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Sample records for bds bacterial detection

  1. An Optimized Method to Detect BDS Satellites' Orbit Maneuvering and Anomalies in Real-Time.

    Science.gov (United States)

    Huang, Guanwen; Qin, Zhiwei; Zhang, Qin; Wang, Le; Yan, Xingyuan; Wang, Xiaolei

    2018-02-28

    The orbital maneuvers of Global Navigation Satellite System (GNSS) Constellations will decrease the performance and accuracy of positioning, navigation, and timing (PNT). Because satellites in the Chinese BeiDou Navigation Satellite System (BDS) are in Geostationary Orbit (GEO) and Inclined Geosynchronous Orbit (IGSO), maneuvers occur more frequently. Also, the precise start moment of the BDS satellites' orbit maneuvering cannot be obtained by common users. This paper presented an improved real-time detecting method for BDS satellites' orbit maneuvering and anomalies with higher timeliness and higher accuracy. The main contributions to this improvement are as follows: (1) instead of the previous two-steps method, a new one-step method with higher accuracy is proposed to determine the start moment and the pseudo random noise code (PRN) of the satellite orbit maneuvering in that time; (2) BDS Medium Earth Orbit (MEO) orbital maneuvers are firstly detected according to the proposed selection strategy for the stations; and (3) the classified non-maneuvering anomalies are detected by a new median robust method using the weak anomaly detection factor and the strong anomaly detection factor. The data from the Multi-GNSS Experiment (MGEX) in 2017 was used for experimental analysis. The experimental results and analysis showed that the start moment of orbital maneuvers and the period of non-maneuver anomalies can be determined more accurately in real-time. When orbital maneuvers and anomalies occur, the proposed method improved the data utilization for 91 and 95 min in 2017.

  2. Inertial Aided Cycle-slip Detection and Repair for BDS Triple-frequency Signal in Severe Multipath Environment

    Directory of Open Access Journals (Sweden)

    NING Yipeng

    2017-05-01

    Full Text Available Inertial information has been proposed to improve the success rate and repair rate for BDS triple-frequency cycle-slip detection in severe environment with multipath effects.At the same time, a BDS/INS loose coupled model has been developed. An innovative INS aided BDS triple-frequency combination method was developed which based on the traditional method of code-phase combination and geometry-free linear combination. The INS aided cycle-slip detection monitoring value was established and the effect of INS positioning error on cycle-slip capacity was analyzed. The proposed method overcomes the shortcoming of cycle-slip detection capacity influenced by the pseudorange observation precision. It also realizes small cycle-slips detection for BDS in severe multipath effects environment. At last, a field test was analysised with INS/BDS triple-frequency integrated positioning system onboard. The results indicate that the method proposed in this paper shows a high cycle-slip detection success rate and repair rate, when traditional triple-frequency detection model losed efficacy above water surface with multipath effects, and it also can be effective in low frequency sampling data.

  3. A New Real-Time Cycle Slip Detection and Repair Method under High Ionospheric Activity for a Triple-Frequency GPS/BDS Receiver

    Directory of Open Access Journals (Sweden)

    Wanke Liu

    2018-02-01

    Full Text Available Cycle slip detection and repair is a prerequisite for high-precision global navigation satellite system (GNSS-based positioning. With the modernization and development of GNSS systems, more satellites are available to transmit triple-frequency signals, which allows the introduction of additional linear combinations and provides new opportunities for cycle slip detection and repair. In this paper, we present a new real-time cycle slip detection and repair method under high ionospheric activity for undifferenced Global Positioning System (GPS/BeiDou Navigation Satellite System (BDS triple-frequency observations collected with a single receiver. First, three optimal linearly independent geometry-free pseudorange minus phase combinations are selected to correctly and uniquely determine the cycle slips on the original triple-frequency carrier phase observations. Then, a second-order time-difference algorithm is employed for the pseudorange minus phase combinations to mitigate the impact of between-epoch ionospheric residuals on cycle slip detection, which is especially beneficial under high ionospheric activity. The performance of the approach is verified with static GPS/BDS triple-frequency observations that are collected with a 30 s sampling interval under active ionospheric conditions, and observations are manually inserted with simulated cycle slips. The results show that the method can correctly detect and repair cycle slips at a resolution as small as 1 cycle. Moreover, kinematic data collected from car-driven and airborne experiments are also processed to verify the performance of the method. The experimental results also demonstrate that the method is effective in processing kinematic data.

  4. A New Real-Time Cycle Slip Detection and Repair Method under High Ionospheric Activity for a Triple-Frequency GPS/BDS Receiver.

    Science.gov (United States)

    Liu, Wanke; Jin, Xueyuan; Wu, Mingkui; Hu, Jie; Wu, Yun

    2018-02-01

    Cycle slip detection and repair is a prerequisite for high-precision global navigation satellite system (GNSS)-based positioning. With the modernization and development of GNSS systems, more satellites are available to transmit triple-frequency signals, which allows the introduction of additional linear combinations and provides new opportunities for cycle slip detection and repair. In this paper, we present a new real-time cycle slip detection and repair method under high ionospheric activity for undifferenced Global Positioning System (GPS)/BeiDou Navigation Satellite System (BDS) triple-frequency observations collected with a single receiver. First, three optimal linearly independent geometry-free pseudorange minus phase combinations are selected to correctly and uniquely determine the cycle slips on the original triple-frequency carrier phase observations. Then, a second-order time-difference algorithm is employed for the pseudorange minus phase combinations to mitigate the impact of between-epoch ionospheric residuals on cycle slip detection, which is especially beneficial under high ionospheric activity. The performance of the approach is verified with static GPS/BDS triple-frequency observations that are collected with a 30 s sampling interval under active ionospheric conditions, and observations are manually inserted with simulated cycle slips. The results show that the method can correctly detect and repair cycle slips at a resolution as small as 1 cycle. Moreover, kinematic data collected from car-driven and airborne experiments are also processed to verify the performance of the method. The experimental results also demonstrate that the method is effective in processing kinematic data.

  5. Precise Positioning of BDS, BDS/GPS: Implications for Tsunami Early Warning in South China Sea

    Directory of Open Access Journals (Sweden)

    Kejie Chen

    2015-11-01

    Full Text Available Global Positioning System (GPS has been proved to be a powerful tool for measuring co-seismic ground displacements with an application to seismic source inversion. Whereas most of the tsunamis are triggered by large earthquakes, GPS can contribute to the tsunami early warning system (TEWS by helping to obtain tsunami source parameters in near real-time. Toward the end of 2012, the second phase of the BeiDou Navigation Satellite System (BDS constellation was accomplished, and BDS has been providing regional positioning service since then. Numerical results indicate that precision of BDS nowadays is equivalent to that of the GPS. Compared with a single Global Satellite Navigation System (GNSS, combined BDS/GPS real-time processing can improve accuracy and especially reliability of retrieved co-seismic displacements. In the present study, we investigate the potential of BDS to serve for the early warning system of tsunamis in the South China Sea region. To facilitate early warnings of tsunamis and forecasting capabilities in this region, we propose to distribute an array of BDS-stations along the Luzon Island (Philippines. By simulating an earthquake with Mw = 8 at the Manila trench as an example, we demonstrate that such an array will be able to detect earthquake parameters in real time with a high degree of accuracy and, hence, contribute to the fast and reliable tsunami early warning system in this region.

  6. Radiometric detection of bacterial metabolism

    International Nuclear Information System (INIS)

    Camargo, E.E.; Wagner Junior, H.N.

    1979-01-01

    The measurement of 14 CO 2 produced by the bacterial oxidation of labelled compounds is discussed as a means of evaluating the bacterial metabolism. The following items are discussed:automated radiometric detection, types of graphs, clinical applications of the radiometric system and influential factors. Complementary studies on bacterial assimilation of substances are presented. (M.A.) [pt

  7. A Geometry-Based Cycle Slip Detection and Repair Method with Time-Differenced Carrier Phase (TDCP for a Single Frequency Global Position System (GPS + BeiDou Navigation Satellite System (BDS Receiver

    Directory of Open Access Journals (Sweden)

    Chuang Qian

    2016-12-01

    Full Text Available As the field of high-precision applications based on carriers continues to expand, the development of low-cost, small, modular receivers and their application in diverse scenarios and situations with complex data quality has increased the requirements of carrier-phase data preprocessing. A new geometry-based cycle slip detection and repair method based on Global Position System (GPS + BeiDou Navigation Satellite System (BDS is proposed. The method uses a Time-differenced Carrier Phase (TDCP model, which eliminates the Inner-System Bias (ISB between GPS and BDS, and it is conducive to the effective combination of GPS and BDS. It avoids the interference of the noise of the pseudo-range with cycle slip detection, while the cycle slips are preserved as integers. This method does not limit the receiver frequency number, and it is applicable to single-frequency data. The process is divided into two steps to detect and repair cycle slip. The first step is cycle slip detection, using the Improved Local Analysis Method (ILAM to find satellites that have cycle slips; The second step is to repair the cycle slips, including estimating the float solution of changes in ambiguities at the satellites that have cycle slips with the least squares method and the integer solution of the cycle slips by rounding. In the process of rounding, in addition to the success probability, a decimal test is carried out to validate the result. Finally, experiments with filed test data are carried out to prove the effectiveness of this method. The results show that the detectable cycle slips number with GPS + BDS is much greater than that with GPS. The method can also detect the non-integer outliers while fixing the cycle slip. The maximum decimal bias in repair is less than that with GPS. It implies that this method takes full advantages of multi-system.

  8. A Geometry-Based Cycle Slip Detection and Repair Method with Time-Differenced Carrier Phase (TDCP) for a Single Frequency Global Position System (GPS) + BeiDou Navigation Satellite System (BDS) Receiver.

    Science.gov (United States)

    Qian, Chuang; Liu, Hui; Zhang, Ming; Shu, Bao; Xu, Longwei; Zhang, Rufei

    2016-12-05

    As the field of high-precision applications based on carriers continues to expand, the development of low-cost, small, modular receivers and their application in diverse scenarios and situations with complex data quality has increased the requirements of carrier-phase data preprocessing. A new geometry-based cycle slip detection and repair method based on Global Position System (GPS) + BeiDou Navigation Satellite System (BDS) is proposed. The method uses a Time-differenced Carrier Phase (TDCP) model, which eliminates the Inner-System Bias (ISB) between GPS and BDS, and it is conducive to the effective combination of GPS and BDS. It avoids the interference of the noise of the pseudo-range with cycle slip detection, while the cycle slips are preserved as integers. This method does not limit the receiver frequency number, and it is applicable to single-frequency data. The process is divided into two steps to detect and repair cycle slip. The first step is cycle slip detection, using the Improved Local Analysis Method (ILAM) to find satellites that have cycle slips; The second step is to repair the cycle slips, including estimating the float solution of changes in ambiguities at the satellites that have cycle slips with the least squares method and the integer solution of the cycle slips by rounding. In the process of rounding, in addition to the success probability, a decimal test is carried out to validate the result. Finally, experiments with filed test data are carried out to prove the effectiveness of this method. The results show that the detectable cycle slips number with GPS + BDS is much greater than that with GPS. The method can also detect the non-integer outliers while fixing the cycle slip. The maximum decimal bias in repair is less than that with GPS. It implies that this method takes full advantages of multi-system.

  9. A Geometry-Based Cycle Slip Detection and Repair Method with Time-Differenced Carrier Phase (TDCP) for a Single Frequency Global Position System (GPS) + BeiDou Navigation Satellite System (BDS) Receiver

    OpenAIRE

    Qian, Chuang; Liu, Hui; Zhang, Ming; Shu, Bao; Xu, Longwei; Zhang, Rufei

    2016-01-01

    As the field of high-precision applications based on carriers continues to expand, the development of low-cost, small, modular receivers and their application in diverse scenarios and situations with complex data quality has increased the requirements of carrier-phase data preprocessing. A new geometry-based cycle slip detection and repair method based on Global Position System (GPS) + BeiDou Navigation Satellite System (BDS) is proposed. The method uses a Time-differenced Carrier Phase (TDCP...

  10. Molecular detection of human bacterial pathogens

    National Research Council Canada - National Science Library

    Liu, Dongyou

    2011-01-01

    .... Molecular Detection of Human Bacterial Pathogens addresses this issue, with international scientists in respective bacterial pathogen research and diagnosis providing expert summaries on current...

  11. Microconductometric Detection of Bacterial Contamination

    Directory of Open Access Journals (Sweden)

    Sarra EL ICHI

    2014-05-01

    Full Text Available Several approaches can be used for the electrochemical detection of bacterial contamination. Their performance can be assessed by the ability to detect bacteria at very low concentrations within a short-time response. We have already demonstrated that a conductometric biosensor based on interdigitated thin-film electrodes is adapted to detect bacteria in clinical samples like serum and compatible with microfluidic fabrication. The type of interdigitated microelectrodes influences the performance of the biosensor. This was shown by the results obtained in this work. A magnetic-nanoparticles based immunosensor was designed using gold screen-printed electrodes. The immunosensor was able to specifically detect E. coli in the range of 1-103 CFU mL-1. The new transducer offered a larger active sensing surface with a lower cost and a robust material. Accuracy of the conductance value was enhanced by differential measurements. The immunosensor is compatible with a microfluidic system.

  12. The eukaryotic enzyme Bds1 is an alkyl but not an aryl sulfohydrolase.

    Science.gov (United States)

    Waddell, Grace L; Gilmer, Caroline R; Taylor, Nicholas G; Reveral, John Randolf S; Forconi, Marcello; Fox, Jennifer L

    2017-09-16

    The eukaryotic enzyme Bds1 in Saccharomyces cerevisiae is a metallo-β-lactamase-related enzyme evolutionarily originating from bacterial horizontal gene transfer that serves an unknown biological role. Previously, Bds1 was reported to be an alkyl and aryl sulfatase. However, we demonstrate here that Bds1 acts on primary alkyl sulfates (of 6-12 carbon atoms) but not the aryl sulfates p-nitrophenyl sulfate and p-nitrocatechol sulfate. The apparent catalytic rate constant for hydrolysis of the substrate 1-hexyl sulfate by Bds1 is over 100 times lower than that of the reaction catalyzed by its bacterial homolog SdsA1. We show that Bds1 shares a catalytic mechanism with SdsA1 in which the carbon atom of the sulfate ester is the subject of nucleophilic attack, rather than the sulfur atom, resulting in C-O bond lysis. In contrast to SdsA1 and another bacterial homolog with selectivity for secondary alkyl sulfates named Pisa1, Bds1 does not show any substantial activity towards secondary alkyl sulfates. Neither Bds1 nor SdsA1 have any significant activity towards a branched primary alkyl sulfate, primary and secondary steroid sulfates, or phosphate diesters. Therefore, the enzymes homologous to SdsA1 that have been identified and characterized thus far vary in their selectivity towards primary and secondary alkyl sulfates but do not exhibit aryl sulfatase activity. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Biosensors for Whole-Cell Bacterial Detection

    Science.gov (United States)

    Rushworth, Jo V.; Hirst, Natalie A.; Millner, Paul A.

    2014-01-01

    SUMMARY Bacterial pathogens are important targets for detection and identification in medicine, food safety, public health, and security. Bacterial infection is a common cause of morbidity and mortality worldwide. In spite of the availability of antibiotics, these infections are often misdiagnosed or there is an unacceptable delay in diagnosis. Current methods of bacterial detection rely upon laboratory-based techniques such as cell culture, microscopic analysis, and biochemical assays. These procedures are time-consuming and costly and require specialist equipment and trained users. Portable stand-alone biosensors can facilitate rapid detection and diagnosis at the point of care. Biosensors will be particularly useful where a clear diagnosis informs treatment, in critical illness (e.g., meningitis) or to prevent further disease spread (e.g., in case of food-borne pathogens or sexually transmitted diseases). Detection of bacteria is also becoming increasingly important in antibioterrorism measures (e.g., anthrax detection). In this review, we discuss recent progress in the use of biosensors for the detection of whole bacterial cells for sensitive and earlier identification of bacteria without the need for sample processing. There is a particular focus on electrochemical biosensors, especially impedance-based systems, as these present key advantages in terms of ease of miniaturization, lack of reagents, sensitivity, and low cost. PMID:24982325

  14. Bacteriophages for detection of bacterial pathogens

    International Nuclear Information System (INIS)

    Kutateladze, M.

    2009-01-01

    The G. Eliava Institute of Bacteriophages, Microbiology and Virology (Tbilisi, Georgia) is one of the most famous institutions focused on bacteriophage research for the elaboration of appropriate phage methodologies for human and animal protection. The main direction of the institute is the study and production of bacteriophages against intestinal disorders (dysentery, typhoid, intesti) and purulent-septic infections (staphylococcus, streptococcus, pyophage, etc.). These preparations were successfully introduced during the Soviet era, and for decades were used throughout the former Soviet Union and in other Socialist countries for the treatment, prophylaxis, and diagnosis of various infectious diseases, including those caused by antibiotic-resistant bacterial strains. Bacteriophages were widely used for identifying and detecting infections caused by the most dangerous pathogens and causative agents of epidemiological outbreaks. The specific topic of this presentation is the phage typing of bacterial species, which can be an important method for epidemiological diagnostics. Together with different genetic methodologies - such as PCR-based methods, PFGE, plasmid fingerprinting, and ribosomal typing - phage typing is one method for identifying bacterial pathogens. The method has a high percentage of determination of phage types, high specificity of reaction, and is easy for interpretation and use by health workers. Phage typing was applied for inter-species differentiation of different species of Salmonella, S. typhi, Brucella spp, Staphylococcus aureus, E. col,i Clostridium deficile, Vibrio cholerae, Yersinia pestis, Yersinia enterocolitica, Lysteria monocytogenes, Clostridium perfringens, Clostridium tetani, plant pathogens, and other bacterial pathogens. In addition to addressing the utility and efficacy of phage typing, the paper will discuss the isolation and selection of diagnostic typing phages for interspecies differentiation of pathogens that is necessary

  15. Modeling Business Development Services (BDS) in the Tanzania ...

    African Journals Online (AJOL)

    These include services that will guide them to innovations, customer satisfaction, business strategies and awareness. The second objective is to examine the extent to which BDS supply-side factors influence the successful provision of BDS. Here, the study hypothesized that factors on the supply-side (i.e., creativity and ...

  16. The BDS iGMAS RIOS station at Observatório Nacional, Rio de Janeiro

    Science.gov (United States)

    Humberto Andrei, Alexandre; Song, Shuli; Junqueira, Selma; Beauvalet, Laurene

    2016-07-01

    position of the satellites by analyzing the pseudo-ranges obtained by C1W code for GPS, and C7I code for BDS. Using the Allan variation a crucial result is obtained. It is shown that the BDS system can perform at the level of the GPS system, provided equal satellite coverage. On the other hand at the Observatório Nacional it is detected a near constant bias of about 35m between the ranges simultaneously derived from the RIOS (iGMAS) and RJEP (GNSS) stations, no matter the observed satellite, or constellation. Both results are presented and discussed. We also present the current status of the installation of a second BDS iGMAS station, in a northern, equatorial location in Brazil. The operational and scientific perspectives are disclosed.

  17. Bacterial contamination of platelet concentrates: pathogen detection and inactivation methods

    Directory of Open Access Journals (Sweden)

    Dana Védy

    2009-04-01

    Full Text Available Whereas the reduction of transfusion related viral transmission has been a priority during the last decade, bacterial infection transmitted by transfusion still remains associated to a high morbidity and mortality, and constitutes the most frequent infectious risk of transfusion. This problem especially concerns platelet concentrates because of their favorable bacterial growth conditions. This review gives an overview of platelet transfusion-related bacterial contamination as well as on the different strategies to reduce this problem by using either bacterial detection or inactivation methods.

  18. Sensitive Detection of Deliquescent Bacterial Capsules through Nanomechanical Analysis.

    Science.gov (United States)

    Nguyen, Song Ha; Webb, Hayden K

    2015-10-20

    Encapsulated bacteria usually exhibit strong resistance to a wide range of sterilization methods, and are often virulent. Early detection of encapsulation can be crucial in microbial pathology. This work demonstrates a fast and sensitive method for the detection of encapsulated bacterial cells. Nanoindentation force measurements were used to confirm the presence of deliquescent bacterial capsules surrounding bacterial cells. Force/distance approach curves contained characteristic linear-nonlinear-linear domains, indicating cocompression of the capsular layer and cell, indentation of the capsule, and compression of the cell alone. This is a sensitive method for the detection and verification of the encapsulation status of bacterial cells. Given that this method was successful in detecting the nanomechanical properties of two different layers of cell material, i.e. distinguishing between the capsule and the remainder of the cell, further development may potentially lead to the ability to analyze even thinner cellular layers, e.g. lipid bilayers.

  19. Detecting Nosocomial Intrinsic Infections through Relating Bacterial ...

    African Journals Online (AJOL)

    Sierra Leone Journal of Biomedical Research ... Surgical procedures often lead to both intrinsic and extrinsic infections. ... This study demonstrated surgical procedures as precursory to intrinsic infections and that bacterial pathogens found on wounds and endogenous indicators of surgery are links to intrinsic infection.

  20. Evaluation of GPS/BDS indoor positioning performance and enhancement

    DEFF Research Database (Denmark)

    He, Zhe; Petovello, Mark; Pei, Ling

    2017-01-01

    This paper assesses the potential of using BDS and GPS signals to position in challenged environments such as indoors. Traditional assisted GNSS approaches that use code phase as measurements (i.e., coarse-time solutions) are shown to be prone to multipath and noise. An enhanced approach that has...... superior sensitivity and positioning performance—the so-called direct positioning receiver architecture—has been implemented and evaluated using live indoor BDS and/or GPS signals. Real indoor experiments have been conducted in Shanghai and significant improvement has been observed with enhanced approaches......: results with BDS constellation show better horizontal positioning performance (biases are less than 10m) than using GPS alone, but are slightly worse in the vertical axis; when using the enhanced approach with BDS and GPS, both horizontal and vertical axes show promising results for the environments...

  1. Illuminating the detection chain of bacterial bioreporters

    NARCIS (Netherlands)

    Meer, J.R. van der; Tropel, D.; Jaspers, M.

    2004-01-01

    Engineering bacteria for measuring chemicals of environmental or toxicological concern (bioreporter bacteria) has grown slowly into a mature research area. Despite many potential advantages, current bioreporters do not perform well enough to comply with environmental detection standards. Basically,

  2. A Printed Multicomponent Paper Sensor for Bacterial Detection.

    Science.gov (United States)

    Ali, M Monsur; Brown, Christine L; Jahanshahi-Anbuhi, Sana; Kannan, Balamurali; Li, Yingfu; Filipe, Carlos D M; Brennan, John D

    2017-09-26

    We present a simple all-in-one paper-based sensor for E. coli detection using a composite ink made of a fluorogenic DNAzyme probe for bacterial recognition and signal generation, lysozyme that lyses whole bacterial cells, and pullulan/trehalose sugars that stabilize printed bioactive molecules. The paper sensor is capable of producing a fluorescence signal as a readout within 5 minutes upon contacting E. coli, can achieve a limit of detection of 100 cells/mL, in a variety of sample matrixes, without sample enrichment, and remains stable for at least 6 months when stored at ambient temperature. Therefore, this simple paper sensor provides rapid bacterial testing on site, and can be shipped and stored under ambient conditions to benefit users living in resource-limited regions.

  3. Molecular analysis of cross-bacterial contamination detected in ...

    African Journals Online (AJOL)

    ... the isolate Delftia acidovorans BP(R2) and it is also coupled to protein with molecular weight 25-26 KDa. As well as, this bacterial contamination was the reason for the false positive results observed during the detection of HCV infections. Journal of Applied Sciences and Environmental Management Vol. 9(1) 2005: 5-10.

  4. Detection of Bacterial Endospores in Soil by Terbium Fluorescence

    Directory of Open Access Journals (Sweden)

    Andrea Brandes Ammann

    2011-01-01

    Full Text Available Spore formation is a survival mechanism of microorganisms when facing unfavorable environmental conditions resulting in “dormant” states. We investigated the occurrence of bacterial endospores in soils from various locations including grasslands (pasture, meadow, allotment gardens, and forests, as well as fluvial sediments. Bacterial spores are characterized by their high content of dipicolinic acid (DPA. In the presence of terbium, DPA forms a complex showing a distinctive photoluminescence spectrum. DPA was released from soil by microwaving or autoclaving. The addition of aluminium chloride reduced signal quenching by interfering compounds such as phosphate. The highest spore content (up to 109 spores per gram of dry soil was found in grassland soils. Spore content is related to soil type, to soil depth, and to soil carbon-to-nitrogen ratio. Our study might provide a basis for the detection of “hot spots” of bacterial spores in soil.

  5. Detection of antibiotic resistance in clinical bacterial strains from pets

    OpenAIRE

    Poeta, P.; Rodrigues, J.

    2008-01-01

    The identification of different bacterial strains and the occurrence of antibiotic resistance were investigated in several infection processes of pets as skin abscess with purulent discharge, bronco alveolar fluid, earwax, urine, mammary, and eye fluid. Streptococcus spp. and Staphylococcus spp. were the most detected in the different samples. A high frequency of antimicrobial resistance has been observed and this could reflect the wide use of antimicrobials in pets, making the effectiveness ...

  6. Nucleic acid detection technologies and marker molecules in bacterial diagnostics.

    Science.gov (United States)

    Scheler, Ott; Glynn, Barry; Kurg, Ants

    2014-05-01

    There is a growing need for quick and reliable methods for microorganism detection and identification worldwide. Although traditional culture-based technologies are trustworthy and accurate at a relatively low cost, they are also time- and labor-consuming and are limited to culturable bacteria. Those weaknesses have created a necessity for alternative technologies that are capable for faster and more precise bacterial identification from medical, food or environmental samples. The most common current approach is to analyze the nucleic acid component of analyte solution and determine the bacterial composition according to the specific nucleic acid profiles that are present. This review aims to give an up-to-date overview of different nucleic acid target sequences and respective analytical technologies.

  7. Smart phone based bacterial detection using bio functionalized fluorescent nanoparticles

    International Nuclear Information System (INIS)

    Rajendran, Vinoth Kumar; Bakthavathsalam, Padmavathy; Ali, Baquir Mohammed Jaffar

    2014-01-01

    We are describing immunochromatographic test strips with smart phone-based fluorescence readout. They are intended for use in the detection of the foodborne bacterial pathogens Salmonella spp. and Escherichia coli O157. Silica nanoparticles (SiNPs) were doped with FITC and Ru(bpy), conjugated to the respective antibodies, and then used in a conventional lateral flow immunoassay (LFIA). Fluorescence was recorded by inserting the nitrocellulose strip into a smart phone-based fluorimeter consisting of a light weight (40 g) optical module containing an LED light source, a fluorescence filter set and a lens attached to the integrated camera of the cell phone in order to acquire high-resolution fluorescence images. The images were analysed by exploiting the quick image processing application of the cell phone and enable the detection of pathogens within few minutes. This LFIA is capable of detecting pathogens in concentrations as low as 10 5 cfu mL −1 directly from test samples without pre-enrichment. The detection is one order of magnitude better compared to gold nanoparticle-based LFIAs under similar condition. The successful combination of fluorescent nanoparticle-based pathogen detection by LFIAs with a smart phone-based detection platform has resulted in a portable device with improved diagnosis features and having potential application in diagnostics and environmental monitoring. (author)

  8. Conventional and molecular methods to detect bacterial pathogens in mussels.

    Science.gov (United States)

    Gugliandolo, C; Lentini, V; Spanò, A; Maugeri, T L

    2011-01-01

    To detect Aeromonas spp., Salmonella spp., Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus in mussels and water samples from a farming area, conventional and molecular methods were applied to enrichment cultures. The aerolysin gene (aero) of Aeromonas spp., the invasion plasmid antigen B (ipaB) gene of Salmonella spp., the enterotoxin secretion protein (epsM) gene of V. cholerae, the species-specific region of 16S rRNA gene of V. vulnificus, the 16S-23S rDNA (IGS) gene of V. parahaemolyticus and the pR72H fragment of V. parahaemolyticus were amplified by multiplex polymerase chain reaction (PCR) assays on DNA extracted from enrichment cultures. The haemolysin gene (tdh) of pathogenic V. parahaemolyticus was also amplified. Conventional culture method allowed the isolation of V. parahaemolyticus and V. vulnificus from water and mussels. The genes aero, epsM and 16S rRNA of V. vulnificus were occasionally detected in the enrichment cultures. In mussels, the ipaB and IGS genes were detected from June to September and from April to November, respectively. All genes, except aero, were amplified from mussels collected in September, when pathogenic V. parahaemolyticus (tdh+) strains were also isolated. Multiplex-PCR assays were more sensitive and faster than conventional procedures. The results emphasize the need of an accurate and rapid detection of bacterial pathogens in mussels to protect human health. © 2010 The Authors. Letters in Applied Microbiology © 2010 The Society for Applied Microbiology.

  9. Biochemical principle of Limulus test for detecting bacterial endotoxins.

    Science.gov (United States)

    Iwanaga, Sadaaki

    2007-05-01

    A hemocyte lysate from horseshoe crab (Limulus) produced a gel, when exposed to Gram-negative bacterial endotoxins, lipopolysaccharides (LPS). This gelation reaction of the lysate, so-called Limulus test, has been widely employed as a simple and very sensitive assay method for endotoxins. Recent biochemical studies on the principle of Limulus test indicate that the hemocytes contain several serine protease zymogens, which constitute a coagulation cascade triggered by endotoxins, and that there is a (1,3)-β-D-glucan-mediated coagulation pathway which also results in the formation of gel. Up to now, six protein components, designated coagulogen, proclotting enzyme, factor B, factor C, and factor G, all of which are closely associated with the endotoxin-mediated coagulation pathway, have been purified and biochemically characterized. The molecular structures of these proteins have also been elucidated. Moreover, the reconstitution experiments using the isolated clotting factors, factor C, factor B, proclotting enzyme and coagulogen in the presence of endotoxin, leads to the formation of coagulin gel. Here, I will focus on the biochemical principle of Limulus test for detecting bacterial endotoxins, and its activation and regulation mechanism on the LPS-mediated coagulation cascade.

  10. Detecting rare gene transfer events in bacterial populations

    Directory of Open Access Journals (Sweden)

    Kaare Magne Nielsen

    2014-01-01

    Full Text Available Horizontal gene transfer (HGT enables bacteria to access, share, and recombine genetic variation, resulting in genetic diversity that cannot be obtained through mutational processes alone. In most cases, the observation of evolutionary successful HGT events relies on the outcome of initially rare events that lead to novel functions in the new host, and that exhibit a positive effect on host fitness. Conversely, the large majority of HGT events occurring in bacterial populations will go undetected due to lack of replication success of transformants. Moreover, other HGT events that would be highly beneficial to new hosts can fail to ensue due to lack of physical proximity to the donor organism, lack of a suitable gene transfer mechanism, genetic compatibility, and stochasticity in tempo-spatial occurrence. Experimental attempts to detect HGT events in bacterial populations have typically focused on the transformed cells or their immediate offspring. However, rare HGT events occurring in large and structured populations are unlikely to reach relative population sizes that will allow their immediate identification; the exception being the unusually strong positive selection conferred by antibiotics. Most HGT events are not expected to alter the likelihood of host survival to such an extreme extent, and will confer only minor changes in host fitness. Due to the large population sizes of bacteria and the time scales involved, the process and outcome of HGT are often not amenable to experimental investigation. Population genetic modeling of the growth dynamics of bacteria with differing HGT rates and resulting fitness changes is therefore necessary to guide sampling design and predict realistic time frames for detection of HGT, as it occurs in laboratory or natural settings. Here we review the key population genetic parameters, consider their complexity and highlight knowledge gaps for further research.

  11. Data for automated, high-throughput microscopy analysis of intracellular bacterial colonies using spot detection

    DEFF Research Database (Denmark)

    Ernstsen, Christina L; Login, Frédéric H; Jensen, Helene H

    2017-01-01

    Quantification of intracellular bacterial colonies is useful in strategies directed against bacterial attachment, subsequent cellular invasion and intracellular proliferation. An automated, high-throughput microscopy-method was established to quantify the number and size of intracellular bacterial...... of cell nuclei were automatically quantified using a spot detection-tool. The spot detection-output was exported to Excel, where data analysis was performed. In this article, micrographs and spot detection data are made available to facilitate implementation of the method....

