl-coenzyme A (CoA) pathway has been implicated as being key to mercury methylation in one SRB strain, Desulfovibrio desulfuricans LS, but this result has not been extended to other SRB species. To probe whether the acetyl-CoA pathway is the controlling biochemical process for methylmercury production in SRB, five incomplete-oxidizing SRB strains and two Desulfobacter strains that do not use the acetyl-CoA pathway for major carbon metabolism were assayed for methylmercury formation and acetyl-CoA pathway enzyme activities. Three of the SRB strains were also incubated with chloroform to inhibit the acetyl-CoA pathway. So far, all species that have been found to have acetyl-CoA activity are complete oxidizers that require the acetyl-CoA pathway for basic metabolism, as well as methylate mercury. Chloroform inhibits Hg methylation in these species either by blocking the methylating enzyme or by indirect effects on metabolism and growth. However, we have identified four incomplete-oxidizing strains that clearly do not utilize the acetyl-CoA pathway either for metabolism or mercury methylation (as confirmed by the absence of chloroform inhibition). Hg methylation is thus independent of the acetyl-CoA pathway and may not require vitamin B₁₂ in some and perhaps many incomplete-oxidizing SRB strains.     

Rapid Identification and Typing of Herpes Simplex Virus Types 1 and 2 by a Direct Immunofluorescence Technique

An immunofluorescence (FA) technique has been developed which can identify herpes simplex virus (HSV) in clinical specimens and also type the virus directly as type 1 or type 2. This test, first applied to cervicovaginal specimens obtained from 80 mice genitally inoculated with HSV, indicated a sensitivity approaching 80% in comparison to standard viral isolation methods. A similar sensitivity was found when the test was applied to 185 clinical specimens with adequate cells for staining, which were obtained from a variety of sites of patients with suspect herpetic infection. In only 1 of 6 specimens positive by both FA and culture methods was the HSV type wrongly identified by the FA technique. There were also six specimens which were negative by culture methods but positive by the FA test, indicating a specificity of 91%. It is likely that these are not instances of false-positive tests but of other factors which may have resulted in negative viral isolations by culture methods. As more specific reagents become available, it is anticipated that the FA technique will have wider usage in diagnostic laboratories for the identification and typing of HSV types 1 and 2.     

Effects of Bacillus thuringiensis var. israelensis on Target and Nontarget Organisms: a Review of Laboratory and Field Experiments

Since the discovery of Bacillus thuringiensis var. israelensis (Bti) in 1976, extensive literature has proved its efficacy to control mosquitoes and black flies, of which many species are known as important vectors of diseases or simply as pests of humans and animals. Since 1978, Bti has been used in many countries on all continents and numerous studies have been made on target mosquitoes and black flies, as well as nontarget organisms (NTO). This review analyses the results of 75 studies on these organisms covering approximately 125 families, 300 genera and 400 species. Different factors such as species, instar, feeding behaviour and environmental parameters (larval density, water temperature, suspended matter etc.) may drastically affect the efficacy of the Bti products. This is addressed in detail by reviewing the main factors affecting mosquitoes as well as black flies. The results of a wide range of laboratory and field experiments using different target and nontarget species, various preparations and formulations of Bti and different biotic or abiotic factors are present in the literature, making the data difficult to compare on a common basis. Our analysis shows that, under different application conditions, the effects of Bti on target and nontarget organisms may be hard to predict. Although Bti has been proclaimed to be relatively highly specific, some studies show that some NTO are affected either by single or repeated Bti treatments. Present use against black flies seems ecologically acceptable. High frequencies of application and/or overdosages against mosquitoes may result in some persistence of the toxin crystals and ultimately this may have adverse effects on the food web. A long-term study (published in 1998) in mosquito habitats has shown that intensive Bti treatments over three years did in fact produce an impact on the food web in wetlands. This raises questions, for the first time, on Bti environmental specificity. The importance of this impact is discussed and the alternatives for practical pest control are considered. Some modifications of Bti use against mosquitoes, guided by research, is probably the best of these alternatives.     

Manipulation of dietary lipids, fatty acids and vitamins in zooplankton cultures

1. A wide range of species that are cultivated in commercial mariculture are planktonic during at least part of their life cycle; for example, the larval stages of shellfish (shrimp and molluscs) and the live feeds (rotifers, brine shrimp, copepods) used in the larviculture of marine fish and shellfish. Over the last decades various techniques have been developed to deliver nutrients to these zooplanktonic organisms either through artificial diets or by manipulating the composition of the live prey fed to the carnivorous stages. This paper reviews the methodology that has allowed aquaculturists to gain knowledge of nutritional requirements and may offer interesting opportunities for ecologists to verify the importance of key nutrients in the natural food chain of marine as well as freshwater ecosystems.
2. Live micro-algae can be replaced partially or completely in the diet of filter-feeders such as rotifers, Artemia , shrimp larvae and bivalves, by various types of preserved algae, micro-encapsulated diets and yeast-based diets, whereas lipid emulsions and liposomes may be utilized to supplement specific lipid-and water-soluble nutrients, respectively. Microbound and micro-encapsulated diets have been designed to supplement live feed in the culture of micro-predators such as fish and shrimp larvae.
3. Live prey organisms, in particular rotifers and Artemia , can be 'bio-encapsulated' with a variety of enrichment diets to manipulate their content in certain nutrients, including ω3 highly unsaturated fatty acids (FA) and the vitamins C, A and E. Nevertheless, the enrichment techniques are not applicable for all nutrients and prey organisms. Phospholipid composition is difficult to manipulate through the diet of live feed and the enrichment of the essential FA docosahexaenoic acid (DHA) is hampered in most Artemia species due to the catabolism of this FA following enrichment.