  12. Improving Ambiguity Resolution for Medium Baselines Using Combined GPS and BDS Dual/Triple-Frequency Observations.

    Science.gov (United States)

    Gao, Wang; Gao, Chengfa; Pan, Shuguo; Wang, Denghui; Deng, Jiadong

    2015-10-30

    The regional constellation of the BeiDou navigation satellite system (BDS) has been providing continuous positioning, navigation and timing services since 27 December 2012, covering China and the surrounding area. Real-time kinematic (RTK) positioning with combined BDS and GPS observations is feasible. Besides, all satellites of BDS can transmit triple-frequency signals. Using the advantages of multi-pseudorange and carrier observations from multi-systems and multi-frequencies is expected to be of much benefit for ambiguity resolution (AR). We propose an integrated AR strategy for medium baselines by using the combined GPS and BDS dual/triple-frequency observations. In the method, firstly the extra-wide-lane (EWL) ambiguities of triple-frequency system, i.e., BDS, are determined first. Then the dual-frequency WL ambiguities of BDS and GPS were resolved with the geometry-based model by using the BDS ambiguity-fixed EWL observations. After that, basic (i.e., L1/L2 or B1/B2) ambiguities of BDS and GPS are estimated together with the so-called ionosphere-constrained model, where the ambiguity-fixed WL observations are added to enhance the model strength. During both of the WL and basic AR, a partial ambiguity fixing (PAF) strategy is adopted to weaken the negative influence of new-rising or low-elevation satellites. Experiments were conducted and presented, in which the GPS/BDS dual/triple-frequency data were collected in Nanjing and Zhengzhou of China, with the baseline distance varying from about 28.6 to 51.9 km. The results indicate that, compared to the single triple-frequency BDS system, the combined system can significantly enhance the AR model strength, and thus improve AR performance for medium baselines with a 75.7% reduction of initialization time on average. Besides, more accurate and stable positioning results can also be derived by using the combined GPS/BDS system.

  13. Preface: BeiDou Navigation Satellite System (BDS)/GNSS+: Recent progress and new applications

    Science.gov (United States)

    Jin, Shuanggen

    2017-02-01

    Nowadays, the new China's BeiDou Navigation Satellite System (BDS) has been developed well. At the end of 2016, over 23 BDS satellites were launched, including five geostationary Earth orbit (GEO) satellites, five inclined geosynchronous orbit (IGSO) satellites and nine medium Earth orbit (MEO) satellites. The current BDS service covers China and most Asia-Pacific regions with accuracy of better than 10 m in positioning, 0.2 m/s in velocity and 50 ns in timing. The BDS with global coverage will be completely established by 2020 with five GEO satellites and 30 MEO satellites. The main function of BDS is the positioning, navigation and timing (PNT) as well as short message communications. Together with the United States' GPS, Russia's GLONASS and the European Union's Galileo system as well as other regional augmentation systems, more new applications of multi-Global Navigation Satellite Systems (GNSS) will be exploited and realized in the next decades.

  14. A novel method to detect bacterial resistance to disinfectants

    Directory of Open Access Journals (Sweden)

    Xiao-Feng He

    2017-09-01

    Full Text Available In clinical practice, the important hygienic prevention of bacterial pathogen spread is disinfection of potentially contaminated area. Benzalkonium bromide and chlorhexidine acetate are commonly used disinfectants with a broad spectrum of anti-microbial effect. It is vital to inhibit the spread of pathogen in hospital. However, a large number of pathogens with the decreased antiseptic susceptibility have been isolated from clinical samples which showed an increased minimal inhibitory concentration (MIC against those antiseptics. These resistant pathogens are the major causes for nosocomial cross-infections in hospital. The present study demonstrated the utility of Oxford plate assay system in determining the potential disinfectant resistance of bacteria. The microbiological assay is based on the inhibitory effect of tested disinfectants upon the strains of Staphylococcus aureus and Escherichia coli. Statistical analysis of the bioassay results indicated the linear correlation (r = 0.87–0.99, P < 0.01 between the diameter of growth inhibition zone and the log dosage of the tested disinfectants. Moreover, comparison of inhibitory efficacy of benzalkonium bromide upon 29 S. aureus strains isolated from clinical samples by both Oxford plate method and broth dilution method showed that the diameter of growth inhibition zone has significantly negative correlation with the minimal inhibitory concentration (MIC (r = −0.574, P < 0.001. These results suggest that the Oxford plate is a simple and time-saving method in detecting potential clinical disinfectant resistance and its usefulness for routine surveillance of pathogenic resistance to disinfectants warrants further investigation.

  15. Rapid detection of bacterial pathogens using flourescence spectroscopy and chemometrics

    Science.gov (United States)

    This work presents the development of a method for rapid bacterial identification based on the fluorescence spectroscopy combined with multivariate analysis. Fluorescence spectra of pure three different genera of bacteria (Escherichia coli, Salmonella, and Campylobacter) were collected from 200...

  16. Procedures involving lipid media for detection of bacterial contamination in breweries.

    Science.gov (United States)

    Van Vuuren, H J; Louw, H A; Loos, M A; Meisel, R

    1977-01-01

    The liquid equivalent of universal beer agar, designated universal beer liquid medium, and its beer-free equivalent, universal liquid medium (UL), were equally effective in demonstrating bacterial contamination in 120 of 200 samples from different stages of commercial brewing process. Growth of the contaminants after 3 days was consistently more luxuriant in the UL medium. A yeast-water substrate medium failed to reveal many contaminants detected with UL in 392 samples from three breweries and revealed only a few not detected with UL. The use of UL and a lactose-peptone medium, with microscope examination of the media for bacterial growth, permitted detection of 93% of the known contaminants compared to 87%, detected with UL alone; this combination or universal beer liquid medium plus lactose-peptone medium can therefore be recommended for the detection of bacterial contaminants in brewery samples. Bacterial contamination of pitching yeasts appeared to be a particular problem in the breweries investigated. PMID:848948

  17. Comparison of enterovirus detection in cerebrospinal fluid with Bacterial Meningitis Score in children

    Science.gov (United States)

    Pires, Frederico Ribeiro; Franco, Andréia Christine Bonotto Farias; Gilio, Alfredo Elias; Troster, Eduardo Juan

    2017-01-01

    ABSTRACT Objective To measure the role of enterovirus detection in cerebrospinal fluid compared with the Bacterial Meningitis Score in children with meningitis. Methods A retrospective cohort based on analysis of medical records of pediatric patients diagnosed as meningitis, seen at a private and tertiary hospital in São Paulo, Brazil, between 2011 and 2014. Excluded were patients with critical illness, purpura, ventricular shunt or recent neurosurgery, immunosuppression, concomitant bacterial infection requiring parenteral antibiotic therapy, and those who received antibiotics 72 hours before lumbar puncture. Results The study included 503 patients. Sixty-four patients were excluded and 94 were not submitted to all tests for analysis. Of the remaining 345 patients, 7 were in the Bacterial Meningitis Group and 338 in the Aseptic Meningitis Group. There was no statistical difference between the groups. In the Bacterial Meningitis Score analysis, of the 338 patients with possible aseptic meningitis (negative cultures), 121 of them had one or more points in the Bacterial Meningitis Score, with sensitivity of 100%, specificity of 64.2%, and negative predictive value of 100%. Of the 121 patients with positive Bacterial Meningitis Score, 71% (86 patients) had a positive enterovirus detection in cerebrospinal fluid. Conclusion Enterovirus detection in cerebrospinal fluid was effective to differentiate bacterial from viral meningitis. When the test was analyzed together with the Bacterial Meningitis Score, specificity was higher when compared to Bacterial Meningitis Score alone. PMID:28767914

  18. Detection of bacterial blight resistant gene xa5 using linked marker ...

    African Journals Online (AJOL)

    Detection of bacterial blight resistant gene xa5 using linked marker approaches. SA Naveed, M Babar, A Arif, Y Zafar, M Sabar, I Ali, M Chragh, M Arif. Abstract. Rice is the primary source of food for 57% of the world's population. Genetic resistance is important to control many kinds of pathogenic diseases. Bacterial blight ...

  19. Improving Ambiguity Resolution for Medium Baselines Using Combined GPS and BDS Dual/Triple-Frequency Observations

    Directory of Open Access Journals (Sweden)

    Wang Gao

    2015-10-01

    Full Text Available The regional constellation of the BeiDou navigation satellite system (BDS has been providing continuous positioning, navigation and timing services since 27 December 2012, covering China and the surrounding area. Real-time kinematic (RTK positioning with combined BDS and GPS observations is feasible. Besides, all satellites of BDS can transmit triple-frequency signals. Using the advantages of multi-pseudorange and carrier observations from multi-systems and multi-frequencies is expected to be of much benefit for ambiguity resolution (AR. We propose an integrated AR strategy for medium baselines by using the combined GPS and BDS dual/triple-frequency observations. In the method, firstly the extra-wide-lane (EWL ambiguities of triple-frequency system, i.e., BDS, are determined first. Then the dual-frequency WL ambiguities of BDS and GPS were resolved with the geometry-based model by using the BDS ambiguity-fixed EWL observations. After that, basic (i.e., L1/L2 or B1/B2 ambiguities of BDS and GPS are estimated together with the so-called ionosphere-constrained model, where the ambiguity-fixed WL observations are added to enhance the model strength. During both of the WL and basic AR, a partial ambiguity fixing (PAF strategy is adopted to weaken the negative influence of new-rising or low-elevation satellites. Experiments were conducted and presented, in which the GPS/BDS dual/triple-frequency data were collected in Nanjing and Zhengzhou of China, with the baseline distance varying from about 28.6 to 51.9 km. The results indicate that, compared to the single triple-frequency BDS system, the combined system can significantly enhance the AR model strength, and thus improve AR performance for medium baselines with a 75.7% reduction of initialization time on average. Besides, more accurate and stable positioning results can also be derived by using the combined GPS/BDS system.

  20. Positioning Accuracy Analysis of GPS/BDS/GLONASS Network RTK Based on DREAMNET

    Directory of Open Access Journals (Sweden)

    YAO Yibin

    2016-09-01

    Full Text Available With BDS being continually providing service in the Asia-Pacific Region, GLONASS being fully operational with 24 satellites in orbit again and GPS modernization, multi-GNSS network RTK will become the development trend of network RTK in the future. The data of multi-GNSS will be process by data reserving, editing and managing system of network RTK (DREAMNET, which developed independently by this research group, to analyze and compare the positioning accuracy between different combinations of global navigation satellite system. According to the experiment, the positioning accuracy of GPS/BDS/GLONASS network RTK and GPS/BDS network RTK is highest, GPS and BDS only second. Besides, with the increasing of the cut-off elevation, the availability of single GPS network RTK significantly reduces. However with 40°cut-off elevations, positioning service with the accuracy of 0.005m in horizontal, 0.025m in vertical will be provided by GPS/BDS/GLONASS network RTK in 99.84% time of a day. Finally, the statistics of positioning accuracy for 15days show that the accuracy of 0.01m in horizontal, 0.025m in vertical could be reached in six situations, which including BDS and BDS/GLONASS network RTK. Besides, the accuracy of 0.006m in horizontal, 0.015m in vertical could be reached by GPS/BDS/GLONASS network RTK, proving that the positioning accuracy and stability of DREAMNET can meet the needs of surveying and mapping.

  1. Detection of bacterial blight resistance genes in basmati rice landraces.

    Science.gov (United States)

    Ullah, I; Jamil, S; Iqbal, M Z; Shaheen, H L; Hasni, S M; Jabeen, S; Mehmood, A; Akhter, M

    2012-07-20

    Aromatic basmati rice is vulnerable to bacterial blight disease. Genes conferring resistance to bacterial blight have been identified in coarse rice; however, their incorporation into basmati varieties compromises the prized basmati aroma. We identified bacterial blight resistance genes Xa4, xa5, Xa7, and xa13 in 52 basmati landraces and five basmati cultivars using PCR markers. The Xa7 gene was found to be the most prevalent among the cultivars and landraces. The cultivars Basmati-385 and Basmati-2000 also contained the Xa4 gene; however, xa5 and xa13 were confined to landraces only. Ten landraces were found to have multiple resistance genes. Landraces Basmati-106, Basmati-189 and Basmati-208 contained Xa4 and Xa7 genes. Whereas, landraces Basmati-122, Basmati-427, Basmati-433 were observed to have xa5 and Xa7 genes. Landraces Basmati-48, Basmati-51A, Basmati-334, and Basmati-370A possessed Xa7 and xa13 genes. The use of landraces containing recessive genes xa5 and xa13 as donor parents in hybridization with cultivars Basmati-385 and Basmati-2000, which contain the genes Xa4 and Xa7, will expedite efforts to develop bacterial blight-resistant basmati rice cultivars through marker assisted selection, based on a pyramiding approach, without compromising aroma and grain quality.

  2. Detecting bacterial endophytes in tropical grasses of the Brachiaria ...

    African Journals Online (AJOL)

    Plant-growth-promoting (PGP) bacteria include a diverse group of soil bacteria thought to stimulate plant growth by various mechanisms. Brachiaria forage grasses, of African origin, are perennials that often grow under low-input conditions and are likely to harbour unique populations of PGP bacteria. Three bacterial strains ...

  3. Bacterial contamination of platelet components not detected by BacT/ALERT®.

    Science.gov (United States)

    Abela, M A; Fenning, S; Maguire, K A; Morris, K G

    2018-02-01

    To investigate the possible causes for false negative results in BacT/ALERT ® 3D Signature System despite bacterial contamination of platelet units. The Northern Ireland Blood Transfusion Service (NIBTS) routinely extends platelet component shelf life to 7 days. Components are sampled and screened for bacterial contamination using an automated microbial detection system, the BacT/ALERT ® 3D Signature System. We report on three platelet components with confirmed bacterial contamination, which represent false negative BacT/ALERT ® results and near-miss serious adverse events. NIBTS protocols for risk reduction of bacterial contamination of platelet components are described. The methodology for bacterial detection using BacT/ALERT ® is outlined. Laboratory tests, relevant patient details and relevant follow-up information are analysed. In all three cases, Staphylococcus aureus was isolated from the platelet residue and confirmed on terminal sub-culture using BacT/ALERT ® . In two cases, S. aureus with similar genetic makeup was isolated from the donors. Risk reduction measures for bacterial contamination of platelet components are not always effective. Automated bacterial culture detection does not eliminate the risk of bacterial contamination. Visual inspection of platelet components prior to release, issue and administration remains an important last line of defence. © 2017 British Blood Transfusion Society.

  4. Suitability of Optical, Physical and Chemical Measurements for Detection of Changes in Bacterial Drinking Water Quality

    Science.gov (United States)

    Ikonen, Jenni; Pitkänen, Tarja; Miettinen, Ilkka T.

    2013-01-01

    In this study, different optical, physical and chemical measurements were tested for their capacity to detect changes in water quality. The tests included UV-absorbance at 254 nm, absorbance at 420 nm, turbidity, particle counting, temperature, pH, electric conductivity (EC), free chlorine concentration and ATP concentration measurements. Special emphasis was given to investigating the potential for measurement tools to detect changes in bacterial concentrations in drinking water. Bacterial colony counts (CFU) and total bacterial cell counts (TBC) were used as reference methods for assessing the bacterial water quality. The study consists of a series of laboratory scale experiments: monitoring of regrowth of Pseudomonas fluorescens, estimation of the detection limits for optical measurements using Escherichia coli dilutions, verification of the relationships by analysing grab water samples from various distribution systems and utilisation of the measurements in the case of an accidentally contaminated distribution network. We found significant correlations between the tested measurements and the bacterial water quality. As the bacterial contamination of water often co-occurs with the intrusion of matrixes containing mainly non-bacterial components, the tested measurement tools can be considered to have the potential to rapidly detect any major changes in drinking water quality. PMID:24284353

  5. Biochemical principle of Limulus test for detecting bacterial endotoxins

    OpenAIRE

    Iwanaga, Sadaaki

    2007-01-01

    A hemocyte lysate from horseshoe crab (Limulus) produced a gel, when exposed to Gram-negative bacterial endotoxins, lipopolysaccharides (LPS). This gelation reaction of the lysate, so-called Limulus test, has been widely employed as a simple and very sensitive assay method for endotoxins. Recent biochemical studies on the principle of Limulus test indicate that the hemocytes contain several serine protease zymogens, which constitute a coagulation cascade triggered by endotoxins, and that ther...

  6. Gallium-67 myocardial imaging for the detection of bacterial endocarditis

    International Nuclear Information System (INIS)

    Wiseman, J.; Rouleau, J.; Rigo, P.; Strauss, H.W.; Pitt, B.

    1976-01-01

    Eleven patients with a clinical diagnosis of bacterial endocarditis underwent scintillation scanning of the precordial region 2--7 days after the intravenous administration of 3 mCi of gallium-67 citrate. Seven had positive scans, 3 of which were confirmed by postmortem imaging at autopsy. Serial images revealed the scans to be frequently negative at 48 hours and positive from 3 to 8 days following injection. Uptake was not seen in the region of the myocardium 48 hours or longer after the injection of 15 patients without endocarditis used as controls

  7. Gallium-67 myocardial imaging for the detection of bacterial endocarditis

    Energy Technology Data Exchange (ETDEWEB)

    Wiseman, J.; Rouleau, J.; Rigo, P.; Strauss, H.W.; Pitt, B.

    1976-07-01

    Eleven patients with a clinical diagnosis of bacterial endocarditis underwent scintillation scanning of the precordial region 2--7 days after the intravenous administration of 3 mCi of gallium-67 citrate. Seven had positive scans, 3 of which were confirmed by postmortem imaging at autopsy. Serial images revealed the scans to be frequently negative at 48 hours and positive from 3 to 8 days following injection. Uptake was not seen in the region of the myocardium 48 hours or longer after the injection of 15 patients without endocarditis used as controls.

  8. High-accuracy Long Arc Almanac Model Design for BDS

    Directory of Open Access Journals (Sweden)

    CHANG Zhiqiao

    2018-03-01

    Full Text Available Almanac parameters can be used to assist signal acquisition for both conventional navigation and autonomous navigation. The extended validity of the almanac parameters not only enables the terrestrial receiver to make full use of almanac data when starting up,but also determines the frequency of the almanac uploaded and the satellite storage resources on-board for autonomous navigation with inter-satellite link observation. Based on analysis of the major perturbations of three types of BeiDou satellites and their effects on the long-term and long-period terms of the orbital elements,an almanac model with six orbital elements and five perturbation parameters is designed. The almanac fitting test is carried out based on the 90-day long arc orbit of BeiDou satellites in orbit throughout 2013. The results show that the new almanac model improves accuracy of almanac fitting. For Geostationary Earth Orbit (GEO and Inclined Geosynchronous Orbit (IGSO satellites,position fitting error is reduced from 200 km to more than 10 km even to several km and velocity error is reduced from 15 m/s to 0.6 m/s. The accuracy of the new model is about 20 to 30 times higher than that of the conventional model. For Medium Earth Orbit (MEO satellite,position fitting error is about 5 km and velocity error is about 0.6 m/s regardless of which model,and the accuracy of the new method is improved about 15%. For 10 km position error upper limit of inter-satellite link,the maximum fitting arc length of the conventional model is about 14 days,and the maximum fitting arc length of the new almanac model can be extended to 45 days. The new almanac model extends the validity of almanac parameters,and optimizes almanac model for BeiDou Navigation Satellite System (BDS.

  9. DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT.

    Science.gov (United States)

    Peña-Castillo, Lourdes; Grüell, Marc; Mulligan, Martin E; Lang, Andrew S

    2016-01-01

    Small non-coding RNAs (sRNAs) are regulatory RNA molecules that have been identified in a multitude of bacterial species and shown to control numerous cellular processes through various regulatory mechanisms. In the last decade, next generation RNA sequencing (RNA-seq) has been used for the genome-wide detection of bacterial sRNAs. Here we describe sRNA-Detect, a novel approach to identify expressed small transcripts from prokaryotic RNA-seq data. Using RNA-seq data from three bacterial species and two sequencing platforms, we performed a comparative assessment of five computational approaches for the detection of small transcripts. We demonstrate that sRNA-Detect improves upon current standalone computational approaches for identifying novel small transcripts in bacteria.

  10. Detection and quantification of intracellular bacterial colonies by automated, high-throughput microscopy.

    Science.gov (United States)

    Ernstsen, Christina L; Login, Frédéric H; Jensen, Helene H; Nørregaard, Rikke; Møller-Jensen, Jakob; Nejsum, Lene N

    2017-08-01

    To target bacterial pathogens that invade and proliferate inside host cells, it is necessary to design intervention strategies directed against bacterial attachment, cellular invasion and intracellular proliferation. We present an automated microscopy-based, fast, high-throughput method for analyzing size and number of intracellular bacterial colonies in infected tissue culture cells. Cells are seeded in 48-well plates and infected with a GFP-expressing bacterial pathogen. Following gentamicin treatment to remove extracellular pathogens, cells are fixed and cell nuclei stained. This is followed by automated microscopy and subsequent semi-automated spot detection to determine the number of intracellular bacterial colonies, their size distribution, and the average number per host cell. Multiple 48-well plates can be processed sequentially and the procedure can be completed in one working day. As a model we quantified intracellular bacterial colonies formed by uropathogenic Escherichia coli (UPEC) during infection of human kidney cells (HKC-8). Urinary tract infections caused by UPEC are among the most common bacterial infectious diseases in humans. UPEC can colonize tissues of the urinary tract and is responsible for acute, chronic, and recurrent infections. In the bladder, UPEC can form intracellular quiescent reservoirs, thought to be responsible for recurrent infections. In the kidney, UPEC can colonize renal epithelial cells and pass to the blood stream, either via epithelial cell disruption or transcellular passage, to cause sepsis. Intracellular colonies are known to be clonal, originating from single invading UPEC. In our experimental setup, we found UPEC CFT073 intracellular bacterial colonies to be heterogeneous in size and present in nearly one third of the HKC-8 cells. This high-throughput experimental format substantially reduces experimental time and enables fast screening of the intracellular bacterial load and cellular distribution of multiple

  11. Broad-Range Bacterial Capture from Fluid-Samples: Implications for Amplification-Free Contamination Detection

    Directory of Open Access Journals (Sweden)

    Monika WEBER

    2016-08-01

    Full Text Available Fluid-Screen, Inc. presents a bacterial concentration and filtration method based on dielectrophoresis and alternating current kinetics. Dielectrophoresis has been previously shown to induce particle motion; however, bacterial capture efficiency and reproducibility have consistently been low, reducing its potential for practical applications. In this study, we introduce a novel, patent-pending electrode system optimized to simultaneously capture a wide range of bacterial species from a variety of aqueous solutions. Specifically, we show that the method of dielectrophoresis used induces responses in both characteristic Gram- negative Escherichia coli and Gram-positive Enterococcus faecalis bacteria, as well as with Bacillus subtilis and Aestuariimicrobium kwangyangense. We have adapted the electrode design to create a bacterial sample preparatio unit, termed the sample sorter, that is able to capture multiple bacterial species and release them simultaneously for bacterial concentration and exchange from complex matrices to defined buffer media. This technology can be used on its own or in conjunction with standard bacterial detection methods such as mass spectroscopy. The Fluid-Screen product will dramatically improve testing and identification of bacterial contaminants in various industrial settings by eliminating the need for amplification of samples and by reducing the time to identification.

  12. Estimation of BDS DCB Combining GIM and Different Zero-mean Constraints

    Directory of Open Access Journals (Sweden)

    YAO Yibin

    2017-02-01

    Full Text Available As the limited number of the BeiDou Navigation Satellite System (BDS satellites and tracking stations currently, it's difficult to attain daily DCBs solution with precisely high accuracy based on BeiDou single system. In order to overcome the weakness above, two different zero-mean constraints for BDS satellites, called constraint one and constraint two, respectively, are used to estimate DCBs of BDS based on BeiDou observations from the multi-GNSS experiment (MGEX network and global ionosphere maps (GIM from the Center for Orbit Determination in Europe (CODE. The results show that the systematic difference of the overall trend under two different constraints is consistent, and the systematic difference of DCBC2I-C7I and DCBC2I-C6I is -3.3 ns and 1.2 ns, respectively. The systematic difference between BDS satellite DCBs and receiver DCBs has the same absolute value, but opposite signs instead. Compared to constraint one, The DCBs estimation of IGSO/MEO satellites under constraint two are more stable (the improvement of satellites DCBC2I-C7I and DCBC2I-C6I STD are up to 21%, 13%, respectively, the stability of IGSO and MEO satellites (STDs are within 0.1 ns, 0.2 ns, respectively is better than that of GEO satellites (STDs are 0.15~0.32 ns. DCB estimation of constraint one is not only consistent with the CAS/DLR products (Bias:-0.4~0.2 ns, but also takes into account the stability of BDS satellites DCB. Under the two different constraints, there is no obvious change in BDS receiver DCBs, meaning that the selection of constraints has no obvious influence on the stability of BDS receivers DCBs. The overall stability of BDS receiver DCBs is better than 1 ns. Due to the accuracy discrepancy of GIM in different latitudes, the stability of BDS receiver DCBs in the middle-high latitude (STDs are within 0.4 ns is better than that in low latitude region (STDs are 0.8~1 ns.

  13. Detection of mastitis pathogens by analysis of volatile bacterial metabolites

    NARCIS (Netherlands)

    Hettinga, K.A.; Valenberg, van H.J.F.; Lam, T.J.G.M.; Hooijdonk, van A.C.M.

    2008-01-01

    The ability to detect mastitis pathogens based on their volatile metabolites was studied. Milk samples from cows with clinical mastitis, caused by Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus uberis, Streptococcus dysgalactiae, and Escherichia coli were collected. In

  14. The BDS Triple Frequency Pseudo-range Correlated Stochastic Model of Single Station Modeling Method

    Directory of Open Access Journals (Sweden)

    HUANG Lingyong

    2017-05-01

    Full Text Available In order to provide a reliable pseudo-range stochastic model, a method is studied to estimate the BDS triple-frequency pseudo-range related stochastic model based on three BDS triple-frequency pseudo-range minus carrier (GIF combinations using the data of a single station. In this algorithm, the low order polynomial fitting method is used to fit the GIF combination in order to eliminate the error and other constants except non pseudo noise at first. And then, multiple linear regression analysis method is used to model the stochastic function of three linearly independent GIF combinations. Finally the related stochastic model of the original BDS triple-frequency pseudo-range observations is obtained by linear transformation. The BDS triple-frequency data verification results show that this algorithm can get a single station related stochastic model of BDS triple-frequency pseudo-range observation, and it is advantageous to provide accurate stochastic model for navigation and positioning and integrity monitoring.

  15. Characteristics of the BDS Carrier Phase Multipath and Its Mitigation Methods in Relative Positioning.

    Science.gov (United States)

    Dai, Wujiao; Shi, Qiang; Cai, Changsheng

    2017-04-07

    The carrier phase multipath effect is one of the most significant error sources in the precise positioning of BeiDou Navigation Satellite System (BDS). We analyzed the characteristics of BDS multipath, and found the multipath errors of geostationary earth orbit (GEO) satellite signals are systematic, whereas those of inclined geosynchronous orbit (IGSO) or medium earth orbit (MEO) satellites are both systematic and random. The modified multipath mitigation methods, including sidereal filtering algorithm and multipath hemispherical map (MHM) model, were used to improve BDS dynamic deformation monitoring. The results indicate that the sidereal filtering methods can reduce the root mean square (RMS) of positioning errors in the east, north and vertical coordinate directions by 15%, 37%, 25% and 18%, 51%, 27% in the coordinate and observation domains, respectively. By contrast, the MHM method can reduce the RMS by 22%, 52% and 27% on average. In addition, the BDS multipath errors in static baseline solutions are a few centimeters in multipath-rich environments, which is different from that of Global Positioning System (GPS) multipath. Therefore, we add a parameter representing the GEO multipath error in observation equation to the adjustment model to improve the precision of BDS static baseline solutions. And the results show that the modified model can achieve an average precision improvement of 82%, 54% and 68% in the east, north and up coordinate directions, respectively.

  16. Convergence Time and Positioning Accuracy Comparison between BDS and GPS Precise Point Positioning

    Directory of Open Access Journals (Sweden)

    ZHANG Xiaohong

    2015-03-01

    Full Text Available BDS/GPS data from MGEX were processed by TriP 2.0 software developed at Wuhan University. Both static and kinematic float PPP are tested by adopting precise satellite orbits and clocks provided by Research Center of GNSS, Wuhan University. The results show that the convergence time of BDS static PPP is about 80min while kinematic PPP is about 100min. For 3h observations, static positioning accuracy of 5 cm and kinematic positioning accuracy of 8 cm in horizontal, about 12 cm in vertical can be achieved. Similar to GPS PPP, precision in east component is worse than north. At present, BDS PPP needs longer convergence time than GPS PPP to reach an absolute positioning accuracy of cm~dm due to the lack of global tracking stations and the limited accuracy of orbit and clock products.

  17. BDS/GPS Dual Systems Positioning Based on the Modified SR-UKF Algorithm

    Directory of Open Access Journals (Sweden)

    JaeHyok Kong

    2016-05-01

    Full Text Available The Global Navigation Satellite System can provide all-day three-dimensional position and speed information. Currently, only using the single navigation system cannot satisfy the requirements of the system’s reliability and integrity. In order to improve the reliability and stability of the satellite navigation system, the positioning method by BDS and GPS navigation system is presented, the measurement model and the state model are described. Furthermore, the modified square-root Unscented Kalman Filter (SR-UKF algorithm is employed in BDS and GPS conditions, and analysis of single system/multi-system positioning has been carried out, respectively. The experimental results are compared with the traditional estimation results, which show that the proposed method can perform highly-precise positioning. Especially when the number of satellites is not adequate enough, the proposed method combine BDS and GPS systems to achieve a higher positioning precision.

  18. A functional gene array for detection of bacterial virulence elements

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, C

    2007-11-01

    We report our development of the first of a series of microarrays designed to detect pathogens with known mechanisms of virulence and antibiotic resistance. By targeting virulence gene families as well as genes unique to specific biothreat agents, these arrays will provide important data about the pathogenic potential and drug resistance profiles of unknown organisms in environmental samples. To validate our approach, we developed a first generation array targeting genes from Escherichia coli strains K12 and CFT073, Enterococcus faecalis and Staphylococcus aureus. We determined optimal probe design parameters for microorganism detection and discrimination, measured the required target concentration, and assessed tolerance for mismatches between probe and target sequences. Mismatch tolerance is a priority for this application, due to DNA sequence variability among members of gene families. Arrays were created using the NimbleGen Maskless Array Synthesizer at Lawrence Livermore National Laboratory. Purified genomic DNA from combinations of one or more of the four target organisms, pure cultures of four related organisms, and environmental aerosol samples with spiked-in genomic DNA were hybridized to the arrays. Based on the success of this prototype, we plan to design further arrays in this series, with the goal of detecting all known virulence and antibiotic resistance gene families in a greatly expanded set of organisms.

  19. Multiplex PCR assay for simultaneous detection of six major bacterial pathogens of rice.

    Science.gov (United States)

    Cui, Z; Ojaghian, M R; Tao, Z; Kakar, K U; Zeng, J; Zhao, W; Duan, Y; Vera Cruz, C M; Li, B; Zhu, B; Xie, G

    2016-05-01

    The aim of this study was to develop a multiplex PCR (mPCR) assay for rapid, sensitive and simultaneous detection of six important rice pathogens: Xanthomonas oryzae pv. oryzae, X. oryzae pv. oryzicola, Pseudomonas fuscovaginae, Burkholderia glumae, Burkholderia gladioli and Acidovorax avenae subsp. avenae. Specific primers were designed through a bioinformatics pipeline. Sensitivity of detection was established using both traditional PCR and quantitative real-time PCR on isolated DNA and on bacterial cells both in vitro and in simulated diseased seeds and the parameters were optimized for an mPCR assay. A total of 150 bacterial strains were tested for specificity. The mPCR assay accurately predicted the presence of pathogens among 44 symptomatic and asymptomatic rice seed, sheath and leaf samples. This study confirmed that this mPCR assay is a rapid, reliable and simple tool for the simultaneous detection of six important rice bacterial pathogens. This study is the first report of a method allowing simultaneous detection of six major rice pathogens. The ability to use crude extracts from plants without bacterial isolation or DNA extraction enhances the value of this mPCR technology for rapid detection and aetiological/epidemiological studies. © 2016 The Society for Applied Microbiology.

  20. Precise orbit determination of Multi-GNSS constellation including GPS GLONASS BDS and GALIEO

    Science.gov (United States)

    Dai, Xiaolei

    2014-05-01

    In addition to the existing American global positioning system (GPS) and the Russian global navigation satellite system (GLONASS), the new generation of GNSS is emerging and developing, such as the Chinese BeiDou satellite navigation system (BDS) and the European GALILEO system. Multi-constellation is expected to contribute to more accurate and reliable positioning and navigation service. However, the application of multi-constellation challenges the traditional precise orbit determination (POD) strategy that was designed usually for single constellation. In this contribution, we exploit a more rigorous multi-constellation POD strategy for the ongoing IGS multi-GNSS experiment (MGEX) where the common parameters are identical for each system, and the frequency- and system-specified parameters are employed to account for the inter-frequency and inter-system biases. Since the authorized BDS attitude model is not yet released, different BDS attitude model are implemented and their impact on orbit accuracy are studied. The proposed POD strategy was implemented in the PANDA (Position and Navigation Data Analyst) software and can process observations from GPS, GLONASS, BDS and GALILEO together. The strategy is evaluated with the multi-constellation observations from about 90 MGEX stations and BDS observations from the BeiDou experimental tracking network (BETN) of Wuhan University (WHU). Of all the MGEX stations, 28 stations record BDS observation, and about 80 stations record GALILEO observations. All these data were processed together in our software, resulting in the multi-constellation POD solutions. We assessed the orbit accuracy for GPS and GLONASS by comparing our solutions with the IGS final orbit, and for BDS and GALILEO by overlapping our daily orbit solution. The stability of inter-frequency bias of GLONASS and inter-system biases w.r.t. GPS for GLONASS, BDS and GALILEO were investigated. At last, we carried out precise point positioning (PPP) using the multi

  1. Simultaneous Detection of Three Bacterial Seed-Borne Diseases in Rice Using Multiplex Polymerase Chain Reaction

    Directory of Open Access Journals (Sweden)

    In Jeong Kang

    2016-12-01

    Full Text Available Burkholderia glumae (bacterial grain rot, Xanthomonas oryzae pv. oryzae (bacterial leaf blight, and Acidovorax avenae subsp. avenae (bacterial brown stripe are major seedborne pathogens of rice. Based on the 16S and 23S rDNA sequences for A. avenae subsp. avenae and B. glumae, and transposase A gene sequence for X. oryzae pv. oryzae, three sets of primers had been designed to produce 402 bp for B. glumae, 490 bp for X. oryzae, and 290 bp for A. avenae subsp. avenae with the 63°C as an optimum annealing temperature. Samples collected from naturally infected fields were detected with two bacteria, B. glumae and A. avenae subsp. avenae but X. oryzae pv. oryzae was not detected. This assay can be used to identify pathogens directly from infected seeds, and will be an effective tool for the identification of the three pathogens in rice plants.

  2. Simultaneous Detection of Three Bacterial Seed-Borne Diseases in Rice Using Multiplex Polymerase Chain Reaction.

    Science.gov (United States)

    Kang, In Jeong; Kang, Mi-Hyung; Noh, Tae-Hwan; Shim, Hyeong Kwon; Shin, Dong Bum; Heu, Suggi

    2016-12-01

    Burkholderia glumae (bacterial grain rot), Xanthomonas oryzae pv. oryzae (bacterial leaf blight), and Acidovorax avenae subsp. avenae (bacterial brown stripe) are major seedborne pathogens of rice. Based on the 16S and 23S rDNA sequences for A. avenae subsp. avenae and B. glumae , and transposase A gene sequence for X. oryzae pv. oryzae , three sets of primers had been designed to produce 402 bp for B. glumae , 490 bp for X. oryzae , and 290 bp for A. avenae subsp. avenae with the 63°C as an optimum annealing temperature. Samples collected from naturally infected fields were detected with two bacteria, B. glumae and A. avenae subsp. avenae but X. oryzae pv. oryzae was not detected. This assay can be used to identify pathogens directly from infected seeds, and will be an effective tool for the identification of the three pathogens in rice plants.

  3. Detection of Peroxynitrite in Plants Exposed to Bacterial Infection.

    Science.gov (United States)

    Bellin, Diana; Delledonne, Massimo; Vandelle, Elodie

    2016-01-01

    Peroxynitrite is a highly reactive derivative of nitric oxide (NO) which is gaining attention in the plant biology community because it may play a role in NO signaling during biotic stress. Peroxynitrite can react with many different biomolecules, but its ability to nitrate the tyrosine residues of proteins is particularly important because this may regulate defense signaling in response to pathogens. The analysis of peroxynitrite levels in the context of its proposed defense role requires an accurate and specific detection method. Here, we describe a photometric assay using the fluorescent dye Hong Kong Green 2 as a specific and quantitative probe for peroxynitrite in Arabidopsis thaliana plants challenged with an avirulent strain of Pseudomonas syringae pv. tomato. This protocol includes the preparation of plant samples, the assay procedure, the measurement of peroxynitrite-specific fluorescence, and data presentation.

  4. Comparative study of anxiety index and stress coping skills in first and second year BDS students of Sinhgad Dental College, Pune

    OpenAIRE

    Rajeev Saxena

    2015-01-01

    Objectives To know the Anxiety index and stress coping skills in first and second year BDS students. Methods 188 students received a pre-validated module by Zung anxiety self-assessment tool, and Coping as measured by “Ways of coping scale by Folkman and Lazarus. Results Overall results show higher anxiety levels amongst first BDS students compared to second BDS. Conclusions Stress coping module should be introduced at the earlier stage i.e. First BDS which would help the...

  5. Bacterial gene expression detected in human faeces by reverse transcription-PCR

    NARCIS (Netherlands)

    Fitzsimons, N.A.; Akkermans, A.D.L.; Vos, de W.M.; Vaughan, E.E.

    2003-01-01

    A method to isolate and specifically detect bacterial messenger RNA (mRNA) in human faeces is presented. The surface layer protein gene slpA of Lactobacillus acidophilus ATCC 4356(T) was chosen as a model system because it is transcribed at a high level to a relatively stable mRNA (Boot et al.,

  6. Detection of bacterial blight resistant gene xa5 using linked marker ...

    African Journals Online (AJOL)

    USER

    2010-06-14

    Jun 14, 2010 ... Detection of bacterial blight resistant gene xa5 using linked marker approaches. Shahzad Amir Naveed2, Muhammad Babar3*, Ajuman Arif1, Yusaf Zafar1, Muhammad Sabar1,. Iftikhar Ali2, Muhammad Chragh1 and Muhammad Arif1. 1National Institute for Biotechnology and Genetic Engineering (NIBGE), ...

  7. Evaluation of a PCR for detection of Actinobacillus pleuropneumoniae in mixed bacterial cultures from tonsils

    DEFF Research Database (Denmark)

    Gram, T.; Ahrens, Peter; Nielsen, J.P.

    1996-01-01

    strains of A. lignieresii. The lower detection limit of the PCR test was 10(3) A. pleuropneumoniae CFU/PCR test tube and was not affected by addition of 10(6) E. coli CFU/PCR test tube. Mixed bacterial cultures from tonsils of 101 pigs from 9 different herds were tested by culture and by PCR using four...

  8. Effect of irradiation on the detection of bacterial DNA in contaminated food samples by DNA hybridization

    International Nuclear Information System (INIS)

    Rowe, T.F.; Towner, K.J.

    1994-01-01

    A membrane-based DNA hybridization technique was used in a model system to examine the effect of irradiation treatment on the detection of bacterial contamination in foodstuffs. Although hybridization signals were reduced compared with otherwise identical unirradiated food samples, artificial contamination levels in excess of 10 5 cfu per test could be distinguished in 12 of the 13 foods examined following the irradiation process. In no case were viable bacteria detected following irradiation treatment. (Author)

  9. An alternative to the BDS test: integration across the correlation integral

    Czech Academy of Sciences Publication Activity Database

    Kočenda, Evžen

    2001-01-01

    Roč. 20, č. 3 (2001), s. 337-351 ISSN 0747-4938 Institutional research plan: CEZ:AV0Z7085904 Keywords : BDS test Subject RIV: BB - Applied Statistics, Operational Research http://search. ebscohost .com/login.aspx?direct=true&db=bth&AN=8533996&site=ehost-live

  10. Evaluation on real-time dynamic performance of BDS in PPP, RTK, and INS tightly aided modes

    Science.gov (United States)

    Gao, Zhouzheng; Li, Tuan; Zhang, Hongping; Ge, Maorong; Schuh, Harald

    2018-05-01

    Since China's BeiDou satellite navigation system (BDS) began to provide regional navigation service for Asia-Pacific region after 2012, more new generation BDS satellites have been launched to further expand BDS's coverage to be global. In this contribution, precise positioning models based on BDS and the corresponding mathematical algorithms are presented in detail. Then, an evaluation on BDS's real-time dynamic positioning and navigation performance is presented in Precise Point Positioning (PPP), Real-time Kinematic (RTK), Inertial Navigation System (INS) tightly aided PPP and RTK modes by processing a set of land-borne vehicle experiment data. Results indicate that BDS positioning Root Mean Square (RMS) in north, east, and vertical components are 2.0, 2.7, and 7.6 cm in RTK mode and 7.8, 14.7, and 24.8 cm in PPP mode, which are close to GPS positioning accuracy. Meanwhile, with the help of INS, about 38.8%, 67.5%, and 66.5% improvements can be obtained by using PPP/INS tight-integration mode. Such enhancements in RTK/INS tight-integration mode are 14.1%, 34.0%, and 41.9%. Moreover, the accuracy of velocimetry and attitude determination can be improved to be better than 1 cm/s and 0.1°, respectively. Besides, the continuity and reliability of BDS in both PPP and RTK modes can also be ameliorated significantly by INS during satellite signal missing periods.

  11. An integrated microfluidic analysis microsystems with bacterial capture enrichment and in-situ impedance detection

    Science.gov (United States)

    Liu, Hai-Tao; Wen, Zhi-Yu; Xu, Yi; Shang, Zheng-Guo; Peng, Jin-Lan; Tian, Peng

    2017-09-01

    In this paper, an integrated microfluidic analysis microsystems with bacterial capture enrichment and in-situ impedance detection was purposed based on microfluidic chips dielectrophoresis technique and electrochemical impedance detection principle. The microsystems include microfluidic chip, main control module, and drive and control module, and signal detection and processing modulet and result display unit. The main control module produce the work sequence of impedance detection system parts and achieve data communication functions, the drive and control circuit generate AC signal which amplitude and frequency adjustable, and it was applied on the foodborne pathogens impedance analysis microsystems to realize the capture enrichment and impedance detection. The signal detection and processing circuit translate the current signal into impendence of bacteria, and transfer to computer, the last detection result is displayed on the computer. The experiment sample was prepared by adding Escherichia coli standard sample into chicken sample solution, and the samples were tested on the dielectrophoresis chip capture enrichment and in-situ impedance detection microsystems with micro-array electrode microfluidic chips. The experiments show that the Escherichia coli detection limit of microsystems is 5 × 104 CFU/mL and the detection time is within 6 min in the optimization of voltage detection 10 V and detection frequency 500 KHz operating conditions. The integrated microfluidic analysis microsystems laid the solid foundation for rapid real-time in-situ detection of bacteria.

  12. Duplex recombinase polymerase amplification assays incorporating competitive internal controls for bacterial meningitis detection.

    Science.gov (United States)

    Higgins, Owen; Clancy, Eoin; Forrest, Matthew S; Piepenburg, Olaf; Cormican, Martin; Boo, Teck Wee; O'Sullivan, Nicola; McGuinness, Claire; Cafferty, Deirdre; Cunney, Robert; Smith, Terry J

    2018-01-30

    Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification technology that provides rapid and robust infectious disease pathogen detection, ideal for point-of-care (POC) diagnostics in disease-prevalent low-resource countries. We have developed and evaluated three duplex RPA assays incorporating competitive internal controls for the detection of leading bacterial meningitis pathogens. Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae singleplex RPA assays were initially developed and evaluated, demonstrating 100% specificity with limits of detection of 4.1, 8.5 and 3.9 genome copies per reaction, respectively. Each assay was further developed into internally controlled duplex RPA assays via the incorporation of internal amplification control templates. Clinical performance of each internally controlled duplex RPA assay was evaluated by testing 64 archived PCR-positive clinical samples. Compared to real-time PCR, all duplex RPA assays demonstrated 100% diagnostic specificity, with diagnostic sensitivities of 100%, 86.3% and 100% for the S. pneumoniae, N. meningitidis and H. influenzae assays, respectively. This study details the first report of internally controlled duplex RPA assays for the detection of bacterial meningitis pathogens: S. pneumoniae, N. meningitidis and H. influenzae. We have successfully demonstrated the clinical diagnostic utility of each duplex RPA assay, introducing effective diagnostic technology for POC bacterial meningitis identification in disease-prevalent developing countries. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. Broad-spectrum biosensor capable of detecting and identifying diverse bacterial and Candida species in blood.

    Science.gov (United States)

    Metzgar, David; Frinder, Mark; Lovari, Robert; Toleno, Donna; Massire, Christian; Blyn, Lawrence B; Ranken, Raymond; Carolan, Heather E; Hall, Thomas A; Moore, David; Hansen, Christian J; Sampath, Rangarajan; Ecker, David J

    2013-08-01

    We describe an assay which uses broad-spectrum, conserved-site PCR paired with mass spectrometry analysis of amplicons (PCR/electrospray ionization-mass spectrometry [ESI-MS]) to detect and identify diverse bacterial and Candida species in uncultured specimens. The performance of the assay was characterized using whole-blood samples spiked with low titers of 64 bacterial species and 6 Candida species representing the breadth of coverage of the assay. The assay had an average limit of detection of 100 CFU of bacteria or Candida per milliliter of blood, and all species tested yielded limits of detection between 20 and 500 CFU per milliliter. Over 99% of all detections yielded correct identifications, whether they were obtained at concentrations well above the limit of detection or at the lowest detectable concentrations. This study demonstrates the ability of broad-spectrum PCR/ESI-MS assays to detect and identify diverse organisms in complex natural matrices that contain high levels of background DNA.

  14. Non-labeled QCM Biosensor for Bacterial Detection using Carbohydrate and Lectin Recognitions

    Science.gov (United States)

    Shen, Zhihong; Huang, Mingchuan; Xiao, Caide; Zhang, Yun; Zeng, Xiangqun; Wang, Peng G.

    2008-01-01

    High percentages of harmful microbes or their secreting toxins bind to specific carbohydrate sequences on human cells at the recognition and attachment sites. A number of studies also show that lectins react with specific structures of bacteria and fungi. In this report, we take advantage of the fact that a high percentage of microorganisms have both carbohydrate and lectin binding pockets at their surface. We demonstrate here for the first time that a carbohydrate non-labeled mass sensor in combination with lectin-bacterial O-antigen recognition can be used for detection of high molecular weight bacterial targets with remarkably high sensitivity and specificity. A functional mannose self-assembled monolayer (SAM) in combination with lectin Con A was used as molecular recognition elements for the detection of E. coli W1485 using Quartz Crytsal Microbalance (QCM) as a transducer. The multivalent binding of Concanavalin A (Con A) to the Escherichia coli (E. coli) surface O-antigen favors the strong adhesion of E. coli to mannose modified QCM surface by forming bridges between these two. As a result, the contact area between cell and QCM surface increases that leads to rigid and strong attachment. Therefore it enhances the binding between E. coli and the mannose. Our results show a significant improvement of the sensitivity and specificity of carbohydrate QCM biosensor with a experimental detection limit of a few hundred bacterial cells. The linear range is from 7.5 × 102 to 7.5 × 107 cells/mL that is four decade wider than the mannose alone QCM sensor. The change of damping resistances for E. coli adhesion experiments was no more than 1.4% suggesting that the bacterial attachment was rigid, rather than a viscoelastic behavior. Little non-specific binding was observed for Staphylococcus aureus and other proteins (Fetal Bovine serum, Erythrina cristagalli lectin). Our approach not only overcomes the challenges of applying QCM technology for bacterial detection but

  15. Real-time detection of antibiotic activity by measuring nanometer-scale bacterial deformation

    Science.gov (United States)

    Iriya, Rafael; Syal, Karan; Jing, Wenwen; Mo, Manni; Yu, Hui; Haydel, Shelley E.; Wang, Shaopeng; Tao, Nongjian

    2017-12-01

    Diagnosing antibiotic-resistant bacteria currently requires sensitive detection of phenotypic changes associated with antibiotic action on bacteria. Here, we present an optical imaging-based approach to quantify bacterial membrane deformation as a phenotypic feature in real-time with a nanometer scale (˜9 nm) detection limit. Using this approach, we found two types of antibiotic-induced membrane deformations in different bacterial strains: polymyxin B induced relatively uniform spatial deformation of Escherichia coli O157:H7 cells leading to change in cellular volume and ampicillin-induced localized spatial deformation leading to the formation of bulges or protrusions on uropathogenic E. coli CFT073 cells. We anticipate that the approach will contribute to understanding of antibiotic phenotypic effects on bacteria with a potential for applications in rapid antibiotic susceptibility testing.

  16. Nile Red Detection of Bacterial Hydrocarbons and Ketones in a High-Throughput Format

    Energy Technology Data Exchange (ETDEWEB)

    Pinzon, NM; Aukema, KG; Gralnick, JA; Wackett, LP

    2011-06-28

    A method for use in high-throughput screening of bacteria for the production of long-chain hydrocarbons and ketones by monitoring fluorescent light emission in the presence of Nile red is described. Nile red has previously been used to screen for polyhydroxybutyrate (PHB) and fatty acid esters, but this is the first report of screening for recombinant bacteria making hydrocarbons or ketones. The microtiter plate assay was evaluated using wild-type and recombinant strains of Shewanella oneidensis and Escherichia coli expressing the enzyme OleA, previously shown to initiate hydrocarbon biosynthesis. The strains expressing exogenous Stenotrophomonas maltophilia oleA, with increased levels of ketone production as determined by gas chromatography-mass spectrometry, were distinguished with Nile red fluorescence. Confocal microscopy images of S. oneidensis oleA-expressing strains stained with Nile red were consistent with a membrane localization of the ketones. This differed from Nile red staining of bacterial PHB or algal lipid droplets that showed intracellular inclusion bodies. These results demonstrated the applicability of Nile red in a high-throughput technique for the detection of bacterial hydrocarbons and ketones. IMPORTANCE In recent years, there has been renewed interest in advanced biofuel sources such as bacterial hydrocarbon production. Previous studies used solvent extraction of bacterial cultures followed by gas chromatography-mass spectrometry (GC-MS) to detect and quantify ketones and hydrocarbons (Beller HR, Goh EB, Keasling JD, Appl. Environ. Microbiol. 76: 1212-1223, 2010; Sukovich DJ, Seffernick JL, Richman JE, Gralnick JA, Wackett LP, Appl. Environ. Microbiol. 76: 3850-3862, 2010). While these analyses are powerful and accurate, their labor-intensive nature makes them intractable to high-throughput screening; therefore, methods for rapid identification of bacterial strains that are overproducing hydrocarbons are needed. The use of high

  17. Detection of respiratory bacterial pathogens causing atypical pneumonia by multiplex Lightmix®RT-PCR.

    Science.gov (United States)

    Wagner, Karoline; Springer, Burkard; Imkamp, Frank; Opota, Onya; Greub, Gilbert; Keller, Peter M

    2018-04-01

    Pneumonia is a severe infectious disease. In addition to common viruses and bacterial pathogens (e.g. Streptococcus pneumoniae), fastidious respiratory pathogens like Chlamydia pneumoniae, Mycoplasma pneumoniae and Legionella spp. can cause severe atypical pneumonia. They do not respond to penicillin derivatives, which may cause failure of antibiotic empirical therapy. The same applies for infections with B. pertussis and B. parapertussis, the cause of pertussis disease, that may present atypically and need to be treated with macrolides. Moreover, these fastidious bacteria are difficult to identify by culture or serology, and therefore often remain undetected. Thus, rapid and accurate identification of bacterial pathogens causing atypical pneumonia is crucial. We performed a retrospective method evaluation study to evaluate the diagnostic performance of the new, commercially available Lightmix ® multiplex RT-PCR assay that detects these fastidious bacterial pathogens causing atypical pneumonia. In this retrospective study, 368 clinical respiratory specimens, obtained from patients suffering from atypical pneumonia that have been tested negative for the presence of common agents of pneumonia by culture and viral PCR, were investigated. These clinical specimens have been previously characterized by singleplex RT-PCR assays in our diagnostic laboratory and were used to evaluate the diagnostic performance of the respiratory multiplex Lightmix ® RT-PCR. The multiplex RT-PCR displayed a limit of detection between 5 and 10 DNA copies for different in-panel organisms and showed identical performance characteristics with respect to specificity and sensitivity as in-house singleplex RT-PCRs for pathogen detection. The Lightmix ® multiplex RT-PCR assay represents a low-cost, time-saving and accurate diagnostic tool with high throughput potential. The time-to-result using an automated DNA extraction device for respiratory specimens followed by multiplex RT-PCR detection was

  18. Comparison of enterovirus detection in cerebrospinal fluid with Bacterial Meningitis Score in children

    OpenAIRE

    Pires, Frederico Ribeiro; Franco, Andréia Christine Bonotto Farias; Gilio, Alfredo Elias; Troster, Eduardo Juan

    2017-01-01

    ABSTRACT Objective To measure the role of enterovirus detection in cerebrospinal fluid compared with the Bacterial Meningitis Score in children with meningitis. Methods A retrospective cohort based on analysis of medical records of pediatric patients diagnosed as meningitis, seen at a private and tertiary hospital in São Paulo, Brazil, between 2011 and 2014. Excluded were patients with critical illness, purpura, ventricular shunt or recent neurosurgery, immunosuppression, concomitant bact...

  19. Rapid detection of bacterial meningitis using a point-of-care glucometer.

    Science.gov (United States)

    Rousseau, Geoffroy; Asmolov, Romain; Grammatico-Guillon, Leslie; Auvet, Adrien; Laribi, Said; Garot, Denis; Jouan, Youenn; Dequin, Pierre-François; Guillon, Antoine

    2017-08-10

    In case of acute bacterial meningitis, a decision on the need for intensive care admission should be made within the first hour. The aim of this study was to assess the ability of a point-of-care glucometer to determine abnormal cerebrospinal fluid (CSF) glucose concentration at the bedside that contributes toward bacterial meningitis diagnosis. We carried out a prospective study and simultaneously measured the glucose concentrations in CSF and blood using a central laboratory and a point-of-care glucometer. We compared CSF/blood glucose ratios obtained at the bedside with a glucometer versus those obtained by the central laboratory. We determined the performance characteristics of the CSF/blood glucose ratio provided by a glucometer to detect bacterial infection in the CSF immediately after CSF sampling. We screened 201 CSF collection procedures during the study period and included 172 samples for analysis. Acute bacterial meningitis was diagnosed in 17/172 (9.9%) of CSF samples. The median turnaround time for a point-of-care glucometer analysis was 5 (interquartile range 2-10) min versus 112 (interquartile range 86-154) min for the central laboratory (P<0.0001). The optimal cut-off of the CSF/blood glucose ratio calculated from a bedside glucometer was 0.46, with a sensitivity of 94.1% (95% confidence interval: 71.3-99.9%), a specificity of 91% (95% confidence interval: 85.3-95%), and a positive likelihood ratio of 10. A glucometer accurately detects an abnormal CSF/blood glucose ratio immediately after the lumbar puncture. This cheap point-of-care method has the potential to speed up the diagnostic process of patients with bacterial meningitis.

  20. Dynamic laser speckle to detect motile bacterial response of Pseudomonas aeruginosa

    International Nuclear Information System (INIS)

    Sendra, H; Murialdo, S; Passoni, L

    2007-01-01

    This proposal deals with the technique for detection of motile response of Pseudomonas aeruginosa using dynamic laser speckle or biospeckle as an alternative method. The study of bacterial displacement plays an essential role in biocatalysts processes and biodegradation. Hence, some biodegrading enzymes are benign catalytic that could be used for the production of industrially useful compounds as well as in wastewater treatments. This work presents an experimental set up and a computational process using frame sequences of dynamic laser speckle as a novel application. The objective was the detection of different levels of motility in bacteria. The encouraging results were achieved through a direct and non invasive observation method of the phenomenon

  1. Application of photostable quantum dots for indirect immunofluorescent detection of specific bacterial serotypes on small marine animals

    International Nuclear Information System (INIS)

    Decho, Alan W; Beckman, Erin M; Chandler, G Thomas; Kawaguchi, Tomohiro

    2008-01-01

    An indirect immunofluorescence approach was developed using semiconductor quantum dot nanocrystals to label and detect a specific bacterial serotype of the bacterial human pathogen Vibrio parahaemolyticus, attached to small marine animals (i.e. benthic harpacticoid copepods), which are suspected pathogen carriers. This photostable labeling method using nanotechnology will potentially allow specific serotypes of other bacterial pathogens to be detected with high sensitivity in a range of systems, and can be easily applied for sensitive detection to other Vibrio species such as Vibrio cholerae

  2. Detection of human bacterial pathogens in ticks collected from Louisiana black bears (Ursus americanus luteolus).

    Science.gov (United States)

    Leydet, Brian F; Liang, Fang-Ting

    2013-04-01

    There are 4 major human-biting tick species in the northeastern United States, which include: Amblyomma americanum, Amblyomma maculatum, Dermacentor variabilis, and Ixodes scapularis. The black bear is a large mammal that has been shown to be parasitized by all the aforementioned ticks. We investigated the bacterial infections in ticks collected from Louisiana black bears (Ursus americanus subspecies luteolus). Eighty-six ticks were collected from 17 black bears in Louisiana from June 2010 to March 2011. All 4 common human-biting tick species were represented. Each tick was subjected to polymerase chain reaction (PCR) targeting select bacterial pathogens and symbionts. Bacterial DNA was detected in 62% of ticks (n=53). Rickettsia parkeri, the causative agent of an emerging spotted fever group rickettsiosis, was identified in 66% of A. maculatum, 28% of D. variabilis, and 11% of I. scapularis. The Lyme disease bacterium, Borrelia burgdorferi, was detected in 2 I. scapularis, while one A. americanum was positive for Borrelia bissettii, a putative human pathogen. The rickettsial endosymbionts Candidatus Rickettsia andeanae, rickettsial endosymbiont of I. scapularis, and Rickettsia amblyommii were detected in their common tick hosts at 21%, 39%, and 60%, respectively. All ticks were PCR-negative for Anaplasma phagocytophilum, Ehrlichia spp., and Babesia microti. This is the first reported detection of R. parkeri in vector ticks in Louisiana; we also report the novel association of R. parkeri with I. scapularis. Detection of both R. parkeri and B. burgdorferi in their respective vectors in Louisiana demands further investigation to determine potential for human exposure to these pathogens. Copyright © 2013 Elsevier GmbH. All rights reserved.

  3. Novel detection system for biomolecules using nano-sized bacterial magnetic particles and magnetic force microscopy.

    Science.gov (United States)

    Amemiya, Yosuke; Tanaka, Tsuyoshi; Yoza, Brandon; Matsunaga, Tadashi

    2005-11-21

    A system for streptavidin detection using biotin conjugated to nano-sized bacterial magnetic particles (BMPs) has been developed. BMPs, isolated from magnetic bacteria, were used as magnetic markers for magnetic force microscopy (MFM) imaging. The magnetic signal was obtained from a single particle using MFM without application of an external magnetic field. The number of biotin conjugated BMPs (biotin-BMPs) bound to streptavidin immobilized on the glass slides increased with streptavidin concentrations up to 100 pg/ml. The minimum streptavidin detection limit using this technique is 1 pg/ml, which is 100 times more sensitive than a conventional fluorescent detection system. This is the first report using single domain nano-sized magnetic particles as magnetic markers for biosensing. This assay system can be used for immunoassay and DNA detection with high sensitivities.

  4. Species Specific Bacterial Spore Detection Using Lateral-Flow Immunoassay with DPA-Triggered Tb Luminescence

    Science.gov (United States)

    Ponce, Adrian

    2003-01-01

    A method of detecting bacterial spores incorporates (1) A method of lateral-flow immunoassay in combination with (2) A method based on the luminescence of Tb3+ ions to which molecules of dipicolinic acid (DPA) released from the spores have become bound. The present combination of lateral-flow immunoassay and DPA-triggered Tb luminescence was developed as a superior alternative to a prior lateral-flow immunoassay method in which detection involves the visual observation and/or measurement of red light scattered from colloidal gold nanoparticles. The advantage of the present combination method is that it affords both (1) High selectivity for spores of the species of bacteria that one seeks to detect (a characteristic of lateral-flow immunoassay in general) and (2) Detection sensitivity much greater (by virtue of the use of DPA-triggered Tb luminescence instead of gold nanoparticles) than that of the prior lateral-flow immunoassay method

  5. Investigation of polymerase chain reaction assays to improve detection of bacterial involvement in bovine respiratory disease.

    Science.gov (United States)

    Bell, Colin J; Blackburn, Paul; Elliott, Mark; Patterson, Tony I A P; Ellison, Sean; Lahuerta-Marin, Angela; Ball, Hywel J

    2014-09-01

    Bovine respiratory disease (BRD) causes severe economic losses to the cattle farming industry worldwide. The major bacterial organisms contributing to the BRD complex are Mannheimia haemolytica, Histophilus somni, Mycoplasma bovis, Pasteurella multocida, and Trueperella pyogenes. The postmortem detection of these organisms in pneumonic lung tissue is generally conducted using standard culture-based techniques where the presence of therapeutic antibiotics in the tissue can inhibit bacterial isolation. In the current study, conventional and real-time polymerase chain reaction (PCR) assays were used to assess the prevalence of these 5 organisms in grossly pneumonic lung samples from 150 animals submitted for postmortem examination, and the results were compared with those obtained using culture techniques. Mannheimia haemolytica was detected in 51 cases (34%) by PCR and in 33 cases (22%) by culture, H. somni was detected in 35 cases (23.3%) by PCR and in 6 cases (4%) by culture, Myc. bovis was detected in 53 cases (35.3%) by PCR and in 29 cases (19.3%) by culture, P. multocida was detected in 50 cases (33.3%) by PCR and in 31 cases (20.7%) by culture, and T. pyogenes was detected in 42 cases (28%) by PCR and in 31 cases (20.7%) by culture, with all differences being statistically significant. The PCR assays indicated positive results for 111 cases (74%) whereas 82 cases (54.6%) were culture positive. The PCR assays have demonstrated a significantly higher rate of detection of all 5 organisms in cases of pneumonia in cattle in Northern Ireland than was detected by current standard procedures. © 2014 The Author(s).

  6. Impact of the Initial State on BDS Real-Time Orbit Determination Filter Convergence

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    Yun Qing

    2018-01-01

    Full Text Available High precision real-time orbit of navigation satellites are usually predicted based on batch estimation solutions, which is highly dependent on the accuracy of the dynamic model. However, for the BDS satellites, the accuracy and reliability of the predicted orbit usually decrease due to the inaccurate dynamic model or orbit maneuvers. To improve this situation, the sequential estimation Square Root Information Filtering (SRIF was applied to determine the real-time BDS orbits. In the filter algorithm, usually a long period is required for the orbit to converge to the final accuracy, due to lake of accurate initial state. This paper focuses on the impact of the initial state with different a priori Standard Deviation (STD on the BDS orbit convergence performance in both normal and abnormal periods. For the normal period, the Ultra-Rapid (UR orbit products and the Broadcast Ephemerides (BRDC used as initial orbits are discussed respectively. For the abnormal period, orbit maneuver is analyzed. Experimental results show that a proper a priori STD of initial state can significantly accelerate the orbit convergence, while a loose a priori STD takes more than 10 h to converge in the radial direction for the BDS GEO/IGSO/MEO satellites. When the UR orbit product is used as the initial orbit, the orbit of the IGSO/MEO satellites can converge to decimeter-level immediately. When the BRDC product is used, the accuracy of meter-level can be obtained for the IGSO/MEO immediately, and converge to decimeter-level in about 6 h. For the period after the orbit maneuver, the real-time orbit accuracy can reach meter-level in about 6 h after the first group of broadcast ephemerides is received.

  7. Three-frequency BDS precise point positioning ambiguity resolution based on raw observables

    Science.gov (United States)

    Li, Pan; Zhang, Xiaohong; Ge, Maorong; Schuh, Harald

    2018-02-01

    All BeiDou navigation satellite system (BDS) satellites are transmitting signals on three frequencies, which brings new opportunity and challenges for high-accuracy precise point positioning (PPP) with ambiguity resolution (AR). This paper proposes an effective uncalibrated phase delay (UPD) estimation and AR strategy which is based on a raw PPP model. First, triple-frequency raw PPP models are developed. The observation model and stochastic model are designed and extended to accommodate the third frequency. Then, the UPD is parameterized in raw frequency form while estimating with the high-precision and low-noise integer linear combination of float ambiguity which are derived by ambiguity decorrelation. Third, with UPD corrected, the LAMBDA method is used for resolving full or partial ambiguities which can be fixed. This method can be easily and flexibly extended for dual-, triple- or even more frequency. To verify the effectiveness and performance of triple-frequency PPP AR, tests with real BDS data from 90 stations lasting for 21 days were performed in static mode. Data were processed with three strategies: BDS triple-frequency ambiguity-float PPP, BDS triple-frequency PPP with dual-frequency (B1/B2) and three-frequency AR, respectively. Numerous experiment results showed that compared with the ambiguity-float solution, the performance in terms of convergence time and positioning biases can be significantly improved by AR. Among three groups of solutions, the triple-frequency PPP AR achieved the best performance. Compared with dual-frequency AR, additional the third frequency could apparently improve the position estimations during the initialization phase and under constraint environments when the dual-frequency PPP AR is limited by few satellite numbers.

  8. Current advances in aptamer-assisted technologies for detecting bacterial and fungal toxins.

    Science.gov (United States)

    Alizadeh, N; Memar, M Y; Mehramuz, B; Abibiglou, S S; Hemmati, F; Samadi Kafil, H

    2018-03-01

    Infectious diseases are among the common leading causes of morbidity and mortality worldwide. Associated with the emergence of new infectious diseases, the increasing number of antimicrobial-resistant isolates presents a serious threat to public health and hospitalized patients. A microbial pathogen may elicit several host responses and use a variety of mechanisms to evade host defences. These methods and mechanisms include capsule, lipopolysaccharides or cell wall components, adhesions and toxins. Toxins inhibit phagocytosis, cause septic shock and host cell damages by binding to host surface receptors and invasion. Bacterial and fungal pathogens are able to apply many different toxin-dependent mechanisms to disturb signalling pathways and the structural integrity of host cells for establishing and maintaining infections Initial techniques for analysis of bacterial toxins were based on in vivo or in vitro assessments. There is a permanent demand for appropriate detection methods which are affordable, practical, careful, rapid, sensitive, efficient and economical. Aptamers are DNA or RNA oligonucleotides that are selected by systematic evolution of ligands using exponential enrichment (SELEX) methods and can be applied in diagnostic applications. This review provides an overview of aptamer-based methods as a novel approach for detecting toxins in bacterial and fungal pathogens. © 2017 The Society for Applied Microbiology.

  9. Comparison of individual and pooled sampling methods for detecting bacterial pathogens of fish

    Science.gov (United States)

    Mumford, Sonia; Patterson, Chris; Evered, J.; Brunson, Ray; Levine, J.; Winton, J.

    2005-01-01

    Examination of finfish populations for viral and bacterial pathogens is an important component of fish disease control programs worldwide. Two methods are commonly used for collecting tissue samples for bacteriological culture, the currently accepted standards for detection of bacterial fish pathogens. The method specified in the Office International des Epizooties Manual of Diagnostic Tests for Aquatic Animals permits combining renal and splenic tissues from as many as 5 fish into pooled samples. The American Fisheries Society (AFS) Blue Book/US Fish and Wildlife Service (USFWS) Inspection Manual specifies the use of a bacteriological loop for collecting samples from the kidney of individual fish. An alternative would be to more fully utilize the pooled samples taken for virology. If implemented, this approach would provide substantial savings in labor and materials. To compare the relative performance of the AFS/USFWS method and this alternative approach, cultures of Yersinia ruckeri were used to establish low-level infections in groups of rainbow trout (Oncorhynchus mykiss) that were sampled by both methods. Yersinia ruckeri was cultured from 22 of 37 groups by at least 1 method. The loop method yielded 18 positive groups, with 1 group positive in the loop samples but negative in the pooled samples. The pooled samples produced 21 positive groups, with 4 groups positive in the pooled samples but negative in the loop samples. There was statistically significant agreement (Spearman coefficient 0.80, P methods to permit detection of low-level bacterial infections of rainbow trout.

  10. Comparison of enterovirus detection in cerebrospinal fluid with Bacterial Meningitis Score in children.

    Science.gov (United States)

    Pires, Frederico Ribeiro; Franco, Andréia Christine Bonotto Farias; Gilio, Alfredo Elias; Troster, Eduardo Juan

    2017-01-01

    To measure the role of enterovirus detection in cerebrospinal fluid compared with the Bacterial Meningitis Score in children with meningitis. A retrospective cohort based on analysis of medical records of pediatric patients diagnosed as meningitis, seen at a private and tertiary hospital in São Paulo, Brazil, between 2011 and 2014. Excluded were patients with critical illness, purpura, ventricular shunt or recent neurosurgery, immunosuppression, concomitant bacterial infection requiring parenteral antibiotic therapy, and those who received antibiotics 72 hours before lumbar puncture. The study included 503 patients. Sixty-four patients were excluded and 94 were not submitted to all tests for analysis. Of the remaining 345 patients, 7 were in the Bacterial Meningitis Group and 338 in the Aseptic Meningitis Group. There was no statistical difference between the groups. In the Bacterial Meningitis Score analysis, of the 338 patients with possible aseptic meningitis (negative cultures), 121 of them had one or more points in the Bacterial Meningitis Score, with sensitivity of 100%, specificity of 64.2%, and negative predictive value of 100%. Of the 121 patients with positive Bacterial Meningitis Score, 71% (86 patients) had a positive enterovirus detection in cerebrospinal fluid. Enterovirus detection in cerebrospinal fluid was effective to differentiate bacterial from viral meningitis. When the test was analyzed together with the Bacterial Meningitis Score, specificity was higher when compared to Bacterial Meningitis Score alone. Avaliar o papel da pesquisa de enterovírus no líquido cefalorraquidiano em comparação com o Escore de Meningite Bacteriana em crianças com meningite. Coorte retrospectiva, realizada pela análise de prontuários, incluindo pacientes pediátricos, com diagnóstico de meningite e atendidos em um hospital privado e terciário, localizado em São Paulo, entre 2011 e 2014. Foram excluídos os pacientes com doença crítica, púrpura, deriva

  11. 'Bioluminescent' reporter phage for the detection of Category A bacterial pathogens.

    Science.gov (United States)

    Schofield, David A; Molineux, Ian J; Westwater, Caroline

    2011-07-08

    Yersinia pestis and Bacillus anthracis are Category A bacterial pathogens that are the causative agents of the plague and anthrax, respectively. Although the natural occurrence of both diseases' is now relatively rare, the possibility of terrorist groups using these pathogens as a bioweapon is real. Because of the disease's inherent communicability, rapid clinical course, and high mortality rate, it is critical that an outbreak be detected quickly. Therefore methodologies that provide rapid detection and diagnosis are essential to ensure immediate implementation of public health measures and activation of crisis management. Recombinant reporter phage may provide a rapid and specific approach for the detection of Y. pestis and B. anthracis. The Centers for Disease Control and Prevention currently use the classical phage lysis assays for the confirmed identification of these bacterial pathogens. These assays take advantage of naturally occurring phage which are specific and lytic for their bacterial hosts. After overnight growth of the cultivated bacterium in the presence of the specific phage, the formation of plaques (bacterial lysis) provides a positive identification of the bacterial target. Although these assays are robust, they suffer from three shortcomings: 1) they are laboratory based; 2) they require bacterial isolation and cultivation from the suspected sample, and 3) they take 24-36 h to complete. To address these issues, recombinant "light-tagged" reporter phage were genetically engineered by integrating the Vibrio harveyi luxAB genes into the genome of Y. pestis and B. anthracis specific phage. The resulting luxAB reporter phage were able to detect their specific target by rapidly (within minutes) and sensitively conferring a bioluminescent phenotype to recipient cells. Importantly, detection was obtained either with cultivated recipient cells or with mock-infected clinical specimens. For demonstration purposes, here we describe the method for the phage

  12. Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations

    Science.gov (United States)

    Law, Jodi Woan-Fei; Ab Mutalib, Nurul-Syakima; Chan, Kok-Gan; Lee, Learn-Han

    2015-01-01

    The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR), multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP) and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA) and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases. PMID:25628612

  13. Rapid Methods for the Detection of Foodborne Bacterial Pathogens: Principles, Applications, Advantages and Limitations

    Directory of Open Access Journals (Sweden)

    Law eJodi Woan-Fei

    2015-01-01

    Full Text Available The incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. Foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. The conventional methods used to detect foodborne pathogen are time consuming and laborious. Hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food analyses. Rapid detection methods can be categorized into nucleic acid-based, biosensor-based and immunological-based methods. This review emphasizes on the principles and application of recent rapid methods for the detection of foodborne bacterial pathogens. Detection methods included are simple polymerase chain reaction (PCR, multiplex PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA, loop-mediated isothermal amplification (LAMP and oligonucleotide DNA microarray which classified as nucleic acid-based methods; optical, electrochemical and mass-based biosensors which classified as biosensor-based methods; enzyme-linked immunosorbent assay (ELISA and lateral flow immunoassay which classified as immunological-based methods. In general, rapid detection methods are generally time-efficient, sensitive, specific and labor-saving. The developments of rapid detection methods are vital in prevention and treatment of foodborne diseases.

  14. Time synchronization of new-generation BDS satellites using inter-satellite link measurements

    Science.gov (United States)

    Pan, Junyang; Hu, Xiaogong; Zhou, Shanshi; Tang, Chengpan; Guo, Rui; Zhu, Lingfeng; Tang, Guifeng; Hu, Guangming

    2018-01-01

    Autonomous satellite navigation is based on the ability of a Global Navigation Satellite System (GNSS), such as Beidou, to estimate orbits and clock parameters onboard satellites using Inter-Satellite Link (ISL) measurements instead of tracking data from a ground monitoring network. This paper focuses on the time synchronization of new-generation Beidou Navigation Satellite System (BDS) satellites equipped with an ISL payload. Two modes of Ka-band ISL measurements, Time Division Multiple Access (TDMA) mode and the continuous link mode, were used onboard these BDS satellites. Using a mathematical formulation for each measurement mode along with a derivation of the satellite clock offsets, geometric ranges from the dual one-way measurements were introduced. Then, pseudoranges and clock offsets were evaluated for the new-generation BDS satellites. The evaluation shows that the ranging accuracies of TDMA ISL and the continuous link are approximately 4 cm and 1 cm (root mean square, RMS), respectively. Both lead to ISL clock offset residuals of less than 0.3 ns (RMS). For further validation, time synchronization between these satellites to a ground control station keeping the systematic time in BDT was conducted using L-band Two-way Satellite Time Frequency Transfer (TWSTFT). System errors in the ISL measurements were calibrated by comparing the derived clock offsets with the TWSTFT. The standard deviations of the estimated ISL system errors are less than 0.3 ns, and the calibrated ISL clock parameters are consistent with that of the L-band TWSTFT. For the regional BDS network, the addition of ISL measurements for medium orbit (MEO) BDS satellites increased the clock tracking coverage by more than 40% for each orbital revolution. As a result, the clock predicting error for the satellite M1S was improved from 3.59 to 0.86 ns (RMS), and the predicting error of the satellite M2S was improved from 1.94 to 0.57 ns (RMS), which is a significant improvement by a factor of 3-4.

  15. Simultaneous Detection of 13 Key Bacterial Respiratory Pathogens by Combination of Multiplex PCR and Capillary Electrophoresis.

    Science.gov (United States)

    Jiang, Lu Xi; Ren, Hong Yu; Zhou, Hai Jian; Zhao, Si Hong; Hou, Bo Yan; Yan, Jian Ping; Qin, Tian; Chen, Yu

    2017-08-01

    Lower respiratory tract infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory bacteria. To compensate for the limits of current respiratory bacteria detection methods, we developed a combination of multiplex polymerase chain reaction (PCR) and capillary electrophoresis (MPCE) assay to detect thirteen bacterial pathogens responsible for lower respiratory tract infections, including Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, Mycoplasma pneumoniae, Legionella spp., Bordetella pertussis, Mycobacterium tuberculosis complex, Corynebacterium diphtheriae, and Streptococcus pyogenes. Three multiplex PCR reactions were built, and the products were analyzed by capillary electrophoresis using the high-throughput DNA analyzer. The specificity of the MPCE assay was examined and the detection limit was evaluated using DNA samples from each bacterial strain and the simulative samples of each strain. This assay was further evaluated using 152 clinical specimens and compared with real-time PCR reactions. For this assay, three nested-multiplex-PCRs were used to detect these clinical specimens. The detection limits of the MPCE assay for the 13 pathogens were very low and ranged from 10-7 to 10-2 ng/μL. Furthermore, analysis of the 152 clinical specimens yielded a specificity ranging from 96.5%-100.0%, and a sensitivity of 100.0% for the 13 pathogens. This study revealed that the MPCE assay is a rapid, reliable, and high-throughput method with high specificity and sensitivity. This assay has great potential in the molecular epidemiological survey of respiratory pathogens. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  16. Novel aptamer-linked nanoconjugate approach for detection of waterborne bacterial pathogens: an update

    Science.gov (United States)

    Singh, Gulshan; Manohar, Murli; Adegoke, Anthony Ayodeji; Stenström, Thor Axel; Shanker, Rishi

    2017-01-01

    The lack of microbiologically safe water in underdeveloped nations is the prime cause of infectious disease outbreaks. The need for the specific identification and detection of microorganisms encourages the development of advanced, rapid, sensitive and highly specific methods for the monitoring of pathogens and management of potential risk to human health. The rapid molecular assays based on detection of specific molecular signatures offer advantages over conventional methods in terms of specificity and sensitivity but require complex instrumentation and skilled personnel. Nanotechnology is an emerging area and provides a robust approach for the identification of pathogenic microorganism utilizing the peculiar properties of nanomaterials, i.e. small size (1-100 nm) and large surface area. This emerging technology promises to fulfill the urgent need of a novel strategy to enhance the bacterial identification and quantitation in the environment. In this context, the peculiar properties of gold nanoparticles, their plasmonic shifts, and changes in magnetic properties have been utilized for the simple and cost-effective detection of bacterial nucleic acids, antigens and toxins with quite improved sensitivity. One of the promising leads to develop an advance detection method might be the coupling of nucleic acid aptamers (capable of interacting specifically with bacteria, protozoa, and viruses) with nanomaterials. Such aptamer-nano conjugate can be used for the specific recognition of infectious agents in different environmental matrices. This review summarizes the application of nanotechnology in the area of pathogen detection and discusses the prospects of coupling nucleic acid aptamers with nanoparticles for the specific detection of targeted pathogens.

  17. Novel aptamer-linked nanoconjugate approach for detection of waterborne bacterial pathogens: an update

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Gulshan, E-mail: gsingh.gulshan@gmail.com [Durban University of Technology, Institute for Water and Wastewater Technology (IWWT) (South Africa); Manohar, Murli [Jamia Hamdard (Hamdard University), Department of Biochemistry (India); Adegoke, Anthony Ayodeji; Stenström, Thor Axel [Durban University of Technology, Institute for Water and Wastewater Technology (IWWT) (South Africa); Shanker, Rishi [Ahmedabad University, Division of Biological & Life Sciences, School of Arts & Sciences (India)

    2017-01-15

    The lack of microbiologically safe water in underdeveloped nations is the prime cause of infectious disease outbreaks. The need for the specific identification and detection of microorganisms encourages the development of advanced, rapid, sensitive and highly specific methods for the monitoring of pathogens and management of potential risk to human health. The rapid molecular assays based on detection of specific molecular signatures offer advantages over conventional methods in terms of specificity and sensitivity but require complex instrumentation and skilled personnel. Nanotechnology is an emerging area and provides a robust approach for the identification of pathogenic microorganism utilizing the peculiar properties of nanomaterials, i.e. small size (1–100 nm) and large surface area. This emerging technology promises to fulfill the urgent need of a novel strategy to enhance the bacterial identification and quantitation in the environment. In this context, the peculiar properties of gold nanoparticles, their plasmonic shifts, and changes in magnetic properties have been utilized for the simple and cost-effective detection of bacterial nucleic acids, antigens and toxins with quite improved sensitivity. One of the promising leads to develop an advance detection method might be the coupling of nucleic acid aptamers (capable of interacting specifically with bacteria, protozoa, and viruses) with nanomaterials. Such aptamer-nano conjugate can be used for the specific recognition of infectious agents in different environmental matrices. This review summarizes the application of nanotechnology in the area of pathogen detection and discusses the prospects of coupling nucleic acid aptamers with nanoparticles for the specific detection of targeted pathogens.

  18. Disposable bioluminescence-based biosensor for detection of bacterial count in food.

    Science.gov (United States)

    Luo, Jinping; Liu, Xiaohong; Tian, Qing; Yue, Weiwei; Zeng, Jing; Chen, Guangquan; Cai, Xinxia

    2009-11-01

    A biosensor for rapid detection of bacterial count based on adenosine 5'-triphosphate (ATP) bioluminescence has been developed. The biosensor is composed of a key sensitive element and a photomultiplier tube used as a detector element. The disposable sensitive element consists of a sampler, a cartridge where intracellular ATP is chemically extracted from bacteria, and a microtube where the extracted ATP reacts with the luciferin-luciferase reagent to produce bioluminescence. The bioluminescence signal is transformed into relevant electrical signal by the detector and further measured with a homemade luminometer. Parameters affecting the amount of the extracted ATP, including the types of ATP extractants, the concentrations of ATP extractant, and the relevant neutralizing reagent, were optimized. Under the optimal experimental conditions, the biosensor showed a linear response to standard bacteria in a concentration range from 10(3) to 10(8) colony-forming units (CFU) per milliliter with a correlation coefficient of 0.925 (n=22) within 5min. Moreover, the bacterial count of real food samples obtained by the biosensor correlated well with those by the conventional plate count method. The proposed biosensor, with characteristics of low cost, easy operation, and fast response, provides potential application to rapid evaluation of bacterial contamination in the food industry, environment monitoring, and other fields.

  19. Development of a bacterial bioassay for atrazine and cyanuric acid detection

    Directory of Open Access Journals (Sweden)

    Anna eHUA

    2015-03-01

    Full Text Available The s-triazine herbicides are compounds which can disseminate into soils and water. Due to their toxic effects on living organisms, their concentrations in drinking water are legislated by WHO recommendations. Here we have developed for the first time, to the best of our knowledge, an alternative method for physicochemical quantification using two bioluminescent bacterial biosensors: E. coli SM003 for cyanuric acid detection and E. coli SM004 for both atrazine and cyanuric acid detection. The concentration of cyanuric acid detection for E. coli SM003 ranges from 7.83 µM to 2.89 mM, and for E. coli SM004 ranges from 0.22 µM to 15 µM. Moreover, atrazine detection by E. coli SM004 ranges from 1.08 µM to 15 µM. According to WHO recommendations, the cyanuric acid detection range is sensitive enough to discriminate between polluted and drinking water. Nevertheless, the detection of atrazine by E. coli SM004 is only applicable for high concentrations of contaminants.

  20. Oxygen measurements in platelet fluids - a new non-invasive method to detect bacterial contaminations in platelets.

    Science.gov (United States)

    Mueller, M M; Hourfar, M K; Huber, E; Sireis, W; Weichert, W; Seifried, E; Tonn, T; Schmidt, M

    2012-06-01

    The residual risk for bacterial contamination in blood components especially in platelets is one to two orders of magnitude higher than for transfusion relevant viral infections. The majority of all bacterial transmitted fatalities occurred at the end of platelet shelf life. Therefore, the maximum shelf life of platelet concentrates (PC) was reduced to 4 days after blood donation in Germany in 2008. A new continuous non-invasive bacterial detection method was developed by O(2) measurements in the platelet fluids and tested with 10 transfusion relevant bacteria species. The bacterial concentration at the time point of a positive signal of PreSense O(2) ranged between 10(2) and 10(5) CFU mL(-1) . Harmful transfusion-transmitted bacterial infection would have probably been prevented by this novel technology. Only strict anaerobic bacteria strains like Clostridium perfringens were not detected within the study period of 72 h. The described non-invasive bacterial detection method represents a new approach to prevent transmission of bacterial infection in platelets. The method is characterised by the advantage that all investigations can be performed until right up to the time of transfusion, and therefore, reduce the risk for sample errors to a minimum. © 2012 The Authors. Transfusion Medicine © 2012 British Blood Transfusion Society.

  1. Comparative study of anxiety index and stress coping skills in first and second year BDS students of Sinhgad Dental College, Pune

    Directory of Open Access Journals (Sweden)

    Rajeev Saxena

    2015-01-01

    Full Text Available Objectives To know the Anxiety index and stress coping skills in first and second year BDS students. Methods 188 students received a pre-validated module by Zung anxiety self-assessment tool, and Coping as measured by “Ways of coping scale by Folkman and Lazarus. Results Overall results show higher anxiety levels amongst first BDS students compared to second BDS. Conclusions Stress coping module should be introduced at the earlier stage i.e. First BDS which would help them to be competent.

  2. Preparation of miniantibodies to Azospirillum brasilense Sp245 surface antigens and their use for bacterial detection.

    Science.gov (United States)

    Dykman, Lev A; Staroverov, Sergei A; Guliy, Olga I; Ignatov, Oleg V; Fomin, Alexander S; Vidyasheva, Irina V; Karavaeva, Olga A; Bunin, Viktor D; Burygin, Gennady L

    2012-01-01

    This article reports the first preparation of miniantibodies to Azospirillum brasilense Sp245 surface antigens by using a combinatorial phage library of sheep antibodies. The prepared phage antibodies were used for the first time for lipopolysaccharide and flagellin detection by dot assay, electro-optical analysis of cell suspensions, and transmission electron microscopy. Interaction of A. brasilense Sp245 with antilipopolysaccharide and antiflagellin phage-displayed miniantibodies caused the magnitude of the electro-optical signal to change considerably. The electro-optical results were in good agreement with the electron microscopic data. This is the first reported possibility of employing phage-displayed miniantibodies in bacterial detection aided by electro-optical analysis of cell suspensions.

  3. Label-free, multiplexed detection of bacterial tmRNA using silicon photonic microring resonators.

    Science.gov (United States)

    Scheler, Ott; Kindt, Jared T; Qavi, Abraham J; Kaplinski, Lauris; Glynn, Barry; Barry, Thomas; Kurg, Ants; Bailey, Ryan C

    2012-01-01

    A label-free biosensing method for the sensitive detection and identification of bacterial transfer-messenger RNA (tmRNA) is presented employing arrays of silicon photonic microring resonators. Species specific tmRNA molecules are targeted by complementary DNA capture probes that are covalently attached to the sensor surface. Specific hybridization is monitored in near real-time by observing the resonance wavelength shift of each individual microring. The sensitivity of the biosensing platform allowed for detection down to 53 fmol of Streptococcus pneumoniae tmRNA, equivalent to approximately 3.16×10(7) CFU of bacteria. The simplicity and scalability of this biosensing approach makes it a promising tool for the rapid identification of different bacteria via tmRNA profiling. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Bacterial and viral pathogens detected in sea turtles stranded along the coast of Tuscany, Italy.

    Science.gov (United States)

    Fichi, G; Cardeti, G; Cersini, A; Mancusi, C; Guarducci, M; Di Guardo, G; Terracciano, G

    2016-03-15

    During 2014, six loggerhead turtles, Caretta caretta and one green turtle, Chelonia mydas, found stranded on the Tuscany coast of Italy, were examined for the presence of specific bacterial and viral agents, along with their role as carriers of fish and human pathogens. Thirteen different species of bacteria, 10 Gram negative and 3 Gram positive, were identified. Among them, two strains of Vibrio parahaemolyticus and one strain of Lactococcus garviae were recovered and confirmed by specific PCR protocols. No trh and tdh genes were detected in V. parahaemolyticus. The first isolation of L. garviae and the first detection of Betanodavirus in sea turtles indicate the possibility for sea turtles to act as carriers of fish pathogens. Furthermore, the isolation of two strains of V. parahaemolyticus highlights the possible role of these animals in human pathogens' diffusion. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Analysis of bacterial metagenomes from the Southwestern Gulf of Mexico for pathogens detection.

    Science.gov (United States)

    Escobedo-Hinojosa, Wendy; Pardo-López, Liliana

    2017-07-31

    Little is known about the diversity of bacteria in the Southwestern Gulf of Mexico. The aim of the study illustrated in this perspective was to search for the presence of bacterial pathogens in this ecosystem, using metagenomic data recently generated by the Mexican research group known as the Gulf of Mexico Research Consortium. Several genera of bacteria annotated as pathogens were detected in water and sediment marine samples. As expected, native and ubiquitous pathogenic bacteria genera such as Burkolderia, Halomonas, Pseudomonas, Shewanella and Vibrio were highly represented. Surprisingly, non-native genera of public health concern were also detected, including Borrelia, Ehrlichia, Leptospira, Mycobacterium, Mycoplasma, Salmonella, Staphylococcus, Streptococcus and Treponema. While there are no previous metagenomics studies of this environment, the potential influences of natural, anthropogenic and ecological factors on the diversity of putative pathogenic bacteria found in it are reviewed. The taxonomic annotation herein reported provides a starting point for an improved understanding of bacterial biodiversity in the Southwestern Gulf of Mexico. It also represents a useful tool in public health as it may help identify infectious diseases associated with exposure to marine water and ingestion of fish or shellfish, and thus may be useful in predicting and preventing waterborne disease outbreaks. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Real-time Bacterial Detection by Single Cell Based Sensors UsingSynchrotron FTIR Spectromicroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Veiseh, Mandana; Veiseh, Omid; Martin, Michael C.; Bertozzi,Carolyn; Zhang, Miqin

    2005-08-10

    Microarrays of single macrophage cell based sensors weredeveloped and demonstrated for real time bacterium detection bysynchrotron FTIR microscopy. The cells were patterned on gold-SiO2substrates via a surface engineering technique by which the goldelectrodes were immobilized with fibronectin to mediate cell adhesion andthe silicon oxide background were passivated with PEG to resist proteinadsorption and cell adhesion. Cellular morphology and IR spectra ofsingle, double, and triple cells on gold electrodes exposed tolipopolysaccharide (LPS) of different concentrations were compared toreveal the detection capabilities of these biosensors. The single-cellbased sensors were found to generate the most significant IR wave numbervariation and thus provide the highest detection sensitivity. Changes inmorphology and IR spectrum for single cells exposed to LPS were found tobe time- and concentration-dependent and correlated with each other verywell. FTIR spectra from single cell arrays of gold electrodes withsurface area of 25 mu-m2, 100 mu-m2, and 400 mu-m2 were acquired usingboth synchrotron and conventional FTIR spectromicroscopes to study thesensitivity of detection. The results indicated that the developedsingle-cell platform can be used with conventional FTIRspectromicroscopy. This technique provides real-time, label-free, andrapid bacterial detection, and may allow for statistic and highthroughput analyses, and portability.

  7. Mass Cytometry for Detection of Silver at the Bacterial Single Cell Level

    Directory of Open Access Journals (Sweden)

    Yuting Guo

    2017-07-01

    Full Text Available Background: Mass cytometry (Cytometry by Time of Flight, CyTOF allows single-cell characterization on the basis of specific metal-based cell markers. In addition, other metals in the mass range such as silver can be detected per cell. Bacteria are known to be sensible to silver and a protocol was developed to measure both the number of affected cells per population and the quantities of silver per cell.Methods: For mass cytometry ruthenium red was used as a marker for all cells of a population while parallel application of cisplatin discriminated live from dead cells. Silver quantities per cell and frequencies of silver containing cells in a population were measured by mass cytometry. In addition, live/dead subpopulations were analyzed by flow cytometry and distinguished by cell sorting based on ruthenium red and propidium iodide double staining. Verification of the cells’ silver load was performed on the bulk level by using ICP-MS in combination with cell sorting. The protocol was developed by conveying both, fast and non-growing Pseudomonas putida cells as test organisms.Results: A workflow for labeling bacteria in order to be analyzed by mass cytometry was developed. Three different parameters were tested: ruthenium red provided counts for all bacterial cells in a population while consecutively applied cisplatin marked the frequency of dead cells. Apparent population heterogeneity was detected by different frequencies of silver containing cells. Silver quantities per cell were also well measurable. Generally, AgNP-10 treatment caused higher frequencies of dead cells, higher frequencies of silver containing cells and higher per-cell silver quantities. Due to an assumed chemical equilibrium of free and bound silver ions live and dead cells were associated with silver in equal quantities and this preferably during exponential growth. With ICP-MS up to 1.5 fg silver per bacterial cell were detected.Conclusion: An effective mass cytometry

  8. Bacterial wetwood detection in Fagus grandifolia and Prunus serotina sapwood using a conducting polymer electronic-nose device

    Science.gov (United States)

    A.D. Wilson

    2014-01-01

    New electronic gas-detection methods were developed and tested for the diagnosis of bacterial wetwood disease in Fagus grandifolia (American beech) and Prunus serotina (black cherry) using a Conducting Polymer (CP)-type electronic nose (e-nose), the Aromascan A32S, based on detection of headspace...

  9. The study and realization of BDS un-differenced network-RTK based on raw observations

    Science.gov (United States)

    Tu, Rui; Zhang, Pengfei; Zhang, Rui; Lu, Cuixian; Liu, Jinhai; Lu, Xiaochun

    2017-06-01

    A BeiDou Navigation Satellite System (BDS) Un-Differenced (UD) Network Real Time Kinematic (URTK) positioning algorithm, which is based on raw observations, is developed in this study. Given an integer ambiguity datum, the UD integer ambiguity can be recovered from Double-Differenced (DD) integer ambiguities, thus the UD observation corrections can be calculated and interpolated for the rover station to achieve the fast positioning. As this URTK model uses raw observations instead of the ionospheric-free combinations, it is applicable for both dual- and single-frequency users to realize the URTK service. The algorithm was validated with the experimental BDS data collected at four regional stations from day of year 080 to 083 in 2016. The achieved results confirmed the high efficiency of the proposed URTK for providing the rover users a rapid and precise positioning service compared to the standard NRTK. In our test, the BDS URTK can provide a positioning service with cm level accuracy, i.e., 1 cm in the horizontal components, and 2-3 cm in the vertical component. Within the regional network, the mean convergence time for the users to fix the UD ambiguities is 2.7 s for the dual-frequency observations and of 6.3 s for the single-frequency observations after the DD ambiguity resolution. Furthermore, due to the feature of realizing URTK technology under the UD processing mode, it is possible to integrate the global Precise Point Positioning (PPP) and the local NRTK into a seamless positioning service.

  10. Multi-GNSS phase delay estimation and PPP ambiguity resolution: GPS, BDS, GLONASS, Galileo

    Science.gov (United States)

    Li, Xingxing; Li, Xin; Yuan, Yongqiang; Zhang, Keke; Zhang, Xiaohong; Wickert, Jens

    2017-10-01

    This paper focuses on the precise point positioning (PPP) ambiguity resolution (AR) using the observations acquired from four systems: GPS, BDS, GLONASS, and Galileo (GCRE). A GCRE four-system uncalibrated phase delay (UPD) estimation model and multi-GNSS undifferenced PPP AR method were developed in order to utilize the observations from all systems. For UPD estimation, the GCRE-combined PPP solutions of the globally distributed MGEX and IGS stations are performed to obtain four-system float ambiguities and then UPDs of GCRE satellites can be precisely estimated from these ambiguities. The quality of UPD products in terms of temporal stability and residual distributions is investigated for GPS, BDS, GLONASS, and Galileo satellites, respectively. The BDS satellite-induced code biases were corrected for GEO, IGSO, and MEO satellites before the UPD estimation. The UPD results of global and regional networks were also evaluated for Galileo and BDS, respectively. As a result of the frequency-division multiple-access strategy of GLONASS, the UPD estimation was performed using a network of homogeneous receivers including three commonly used GNSS receivers (TRIMBLE NETR9, JAVAD TRE_G3TH DELTA, and LEICA). Data recorded from 140 MGEX and IGS stations for a 30-day period in January in 2017 were used to validate the proposed GCRE UPD estimation and multi-GNSS dual-frequency PPP AR. Our results show that GCRE four-system PPP AR enables the fastest time to first fix (TTFF) solutions and the highest accuracy for all three coordinate components compared to the single and dual system. An average TTFF of 9.21 min with 7{°} cutoff elevation angle can be achieved for GCRE PPP AR, which is much shorter than that of GPS (18.07 min), GR (12.10 min), GE (15.36 min) and GC (13.21 min). With observations length of 10 min, the positioning accuracy of the GCRE fixed solution is 1.84, 1.11, and 1.53 cm, while the GPS-only result is 2.25, 1.29, and 9.73 cm for the east, north, and vertical

  11. Comparative study of sequence aligners for detecting antibiotic resistance in bacterial metagenomes.

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    McCall, C; Xagoraraki, I

    2018-03-01

    We aim to compare the performance of Bowtie2, bwa-mem, blastn and blastx when aligning bacterial metagenomes against the Comprehensive Antibiotic Resistance Database (CARD). Simulated reads were used to evaluate the performance of each aligner under the following four performance criteria: correctly mapped, false positives, multi-reads and partials. The optimal alignment approach was applied to samples from two wastewater treatment plants to detect antibiotic resistance genes using next generation sequencing. blastn mapped with greater accuracy among the four sequence alignment approaches considered followed by Bowtie2. blastx generated the greatest number of false positives and multi-reads when aligned against the CARD. The performance of each alignment tool was also investigated using error-free reads. Although each aligner mapped a greater number of error-free reads as compared to Illumina-error reads, in general, the introduction of sequencing errors had little effect on alignment results when aligning against the CARD. Given each performance criteria, blastn was found to be the most favourable alignment tool and was therefore used to assess resistance genes in sewage samples. Beta-lactam and aminoglycoside were found to be the most abundant classes of antibiotic resistance genes in each sample. Antibiotic resistance genes (ARGs) are pollutants known to persist in wastewater treatment plants among other environments, thus methods for detecting these genes have become increasingly relevant. Next generation sequencing has brought about a host of sequence alignment tools that provide a comprehensive look into antimicrobial resistance in environmental samples. However, standardizing practices in ARG metagenomic studies is challenging since results produced from alignment tools can vary significantly. Our study provides sequence alignment results of synthetic, and authentic bacterial metagenomes mapped against an ARG database using multiple alignment tools, and the

  12. A Genoproteomic Approach to Detect Peptide Markers of Bacterial Respiratory Pathogens.

    Science.gov (United States)

    Wang, Honghui; Drake, Steven K; Yong, Chen; Gucek, Marjan; Lyes, Matthew A; Rosenberg, Avi Z; Soderblom, Erik; Arthur Moseley, M; Dekker, John P; Suffredini, Anthony F

    2017-08-01

    Rapid identification of respiratory pathogens may facilitate targeted antimicrobial therapy. Direct identification of bacteria in bronchoalveolar lavage (BAL) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is confounded by interfering substances. We describe a method to identify unique peptide markers of 5 gram-negative bacteria by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for direct pathogen identification in BAL. In silico translation and digestion were performed on 14-25 whole genomes representing strains of Acinetobacter baumannii , Moraxella catarrhalis , Pseudomonas aeruginosa , Stenotrophomonas maltophilia , and Klebsiella pneumoniae . Peptides constituting theoretical core peptidomes in each were identified. Rapid tryptic digestion was performed; peptides were analyzed by LC-MS/MS and compared with the theoretical core peptidomes. High-confidence core peptides (false discovery rate identified and analyzed with the lowest common ancestor search to yield potential species-specific peptide markers. The species specificity of each peptide was verified with protein BLAST. Further, 1 or 2 pathogens were serially diluted into pooled inflamed BAL, and a targeted LC-MS/MS assay was used to detect 25 peptides simultaneously. Five unique peptides with the highest abundance for each pathogen distinguished these pathogens with varied detection sensitivities. Peptide markers for A. baumannii and P. aeruginosa , when spiked simultaneously into inflamed BAL, were detected with as few as 3.6 (0.2) × 10 3 and 2.2 (0.6) × 10 3 colony-forming units, respectively, by targeted LC-MS/MS. This proof-of-concept study shows the feasibility of identifying unique peptides in BAL for 5 gram-negative bacterial pathogens, and it may provide a novel approach for rapid direct identification of bacterial pathogens in BAL. © 2017 American Association for Clinical Chemistry.

  13. Evaluation of vaginal pH for detection of bacterial vaginosis

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    R Hemalatha

    2013-01-01

    Full Text Available Background & objectives : Bacterial vaginosis (BV is highly prevalent among women in reproductive age group. Little information exists on routine vaginal p H measurement in women with BV. We undertook this study to assess the utility of vaginal p H determination for initial evaluation of bacterial vaginosis. Methods : In this cross-sectional study vaginal swabs were collected from women with complaints of white discharge, back ache and pain abdomen attending a government hospital and a community health clinic, and subjected to vaginal p H determination, Gram stain, wet mount and whiff test. Nugent score and Amsel criteria were used for BV confirmation. Results : Of the 270 women included in the analysis, 154 had BV based on Nugents′ score. The mean vaginal p H in women with BV measured by p H strips and p H glove was 5 and 4.9, respectively. The vaginal p H was significantly higher in women with BV. Vaginal discharge was prevalent in 84.8 per cent women, however, only 56.8 per cent of these actually had BV by Nugent score (NS. Presence of clue cells and positive whiff test were significant for BV. Vaginal p H >4.5 by p H strips and p H Glove had a sensitivity of 72 and 79 per cent and specificity of 60 and 53 per cent, respectively to detect BV. Among the combination criteria, clue cells and glove p H >4.5 had highest sensitivity and specificity to detect BV. Interpretation & conclusions : Vaginal p H determination is relatively sensitive, but less specific in detecting women with BV. Inclusion of whiff test along with p H test reduced the sensitivity, but improved specificity. Both, the p H strip and p H glove are equally suitable for screening women with BV on outpatient basis.

  14. Application of Recombinant Factor C Reagent for the Detection of Bacterial Endotoxins in Pharmaceutical Products.

    Science.gov (United States)

    Bolden, Jay; Smith, Kelly

    2017-01-01

    Recombinant Factor C (rFC) is non-animal-derived reagent used to detect bacterial endotoxins in pharmaceutical products. Despite the fact that the reagent was first commercially available nearly 15 years ago, the broad use of rFC in pharmaceutical industry has long been lagging, presumably due to historical single-source supplier concerns and the lack of inclusion in worldwide pharmacopeias. Commercial rFC reagents are now available from multiple manufacturers, thus single sourcing is no longer an issue. We report here the successful validation of several pharmaceutical products by an end-point florescence-based endotoxin method using the rFC reagent. The method is equivalent or superior to the compendia bacterial endotoxins test method. Based on the comparability data and extenuating circumstances, the incorporation of the end point fluorescence technique and rFC reagent in global compendia bacterial endotoxins test chapters is desired and warranted. LAY ABSTRACT: Public health has been protected for over 30 years with the use of a purified blood product of the horseshoe crab, limulus amebocyte lysate. More recently, this blood product can be produced in biotech manufacturing processes, which reduces potential impacts to the horseshoe crab and related species dependent upon the crab, for example, migrating shorebirds. The pharmaceutical industry has been slow to adopt the use of this reagent, Recombinant Factor C (rFC), for various reasons. We evaluated the use of rFC across many pharmaceutical products, and in other feasibility demonstration experiments, and found rFC to be a suitable alternative to the animal-derived limulus amebocyte lysate. Incorporation of rFC and its analytical method into national testing standards would provide an equivalent or better test while continuing to maintain patient safety for those who depend on medicines and while securing pharmaceutical supply chains. In addition, widespread use of this method would benefit existing animal

  15. Beetroot-Pigment-Derived Colorimetric Sensor for Detection of Calcium Dipicolinate in Bacterial Spores

    Science.gov (United States)

    Gonçalves, Letícia Christina Pires; Da Silva, Sandra Maria; DeRose, Paul C.; Ando, Rômulo Augusto; Bastos, Erick Leite

    2013-01-01

    In this proof-of-concept study, we describe the use of the main red beet pigment betanin for the quantification of calcium dipicolinate in bacterial spores, including Bacillus anthracis. In the presence of europium(III) ions, betanin is converted to a water-soluble, non-luminescent orange 1∶1 complex with a stability constant of 1.4×105 L mol–1. The addition of calcium dipicolinate, largely found in bacterial spores, changes the color of the aqueous solution of [Eu(Bn)+] from orange to magenta. The limit of detection (LOD) of calcium dipicolinate is around 2.0×10–6 mol L–1 and the LOD determined for both spores, B. cereus and B. anthracis, is (1.1±0.3)×106 spores mL–1. This simple, green, fast and low cost colorimetric assay was selective for calcium dipicolinate when compared to several analogous compounds. The importance of this work relies on the potential use of betalains, raw natural pigments, as colorimetric sensors for biological applications. PMID:24019934

  16. A Feasibility Study for Microwave Breast Cancer Detection Using Contrast-Agent-Loaded Bacterial Microbots

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    Yifan Chen

    2013-01-01

    Full Text Available We propose a new approach to microwave breast tumor sensing and diagnosis based on the use of biocompatible flagellated magnetotactic bacteria (MTB adapted to operate in human microvasculature. It has been verified experimentally by Martel et al. that externally generated magnetic gradients could be applied to guide the MTB along preplanned routes inside the human body, and a nanoload could be attached to these bacterial microbots. Motivated by these useful properties, we suggest loading a nanoscale microwave contrast agent such as carbon nanotubes (CNTs or ferroelectric nanoparticles (FNPs onto the MTB in order to modify the dielectric properties of tissues near the agent-loaded bacteria. Subsequently, we propose a novel differential microwave imaging (DMI technique to track simultaneously multiple swarms of MTB microbots injected into the breast. We also present innovative strategies to detect and localize a breast tissue malignancy and estimate its size via this DMI-trackable bacterial microrobotic system. Finally, we use an anatomically realistic numerical breast phantom as a platform to demonstrate the feasibility of this tumor diagnostic method.

  17. Recent Developments in Antibody-Based Assays for the Detection of Bacterial Toxins

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    Kui Zhu

    2014-04-01

    Full Text Available Considering the urgent demand for rapid and accurate determination of bacterial toxins and the recent promising developments in nanotechnology and microfluidics, this review summarizes new achievements of the past five years. Firstly, bacterial toxins will be categorized according to their antibody binding properties into low and high molecular weight compounds. Secondly, the types of antibodies and new techniques for producing antibodies are discussed, including poly- and mono-clonal antibodies, single-chain variable fragments (scFv, as well as heavy-chain and recombinant antibodies. Thirdly, the use of different nanomaterials, such as gold nanoparticles (AuNPs, magnetic nanoparticles (MNPs, quantum dots (QDs and carbon nanomaterials (graphene and carbon nanotube, for labeling antibodies and toxins or for readout techniques will be summarized. Fourthly, microscale analysis or minimized devices, for example microfluidics or lab-on-a-chip (LOC, which have attracted increasing attention in combination with immunoassays for the robust detection or point-of-care testing (POCT, will be reviewed. Finally, some new materials and analytical strategies, which might be promising for analyzing toxins in the near future, will be shortly introduced.

  18. [Clinical analysis of patients with bacterial meningitis in childhood and reevaluation of rapid antigen detection methods].

    Science.gov (United States)

    Nakamura, A; Kuroki, H; Ohshima, H; Sugioka, T; Ishiwada, N; Takeda, N; Aizawa, J; Ohkusu, K

    1999-09-01

    Twenty-eight cases of bacterial meningitis during the recent ten years were analyzed retrospectively, and the following results were obtained. 1. Pathogens were as follows; H. influenzae 13 (46.4%), S. pneumoniae 8 (28.6%), S. agalactiae 4 (14.3%), E. coli 2 (7.1%), and L. monocytogenes 1 case (3.6%). 2. Twelve out of the thirteen H. influenzae cases were caused by serotype b (Hib), and 2 strains were beta-lactamase producer. Fifty percent of the S. pneumoniae cases were caused by penicillin-resistant strains. And all these resistant strains belonged to serotype 19 or 23. 3. Underlying diseases related to the onset of meningitis were found in 46% of the cases, and these consisted of CNS shunt operated 5, asplenia or polysplenia 2, Mondini's anomaly 1, sacral dermal sinus 1, and neonate 4 cases. 4. Prognosis of these cases were three deaths, four with neurologic sequelae, and twenty-one complete recoveries. 5. On admission, 85% (17/20) of the cases were diagnosed correctly by the rapid antigen detection. Sensitivity and specificity of the rapid antigen detection by using latex particle agglutination is 90% and 100% in the Hib cases, and 83% and 100% in the S. pneumoniae cases respectively. Moreover, the bacteriologically unknown 2 cases caused by parenteral partial treatment were also diagnosed by the detection of antigen in concentrated urine.

  19. Preparation of Pd/Bacterial Cellulose Hybrid Nanofibers for Dopamine Detection

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    Dawei Li

    2016-05-01

    Full Text Available Palladium nanoparticle-bacterial cellulose (PdBC hybrid nanofibers were synthesized by in-situ chemical reduction method. The obtained PdBC nanofibers were characterized by a series of analytical techniques. The results revealed that Pd nanoparticles were evenly dispersed on the surfaces of BC nanofibers. Then, the as-prepared PdBC nanofibers were mixed with laccase (Lac and Nafion to obtain mixture suspension, which was further modified on electrode surface to construct novel biosensing platform. Finally, the prepared electrochemical biosensor was employed to detect dopamine. The analysis result was satisfactory, the sensor showed excellent electrocatalysis towards dopamine with high sensitivity (38.4 µA·mM−1, low detection limit (1.26 µM, and wide linear range (5–167 µM. Moreover, the biosensor also showed good repeatability, reproducibility, selectivity and stability and was successfully used in the detection of dopamine in human urine, thus providing a promising method for dopamine analysis in clinical application.

  20. High-Precision Ionosphere Monitoring Using Continuous Measurements from BDS GEO Satellites

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    Haiyan Yang

    2018-02-01

    Full Text Available The current constellation of the BeiDou Navigation Satellite System (BDS consists of five geostationary earth orbit (GEO satellites, five inclined geosynchronous satellite orbit (IGSO satellites, and four medium earth orbit (MEO satellites. The advantage of using GEO satellites to monitor the ionosphereis the almost motionless ionospheric pierce point (IPP, which is analyzed in comparison with the MEO and IGSO satellites. The results from the analysis of the observations using eight tracking sites indicate that the ionospheric total electron content (TEC sequence derived from each GEO satellite at their respective fixed IPPs is always continuous. The precision of calculated vertical TEC (VTEC using BDS B1/B2, B1/B3, and B2/B3 dual-frequency combinationsis compared and analyzed. The VTEC12 precision based on the B1/B2 dual-frequency measurements using the smoothed code and the raw code combination is 0.69 and 5.54 TECU, respectively, which is slightly higher than VTEC13 and much higher than VTEC23. Furthermore, the ionospheric monitoring results of site JFNG in the northern hemisphere, and CUT0 in the southern hemisphere during the period from 1 January to 31 December 2015 are presented and discussed briefly.

  1. High-Precision Ionosphere Monitoring Using Continuous Measurements from BDS GEO Satellites.

    Science.gov (United States)

    Yang, Haiyan; Yang, Xuhai; Zhang, Zhe; Zhao, Kunjuan

    2018-02-27

    The current constellation of the BeiDou Navigation Satellite System (BDS) consists of five geostationary earth orbit (GEO) satellites, five inclined geosynchronous satellite orbit (IGSO) satellites, and four medium earth orbit (MEO) satellites. The advantage of using GEO satellites to monitor the ionosphereis the almost motionless ionospheric pierce point (IPP), which is analyzed in comparison with the MEO and IGSO satellites. The results from the analysis of the observations using eight tracking sites indicate that the ionospheric total electron content (TEC) sequence derived from each GEO satellite at their respective fixed IPPs is always continuous. The precision of calculated vertical TEC (VTEC) using BDS B1/B2, B1/B3, and B2/B3 dual-frequency combinationsis compared and analyzed. The VTEC 12 precision based on the B1/B2 dual-frequency measurements using the smoothed code and the raw code combination is 0.69 and 5.54 TECU, respectively, which is slightly higher than VTEC 13 and much higher than VTEC 23 . Furthermore, the ionospheric monitoring results of site JFNG in the northern hemisphere, and CUT0 in the southern hemisphere during the period from 1 January to 31 December 2015 are presented and discussed briefly.

  2. Preface: BeiDou Navigation Satellite System (BDS)/GNSS+: New developments and emerging applications

    Science.gov (United States)

    Jin, Shuanggen

    2017-12-01

    The China's BeiDou Navigation Satellite System (BDS) has been developed and operated well with over 25 launched satellites in 2017, including fifteen Medium Earth orbit (MEO) satellites, five geostationary Earth orbit (GEO) satellites and five inclined geosynchronous orbit (IGSO) satellites. Together with the United States' GPS, European Union's Galileo and Russia's GLONASS as well as other regional augmentation systems, e.g., Indian Regional Navigation Satellite System (IRNSS) and Japan Quasi-Zenith Satellite System (QZSS), more emerging applications of multi-Global Navigation Satellite Systems (GNSS) will be exploited and realized in the coming years. The papers in this issue of Advances in Space Research present new advances in the system, techniques and emerging applications of BDS/GNSS+. These papers were from an open call and a special call for participants at the 8th China Satellite Navigation Conference (CSNC 2017) held on May 23-25, 2017, Shanghai, China. This conference series provides a good platform for academic and technique exchanges as well as collaboration in satellite navigation. CSNC 2017 was well attend with more than 3000 participants and over 800 papers in 12 sessions.

  3. Concurrent Detection of Human Norovirus and Bacterial Pathogens in Water Samples from an Agricultural Region in Central California Coast

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    Peng Tian

    2017-08-01

    Full Text Available Bacterial pathogens and human norovirus (HuNoV are major cause for acute gastroenteritis caused by contaminated food and water. Public waterways can become contaminated from a variety of sources and flood after heavy rain events, leading to pathogen contamination of produce fields. We initiated a survey of several public watersheds in a major leafy green produce production region of the Central California Coast to determine the prevalence of HuNoV as well as bacterial pathogens. Moore swabs were used to collect environmental samples bi-monthly at over 30 sampling sites in the region. High prevalence of HuNoV and bacterial pathogens were detected in environmental water samples in the region. The overall detection rates of HuNoV, O157 Shiga toxin-producing Escherichia coli (STEC, non-O157 STEC, Salmonella, and Listeria were 25.58, 7.91, 9.42, 59.65, and 44.30%, respectively. The detection rates of Salmonella and L. monocytogenes were significantly higher in the spring. Fall and spring had elevated detection rates of O157 STEC. The overall detection rates of non-O157 STEC in the fall were lower than the other seasons but not significant. The overall detection rates of HuNoV were highest in fall, followed by spring and winter, with summer being lowest and significantly lower than other seasons. This study presented the first study of evaluating the correlation between the detection rate of HuNoV and the detection rates of four bacterial pathogens from environmental water. Overall, there was no significant difference in HuNoV detection rates between samples testing positive or negative for the four bacterial pathogens tested. Pathogens in animal-impacted and human-impacted areas were investigated. There were significant higher detection rates in animal-impacted areas than that of human-impacted areas for bacterial pathogens. However, there was no difference in HuNoV detection rates between these two areas. The overall detection levels of generic E

  4. Rapid detection of Mannheimia haemolytica in lung tissues of sheep and from bacterial culture

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    Jyoti Kumar

    2015-09-01

    Full Text Available Aim: This study was aimed to detect Mannheimia haemolytica in lung tissues of sheep and from a bacterial culture. Introduction: M. haemolytica is one of the most important and well-established etiological agents of pneumonia in sheep and other ruminants throughout the world. Accurate diagnosis of M. haemolytica primarily relies on bacteriological examination, biochemical characteristics and, biotyping and serotyping of the isolates. In an effort to facilitate rapid M. haemolytica detection, polymerase chain reaction assay targeting Pasteurella haemolytica serotype-1 specific antigens (PHSSA, Rpt2 and 12S ribosomal RNA (rRNA genes were used to detect M. haemolytica directly from lung tissues and from bacterial culture. Materials and Methods: A total of 12 archived lung tissues from sheep that died of pneumonia on an organized farm were used. A multiplex polymerase chain reaction (mPCR based on two-amplicons targeted PHSSA and Rpt2 genes of M. haemolytica were used for identification of M. haemolytica isolates in culture from the lung samples. All the 12 lung tissue samples were tested for the presence M. haemolytica by PHSSA and Rpt2 genes based PCR and its confirmation by sequencing of the amplicons. Results: All the 12 lung tissue samples tested for the presence of PHSSA and Rpt2 genes of M. haemolytica by mPCR were found to be positive. Amplification of 12S rRNA gene fragment as internal amplification control was obtained with each mPCR reaction performed from DNA extracted directly from lung tissue samples. All the M. haemolytica were also positive for mPCR. No amplified DNA bands were observed for negative control reactions. All the three nucleotide sequences were deposited in NCBI GenBank (Accession No. KJ534629, KJ534630 and KJ534631. Sequencing of the amplified products revealed the identity of 99-100%, with published sequence of PHSSA and Rpt2 genes of M. haemolytica available in the NCBI database. Sheep specific mitochondrial 12S r

  5. Liquid-liquid extraction and liquid chromatography-mass spectrometry detection of curcuminoids from bacterial culture medium.

    Science.gov (United States)

    Tan, Suryani; Rupasinghe, Thusitha W T; Tull, Dedreia L; Augustin, Mary Ann; Gras, Sally L

    2015-04-15

    Liquid chromatography-mass spectrometry (LC-MS) has been used to detect polyphenolic curcuminoids found in turmeric but studies of metabolism by bacterial and mammalian cells in vitro are compromised by poor recovery from the culture medium. We report a liquid-liquid extraction procedure with ethyl acetate and use LC-MS to quantify extracted curcuminoids. Ethyl acetate allows recoveries of ∼ 80-86% of curcuminoids from the bacterial growth medium, bacterial cell lysate and combined bacterial cell and growth medium matrices; a clear improvement over acetonitrile where recoveries were ∼ 25-66%. This optimised method will enable studies of curcuminoid metabolism and may be applicable to other hydrophobic polyphenolic compounds. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Comparison of PCR with Standard Method (MPN for detection of bacterial contamination in drinking water

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    Fatemeh Dehghan

    2014-11-01

    Full Text Available Background: Detection of bacterial contamination in drinking water by culture method is a time and cost consuming method and spends a few days depending on contamination degree. However, the people use the tap water during that time. Molecular methods are rapid and sensitive. In this study a rapid Multiplex PCR method was used for rapid analysis both coliform bacteria and E.coli, and probable detection of VBNC bacteria in drinking water, the experiments were performed in bacteriological lab of water and Wastewater Corporation in Markazi province. Material and Methods:Amplification of a fragment from each of lacZ and uidA genes in a Multiplex PCR was used for detection of coliforms. Eight samples was taken from Arak drinking water system including 36 samples of wells, 41 samples of water distribution network and 3 samples from water storages were examined by amplification of lacZ and uidA genes in a Multiplex PCR. Equivalently, the MPN test was applied as a standard method for all samples for comparison of results. Standard bacteria, pure bacteria isolated from positive MPN and CRM were examined by PCR and MPN method. Results: The result of most samples water network, water storages, and water well were same in both MPN and PCR method .The results of standard bacteria and pure cultures of bacteria isolated from positive MPN and CRM confirmed the PCR method. Five samples were positive in PCR but negative in MPN method. Duration time of PCR was decreased about 105 min by changing the PCR program and electrophoreses factors. Conclusion: The Multiplex PCR can detect coliform bacteria and E.coli synchronous in drinking water.

  7. Diagnostic Accuracy of Ascites Fluid Gross Appearance in Detection of Spontaneous Bacterial Peritonitis

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    Hamed Aminiahidashti

    2014-08-01

    Full Text Available Introduction: Spontaneous bacterial peritonitis (SBP as a monomicrobial infection of ascites fluid is one of the most important causes of morbidity and mortality in cirrhotic patients. This study was aimed to determine the diagnostic accuracy of ascites fluid color in detection of SBP in cirrhotic cases referred to the emergency department. Methods: Cirrhotic patients referred to the ED for the paracentesis of ascites fluid were enrolled. For all studied patients, the results of laboratory analysis and gross appearance of ascites fluid registered and reviewed by two emergency medicine specialists. The sensitivity, specificity, positive and negative predictive value, and positive and negative likelihood ration of the ascites fluid gross appearance in detection of SBP were measured with 95% confidence interval. Results: The present project was performed in 80 cirrhotic patients with ascites (52.5 female. The mean of the subjects’ age was 56.25±12.21 years (35-81. Laboratory findings revealed SBP in 23 (29% cases. Fifty nine (73% cases had transparent ascites fluid appearance of whom 17 (29% ones suffered from SBP. From 21 (26% cases with opaque ascites appearance, 15 (71% had SBP. The sensitivity and specificity of the ascites fluid appearance in detection of SBP were 46.88% (Cl: 30.87-63.55 and 87.50% (95% Cl: 75.3-94.14, respectively. Conclusion: It seems that the gross appearance of ascites fluid had poor diagnostic accuracy in detection of SBP and considering its low sensitivity, it could not be used as a good screening tool for this propose.

  8. Evaluation of two real time PCR assays for the detection of bacterial DNA in amniotic fluid.

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    Girón de Velasco-Sada, Patricia; Falces-Romero, Iker; Quiles-Melero, Inmaculada; García-Perea, Adela; Mingorance, Jesús

    2018-01-01

    The aim of this study was to evaluate two non-commercial Real-Time PCR assays for the detection of microorganisms in amniotic fluid followed by identification by pyrosequencing. We collected 126 amniotic fluids from 2010 to 2015 for the evaluation of two Real-Time PCR assays for detection of bacterial DNA in amniotic fluid (16S Universal PCR and Ureaplasma spp. specific PCR). The method was developed in the Department of Microbiology of the University Hospital La Paz. Thirty-seven samples (29.3%) were positive by PCR/pyrosequencing and/or culture, 4 of them were mixed cultures with Ureaplasma urealyticum. The Universal 16S Real-Time PCR was compared with the standard culture (81.8% sensitivity, 97.4% specificity, 75% positive predictive value, 98% negative predictive value). The Ureaplasma spp. specific Real-Time PCR was compared with the Ureaplasma/Mycoplasma specific culture (92.3% sensitivity, 89.4% specificity, 50% positive predictive value, 99% negative predictive value) with statistically significant difference (p=0.005). Ureaplasma spp. PCR shows a rapid response time (5h from DNA extraction until pyrosequencing) when comparing with culture (48h). So, the response time of bacteriological diagnosis in suspected chorioamnionitis is reduced. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Engineering Rugged Field Assays to Detect Hazardous Chemicals Using Spore-Based Bacterial Biosensors.

    Science.gov (United States)

    Wynn, Daniel; Deo, Sapna; Daunert, Sylvia

    2017-01-01

    Bacterial whole cell-based biosensors have been genetically engineered to achieve selective and reliable detection of a wide range of hazardous chemicals. Although whole-cell biosensors demonstrate many advantages for field-based detection of target analytes, there are still some challenges that need to be addressed. Most notably, their often modest shelf life and need for special handling and storage make them challenging to use in situations where access to reagents, instrumentation, and expertise are limited. These problems can be circumvented by developing biosensors in Bacillus spores, which can be engineered to address all of these concerns. In its sporulated state, a whole cell-based biosensor has a remarkably long life span and is exceptionally resistant to environmental insult. When these spores are germinated for use in analytical techniques, they show no loss in performance, even after long periods of storage under harsh conditions. In this chapter, we will discuss the development and use of whole cell-based sensors, their adaptation to spore-based biosensors, their current applications, and future directions in the field. © 2017 Elsevier Inc. All rights reserved.

  10. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes.

    Science.gov (United States)

    Scheler, Ott; Kaplinski, Lauris; Glynn, Barry; Palta, Priit; Parkel, Sven; Toome, Kadri; Maher, Majella; Barry, Thomas; Remm, Maido; Kurg, Ants

    2011-02-28

    We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  11. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

    Directory of Open Access Journals (Sweden)

    Toome Kadri

    2011-02-01

    Full Text Available Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  12. Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes

    LENUS (Irish Health Repository)

    Scheler, Ott

    2011-02-28

    Abstract Background We present a comprehensive technological solution for bacterial diagnostics using tmRNA as a marker molecule. A robust probe design algorithm for microbial detection microarray is implemented. The probes were evaluated for specificity and, combined with NASBA (Nucleic Acid Sequence Based Amplification) amplification, for sensitivity. Results We developed a new web-based program SLICSel for the design of hybridization probes, based on nearest-neighbor thermodynamic modeling. A SLICSel minimum binding energy difference criterion of 4 kcal\\/mol was sufficient to design of Streptococcus pneumoniae tmRNA specific microarray probes. With lower binding energy difference criteria, additional hybridization specificity tests on the microarray were needed to eliminate non-specific probes. Using SLICSel designed microarray probes and NASBA we were able to detect S. pneumoniae tmRNA from a series of total RNA dilutions equivalent to the RNA content of 0.1-10 CFU. Conclusions The described technological solution and both its separate components SLICSel and NASBA-microarray technology independently are applicative for many different areas of microbial diagnostics.

  13. A Police and Insurance Joint Management System Based on High Precision BDS/GPS Positioning

    Directory of Open Access Journals (Sweden)

    Wenwei Zuo

    2018-01-01

    Full Text Available Car ownership in China reached 194 million vehicles at the end of 2016. The traffic congestion index (TCI exceeds 2.0 during rush hour in some cities. Inefficient processing for minor traffic accidents is considered to be one of the leading causes for road traffic jams. Meanwhile, the process after an accident is quite troublesome. The main reason is that it is almost always impossible to get the complete chain of evidence when the accident happens. Accordingly, a police and insurance joint management system is developed which is based on high precision BeiDou Navigation Satellite System (BDS/Global Positioning System (GPS positioning to process traffic accidents. First of all, an intelligent vehicle rearview mirror terminal is developed. The terminal applies a commonly used consumer electronic device with single frequency navigation. Based on the high precision BDS/GPS positioning algorithm, its accuracy can reach sub-meter level in the urban areas. More specifically, a kernel driver is built to realize the high precision positioning algorithm in an Android HAL layer. Thus the third-party application developers can call the general location Application Programming Interface (API of the original standard Global Navigation Satellite System (GNSS to get high precision positioning results. Therefore, the terminal can provide lane level positioning service for car users. Next, a remote traffic accident processing platform is built to provide big data analysis and management. According to the big data analysis of information collected by BDS high precision intelligent sense service, vehicle behaviors can be obtained. The platform can also automatically match and screen the data that uploads after an accident to achieve accurate reproduction of the scene. Thus, it helps traffic police and insurance personnel to complete remote responsibility identification and survey for the accident. Thirdly, a rapid processing flow is established in this article to

  14. A Police and Insurance Joint Management System Based on High Precision BDS/GPS Positioning.

    Science.gov (United States)

    Zuo, Wenwei; Guo, Chi; Liu, Jingnan; Peng, Xuan; Yang, Min

    2018-01-10

    Car ownership in China reached 194 million vehicles at the end of 2016. The traffic congestion index (TCI) exceeds 2.0 during rush hour in some cities. Inefficient processing for minor traffic accidents is considered to be one of the leading causes for road traffic jams. Meanwhile, the process after an accident is quite troublesome. The main reason is that it is almost always impossible to get the complete chain of evidence when the accident happens. Accordingly, a police and insurance joint management system is developed which is based on high precision BeiDou Navigation Satellite System (BDS)/Global Positioning System (GPS) positioning to process traffic accidents. First of all, an intelligent vehicle rearview mirror terminal is developed. The terminal applies a commonly used consumer electronic device with single frequency navigation. Based on the high precision BDS/GPS positioning algorithm, its accuracy can reach sub-meter level in the urban areas. More specifically, a kernel driver is built to realize the high precision positioning algorithm in an Android HAL layer. Thus the third-party application developers can call the general location Application Programming Interface (API) of the original standard Global Navigation Satellite System (GNSS) to get high precision positioning results. Therefore, the terminal can provide lane level positioning service for car users. Next, a remote traffic accident processing platform is built to provide big data analysis and management. According to the big data analysis of information collected by BDS high precision intelligent sense service, vehicle behaviors can be obtained. The platform can also automatically match and screen the data that uploads after an accident to achieve accurate reproduction of the scene. Thus, it helps traffic police and insurance personnel to complete remote responsibility identification and survey for the accident. Thirdly, a rapid processing flow is established in this article to meet the

  15. Detection of bacterial DNA in serial synovial samples obtained during antibiotic treatment from patients with septic arthritis

    NARCIS (Netherlands)

    van der Heijden, I. M.; Wilbrink, B.; Vije, A. E.; Schouls, L. M.; Breedveld, F. C.; Tak, P. P.

    1999-01-01

    The management of septic arthritis could benefit from sensitive tests that detect the persistence of microorganisms in the joint. The aim of this study was to determine the feasibility of monitoring the presence of bacterial DNA in synovial samples from septic arthritis patients during antibiotic

  16. Detection of Pneumocystis DNA in samples from patients suspected of bacterial pneumonia--a case-control study

    DEFF Research Database (Denmark)

    Helweg-Larsen, Jannik; Jensen, Jørgen Skov; Dohn, Birthe

    2002-01-01

    Pneumocystis jiroveci (formerly known as P. carinii f.sp. hominis) is an opportunistic fungus that causes Pneumocystis pneumonia (PCP) in immunocompromised individuals. Pneumocystis jiroveci can be detected by polymerase chain reaction (PCR). To investigate the clinical importance of a positive P...... Pneumocystis-PCR among HIV-uninfected patients suspected of bacterial pneumonia, a retrospective matched case-control study was conducted....

  17. Detection of Pneumocystis DNA in samples from patients suspected of bacterial pneumonia – a case-control study

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Jensen, JS; Dohn, G

    2002-01-01

    Pneumocystis jiroveci (formerly known as P. carinii f.sp. hominis) is an opportunistic fungus that causes Pneumocystis pneumonia (PCP) in immunocompromised individuals. Pneumocystis jiroveci can be detected by polymerase chain reaction (PCR). To investigate the clinical importance of a positive P...... Pneumocystis-PCR among HIV-uninfected patients suspected of bacterial pneumonia, a retrospective matched case-control study was conducted....

  18. Multiplex detection and identification of bacterial pathogens causing potato blackleg and soft rot in Europe, using padlock probes

    NARCIS (Netherlands)

    Slawiak, M.; Doorn, van R.; Szemes, M.; Speksnijder, A.G.C.L.; Waleron, M.; Wolf, van der J.M.; Lojkowska, E.; Schoen, C.D.

    2013-01-01

    The objective of this study was to develop a multiplex detection and identification protocol for bacterial soft rot coliforms, namely Pectobacterium wasabiae (Pw), Pectobacterium atrosepticum (Pba) and Dickeya spp., responsible for potato blackleg and tuber soft rot. The procedures were derived from

  19. Bacterial overgrowth can be detected by breath hydrogen measurement before clinical manifestations in suckling lambs

    Directory of Open Access Journals (Sweden)

    András Jávor

    2015-01-01

    Full Text Available Hydrogen breath test is a non-invasive and inexpensive method for estimation of small bowel transit time, detection of excess bacteria in the small intestine and demonstration of maldigestion or malabsorption. Until now, little has been known about breath hydrogen excretion in lambs. The aim of our study was to assess the patterns of breath hydrogen excretion in lambs before and after feeding ewe’s milk, and to evaluate pathological and/or physiological alterations in the lambs’ gastrointestinal function. We assumed that intestinal disorders may influence the breath hydrogen concentrations, which could be detected early in the subclinical stage. A total of 52 healthy black-headed Dorper lambs were included in the study. Breath hydrogen was measured after overnight fasting and at 30, 60 and 90 min after the start of feeding. There was a 2-week follow-up period after the measurements to assess the gastrointestinal health of lambs. During the follow-up period, clinical signs of diarrhoea developed in 6 lambs. Based on our results in healthy lambs, the median concentration of baseline breath hydrogen was 1.00 parts per million (minimum: 0.00, maximum: 2.00. We observed a significant elevation in breath hydrogen concentrations 60 min after feeding (P = 0.004, whereas the values detected 30 min after feeding were similar to the baseline values. Regarding the lambs in which clinical signs of diarrhoea developed, we revealed significantly higher baseline breath hydrogen concentrations compared to those which remained healthy (P < 0.001. Our observations underline that hydrogen breath test may be a useful tool for indicating potential bacterial overgrowth before any clinical signs of diarrhoea.

  20. A Kalman Filter-Based Short Baseline RTK Algorithm for Single-Frequency Combination of GPS and BDS

    Directory of Open Access Journals (Sweden)

    Sihao Zhao

    2014-08-01

    Full Text Available The emerging Global Navigation Satellite Systems (GNSS including the BeiDou Navigation Satellite System (BDS offer more visible satellites for positioning users. To employ those new satellites in a real-time kinematic (RTK algorithm to enhance positioning precision and availability, a data processing model for the dual constellation of GPS and BDS is proposed and analyzed. A Kalman filter-based algorithm is developed to estimate the float ambiguities for short baseline scenarios. The entire work process of the high-precision algorithm based on the proposed model is deeply investigated in detail. The model is validated with real GPS and BDS data recorded from one zero and two short baseline experiments. Results show that the proposed algorithm can generate fixed baseline output with the same precision level as that of either a single GPS or BDS RTK algorithm. The significantly improved fixed rate and time to first fix of the proposed method demonstrates a better availability and effectiveness on processing multi-GNSSs.

  1. A Kalman filter-based short baseline RTK algorithm for single-frequency combination of GPS and BDS.

    Science.gov (United States)

    Zhao, Sihao; Cui, Xiaowei; Guan, Feng; Lu, Mingquan

    2014-08-20

    The emerging Global Navigation Satellite Systems (GNSS) including the BeiDou Navigation Satellite System (BDS) offer more visible satellites for positioning users. To employ those new satellites in a real-time kinematic (RTK) algorithm to enhance positioning precision and availability, a data processing model for the dual constellation of GPS and BDS is proposed and analyzed. A Kalman filter-based algorithm is developed to estimate the float ambiguities for short baseline scenarios. The entire work process of the high-precision algorithm based on the proposed model is deeply investigated in detail. The model is validated with real GPS and BDS data recorded from one zero and two short baseline experiments. Results show that the proposed algorithm can generate fixed baseline output with the same precision level as that of either a single GPS or BDS RTK algorithm. The significantly improved fixed rate and time to first fix of the proposed method demonstrates a better availability and effectiveness on processing multi-GNSSs.

  2. Parallel reaction monitoring on a Q Exactive mass spectrometer increases reproducibility of phosphopeptide detection in bacterial phosphoproteomics measurements.

    Science.gov (United States)

    Taumer, Christoph; Griesbaum, Lena; Kovacevic, Alen; Soufi, Boumediene; Nalpas, Nicolas C; Macek, Boris

    2018-03-29

    Increasing number of studies report the relevance of protein Ser/Thr/Tyr phosphorylation in bacterial physiology, yet the analysis of this type of modification in bacteria still presents a considerable challenge. Unlike in eukaryotes, where tens of thousands of phosphorylation events likely occupy more than two thirds of the proteome, the abundance of protein phosphorylation is much lower in bacteria. Even the state-of-the-art phosphopeptide enrichment protocols fail to remove the high background of abundant unmodified peptides, leading to low signal intensity and undersampling of phosphopeptide precursor ions in consecutive data-dependent MS runs. Consequently, large-scale bacterial phosphoproteomic datasets often suffer from poor reproducibility and a high number of missing values. Here we explore the application of parallel reaction monitoring (PRM) on a Q Exactive mass spectrometer in bacterial phosphoproteome analysis, focusing especially on run-to-run sampling reproducibility. In multiple measurements of identical phosphopeptide-enriched samples, we show that PRM outperforms data-dependent acquisition (DDA) in terms of detection frequency, reaching almost complete sampling efficiency, compared to 20% in DDA. We observe a similar trend over multiple heterogeneous phosphopeptide-enriched samples and conclude that PRM shows a great promise in bacterial phosphoproteomics analyses where reproducible detection and quantification of a relatively small set of phosphopeptides is desired. Bacterial phosphorylated peptides occur in low abundance compared to their unmodified counterparts, and are therefore rarely reproducibly detected in shotgun (DDA) proteomics measurements. Here we show that parallel reaction monitoring complements DDA analyses and makes detection of known, targeted phosphopeptides more reproducible. This will be of significance in replicated MS measurements that have a goal to reproducibly detect and quantify phosphopeptides of interest. Copyright

  3. Cooperating the BDS, GPS, GLONASS and strong-motion observations for real-time deformation monitoring

    Science.gov (United States)

    Tu, Rui

    2017-04-01

    An approach of cooperating the BDS, GPS, GLONASS and Strong-Motion (SM) records for real-time deformation monitoring was presented, and it was validated by an experiment data. For this approach, the GNSS data was processed by the RTK technology to retrieve the GNSS displacement, and the SM data was calibrated to get the raw acceleration, a Kalman filter was used to combine the GNSS displacement and the SM acceleration to obtain the integrated displacement, velocity and acceleration. The validation results show that the advantages of each sensors are completely complement; for the SM, the baseline shifts are estimated and corrected, high-precision velocity and displacement are recovered, and for the GNSS, the SM's high-resolution acceleration are used to reduce the GNSS noise, thus high-precision and broadband deformation information can be real-time obtained, it will be useful for the high-building, dam, bridge, landslide's deformation monitoring.

  4. Chemical polyglycosylation and nanolitre detection enables single-molecule recapitulation of bacterial sugar export

    Science.gov (United States)

    Kong, Lingbing; Almond, Andrew; Bayley, Hagan; Davis, Benjamin G.

    2016-05-01

    The outermost protective layer of both Gram-positive and Gram-negative bacteria is composed of bacterial capsular polysaccharides. Insights into the interactions between the capsular polysaccharide and its transporter and the mechanism of sugar export would not only increase our understanding of this key process, but would also help in the design of novel therapeutics to block capsular polysaccharide export. Here, we report a nanolitre detection system that makes use of the bilayer interface between two droplets, and we use this system to study single-molecule recapitulation of sugar export. A synthetic strategy of polyglycosylation based on tetrasaccharide monomers enables ready synthetic access to extended fragments of K30 oligosaccharides and polysaccharides. Examination of the interactions between the Escherichia coli sugar transporter Wza and very small amounts of fragments of the K30 capsular polysaccharide substrate reveal the translocation of smaller but not larger fragments. We also observe capture events that occur only on the intracellular side of Wza, which would complement coordinated feeding by adjunct biosynthetic machinery.

  5. Development of Simple Bacterial Biosensor for Phenol Detection in Water at Medium Concentration using Glass Microelectrode

    Directory of Open Access Journals (Sweden)

    Setyawan Purnomo Sakti

    2016-01-01

    Full Text Available Water is one of the most fundamental natural resources in earth. The availability of clean water becomes a global interest. Many human activities result in water pollution. One from many pollution substances in water is phenol. Phenol is a very common residual compound in industrial activity. Extensive use of phenol in industry degrades water quality. Regulation has been set in many countries to prevent further damage to the water resource caused by phenol and limiting phenol concentration in water before released into the environment. Therefor it is importance to develop a sensor which can detect phenol concentration in water to be used as a wastewater quality control system. This paper presents a development of bacterial biosensor using Pseudomonas putida and Pseudomonas fluorescens as a biological sensitive material. The sensor was made from glass micro electrode using Ag/AgCl electrode as reference electrode, silver electrode and cellulose ester. The Pseudomonas putida was entrapped inside the nutrient solution and separated by cellulose ester membrane from water containing phenol. It was found that the Pseudomonas putida in used must be growth in 10 hours to reach its optimum growth condition. Linear relationship between biosensor output voltages to phenol concentration was measured for phenol concentration below 200 ppm. The sensitivity of the developed biosensor was 72mV/ppm for Pseudomonas putida and 68.8 mV/ppm for Pseudomonas fluorescens.

  6. A novel multiplex PCR assay for simultaneous detection of nine clinically significant bacterial pathogens associated with bovine mastitis.

    Science.gov (United States)

    Ashraf, Aqeela; Imran, Muhammad; Yaqub, Tahir; Tayyab, Muhammad; Shehzad, Wasim; Thomson, Peter C

    2017-06-01

    For rapid and simultaneous detection of nine bovine mastitic pathogens, a sensitive and specific multiplex PCR assay was developed. The assay was standardized using reference strains and validated on mastitic milk cultures which were identified to species level based on 16S rRNA sequencing. Multiplex PCR assay also efficiently detected the target bacterial strains directly from milk. The detection limit of the assay was up to 50 pg for DNA isolated from pure cultures and 10 4  CFU/ml for spiked milk samples. As estimated by latent class analysis, the assay was sensitive up to 88% and specific up to 98% for targeted mastitic pathogens, compared with the bacterial culture method and the 16S rRNA sequence analysis. This novel molecular assay could be useful for monitoring and maintaining the bovine udder health, ensuring the bacteriological safety of milk, and conducting epidemiological studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Nanolitre real-time PCR detection of bacterial, parasitic, and viral agents from patients with diarrhoea in Nunavut, Canada

    Directory of Open Access Journals (Sweden)

    David M. Goldfarb

    2013-04-01

    Full Text Available Background. Little is known about the microbiology of diarrhoeal disease in Canada's Arctic regions. There are a number of limitations of conventional microbiology testing techniques for diarrhoeal pathogens, and these may be further compromised in the Arctic, given the often long distances for specimen transport. Objective. To develop a novel multiple-target nanolitre real-time reverse transcriptase (RT-PCR platform to simultaneously test diarrhoeal specimens collected from residents of the Qikiqtani (Baffin Island Region of Nunavut, Canada, for a wide range of bacterial, parasitic and viral agents. Study design/methods. Diarrhoeal stool samples submitted for bacterial culture to Qikiqtani General Hospital in Nunavut over an 18-month period were tested with a multiple-target nanolitre real-time PCR panel for major diarrhoeal pathogens including 8 bacterial, 6 viral and 2 parasitic targets. Results. Among 86 stool specimens tested by PCR, a total of 50 pathogens were detected with 1 or more pathogens found in 40 (46.5% stool specimens. The organisms detected comprised 17 Cryptosporidium spp., 5 Clostridium difficile with toxin B, 6 Campylobacter spp., 6 Salmonella spp., 4 astroviruses, 3 noroviruses, 1 rotavirus, 1 Shigella spp. and 1 Giardia spp. The frequency of detection by PCR and bacterial culture was similar for Salmonella spp., but discrepant for Campylobacter spp., as Campylobacter was detected by culture from only 1/86 specimens. Similarly, Cryptosporidium spp. was detected in multiple samples by PCR but was not detected by microscopy or enzyme immunoassay. Conclusions. Cryptosporidium spp., Campylobacter spp. and Clostridium difficile may be relatively common but possibly under-recognised pathogens in this region. Further study is needed to determine the regional epidemiology and clinical significance of these organisms. This method appears to be a useful tool for gastrointestinal pathogen research and may also be helpful for clinical

  8. Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system.

    Science.gov (United States)

    Dunbar, Sherry A; Vander Zee, Coe A; Oliver, Kerry G; Karem, Kevin L; Jacobson, James W

    2003-05-01

    Escherichia coli, Salmonella, Listeria monocytogenes and Campylobacter jejuni are bacterial pathogens commonly implicated in foodborne illnesses. Generally used detection methods (i.e., culture, biochemical testing, ELISA and nucleic acid amplification) can be laborious, time-consuming and require multiple tests to detect all of the pathogens. Our objective was to develop rapid assays to simultaneously detect these four organisms through the presence of antigen or DNA using the Luminex LabMAP system. For nucleic acid detection, organism-specific capture probes corresponding to the 23S ribosomal RNA gene (rrl) were coupled covalently to LabMAP microspheres. Target molecules included synthetic complementary oligonucleotides and genomic DNA isolated from ATCC type strains or other well-characterized strains of each organism. Universal PCR primers were designed to amplify variable regions of bacterial 23S ribosomal DNA, yielding biotinylated amplicons of 86 to 109 bp in length. Varying quantities of targets were hybridized to the combined microsphere sets, labeled with streptavidin-R-phycoerythrin and analyzed on the Luminex(100) system. Results of nucleic acid detection assays, obtained in 30 to 40 min following amplification, correctly and specifically identified each bacterial species with a detection sensitivity of 10(3) to 10(5) genome copies. Capture-sandwich immunoassays were developed with organism-specific antibodies coupled to different microsphere sets. Microspheres were incubated with organism-specific standards and reactivity was assessed with biotinylated detection antibodies and streptavidin-R-phycoerythrin. In the immunoassays, microsphere-associated fluorescence was organism concentration dependent with detectable response at detection of pathogens. The practical significance of this multiplexing approach would be to provide more timely, economical and comprehensive information than is available with conventional isolation and identification

  9. Simultaneous Detection of Three Bacterial Seed-Borne Diseases in Rice Using Multiplex Polymerase Chain Reaction

    OpenAIRE

    Kang, In Jeong; Kang, Mi-Hyung; Noh, Tae-Hwan; Shim, Hyeong Kwon; Shin, Dong Bum; Heu, Suggi

    2016-01-01

    Burkholderia glumae (bacterial grain rot), Xanthomonas oryzae pv. oryzae (bacterial leaf blight), and Acidovorax avenae subsp. avenae (bacterial brown stripe) are major seedborne pathogens of rice. Based on the 16S and 23S rDNA sequences for A. avenae subsp. avenae and B. glumae, and transposase A gene sequence for X. oryzae pv. oryzae, three sets of primers had been designed to produce 402 bp for B. glumae, 490 bp for X. oryzae, and 290 bp for A. avenae subsp. avenae with the 63°C as an opti...

  10. Detection and quantification of intracellular bacterial colonies by automated, high-throughput microscopy

    DEFF Research Database (Denmark)

    Ernstsen, Christina L; Login, Frédéric H; Jensen, Helene H.

    2017-01-01

    cell disruption or transcellular passage, to cause sepsis. Intracellular colonies are known to be clonal, originating from single invading UPEC. In our experimental setup, we found UPEC CFT073 intracellular bacterial colonies to be heterogeneous in size and present in nearly one third of the HKC-8...... day. As a model we quantified intracellular bacterial colonies formed by uropathogenic Escherichia coli (UPEC) during infection of human kidney cells (HKC-8). Urinary tract infections caused by UPEC are among the most common bacterial infectious diseases in humans. UPEC can colonize tissues...

  11. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, Mark T.

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  12. The Effect of Antibiotic Exposure and Specimen Volume on the Detection of Bacterial Pathogens in Children With Pneumonia.

    Science.gov (United States)

    Driscoll, Amanda J; Deloria Knoll, Maria; Hammitt, Laura L; Baggett, Henry C; Brooks, W Abdullah; Feikin, Daniel R; Kotloff, Karen L; Levine, Orin S; Madhi, Shabir A; O'Brien, Katherine L; Scott, J Anthony G; Thea, Donald M; Howie, Stephen R C; Adrian, Peter V; Ahmed, Dilruba; DeLuca, Andrea N; Ebruke, Bernard E; Gitahi, Caroline; Higdon, Melissa M; Kaewpan, Anek; Karani, Angela; Karron, Ruth A; Mazumder, Razib; McLellan, Jessica; Moore, David P; Mwananyanda, Lawrence; Park, Daniel E; Prosperi, Christine; Rhodes, Julia; Saifullah, Md; Seidenberg, Phil; Sow, Samba O; Tamboura, Boubou; Zeger, Scott L; Murdoch, David R

    2017-06-15

    Antibiotic exposure and specimen volume are known to affect pathogen detection by culture. Here we assess their effects on bacterial pathogen detection by both culture and polymerase chain reaction (PCR) in children. PERCH (Pneumonia Etiology Research for Child Health) is a case-control study of pneumonia in children aged 1-59 months investigating pathogens in blood, nasopharyngeal/oropharyngeal (NP/OP) swabs, and induced sputum by culture and PCR. Antibiotic exposure was ascertained by serum bioassay, and for cases, by a record of antibiotic treatment prior to specimen collection. Inoculated blood culture bottles were weighed to estimate volume. Antibiotic exposure ranged by specimen type from 43.5% to 81.7% in 4223 cases and was detected in 2.3% of 4863 controls. Antibiotics were associated with a 45% reduction in blood culture yield and approximately 20% reduction in yield from induced sputum culture. Reduction in yield of Streptococcus pneumoniae from NP culture was approximately 30% in cases and approximately 32% in controls. Several bacteria had significant but marginal reductions (by 5%-7%) in detection by PCR in NP/OP swabs from both cases and controls, with the exception of S. pneumoniae in exposed controls, which was detected 25% less frequently compared to nonexposed controls. Bacterial detection in induced sputum by PCR decreased 7% for exposed compared to nonexposed cases. For every additional 1 mL of blood culture specimen collected, microbial yield increased 0.51% (95% confidence interval, 0.47%-0.54%), from 2% when volume was ≤1 mL to approximately 6% for ≥3 mL. Antibiotic exposure and blood culture volume affect detection of bacterial pathogens in children with pneumonia and should be accounted for in studies of etiology and in clinical management. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

  13. An Internal Reference Control Duplex Real-Time Polymerase Chain Reaction Assay for Detecting Bacterial Contamination in Blood Products.

    Directory of Open Access Journals (Sweden)

    Jin-Ju Zhang

    Full Text Available Real-time polymerase chain reaction (RT-PCR enables effective and sensitive screening for infectious risk in the field of blood safety. However, when using RT-PCR to detect bacterial contamination, several intractable points must be considered, one of which is the lack of appropriate quality control. In this study, we developed a simplified RT-PCR assay in which the same primer set and two distinct probes were used to detect both, an internal reference control and the target in a reaction. The copy number of the internal reference control represents the positive detection limit of the assay; therefore, when the threshold-cycle value of the target is less than or equal to that of the internal reference control, the result obtained for the target can be considered to be a true positive. When human gDNA was spiked with Escherichia coli gDNA and the detection limit for the internal reference control was set to five copies, the measured detection limit for E. coli gDNA was two copies. The internal reference control duplex RT-PCR assay showed high efficiency (0.91-1.02, high linearity (R2 > 0.99, and good reproducibility in intra- and inter-assay comparisons. Lastly, when human platelet-rich plasma samples were spiked with E. coli or other bacterial species, all species were detected efficiently, and the results of a two-sample pooled t test showed that the limit of detection for E. coli was 1 cfu/mL. Here, we present a synthetic internal reference control molecule and a new statistical method for improving the reliability of RT-PCR assays when screening for bacterial contamination in blood products.

  14. Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

    Directory of Open Access Journals (Sweden)

    Simon M. Dittami

    2017-11-01

    Full Text Available Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast.

  15. Detection of irradiated chicken and fish meats by the determination of Gram negative bacterial count and bacterial endotoxins

    International Nuclear Information System (INIS)

    Badr, H.M.

    2010-01-01

    The aim of this investigation was to study the possibility of detecting irradiated chicken and fish meats by the determination of Gram negative bacteria combined with the determination of endotoxin concentrations. Samples of chicken breast with skin, skinless chicken breast and eviscerated Bolti fish (Tilabia nilotica) were irradiated at room temperature at doses of 0, 1.5 and 3 kGy followed by storage at refrigeration temperature (4 ± 1 degree C) for 12 days or frozen storage at -18 degree C for 60 days. Furthermore, other samples of chicken and Bolti fish were irradiated in the frozen sate at doses of 0, 3, and 7 kGy followed by frozen storage at - 18 degree C for 60 days. Then the enumeration of Gram negative bacteria in conjunction with the determination of endotoxin concentrations were carried out for both irradiated and non-irradiated samples post treatments and during storage in addition to the discovery of Pseudomonas spp. The obtained results showed that chicken and fish samples irradiated at dose of 1.5 kGy could be identified during refrigerated storage for 6 and 9 days, respectively, while all samples irradiated at dose of 3 kGy were identifiable during 12 days of refrigerated storage. Moreover, all irradiated and frozen stored samples were identifiable during their frozen storage (- 18 degree C). The absence of Pseudomonads in all irradiated samples may aid in the differentiation of irradiated and non-irradiated samples especially during refrigerated storage. This method can be applied as a general screening method to predict the possible treatment of chicken and fish meats by ionizing radiation

  16. Detection of a pathogen shift among the pectolytic bacterial pathogens of potato in Washington State

    Science.gov (United States)

    Bacterial tuber soft rot, aerial stem rot and blackleg are significant diseases of potatoes in Washington State. These diseases are caused by Pectobacterium carotovorum subsp. carotovorum, Pectobacterium atrosepticum, and Dickeya chrysanthemi, all characterized by the ability to produce pectolytic ...

  17. Clinical usefulness and accuracy of polymerase chain reaction in the detection of bacterial meningitis agents in pediatric cerebrospinal fluid.

    Science.gov (United States)

    Nour, M; Alaidarous, A

    2018-02-16

    Bacterial meningitis poses enormous healthcare challenges due to a high mortality, morbidity and sequelae. Neisseria (N.) meningitidis, Haemophilus (H.) influenzae, Streptococcus (S.) pneumoniae and S. agalactiae remain among the most prevalent infectious agents that cause bacterial meningitis in children. The objective of this study was the simultaneous detection of these pathogens in suspected cerebrospinal fluid (CSF) by using multiplex polymerase chain reaction (mPCR) and compare PCR results with standard diagnostics currently used in clinical practice. CSF specimens were obtained from 515 children (<5 years) clinically suspected of having acute bacterial meningitis. Based on bacterial culture, four isolates of salmonella sp and one Citrobacter freundii isolate were identified. The remaining 510 CSF specimens, having negative culture, were subjected to mPCR. Twenty-three (4.51%) CSF samples yielded a PCR positive signal. The pathogens identified were: S. pneumoniae (n=13), H. influenzae (n=7) and N. meningitidis (n=3). S. agalactiae was not detected. Using sequential multiplex PCR, serogrouping of S. pneumoniae revealed 3 different serotypes: serotype 19A (n=6), 19F (n=4) and serotype 23F (n=3). Only the serotype A was identified for the 3N. meningitidis isolates. Despite vaccination, S. pneumoniae remains a leading cause of pediatric invasive disease. Detecting causative organism remains the most critical aspect for management of children with suspected meningitis. PCR method is more sensitive and rapid than culture for detecting the infectious agents. Institution of PCR diagnostics is recommended for early and appropriate therapy. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  18. Observation Weight Function Design for Fusing BDS/GPS Data to Estimate the Real-time Clock with Regard to the Orbit Errors

    Directory of Open Access Journals (Sweden)

    GU Shouzhou

    2017-05-01

    Full Text Available The real-time clock product is one of the basis products for wide-area positioning service of high precision. Considering the difference between BDS orbit precision and GPS precision, we design a new observation weight function, in order to optimize the stochastic model of real time BDS/GPS clock estimation. The BDS/GPS observations of 78 MGEX global stations and 2 iGMAS stations were collected to generate the real time clock, and then the calculation results were compared with the final iGMAS precise clock product in two strategies (the old stochastic model and the new stochastic model.It shows that the method based the proposed stochastic model can improve the precision of satellite clock about 9% for GPS and 10%for BDS.

  19. Detecting the dormant: a review of recent advances in molecular techniques for assessing the viability of bacterial endospores.

    Science.gov (United States)

    Mohapatra, Bidyut R; La Duc, Myron T

    2013-09-01

    Due to their contribution to gastrointestinal and pulmonary disease, their ability to produce various deadly exotoxins, and their resistance to extreme temperature, pressure, radiation, and common chemical disinfecting agents, bacterial endospores of the Firmicutes phylum are a major concern for public and environmental health. In addition, the hardy and dormant nature of endospores renders them a particularly significant threat to the integrity of robotic extraterrestrial life-detection investigations. To prevent the contamination of critical surfaces with seemingly ubiquitous bacterial endospores, clean rooms maintained at exceedingly stringent cleanliness levels (i.e., fewer than 100,000 airborne particles per ft(3)) are used for surgical procedures, pharmaceutical processing and packaging, and fabrication and assembly of medical devices and spacecraft components. However, numerous spore-forming bacterial species have been reported to withstand typical clean room bioreduction strategies (e.g., UV lights, maintained humidity, paucity of available nutrients), which highlights the need for rapid and reliable molecular methods for detecting, enumerating, and monitoring the incidence of viable endospores. Robust means of evaluating and tracking spore burden not only provide much needed information pertaining to endospore ecophysiology in different environmental niches but also empower decontamination and bioreduction strategies aimed at sustaining the reliability and integrity of clean room environments. An overview of recent molecular advances in detecting and enumerating viable endospores, as well as the expanding phylogenetic diversity of pathogenic and clean room-associated spore-forming bacteria, ensues.

  20. Analysis on BDS Satellite Internal Multipath and Its Impact on Wide-lane FCB Estimation

    Directory of Open Access Journals (Sweden)

    RUAN Rengui

    2017-08-01

    Full Text Available To the issue of the satellite internal multipath (SIMP of BeiDou satellites, it proposed and emphasized that the SIMP model should be established as a function of the nadir angle with respect to the observed satellite rather than the elevation of the measurement, so that it can be used for receivers at various altitude. BDS data from global distributed stations operated by the International Monitoring and Assessment System (iGMAS and the Multi-GNSS Experiment (MGEX of the International GNSS Service (IGS are collected and a new SIMP model as a piece-wise linear function of the nadir angle is released for the IGSO-and MEO-satellite groups and for B1, B2 and B3 frequency band individually. The SIMP of GEO,IGSO and MEO satellites is further analyzed with B1/B2 dual-frequency data onboard the FengYun-3 C(FY3C satellite at an altitude of~830 km, and it showed that, for nadir angles smaller than 7°, the SIMP values for GEO is quite close to the IGSO's, especially for B2, which may suggest that the SIMP model for IGSO satellites possibly also works for GEO satellites. It also demonstrated that, when the nadir angle is smaller than 12°for the MEO and 7°for the IGSO, the estimated SIMP model with data from FY3C is considerable consistent with that estimated with data collected at ground stations. Experiments are carried out to investigate the impacts of the SIMP on wide-lane fractional cycle bias (FCB estimation for BDS satellites. The result indicates that, with the correction of the estimated SIMP, the repeatability of the FCB series is significantly improved by more than 60% for all satellites. Specifically, for the MEO and IGSO satellites, the repeatability is smaller than 0.05 cycle; the repeatability of 0.023 and 0.068 cycles achieved for GEO satellites C01 and C02 respectively with the estimated SIMP model for IGSO satellites.

  1. Lateral flow assay-based bacterial detection using engineered cell wall binding domains of a phage endolysin.

    Science.gov (United States)

    Kong, Minsuk; Shin, Joong Ho; Heu, Sunggi; Park, Je-Kyun; Ryu, Sangryeol

    2017-10-15

    The development of a cost-effective and efficient bacterial detection assay is essential for diagnostic fields, particularly in resource-poor settings. Although antibodies have been widely used for bacterial capture, the production of soluble antibodies is still expensive and time-consuming. Here, we developed a nitrocellulose-based lateral flow assay using cell wall binding domains (CBDs) from phage as a recognition element and colloidal gold nanoparticles as a colorimetric signal for the detection of a model pathogenic bacterium, Bacillus cereus (B. cereus). To improve conjugation efficiency and detection sensitivity, cysteine-glutathione-S-transferase-tagged CBDs and maltose-binding protein-tagged CBDs were produced in Escherichia coli (E. coli) and incorporated in our assays. The sensitivity of the strip to detect B. cereus was 1×10 4 CFU/mL and the overall assay time was 20min. The assay showed superior results compared to the antibody-based approach, and did not show any significant cross-reactivity. This proof of concept study indicates that the lateral flow assay using engineered CBDs hold considerable promise as simple, rapid, and cost-effective biosensors for whole cell detection. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Kinematic Orbit Determination Method Optimization and Test Analysis for BDS Satellites with Short-arc Tracking Data

    Directory of Open Access Journals (Sweden)

    GUO Rui

    2017-04-01

    Full Text Available Rapid orbit recovery is a puzzle for the BDS satellites after orbit maneuvers. Two kinematic orbit determination methods are studied, with two orbit determination models being established. The receiver system error and serious multipath error exist in the BDS system. The co-location method is proposed to estimate and calibrate the receiver system errors. A CNMC (code noise and multipath correction method is introduced to weaken the multipath error. Therefore the data quality is controlled efficiently for the receivers in the short tracking arc. The GEO/IGSO/MEO real data is emploied to carry out tests and validation. Using 10 min short tracking arc, the kinematic precise orbit determination accuracy is about 3.27 m for the GEOs, and 8.19 m for the IGSOs, and 5.9 m for the MEOs. Rapid orbit determination is achieved, which satisfying the orbit requirements from the BDS RDSS services. The kinematic precise orbit determination method also supports the RDSS service walking up to the global world.

  3. Development of Nested-PCR Assay to Detect Acidovorax citrulli, a Causal Agent of Bacterial Fruit Blotch at Cucurbitaceae

    Directory of Open Access Journals (Sweden)

    Young-Tak Kim

    2015-06-01

    Full Text Available The specific and sensitive nested-PCR method to detect Acidovorax citrulli, a causal agent of bacterial fruit blotch on cucurbitaceae, was developed. PCR primers were designed from the draft genome sequence which was obtained with the Next Generation Sequencing of A. citrulli KACC10651, and the nested-PCR primer set (Ac-ORF 21F/Ac-ORF 21R were selected by checking of specificity to A. citrulli with PCR assays. The selected nested-PCR primer amplified the 140 bp DNA only from A. citrulli strains, and detection sensitivity of the nested PCR increased 10,000 times of 1st PCR detection limit (10 ng genomic DNA/PCR. The nested PCR detected A. citrulli from the all samples of seed surface wash (external seed detection of the artificially inoculated watermelon seeds with 101 cfu/ml and above population of A. citrulli while the nested PCR could not detected A. citrulli from the mashed seed suspension (internal seed detection of the all artificially inoculated watermelon seeds. When the naturally infested watermelon seeds (10% seed infested rate with grow-out test used, the nested PCR detected A. citrulli from 2 seed samples out of 10 replication samples externally and 5 seed samples out of 10 replication samples internally. We believe that the nested-PCR developed in this study will be useful method to detect A. citrulli from the Cucurbitaceae seeds.

  4. Perception of BDS students and fresh graduates about significance of professional ethics in dentistry.

    Science.gov (United States)

    Al-Zain, Sahar Asaad; Al-Sadhan, Salwa Abdul Rahman; Ahmedani, Muhammad Shoaib

    2014-02-01

    To assess the awareness level of undergraduate dentistry students as well as fresh graduates about the significance of professional ethics. The cross sectional study was conducted among the 3rd, 4th and final year male and female BDS students as well as fresh graduate Interns from the College of Dentistry, King Saud University from January to June 2011. The students were asked to give their opinion about need for applications of professional ethics in dental practice on a five point Likert Scale varying from 'strongly agree' to 'strongly disagree'. Minitab statistical software was used for data analysis. Students at all levels considered professional ethics a very important prerequisite for dental practice with overall mean value of 4.42 +/- 0.36. However, the responses from the senior academic levels were significantly on the higher side compared to those from the junior grades. Generally the religious teachings and spirituality was considered as one of the top most motives for practicing professional ethics in dentistry followed by reputation, financial benefits, fear of punishment and self projection, with overall mean values of 3.93 +/- 0.58, 3.81 +/- 0.49, 3.25 +/- 0.94, 3.21 +/- 1.07 and 3.16 +/- 1.04, respectively. The present findings revealed that Professional Ethics is appreciated by the students as a highly significant factor for their success in dental practice as well as acquiring a good name and position in the society.

  5. Perception of BDS students and fresh graduates about significance of professional ethics in dentistry

    International Nuclear Information System (INIS)

    Zain, S.A.A.; Sadhan, S.A.R.A.; Ahmedani, M.S.

    2014-01-01

    Objective: To assess the awareness level of undergraduate dentistry students as well as fresh graduates about the significance of professional ethics. Methods: The cross sectional study was conducted among the 3rd, 4th and final year male and female BDS students as well as fresh graduate Interns from the College of Dentistry, King Saud University from January to June 2011. The students were asked to give their opinion about need for applications of professional ethics in dental practice on a five point Likert Scale varying from strongly agree to strongly disagree. Minitab statistical software was used for data analysis. Results: Students at all levels considered professional ethics a very important prerequisite for dental practice with overall mean value of 4.42+-0.36. However, the responses from the senior academic levels were significantly on the higher side compared to those from the junior grades. Generally the religious teachings and spirituality was considered as one of the top most motives for practicing professional ethics in dentistry followed by reputation, financial benefits, fear of punishment and self projection, with overall mean values of 3.93+-0.58, 3.81+-0.49, 3.25+-0.94, 3.21+-1.07 and 3.16+-1.04, respectively. Conclusion: The present findings revealed that Professional Ethics is appreciated by the students as a highly significant factor for their success in dental practice as well as acquiring a good name and position in the society. (author)

  6. Cooperating the BDS, GPS, GLONASS and strong-motion observations for real-time deformation monitoring

    Science.gov (United States)

    Tu, Rui; Liu, Jinhai; Lu, Cuixian; Zhang, Rui; Zhang, Pengfei; Lu, Xiaochun

    2017-06-01

    An approach of cooperating the BDS, GPS, GLONASS and strong-motion (SM) records for real-time deformation monitoring was presented, which was validated by the experimental data. In this approach, the Global Navigation Satellite System (GNSS) data were processed with the real-time kinematic positioning technology to retrieve the GNSS displacement, and the SM data were calibrated to acquire the raw acceleration; a Kalman filter was then applied to combine the GNSS displacement and the SM acceleration to obtain the integrated displacement, velocity and acceleration. The validation results show that the advantages of each sensor are completely complementary. For the SM, the baseline shifts are estimated and corrected, and the high-precision velocity and displacement are recovered. While the noise of GNSS can be reduced by using the SM-derived high-resolution acceleration, thus the high-precision and broad-band deformation information can be obtained in real time. The proposed method indicates a promising potential and capability in deformation monitoring of the high-building, dam, bridge and landslide.

  7. Fluorescent detection of dipicolinic acid as a biomarker of bacterial spores using lanthanide-chelated gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Donmez, Mert [Department of Chemistry, Faculty of Art and Sciences, Duzce University, Duzce 81620 (Turkey); Yilmaz, M. Deniz, E-mail: deniz.yilmaz@gidatarim.edu.tr [Department of Bioengineering, Faculty of Engineering and Architecture, Konya Food and Agriculture University, Konya 42080 (Turkey); Kilbas, Benan, E-mail: benankilbas@duzce.edu.tr [Department of Chemistry, Faculty of Art and Sciences, Duzce University, Duzce 81620 (Turkey)

    2017-02-15

    Highlights: • The nanosensors based on gold nanoparticles functionalized with lanthanide complexes were synthesized. • The nanosensors selectively and sensitively detected DPA, a biomarker of bacterial spores. • Ratiometric sensing of DPA by a ternary complex was achieved by ligand displacement strategy. - Abstract: Gold nanoparticles (GNPs) functionalized with ethylenediamine-lanthanide complexes (Eu-GNPs and Tb-GNPs) were used for the selective fluorescent detection of dipicolinic acid (DPA), a unique biomarker of bacterial spores, in water. Particles were characterized by transmission electron microscopy and zeta potential measurements. The coordination of DPA to the lanthanides resulted in the enhancement of the fluorescence. A selective response to DPA was observed over the nonselective binding of aromatic ligands. The ligand displacement strategy were also employed for the ratiometric fluorescent detection of DPA. 4,4,4-trifluoro-1-(2-naphthyl)-1,3-butanedion (TFNB) was chosen as an antenna to synthesize ternary complexes. The addition of DPA on EuGNP:TFNB ternary complex quenched the initial emission of the complex at 615 nm and increased the TFNB emission at 450 nm when excited at 350 nm. The results demonstrated that the ratiometric fluorescent detection of DPA was achieved by ligand displacement strategy.

  8. Simultaneous Detection of Brown Rot- and Soft Rot-Causing Bacterial Pathogens from Potato Tubers Through Multiplex PCR.

    Science.gov (United States)

    Ranjan, R K; Singh, Dinesh; Baranwal, V K

    2016-11-01

    Ralstonia solanacearum (Smith) Yabuuchi et al. and Erwinia carotovora subsp. carotovora (Jones) Bergey et al. (Pectobacterium carotovorum subsp. carotovorum) are the two major bacterial pathogens of potato causing brown rot (wilt) and soft rot diseases, respectively, in the field and during storage. Reliable and early detection of these pathogens are keys to avoid occurrence of these diseases in potato crops and reduce yield loss. In the present study, multiplex polymerase chain reaction (PCR) protocol was developed for simultaneous detection of R. solanacearum and E. carotovora subsp. carotovora from potato tubers. A set of oligos targeting the pectatelyase (pel) gene of E. carotovora subsp. carotovora and the universal primers based on 16S r RNA gene of R. solanacearum were used. The standardized multiplex PCR protocol could detect R. solanacearum and E. carotovora subsp. carotovora up to 0.01 and 1.0 ng of genomic DNA, respectively. The protocol was further validated on 96 stored potato tuber samples, collected from different potato-growing states of India, viz. Uttarakhand, Odisha, Meghalaya and Delhi. 53.1 % tuber samples were positive for R. solanacearum, and 15.1 % of samples were positive for E. carotovora subsp. carotovora, and both the pathogens were positive in 26.0 % samples when BIO-PCR was used. This method offers sensitive, specific, reliable and fast detection of two major bacterial pathogens from potato tubers simultaneously, particularly pathogen-free seed certification in large scale.

  9. Development of a panel of recombinase polymerase amplification assays for detection of common bacterial urinary tract infection pathogens.

    Science.gov (United States)

    Raja, B; Goux, H J; Marapadaga, A; Rajagopalan, S; Kourentzi, K; Willson, R C

    2017-08-01

    To develop and evaluate the performance of a panel of isothermal real-time recombinase polymerase amplification (RPA) assays for detection of common bacterial urinary tract infection (UTI) pathogens. The panel included RPAs for Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa and Enterococcus faecalis. All five RPAs required reaction times of under 12 min to reach their lower limit of detection of 100 genomes per reaction or less, and did not cross-react with high concentrations of nontarget bacterial genomic DNA. In a 50-sample retrospective clinical study, the five-RPA assay panel was found to have a specificity of 100% (95% CI, 78-100%) and a sensitivity of 89% (95% CI, 75-96%) for UTI detection. The analytical and clinical validity of RPA for the rapid and sensitive detection of common UTI pathogens was established. Rapid identification of the causative pathogens of UTIs can be valuable in preventing serious complications by helping avoid the empirical treatment necessitated by traditional urine culture's 48-72-h turnaround time. The routine and widespread use of RPA to supplement or replace culture-based methods could profoundly impact UTI management and the emergence of multidrug-resistant pathogens. © 2017 The Society for Applied Microbiology.

  10. Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing

    Science.gov (United States)

    Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellites genome scan we have previously detected significant and suggestive QTL with major effects on the phenotypic variation of survival following challenge with Flavobacterium psychrophilum...

  11. Sponge-specific unknown bacterial groups detected in marine sponges collected from Korea through barcoded pyrosequencing.

    Science.gov (United States)

    Jeong, Jong-Bin; Kim, Kyoung-Ho; Park, Jin-Sook

    2015-01-01

    The bacterial diversity of 10 marine sponges belonging to the species Cliona celata, an unidentified Cliona species, Haliclona cinerea, Halichondria okadai, Hymeniacidon sinapium, Lissodendoryx isodictyalis, Penares incrustans, Spirastrella abata, and Spirastrella panis collected from Jeju Island and Chuja Island was investigated using amplicon pyrosequencing of the 16S rRNA genes. The microbial diversity of these sponges has as of yet rarely or never been investigated. All sponges, except Cliona celata, Lissodendoryx isodictyalis, and Penares incrustans, showed simple bacterial diversity, in which one or two bacterial OTUs occupied more than 50% of the pyrosequencing reads and their OTU rank abundance curves saturated quickly. Most of the predominant OTUs belonged to Alpha-, Beta-, or Gammaproteobacteria. Some of the OTUs from the sponges with low diversity were distantly (88%~89%) or moderately (93%~97%) related to known sequences in the GenBank nucleotide database. Phylogenetic analysis showed that many of the representative sequences of the OTUs were related to the sequences originating from sponges and corals, and formed sponge-specific or -related clades. The marine sponges investigated herein harbored unexplored bacterial diversity, and further studies should be done to understand the microbes present in sponges.

  12. System automation for a bacterial colony detection and identification instrument via forward scattering

    International Nuclear Information System (INIS)

    Bae, Euiwon; Hirleman, E Daniel; Aroonnual, Amornrat; Bhunia, Arun K; Robinson, J Paul

    2009-01-01

    A system design and automation of a microbiological instrument that locates bacterial colonies and captures the forward-scattering signatures are presented. The proposed instrument integrates three major components: a colony locator, a forward scatterometer and a motion controller. The colony locator utilizes an off-axis light source to illuminate a Petri dish and an IEEE1394 camera to capture the diffusively scattered light to provide the number of bacterial colonies and two-dimensional coordinate information of the bacterial colonies with the help of a segmentation algorithm with region-growing. Then the Petri dish is automatically aligned with the respective centroid coordinate with a trajectory optimization method, such as the Traveling Salesman Algorithm. The forward scatterometer automatically computes the scattered laser beam from a monochromatic image sensor via quadrant intensity balancing and quantitatively determines the centeredness of the forward-scattering pattern. The final scattering signatures are stored to be analyzed to provide rapid identification and classification of the bacterial samples

  13. An iron detection system determines bacterial swarming initiation and biofilm formation

    NARCIS (Netherlands)

    Lin, Chuan-Sheng; Tsai, Yu-Huan; Chang, Chih-Jung; Tseng, Shun-Fu; Wu, Tsung-Ru; Lu, Chia-Chen; Wu, Ting-Shu; Lu, Jang-Jih; Horng, Jim-Tong; Martel, Jan; Ojcius, David M.; Lai, Hsin-Chih; Young, John D.; Andrews, S. C.; Robinson, A. K.; Rodriguez-Quinones, F.; Touati, D.; Yeom, J.; Imlay, J. A.; Park, W.; Marx, J. J.; Braun, V.; Hantke, K.; Cornelis, P.; Wei, Q.; Vinckx, T.; Troxell, B.; Hassan, H. M.; Verstraeten, N.; Lewis, K.; Hall-Stoodley, L.; Costerton, J. W.; Stoodley, P.; Kearns, D. B.; Losick, R.; Butler, M. T.; Wang, Q.; Harshey, R. M.; Lai, S.; Tremblay, J.; Deziel, E.; Overhage, J.; Bains, M.; Brazas, M. D.; Hancock, R. E.; Partridge, J. D.; Kim, W.; Surette, M. G.; Givskov, M.; Rather, P. N.; Houdt, R. Van; Michiels, C. W.; Mukherjee, S.; Inoue, T.; Frye, J. G.; McClelland, M.; McCarter, L.; Silverman, M.; Matilla, M. A.; Wu, Y.; Outten, F. W.; Singh, P. K.; Parsek, M. R.; Greenberg, E. P.; Welsh, M. J.; Banin, E.; Vasil, M. L.; Wosten, M. M.; Kox, L. F.; Chamnongpol, S.; Soncini, F. C.; Groisman, E. A.; Laub, M. T.; Goulian, M.; Krell, T.; Lai, H. C.; Lin, C. S.; Soo, P. C.; Tsai, Y. H.; Wei, J. R.; Wyckoff, E. E.; Mey, A. R.; Leimbach, A.; Fisher, C. F.; Payne, S. M.; Livak, K. J.; Schmittgen, T. D.; Clarke, M. B.; Hughes, D. T.; Zhu, C.; Boedeker, E. C.; Sperandio, V.; Stintzi, A.; Clarke-Pearson, M. F.; Brady, S. F.; Drake, E. J.; Gulick, A. M.; Qaisar, U.; Rowland, M. A.; Deeds, E. J.; Garcia, C. A.; Alcaraz, E. S.; Franco, M. A.; Rossi, B. N. Passerini de; Mehi, O.; Skaar, E. P.; Visaggio, D.; Nishino, K.; Dietz, P.; Gerlach, G.; Beier, D.; Bustin, S. A.; Schwyn, B.; Neilands, J. B.

    2016-01-01

    Iron availability affects swarming and biofilm formation in various bacterial species. However, how bacteria sense iron and coordinate swarming and biofilm formation remains unclear. Using Serratia marcescens as a model organism, we identify here a stage-specific iron-regulatory machinery comprising

  14. Point-Counterpoint: A Nucleic Acid Amplification Test for Streptococcus pyogenes Should Replace Antigen Detection and Culture for Detection of Bacterial Pharyngitis.

    Science.gov (United States)

    Pritt, Bobbi S; Patel, Robin; Kirn, Thomas J; Thomson, Richard B

    2016-10-01

    Nucleic acid amplification tests (NAATs) have frequently been the standard diagnostic approach when specific infectious agents are sought in a clinic specimen. They can be applied for specific agents such as S. pyogenes, or commercial multiplex NAATs for detection of a variety of pathogens in gastrointestinal, bloodstream, and respiratory infections may be used. NAATs are both rapid and sensitive. For many years, S. pyogenes testing algorithms used a rapid and specific group A streptococcal antigen test to screen throat specimens, followed, in some clinical settings, by a throat culture for S. pyogenes to increase the sensitivity of its detection. Now S. pyogenes NAATs are being used with increasing frequency. Given their accuracy, rapidity, and ease of use, should they replace antigen detection and culture for the detection of bacterial pharyngitis? Bobbi Pritt and Robin Patel of the Mayo Clinic, where S. pyogenes NAATs have been used for well over a decade with great success, will explain the advantages of this approach, while Richard (Tom) Thomson and Tom Kirn of the NorthShore University HealthSystem will discuss their concerns about this approach to diagnosing bacterial pharyngitis. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  15. LHCb: Measurement of the relative yields of the decay modes $B_{d,s} \\to D^{\\pm}_{(s)}\\pi^{\\mp}$ and $B_{d,s} \\to D^{\\pm}_{(s)} K^{\\pm}$ and determination of $f_d /f_s$ for 7 TeV $pp$ collisions

    CERN Multimedia

    David, P; Morawski, P; Witek, M; Akiba, K; Serra, N; Storaci, B; Tuning, N; Williams, M; Easo, S; Carson, L; Poluektov, A

    2011-01-01

    A fit to the invariant mass distributions is used to determine the relative abundances of the four decay modes $B_{d,s} \\to D^{\\pm}_{(s)}\\pi^{\\mp}$ and $B_{d,s} \\to D^{\\pm}_{(s)} K^{\\mp}$ for $B_{d,s}$ mesons produced in 7 TeV $pp$ collisions at the LHC. From these, the relative branching fractions of the kaon modes with respect to the pion modes, and the value of $f_d /f_s$, are determined.

  16. Molecular Detection of Leptospira in Two Returned Travelers: Higher Bacterial Load in Cerebrospinal Fluid versus Serum or Plasma

    Science.gov (United States)

    Waggoner, Jesse J.; Soda, Elizabeth A.; Seibert, Ryan; Grant, Philip; Pinsky, Benjamin A.

    2015-01-01

    Leptospirosis is a potentially severe illness in returned travelers. Patients often present with fever, headache, and neck pain, which may lead to a workup for meningitis including the acquisition of cerebrospinal fluid (CSF). Although Leptospira DNA has been detected in CSF by polymerase chain reaction (PCR), little data exist regarding the utility of testing CSF in addition to serum or plasma obtained on presentation. In this report, we present two cases of leptospirosis in returned travelers presenting with fever and headache. Our first patient had neutrophilic meningitis, and Leptospira was detectable only in CSF obtained on admission. The second patient had a normal CSF profile, but Leptospira was detected in CSF at a bacterial load 5- to 10-fold higher than that in plasma. CSF is an important specimen for the diagnosis of Leptospira by molecular methods and may yield an actionable diagnosis in the absence of leptospiremia. PMID:26033024

  17. Development and application of a multiplex PCR assay for rapid detection of 4 major bacterial pathogens in ducks.

    Science.gov (United States)

    Wei, B; Cha, S-Y; Kang, M; Park, I-J; Moon, O-K; Park, C-K; Jang, H-K

    2013-05-01

    Infections with Pasteurella multocida, Salmonella enterica, Riemerella anatipestifer, and Escherichia coli result in high morbidity and mortality, which cause significant economic loss in the poultry industry. It can be difficult to distinguish these pathogens based on clinical signs because these pathogens can cause similar clinical signs and coinfections can occur. Thus, rapid and sensitive detection of these 4 major bacterial pathogens are important in ducks. The aim of this study was to develop a multiplex PCR (mPCR) assay for simultaneously detecting and identifying these 4 pathogenic bacteria in a single tube reaction. The target genes used were KMT1 of P. multocida, the invasion protein gene of S. enterica, 16S rDNA of R. anatipestifer, and the alkaline phosphatase gene of E. coli. The detection limit of the assay for all bacterial DNA was 10 pg. The mPCR did not produce any nonspecific amplification products when tested against other related pathogens, including Staphylococcus aureus, Streptococcus pyogenes, Clostridium perfringens, Mycoplasma gallinarum, Mycoplasma synoviae, and Mycoplasma gallisepticum, which can also infect ducks. We applied mPCR to field samples, and the results were the same as the single PCR results. These results suggest that mPCR for the 4 bacteria is a useful and rapid technique to apply to field samples.

  18. A Two-Tube Multiplex Reverse Transcription PCR Assay for Simultaneous Detection of Viral and Bacterial Pathogens of Infectious Diarrhea

    Directory of Open Access Journals (Sweden)

    Ji Wang

    2014-01-01

    Full Text Available Diarrhea caused by viral and bacterial infections is a major health problem in developing countries. The purpose of this study is to develop a two-tube multiplex PCR assay using automatic electrophoresis for simultaneous detection of 13 diarrhea-causative viruses or bacteria, with an intended application in provincial Centers for Diseases Control and Prevention, China. The assay was designed to detect rotavirus A, norovirus genogroups GI and GII, human astrovirus, enteric adenoviruses, and human bocavirus (tube 1, and Salmonella, Vibrio parahaemolyticus, diarrheagenic Escherichia coli, Campylobacter jejuni, Shigella, Yersinia, and Vibrio cholera (tube 2. The analytical specificity was examined with positive controls for each pathogen. The analytical sensitivity was evaluated by performing the assay on serial tenfold dilutions of in vitro transcribed RNA, recombinant plasmids, or bacterial culture. A total of 122 stool samples were tested by this two-tube assay and the results were compared with those obtained from reference methods. The two-tube assay achieved a sensitivity of 20–200 copies for a single virus and 102-103 CFU/mL for bacteria. The clinical performance demonstrated that the two-tube assay had comparable sensitivity and specificity to those of reference methods. In conclusion, the two-tube assay is a rapid, cost-effective, sensitive, specific, and high throughput method for the simultaneous detection of enteric bacteria and virus.

  19. RIG-I detects infection with live Listeria by sensing secreted bacterial nucleic acids

    Science.gov (United States)

    Abdullah, Zeinab; Schlee, Martin; Roth, Susanne; Mraheil, Mobarak Abu; Barchet, Winfried; Böttcher, Jan; Hain, Torsten; Geiger, Sergej; Hayakawa, Yoshihiro; Fritz, Jörg H; Civril, Filiz; Hopfner, Karl-Peter; Kurts, Christian; Ruland, Jürgen; Hartmann, Gunther; Chakraborty, Trinad; Knolle, Percy A

    2012-01-01

    Immunity against infection with Listeria monocytogenes is not achieved from innate immune stimulation by contact with killed but requires viable Listeria gaining access to the cytosol of infected cells. It has remained ill-defined how such immune sensing of live Listeria occurs. Here, we report that efficient cytosolic immune sensing requires access of nucleic acids derived from live Listeria to the cytoplasm of infected cells. We found that Listeria released nucleic acids and that such secreted bacterial RNA/DNA was recognized by the cytosolic sensors RIG-I, MDA5 and STING thereby triggering interferon β production. Secreted Listeria nucleic acids also caused RIG-I-dependent IL-1β-production and inflammasome activation. The signalling molecule CARD9 contributed to IL-1β production in response to secreted nucleic acids. In conclusion, cytosolic recognition of secreted bacterial nucleic acids by RIG-I provides a mechanistic explanation for efficient induction of immunity by live bacteria. PMID:23064150

  20. Bacterial Biofilm Infection Detected in Breast Implant-Associated Anaplastic Large-Cell Lymphoma.

    Science.gov (United States)

    Hu, Honghua; Johani, Khalid; Almatroudi, Ahmad; Vickery, Karen; Van Natta, Bruce; Kadin, Marshall E; Brody, Garry; Clemens, Mark; Cheah, Chan Yoon; Lade, Stephen; Joshi, Preeti Avinash; Prince, H Miles; Deva, Anand K

    2016-06-01

    A recent association between breast implants and the development of anaplastic large-cell lymphoma (ALCL) has been observed. The purpose of this study was to identify whether bacterial biofilm is present in breast implant-associated ALCL and, if so, to compare the bacterial microbiome to nontumor capsule samples from breast implants with contracture. Twenty-six breast implant-associated ALCL samples were analyzed for the presence of biofilm by real-time quantitative polymerase chain reaction, next-generation sequencing, fluorescent in situ hybridization, and scanning electron microscopy, and compared to 62 nontumor capsule specimens. Both the breast implant-associated ALCL and nontumor capsule samples yielded high mean numbers of bacteria (breast implant-associated ALCL, 4.7 × 10 cells/mg of tissue; capsule, 4.9 × 10 cells/mg of tissue). Analysis of the microbiome in breast implant-associated ALCL specimens showed significant differences with species identified in nontumor capsule specimens. There was a significantly greater proportion of Ralstonia spp. present in ALCL specimens compared with nontumor capsule specimens (p capsule specimens compared with breast implant-associated ALCL specimens (p < 0.001). Bacterial biofilm was visualized both on scanning electron microscopy and fluorescent in situ hybridization. This novel finding of bacterial biofilm and a distinct microbiome in breast implant-associated ALCL samples points to a possible infectious contributing cause. Breast implants are widely used in both reconstructive and aesthetic surgery, and strategies to reduce their contamination should be more widely studied and practiced. Risk, V.

  1. Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction

    Directory of Open Access Journals (Sweden)

    Consolandi Clarissa

    2002-09-01

    Full Text Available Abstract Background PCR amplification of bacterial 16S rRNA genes provides the most comprehensive and flexible means of sampling bacterial communities. Sequence analysis of these cloned fragments can provide a qualitative and quantitative insight of the microbial population under scrutiny although this approach is not suited to large-scale screenings. Other methods, such as denaturing gradient gel electrophoresis, heteroduplex or terminal restriction fragment analysis are rapid and therefore amenable to field-scale experiments. A very recent addition to these analytical tools is represented by microarray technology. Results Here we present our results using a Universal DNA Microarray approach as an analytical tool for bacterial discrimination. The proposed procedure is based on the properties of the DNA ligation reaction and requires the design of two probes specific for each target sequence. One oligo carries a fluorescent label and the other a unique sequence (cZipCode or complementary ZipCode which identifies a ligation product. Ligated fragments, obtained in presence of a proper template (a PCR amplified fragment of the 16s rRNA gene contain either the fluorescent label or the unique sequence and therefore are addressed to the location on the microarray where the ZipCode sequence has been spotted. Such an array is therefore "Universal" being unrelated to a specific molecular analysis. Here we present the design of probes specific for some groups of bacteria and their application to bacterial diagnostics. Conclusions The combined use of selective probes, ligation reaction and the Universal Array approach yielded an analytical procedure with a good power of discrimination among bacteria.

  2. PMA-Linked Fluorescence for Rapid Detection of Viable Bacterial Endospores

    Science.gov (United States)

    LaDuc, Myron T.; Venkateswaran, Kasthuri; Mohapatra, Bidyut

    2012-01-01

    The most common approach for assessing the abundance of viable bacterial endospores is the culture-based plating method. However, culture-based approaches are heavily biased and oftentimes incompatible with upstream sample processing strategies, which make viable cells/spores uncultivable. This shortcoming highlights the need for rapid molecular diagnostic tools to assess more accurately the abundance of viable spacecraft-associated microbiota, perhaps most importantly bacterial endospores. Propidium monoazide (PMA) has received a great deal of attention due to its ability to differentiate live, viable bacterial cells from dead ones. PMA gains access to the DNA of dead cells through compromised membranes. Once inside the cell, it intercalates and eventually covalently bonds with the double-helix structures upon photoactivation with visible light. The covalently bound DNA is significantly altered, and unavailable to downstream molecular-based manipulations and analyses. Microbiological samples can be treated with appropriate concentrations of PMA and exposed to visible light prior to undergoing total genomic DNA extraction, resulting in an extract comprised solely of DNA arising from viable cells. This ability to extract DNA selectively from living cells is extremely powerful, and bears great relevance to many microbiological arenas.

  3. Detection of bacterial soft-rot of crown imperial caused by Pectobacterium carotovorum subsp. carotovorum using specific PCR primers

    Directory of Open Access Journals (Sweden)

    E. Mahmoudi

    2007-08-01

    Full Text Available Pectobacterium is one of the major destructive causal agent in most crop plants throughout the world. During a survey in spring of 2005 in the rangeland of Kermanshah and Isfahan, provinces of Iran, samples of bulbs and stems of crown imperial with brown spot and soft rot were collected. Eight strains of pectolytic Erwinia were isolated and purified from these samples. Phenotypic tests indicated that the strains were gram-negative, facultative anaerobic, rod shaped, motile with peritrichous flagella. They were oxidase negative, catalase positive and also able to macerate potato slices. Pathogenicity of all the strains were confirmed on corn, philodendron and crown imperial by inoculation of these crops with a bacterial suspension and reisolation of the strain from symptomatic tissues. A pair of specific PCR primers was used to detect these bacterial strains. The primer set (EXPCCF/EXPCCR amplified a single fragment of the expected size (0.55 kb from genomic DNA of all strains used in this study. In nested PCR, the primer set (INPCCR/INPCCF amplified the expected single fragment (0.4 kb from the PCR product of first PCR amplification. On the basis of the biochemical and phenotypic characteristics and PCR amplification by the specific PCR primers, these strains were identified as Pectobacterium carotovorum subsp. carotovorum. This is the first report of occurrence of crown imperial bacterial soft-rot in Iran.

  4. Evaluation on the impact of IMU grades on BDS + GPS PPP/INS tightly coupled integration

    Science.gov (United States)

    Gao, Zhouzheng; Ge, Maorong; Shen, Wenbin; Li, You; Chen, Qijin; Zhang, Hongping; Niu, Xiaoji

    2017-09-01

    The unexpected observing environments in dynamic applications may lead to partial and/or complete satellite signal outages frequently, which can definitely impact on the positioning performance of the Precise Point Positioning (PPP) in terms of decreasing available satellite numbers, breaking the continuity of observations, and degrading PPP's positioning accuracy. Generally, both the Inertial Navigation System (INS) and the multi-constellation Global Navigation Satellite System (GNSS) can be used to enhance the performance of PPP. This paper introduces the mathematical models of the multi-GNSS PPP/INS Tightly Coupled Integration (TCI), and investigates its performance from several aspects. Specifically, it covers (1) the use of the BDS/GPS PPP, PPP/INS, and their combination; (2) three positioning modes including PPP, PPP/INS TCI, and PPP/INS Loosely Coupled Integration (LCI); (3) the use of four various INS systems named navigation grade, tactical grade, auto grade, and Micro-Electro-Mechanical-Sensors (MEMS) one; (4) three PPP observation scenarios including PPP available, partially available, and fully outage. According to the statistics results, (1) the positioning performance of the PPP/INS (either TCI or LCI) mode is insignificantly depended on the grade of inertial sensor, when there are enough available satellites; (2) after the complete GNSS outages, the TCI mode expresses both higher convergence speed and more accurate positioning solutions than the LCI mode. Furthermore, in the TCI mode, using a higher grade inertial sensor is beneficial for the PPP convergence; (3) under the partial GNSS outage situations, the PPP/INS TCI mode position divergence speed is also restrained significantly; and (4) the attitude determination accuracy of the PPP/INS integration is highly correlated with the grade of inertial sensor.

  5. Evaluation of the line probe assay for the rapid detection of bacterial meningitis pathogens in cerebrospinal fluid samples from children.

    Science.gov (United States)

    Soysal, Ahmet; Toprak, Demet Gedikbasi; Türkoğlu, Salih; Bakir, Mustafa

    2017-01-11

    The aim of this study is to compare the diagnostic performance of the line probe assay (LPA) with conventional multiplex polymerase chain reaction (PCR) for Streptococcus pneumoniae as well as real-time PCR for Neisseria meningitidis and Haemophilus influenzae type b (Hib) in cerebrospinal fluid (CSF) samples from children during the multicenter national surveillance of bacterial meningitis between the years 2006 and 2009 in Turkey. During the study period 1460 subjects were enrolled and among them 841 (57%) met the criteria for probable bacterial meningitis. The mean age of subjects was 51 ± 47 months (range, 1-212 months). We performed the line probe assay in 751 (89%) CSF samples of 841 probable bacterial meningitis cases, of whom 431 (57%) were negative, 127 (17%) were positive for S. pneumoniae, 53 (7%) were positive for H. influenzae type b, and 41 (5%) were positive for N. meningitidis. The LPA was positive in 19 of 23 (82%) S. pneumoniae samples, 4 of 6 (67%) N. meningitidis samples and 2 of 2 (100%) Hib samples in CSF culture-positive cases. The specificity of the LPA for all of S. pneumoniae, H. influenzae type b, and N. meningitidis was 88% (95% CI: 85-91%), when using the standard PCR as a reference. The specificity of LPA for each of S. pneumoniae, H. influenzae type b, and N. meningitidis was 93% (95% CI: 89-95%), 96% (95% CI: 94-98%), and 99% (95% CI: 97-99%), respectively. For all of S. pneumoniae, H. influenzae type b and N. meningitidis the sensitivity of the LPA was 76% (95% CI: 70-82%) and for each of S. pneumoniae, H. influenzae type b and N. meningitidis was 72% (95% CI:63-79%), 88% (95% CI: 73-95%), and 81% (95% CI:67-92%), respectively. The LPA assay can be used to detect common bacterial meningitis pathogens in CSF samples, but the assay requires further improvement.

  6. The use of magnetic resonance and MR angiography in the detection of cerebral infarction: A complication of pediatric bacterial meningitis

    Directory of Open Access Journals (Sweden)

    Stošić-Opinćal Tatjana

    2005-01-01

    Full Text Available Bacground. Association of both cerebral infarction and acute bacterial meningitis is more common in younger patients than in the elderly. The rate of mortality and the frequency of sequel are very high inspite of the use of modern antibiotic therapy. In more than 30% of the cases of childhood bacterial meningitis, both arterial and venous infarctions can occur. The aim of this study was to present the role of the use of magnetic resonance (MRI, and MR angiography (MRA in the detection of bacterial meningitis in children complicated with cerebral infarctions. Method. In the Centre for MR, the Clinical Centre of Serbia, 25 patients with the diagnosis of bacterial meningitis, of which 9 children with cerebral infarction whose clinical conditon deteriorated acutely, despite the antibiotic therapy, underwent MRI and MR angiography examination on a 1T scanner. Examination included the conventional spin-echo techniques with T1-weighted saggital and coronal, and T2- weighted axial and coronal images. Coronal fluid attenuated inversion recovery (FLAIR and the postcontrast T1-weighted images in three orthogonal planes were also used. The use MR angiography was accomplished by the three-dimensional time-of-flight (3D TOF technique. Results. The findings included: multiple hemorrhagic infarction in 4 patients, multiple infarctions in 3 patients, focal infarction in 1 patient and diffuse infarction (1 patient. Common sites of involvement were: the frontal lobes, temporal lobes and basal ganglia. The majority of infarctions were bilateral. In 3 of the patients empyema was found, and in 1 patient bitemporal abscess was detected. In 8 of the patients MR angiography confirmed inflammatory vasculitis. Conclusion. Infarction is the most common sequel of severe meningitis in children. Since the complication of cerebral infarction influences the prognosis of meningitis, repetitive MRI examinations are very significant for the evaluation of the time course of

  7. Automated lanes detection and comparison of bacterial electrophoretic protein fingerprints using fast Fourier transformation.

    Science.gov (United States)

    Millership, S; Ragoonaden, K

    1992-08-01

    A method of computer-automated analysis of bacterial fingerprints produced by electrophoresis of proteins in a one-dimensional slab gel system is described. Proteins were visualized by silver staining. Western blotting, or autoradiography. Gels were recorded with a CCD camera, and after initial manual removal of the unwanted image margins, track margins were identified and extracted and a normalized trace was produced automatically using Fourier routines to smooth plots required for this process. Normalized traces were then compared by Fourier correlation after application of a high-pass step filter.

  8. Low-cost, 4-system, precise GNSS positioning: a GPS, Galileo, BDS and QZSS ionosphere-weighted RTK analysis

    Science.gov (United States)

    Odolinski, Robert; Teunissen, Peter J. G.

    2017-12-01

    With the combination of emerging GNSSs, single-frequency (SF) precise RTK positioning becomes possible. In this contribution we evaluate such low-cost ublox receiver and antenna performance when combining real data of four CDMA systems, namely L1 GPS, E1 Galileo, L1 QZSS, and B1 BDS. Comparisons are made to more expensive dual-frequency (DF) GPS receivers and antennas. The formal and empirical ambiguity success rates and positioning precisions will first be evaluated while making use of L1+E1, so as to investigate whether instantaneous SF RTK is possible without the need of B1 BDS or L1 QZSS. This is followed by an analysis of the SF 4-system model performance when the residual ionosphere can be ignored and modeled as a function of the baseline length, respectively. The analyses are conducted for a location in Dunedin, New Zealand, and compared to Perth, Australia with the better visibility of BDS and QZSS. The results indicate that successful instantaneous and precise RTK positioning is feasible while using L1 GPS and E1 Galileo data, and that the SF 4-system model is competitive to DF GPS even when residual ionospheric delays are present. We finally demonstrate that when the impact from the ionosphere increases and more than one epoch is needed for successful ambiguity resolution, the SF 4-system model performance can still remain competitive with the DF GPS receivers. This is particularly true in Perth with more satellites and when higher than customary elevation cut-off angles need to be used to avoid low-elevation multipath.

  9. Preparation and surface functionalisation of poly(styrene maleimide) nanoparticles for bacterial detection

    CSIR Research Space (South Africa)

    Barnard, A

    2012-10-01

    Full Text Available .kashan.co.za] INTRODUCTION The detection of bacteria in water is essential for the prevention of water-borne disease outbreaks. Conventionally, culturing methods are used to detect bacteria in water, whereby the number of bacteria present in a sample is multiplied to a... to the particle surfaces for attachment of fluorescent markers and antibodies. Figure 1: Process diagram of proposed development method of nanoparticles for bacteria detection Particle characterisation was performed with transmission electron microscopy (TEM...

  10. BeiDou/GPS Displacement Detection Using Robust Weighting Based on Moving Window

    Directory of Open Access Journals (Sweden)

    ZHANG Yunlong

    2017-05-01

    Full Text Available The positioning accuracy of Kalman model under creep deformation condition is closely related to the observation variance, which can be affected by the accuracy of weight ratio of GPS and BDS observations. To improve displacement detection accuracy, shorten convergence time of initial coordinate and reduce monitoring cost, firstly the BDS/GPS single-frequency single-difference combination model is set up by using clock-synchronized dual-antenna BDS/GPS receiver. Then the equivalent weights of GPS and BDS observations are robustly determined respectively, and the Helmert variance component estimated by introducing time-correlated forgetting factor is used to achieve the precise weight ratio between GPS and BDS observations. Finally the coordinates are calculated using the extended Kalman filter by updating observed variance in real-time. According to the experiment, for the short baseline (1 km, BDS/GPS robust precise weighting Kalman method can shorten convergence time of initial coordinate significantly, which is suitable for monitoring the deformation body with creep characteristics, and the displacement detection accuracy can reach sub-millimeter level. Moreover the displacement convergence rate is inversely related to the length of moving window approximately.

  11. Scalable DNA-Based Magnetic Nanoparticle Agglutination Assay for Bacterial Detection in Patient Samples

    DEFF Research Database (Denmark)

    Mezger, Anja; Fock, Jeppe; Antunes, Paula Soares Martins

    2015-01-01

    (MNPs) using low-cost optoelectronic components from Blu-ray drives. We implement a detection approach, which relies on the monomerization of the RCA products, the use of the monomers to link and agglutinate two populations of MNPs functionalized with universal nontarget specific detection probes...

  12. Detection of Bundle Branch Block using Adaptive Bacterial Foraging Optimization and Neural Network

    Directory of Open Access Journals (Sweden)

    Padmavthi Kora

    2017-03-01

    Full Text Available The medical practitioners analyze the electrical activity of the human heart so as to predict various ailments by studying the data collected from the Electrocardiogram (ECG. A Bundle Branch Block (BBB is a type of heart disease which occurs when there is an obstruction along the pathway of an electrical impulse. This abnormality makes the heart beat irregular as there is an obstruction in the branches of heart, this results in pulses to travel slower than the usual. Our current study involved is to diagnose this heart problem using Adaptive Bacterial Foraging Optimization (ABFO Algorithm. The Data collected from MIT/BIH arrhythmia BBB database applied to an ABFO Algorithm for obtaining best(important feature from each ECG beat. These features later fed to Levenberg Marquardt Neural Network (LMNN based classifier. The results show the proposed classification using ABFO is better than some recent algorithms reported in the literature.

  13. Use of o-phthalaldehyde to detect O-phosphorylethanolamine in bacterial lipopolysaccharide.

    Science.gov (United States)

    Yeh, H Y; Price, R M; Jacobs, D M

    1992-06-01

    We have developed a method to measure O-phosphorylethanolamine groups in bacterial lipopolysaccharide using a fluorescent reagent, o-phthalaldehyde. The optimal excitation and emission wavelengths were 335 nm and 450 nm, respectively. The reaction was pH-dependent with an optimum at pH 10.5. The maximum fluorescence intensity occurred two min after mixing lipopolysaccharide with the reagent at pH 10.5. The assay was linear over a range of 1 microgram to 100 micrograms of lipopolysaccharide. When we compared the amount of primary amine (as O-phosphorylethanolamine) in native and p-hydroxyphenylacetic acid-derivatized lipopolysaccharide, we found that 97% of amine groups in native lipopolysaccharide were derivatized by p-hydroxyphenylacetic acid in the presence of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide.

  14. Evaluation of leukocyte esterase and nitrite strip tests to detect spontaneous bacterial peritonitis in cirrhotic patients.

    Science.gov (United States)

    Torun, Serkan; Dolar, Enver; Yilmaz, Yusuf; Keskin, Murat; Kiyici, Murat; Sinirtas, Melda; Sarandol, Emre; Gurel, Selim; Nak, Selim-Giray; Gulten, Macit

    2007-12-07

    To investigate the diagnostic efficacy of leukocyte esterase and nitrite reagent strips for bedside diagnosis of spontaneous bacterial peritonitis (SBP). A total of 63 consecutive patients with cirrhotic ascites (38 male, 25 female) tested between April 2005 and July 2006 were included in the study. Bedside reagent strip testing was performed on ascitic fluid and the results compared to manual cell counting and ascitic fluid culture. SBP was defined as having a polymorphonuclear ascites count of >or= 250/mm(3). Fifteen samples showed SBP. The sensitivity, specificity, positive and negative predictive values of the leukocyte esterase reagent strips were; 93%, 100%, 100%, and 98%, respectively. The sensitivity, specificity, positive and negative predictive value of the nitrite reagent strips were 13%, 93%, 40%, and 77%, respectively. The combination of leukocyte esterase and nitrite reagents strips did not yield statistically significant effects on diagnostic accuracy. Leukocyte esterase reagent strips may provide a rapid, bedside diagnostic test for SBP.

  15. Quantitative Mass Spectrometry for Bacterial Protein Toxins — A Sensitive, Specific, High-Throughput Tool for Detection and Diagnosis

    Directory of Open Access Journals (Sweden)

    Suzanne Kalb

    2011-03-01

    Full Text Available Matrix-assisted laser-desorption time-of-flight (MALDI-TOF mass spectrometry (MS is a valuable high-throughput tool for peptide analysis. Liquid chromatography electrospray ionization (LC-ESI tandem-MS provides sensitive and specific quantification of small molecules and peptides. The high analytic power of MS coupled with high-specificity substrates is ideally suited for detection and quantification of bacterial enzymatic activities. As specific examples of the MS applications in disease diagnosis and select agent detection, we describe recent advances in the analyses of two high profile protein toxin groups, the Bacillus anthracis toxins and the Clostridium botulinum neurotoxins. The two binary toxins produced by B. anthracis consist of protective antigen (PA which combines with lethal factor (LF and edema factor (EF, forming lethal toxin and edema toxin respectively. LF is a zinc-dependent endoprotease which hydrolyzes specific proteins involved in inflammation and immunity. EF is an adenylyl cyclase which converts ATP to cyclic-AMP. Toxin-specific enzyme activity for a strategically designed substrate, amplifies reaction products which are detected by MALDI-TOF-MS and LC-ESI-MS/MS. Pre-concentration/purification with toxin specific monoclonal antibodies provides additional specificity. These combined technologies have achieved high specificity, ultrasensitive detection and quantification of the anthrax toxins. We also describe potential applications to diseases of high public health impact, including Clostridium difficile glucosylating toxins and the Bordetella pertussis adenylyl cyclase.

  16. Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dae-Young [National Water Research Institute, Environment Canada, 867 Lakeshore Road, Burlington, Ontario, L7R 4A6 (Canada)], E-mail: daeyoung.lee@ec.gc.ca; Lauder, Heather; Cruwys, Heather; Falletta, Patricia [National Water Research Institute, Environment Canada, 867 Lakeshore Road, Burlington, Ontario, L7R 4A6 (Canada); Beaudette, Lee A. [Environmental Science and Technology Centre, Environment Canada, 335 River Road South, Ottawa, Ontario, K1A 0H3 (Canada)], E-mail: lee.beaudette@ec.gc.ca

    2008-07-15

    Conventional microbial water quality test methods are well known for their technical limitations, such as lack of direct pathogen detection capacity and low throughput capability. The microarray assay has recently emerged as a promising alternative for environmental pathogen monitoring. In this study, bacterial pathogens were detected in municipal wastewater using a microarray equipped with short oligonucleotide probes targeting 16S rRNA sequences. To date, 62 probes have been designed against 38 species, 4 genera, and 1 family of pathogens. The detection sensitivity of the microarray for a waterborne pathogen Aeromonas hydrophila was determined to be approximately 1.0% of the total DNA, or approximately 10{sup 3}A. hydrophila cells per sample. The efficacy of the DNA microarray was verified in a parallel study where pathogen genes and E. coli cells were enumerated using real-time quantitative PCR (qPCR) and standard membrane filter techniques, respectively. The microarray and qPCR successfully detected multiple wastewater pathogen species at different stages of the disinfection process (i.e. secondary effluents vs. disinfected final effluents) and at two treatment plants employing different disinfection methods (i.e. chlorination vs. UV irradiation). This result demonstrates the effectiveness of the DNA microarray as a semi-quantitative, high throughput pathogen monitoring tool for municipal wastewater.

  17. Development and application of an oligonucleotide microarray and real-time quantitative PCR for detection of wastewater bacterial pathogens

    International Nuclear Information System (INIS)

    Lee, Dae-Young; Lauder, Heather; Cruwys, Heather; Falletta, Patricia; Beaudette, Lee A.

    2008-01-01

    Conventional microbial water quality test methods are well known for their technical limitations, such as lack of direct pathogen detection capacity and low throughput capability. The microarray assay has recently emerged as a promising alternative for environmental pathogen monitoring. In this study, bacterial pathogens were detected in municipal wastewater using a microarray equipped with short oligonucleotide probes targeting 16S rRNA sequences. To date, 62 probes have been designed against 38 species, 4 genera, and 1 family of pathogens. The detection sensitivity of the microarray for a waterborne pathogen Aeromonas hydrophila was determined to be approximately 1.0% of the total DNA, or approximately 10 3 A. hydrophila cells per sample. The efficacy of the DNA microarray was verified in a parallel study where pathogen genes and E. coli cells were enumerated using real-time quantitative PCR (qPCR) and standard membrane filter techniques, respectively. The microarray and qPCR successfully detected multiple wastewater pathogen species at different stages of the disinfection process (i.e. secondary effluents vs. disinfected final effluents) and at two treatment plants employing different disinfection methods (i.e. chlorination vs. UV irradiation). This result demonstrates the effectiveness of the DNA microarray as a semi-quantitative, high throughput pathogen monitoring tool for municipal wastewater

  18. A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes.

    Science.gov (United States)

    Tsirigos, Aristotelis; Rigoutsos, Isidore

    2005-01-01

    In earlier work, we introduced and discussed a generalized computational framework for identifying horizontal transfers. This framework relied on a gene's nucleotide composition, obviated the need for knowledge of codon boundaries and database searches, and was shown to perform very well across a wide range of archaeal and bacterial genomes when compared with previously published approaches, such as Codon Adaptation Index and C + G content. Nonetheless, two considerations remained outstanding: we wanted to further increase the sensitivity of detecting horizontal transfers and also to be able to apply the method to increasingly smaller genomes. In the discussion that follows, we present such a method, Wn-SVM, and show that it exhibits a very significant improvement in sensitivity compared with earlier approaches. Wn-SVM uses a one-class support-vector machine and can learn using rather small training sets. This property makes Wn-SVM particularly suitable for studying small-size genomes, similar to those of viruses, as well as the typically larger archaeal and bacterial genomes. We show experimentally that the new method results in a superior performance across a wide range of organisms and that it improves even upon our own earlier method by an average of 10% across all examined genomes. As a small-genome case study, we analyze the genome of the human cytomegalovirus and demonstrate that Wn-SVM correctly identifies regions that are known to be conserved and prototypical of all beta-herpesvirinae, regions that are known to have been acquired horizontally from the human host and, finally, regions that had not up to now been suspected to be horizontally transferred. Atypical region predictions for many eukaryotic viruses, including the alpha-, beta- and gamma-herpesvirinae, and 123 archaeal and bacterial genomes, have been made available online at http://cbcsrv.watson.ibm.com/HGT_SVM/.

  19. Simultaneous Detection of Key Bacterial Pathogens Related to Pneumonia and Meningitis Using Multiplex PCR Coupled With Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Chi Zhang

    2018-04-01

    Full Text Available Pneumonia and meningitis continue to present an enormous public health burden and pose a major threat to young children. Among the causative organisms of pneumonia and meningitis, bacteria are the most common causes of serious disease and deaths. It is challenging to accurately and rapidly identify these agents. To solve this problem, we developed and validated a 12-plex PCR coupled with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS method (bacterial pathogen-mass spectrometry, BP-MS that can be used to simultaneously screen for 11 key bacterial pathogens related to pneumonia and meningitis. Forty-six nasopharyngeal swabs and 12 isolates were used to determine the specificity of the method. The results showed that, using the BP-MS method, we could accurately identify the expected bacteria without cross-reactivity with other pathogens. For the 11 target bacterial pathogens, the analytical sensitivity of the BP-MS method was as low as 10 copies/reaction. To further evaluate the clinical effectiveness of this method, 204 nasopharyngeal swabs from hospitalized children with suspected pneumonia were tested using this method. In total, 81.9% (167/204 of the samples were positive for at least one of the 11 target pathogens. Among the 167 bacteria-positive samples, the rate of multiple infections was 55.7% (93/167, and the most frequent combination was Streptococcus pneumoniae with Haemophilus influenzae, representing 46.2% (43/93 two-pathogen mixed infections. We used real-time PCR and nested PCR to confirm positive results, with identical results obtained for 81.4% (136/167 of the samples. The BP-MS method is a sensitive and specific molecular detection technique in a multiplex format and with high sample throughput. Therefore, it will be a powerful tool for pathogen screening and antibiotic selection at an early stage of disease.

  20. Specific detection of common pathogens of acute bacterial meningitis using an internally controlled tetraplex-PCR assay.

    Science.gov (United States)

    Farahani, Hamidreza; Ghaznavi-Rad, Ehsanollah; Mondanizadeh, Mahdieh; MirabSamiee, Siamak; Khansarinejad, Behzad

    2016-08-01

    Accurate and timely diagnosis of acute bacterial meningitis is critical for antimicrobial treatment of patients. Although PCR-based methods have been widely used for the diagnosis of acute meningitis caused by bacterial pathogens, the main disadvantage of these methods is their high cost. This disadvantage has hampered the widespread use of molecular assays in many developing countries. The application of multiplex assays and "in-house" protocols are two main approaches that can reduce the overall cost of a molecular test. In the present study, an internally controlled tetraplex-PCR was developed and validated for the specific detection of Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae in cerebrospinal fluid (CSF) samples. The analysis of a panel of other human pathogens showed no cross-reactivity in the assay. The analytical sensitivity of the in-house assay was 792.3 copies/ml, when all three bacteria were presentin the specimens. This value was calculated as 444.5, 283.7, 127.8 copies/ml when only S. pneumoniae, N. meningitidis and H. influenzae, respectively, were present. To demonstrate the diagnostic performance of the assay, a total of 150 archival CSF samples were tested and compared with a commercial multiplex real-time PCR kit. A diagnostic sensitivity of 92.8% and a specificity of 95.1% were determined for the present tetraplex-PCR assay. The results indicate that the established method is sensitive, specific and cost-effective, and can be used particularly in situations where the high cost of commercial kits prevents the use of molecular methods for the diagnosis of bacterial meningitis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Shear horizontal surface acoustic wave microsensor for Class A viral and bacterial detection.

    Energy Technology Data Exchange (ETDEWEB)

    Branch, Darren W.; Huber, Dale L.; Brozik, Susan Marie; Edwards, Thayne L.

    2008-10-01

    The rapid autonomous detection of pathogenic microorganisms and bioagents by field deployable platforms is critical to human health and safety. To achieve a high level of sensitivity for fluidic detection applications, we have developed a 330 MHz Love wave acoustic biosensor on 36{sup o} YX Lithium Tantalate (LTO). Each die has four delay-line detection channels, permitting simultaneous measurement of multiple analytes or for parallel detection of single analyte containing samples. Crucial to our biosensor was the development of a transducer that excites the shear horizontal (SH) mode, through optimization of the transducer, minimizing propagation losses and reducing undesirable modes. Detection was achieved by comparing the reference phase of an input signal to the phase shift from the biosensor using an integrated electronic multi-readout system connected to a laptop computer or PDA. The Love wave acoustic arrays were centered at 330 MHz, shifting to 325-328 MHz after application of the silicon dioxide waveguides. The insertion loss was -6 dB with an out-of-band rejection of 35 dB. The amplitude and phase ripple were 2.5 dB p-p and 2-3{sup o} p-p, respectively. Time-domain gating confirmed propagation of the SH mode while showing suppression of the triple transit. Antigen capture and mass detection experiments demonstrate a sensitivity of 7.19 {+-} 0.74{sup o} mm{sup 2}/ng with a detection limit of 6.7 {+-} 0.40 pg/mm{sup 2} for each channel.

  2. A locked nucleic acid (LNA)-based real-time PCR assay for the rapid detection of multiple bacterial antibiotic resistance genes directly from positive blood culture.

    Science.gov (United States)

    Zhu, Lingxiang; Shen, Dingxia; Zhou, Qiming; Li, Zexia; Fang, Xiangdong; Li, Quan-Zhen

    2015-01-01

    Bacterial strains resistant to various antibiotic drugs are frequently encountered in clinical infections, and the rapid identification of drug-resistant strains is highly essential for clinical treatment. We developed a locked nucleic acid (LNA)-based quantitative real-time PCR (LNA-qPCR) method for the rapid detection of 13 antibiotic resistance genes and successfully used it to distinguish drug-resistant bacterial strains from positive blood culture samples. A sequence-specific primer-probe set was designed, and the specificity of the assays was assessed using 27 ATCC bacterial strains and 77 negative blood culture samples. No cross-reaction was identified among bacterial strains and in negative samples, indicating 100% specificity. The sensitivity of the assays was determined by spiking each bacterial strain into negative blood samples, and the detection limit was 1-10 colony forming units (CFU) per reaction. The LNA-qPCR assays were first applied to 72 clinical bacterial isolates for the identification of known drug resistance genes, and the results were verified by the direct sequencing of PCR products. Finally, the LNA-qPCR assays were used for the detection in 47 positive blood culture samples, 19 of which (40.4%) were positive for antibiotic resistance genes, showing 91.5% consistency with phenotypic susceptibility results. In conclusion, LNA-qPCR is a reliable method for the rapid detection of bacterial antibiotic resistance genes and can be used as a supplement to phenotypic susceptibility testing for the early detection of antimicrobial resistance to allow the selection of appropriate antimicrobial treatment and to prevent the spread of resistant isolates.

  3. A locked nucleic acid (LNA-based real-time PCR assay for the rapid detection of multiple bacterial antibiotic resistance genes directly from positive blood culture.

    Directory of Open Access Journals (Sweden)

    Lingxiang Zhu

    Full Text Available Bacterial strains resistant to various antibiotic drugs are frequently encountered in clinical infections, and the rapid identification of drug-resistant strains is highly essential for clinical treatment. We developed a locked nucleic acid (LNA-based quantitative real-time PCR (LNA-qPCR method for the rapid detection of 13 antibiotic resistance genes and successfully used it to distinguish drug-resistant bacterial strains from positive blood culture samples. A sequence-specific primer-probe set was designed, and the specificity of the assays was assessed using 27 ATCC bacterial strains and 77 negative blood culture samples. No cross-reaction was identified among bacterial strains and in negative samples, indicating 100% specificity. The sensitivity of the assays was determined by spiking each bacterial strain into negative blood samples, and the detection limit was 1-10 colony forming units (CFU per reaction. The LNA-qPCR assays were first applied to 72 clinical bacterial isolates for the identification of known drug resistance genes, and the results were verified by the direct sequencing of PCR products. Finally, the LNA-qPCR assays were used for the detection in 47 positive blood culture samples, 19 of which (40.4% were positive for antibiotic resistance genes, showing 91.5% consistency with phenotypic susceptibility results. In conclusion, LNA-qPCR is a reliable method for the rapid detection of bacterial antibiotic resistance genes and can be used as a supplement to phenotypic susceptibility testing for the early detection of antimicrobial resistance to allow the selection of appropriate antimicrobial treatment and to prevent the spread of resistant isolates.

  4. Enhanced green fluorescent protein in optofluidic Fabry-Perot microcavity to detect laser induced temperature changes in a bacterial culture

    Science.gov (United States)

    Lahoz, F.; Martín, I. R.; Walo, D.; Freire, R.; Gil-Rostra, J.; Yubero, F.; Gonzalez-Elipe, A. R.

    2017-09-01

    Thermal therapy using laser sources can be used in combination with other cancer therapies to eliminate tumors. However, high precision temperature control is required to avoid damage in healthy surrounding tissues. Therefore, in order to detect laser induced temperature changes, we have used the fluorescence signal of the enhanced Green Fluorescent Protein (eGFP) over-expressed in an E. coli bacterial culture. For that purpose, the bacteria expressing eGFP are injected in a Fabry-Perot (FP) optofluidic planar microcavity. In order to locally heat the bacterial culture, external infrared or ultraviolet lasers were used. Shifts in the wavelengths of the resonant FP modes are used to determine the temperature increase as a function of the heating laser pump power. Laser induced local temperature increments up to 6-7 °C were measured. These results show a relatively easy way to measure laser induced local temperature changes using a FP microcavity and using eGFP as a molecular probe instead of external nanoparticles, which could damage/alter the cell. Therefore, we believe that this approach can be of interest for the study of thermal effects in laser induced thermal therapies.

  5. "DETECTION OF BACTERIAL, METHICILLIN RESISTANCE, AND β-LACTAMASE GENES FOUND IN WOUND SWABS BY MULTIPLEX POLYMERASE CHAIN REACTION"

    Directory of Open Access Journals (Sweden)

    S. Sadeghian

    2004-05-01

    Full Text Available Coagulase-positive and coagulase negative, methicillin-resistant staphylococci are major causes of serious nosocomial infections and it is very important to have a reliable test to detect these bacteria. A multiplex polymerase chain reaction (mPCR was used on 100 clinical samples for simultaneous amplification of the universal bacterial, mec-A encoding the penicillin binding protein 2a, which is associated with staphylococcal methicillin resistance and TEM-1 encoding the β-lactamase, which accounts for the majority of all cases of the plasmid β-lactamase resistance worldwide. Out of 100 wound swabs tested, 99% with universal primers, 26% with TEM-1 primers and 6% with mec-A primers were positive. Dot blot Digoxigenin hybridization on the 30 samples was carried out to confirm identified bacteria with specific bacterial probes. Out of 100 wound swabs, 38% were positive with Staphylococcus aureus probe, 23% were positive with enteric bacteria probe, 7% were positive with Streptococcus agalactia probe and 1% were positive with Haemophilus influenza probe. The mPCR method used in this study, was designed to be incorporated into the workflow of the clinical microbiology laboratory and allows for the identification of intrinsic resistance in a timely and reliable manner.

  6. DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays

    Directory of Open Access Journals (Sweden)

    Kenjiro Nagamine

    2015-01-01

    Full Text Available Using Streptococcus pyogenes as a model, we previously established a stepwise computational workflow to effectively identify species-specific DNA signatures that could be used as PCR primer sets to detect target bacteria with high specificity and sensitivity. In this study, we extended the workflow for the rapid development of PCR assays targeting Enterococcus faecalis, Enterococcus faecium, Clostridium perfringens, Clostridium difficile, Clostridium tetani , and Staphylococcus aureus , which are of safety concern for human tissue intended for transplantation. Twenty-one primer sets that had sensitivity of detecting 5–50 fg DNA from target bacteria with high specificity were selected. These selected primer sets can be used in a PCR array for detecting target bacteria with high sensitivity and specificity. The workflow could be widely applicable for the rapid development of PCR-based assays for a wide range of target bacteria, including those of biothreat agents.

  7. A disposable bacterial lysis cartridge (BLC) suitable for an in situ water-borne pathogen detection system.

    Science.gov (United States)

    Lee, Eun-Hee; Lim, Hyun Jeong; Son, Ahjeong; Chua, Beelee

    2015-11-21

    We constructed a disposable bacterial lysis cartridge (BLC) suitable for an in situ pathogen detection system. It had an in-built micro corona discharge based ozone generator that provided ozone for cell lysis. Using a custom sample handling platform, its performance was evaluated with a Gram-positive bacterium of Bacillus subtilis. It was capable of achieving a similar degree of lysis as a commercial ultrasonic dismembrator with a P-1 microprobe in 10 min at an air pump flow rate of 29.4 ml min(-1) and an ozone generator operating voltage of 1600 V. The lysing duration could be significantly reduced to 5 min by increasing the air pump flow rate and the ozone generator operating voltage as well as by the addition of sodium dodecyl sulfate (SDS).

  8. An integrated flow cytometry-based system for real-time, high sensitivity bacterial detection and identification.

    Directory of Open Access Journals (Sweden)

    Dan A Buzatu

    Full Text Available Foodborne illnesses occur in both industrialized and developing countries, and may be increasing due to rapidly evolving food production practices. Yet some primary tools used to assess food safety are decades, if not centuries, old. To improve the time to result for food safety assessment a sensitive flow cytometer based system to detect microbial contamination was developed. By eliminating background fluorescence and improving signal to noise the assays accurately measure bacterial load or specifically identify pathogens. These assays provide results in minutes or, if sensitivity to one cell in a complex matrix is required, after several hours enrichment. Conventional assessments of food safety require 48 to 56 hours. The assays described within are linear over 5 orders of magnitude with results identical to culture plates, and report live and dead microorganisms. This system offers a powerful approach to real-time assessment of food safety, useful for industry self-monitoring and regulatory inspection.

  9. Performance of BVBlue Rapid Test in Detecting Bacterial Vaginosis among Women in Mysore, India

    Directory of Open Access Journals (Sweden)

    Purnima Madhivanan

    2014-01-01

    Full Text Available Bacterial vaginosis (BV is the most common cause of abnormal vaginal discharge in reproductive age women. It is associated with increased susceptibility to HIV/STI and adverse birth outcomes. Diagnosis of BV in resource-poor settings like India is challenging. With little laboratory infrastructure there is a need for objective point-of-care diagnostic tests. Vaginal swabs were collected from women 18 years and older, with a vaginal pH > 4.5 attending a reproductive health clinic. BV was diagnosed with Amsel’s criteria, Nugent scores, and the OSOM BVBlue test. Study personnel were blinded to test results. There were 347 participants enrolled between August 2009 and January 2010. BV prevalence was 45.1% (95% confidence interval (CI: 41.5%–52.8% according to Nugent score. When compared with Nugent score, the sensitivity, specificity, positive predictive value, negative predictive value for Amsel’s criteria and BVBlue were 61.9%, 88.3%, 81.5%, 73.7% and 38.1%, 92.7%, 82.1%, 63.9%, respectively. Combined with a “whiff” test, the performance of BVBlue increased sensitivity to 64.4% and negative predictive value to 73.8%. Despite the good specificity, poor sensitivity limits the usefulness of the BVBlue as a screening test in this population. There is a need to examine the usefulness of this test in other Indian populations.

  10. Detection of antibodies to bacterial cell wall peptidoglycan in human sera

    International Nuclear Information System (INIS)

    Heymer, B.; Schleifer, K.H.; Read, S.; Zabriskie, J.B.; Krause, R.M.

    1976-01-01

    A radioimmunoassay has been developed for the measurement of antibodies to peptidoglycan in human sera including patients with rheumatic feaver and juvenile rheumatoid arthritis. The assay is based on the percentage of binding of the hapten 125 I-L-Ala-γ-D-Glu-L-Lys-D-Ala-D-Ala, the major peptide determinant of peptidoglycan. Because of differences in the avidity of the antibodies in different sera, the amount of antibody was expressed as pentapeptide hapten-binding capacity (pentapeptide-HBC in ng/ml of serum). Fourteen out of 105 normal blood donors had a pentapeptide-HBC value greater than or equal to 75 ng/ml serum. Values in healthy children 5 to 18 years of age were less than or equal to 50 ng/ml. Sixty-eight percent of the individuals with rheumatic fever had values greater than or equal to 75 ng/ml, an indication that streptococcal infections can stimulate an immune response to peptidoglycan. Thirty-five percent of the patients with juvenile rheumatoid arthritis had values greater than or equal to 75 ng/ml. Such a finding points to a possible association between bacterial infections and juvenile rheumatoid arthritis

  11. Real-Time PCR Detection ofBurkholderia cepaciain Pharmaceutical Products Contaminated with Low Levels of Bacterial Contamination.

    Science.gov (United States)

    Jimenez, Luis; Jashari, Theranda; Vasquez, Jenifer; Zapata, Stephanie; Bochis, Joy; Kulko, Margarita; Ellman, Victoria; Gardner, Matthew; Choe, Tina

    2018-01-01

    A real-time polymerase chain reaction (RT-PCR) assay was developed to detect Burkholderia cepacia in pharmaceutical products contaminated with low levels of bacteria. Different pharmaceutical suspensions were artificially contaminated with B. cepacia , Escherichia coli , Staphylococcus aureus , and Bacillus megaterium After a 24 h incubation in trypticase soy broth with Tween 20, samples were streaked on mannitol salt, phenyl ethyl alcohol, eosin methylene blue, MacConkey, and pseudomonas isolation agar. Microbial DNA was extracted from each sample by using a Tris-EDTA, proteinase K, Tween 20 buffer. Regular PCR targeting the 1.5 kilobases 16S rRNA eubacterial gene and cloning showed the predominant DNA in the extracted mix belonged to E. coli Selective media isolation of bacterial contamination showed B. cepacia only detected on pseudomonas isolation while eosin methylene blue and MacConkey detected only E. coli RT-PCR using primers PSL1 and PSR1 amplified a 209 bp 16S rRNA fragment using a Roche LightCycler 96 ® system with SYBR green I, a common double-stranded binding dye. The cycle at which fluorescence from amplification exceeds the background fluorescence was referred to as quantification cycle. All samples were found to be positive by standard microbiological testing and RT-PCR. B. cepacia was detected within 30 h in all contaminated samples using RT-PCR. Based upon standard curve analysis of B. cepacia DNA, the minimum DNA concentration that could be detected was 10 fg/uL with a correlation value of 0.98. RT-PCR detection of B. cepacia allowed faster quality control analysis, corrective actions, and process optimization. LAY ABSTRACT: A real-time polymerase chain reaction (RT-PCR) assay was developed to detect Burkholderia cepacia in pharmaceutical products contaminated with low levels of bacteria. B. cepacia is the number one reason for microbial contamination recalls of non-sterile drug products in the USA. RT-PCR using primers PSL1 and PSR1 amplified a

  12. Detection and quantification of bacterial spoilage in milk and pork meat using MALDI-TOF-MS and multivariate analysis.

    Science.gov (United States)

    Nicolaou, Nicoletta; Xu, Yun; Goodacre, Royston

    2012-07-17

    Microbiological safety is one of the cornerstones of quality control in the food industry. Identification and quantification of spoilage bacteria in pasteurized milk and meat in the food industry currently relies on accurate and sensitive yet time-consuming techniques which give retrospective values for microbial contamination. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), a proven technique in the field of protein and peptide identification and quantification, may be a valuable alternative approach for the rapid assessment of microbial spoilage. In this work we therefore developed MALDI-TOF-MS as a novel analytical approach for the assessment of food that when combined with chemometrics allows for the detection and quantification of milk and pork meat spoilage bacteria. To develop this approach, natural spoilage of pasteurized milk and raw pork meat samples incubated at 15 °C and at room temperature, respectively, was conducted. Samples were collected for MALDI-TOF-MS analysis (which took 4 min per sample) at regular time intervals throughout the spoilage process, with concurrent calculation and documentation of reference total viable counts using traditional microbiological methods (these took 2 days). Multivariate statistical techniques such as principal component discriminant function analysis, canonical correlation analysis, partial least-squares (PLS) regression, and kernel PLS (KPLS) were used to analyze the data. The results from MALDI-TOF-MS combined with PLS or KPLS gave excellent bacterial quantification results for both milk and meat spoilage, and typical root mean squared errors for prediction in test spectra were between 0.53 and 0.79 log unit. Overall these novel findings strongly indicate that MALDI-TOF-MS when combined with chemometric approaches would be a useful adjunct for routine use in the milk and meat industry as a fast and accurate viable bacterial detection and quantification method.

  13. Detection of bacterial 16S rRNA and identification of four clinically important bacteria by real-time PCR.

    Directory of Open Access Journals (Sweden)

    Robert J Clifford

    Full Text Available Within the paradigm of clinical infectious disease research, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa represent the four most clinically relevant, and hence most extensively studied bacteria. Current culture-based methods for identifying these organisms are slow and cumbersome, and there is increasing need for more rapid and accurate molecular detection methods. Using bioinformatic tools, 962,279 bacterial 16S rRNA gene sequences were aligned, and regions of homology were selected to generate a set of real-time PCR primers that target 93.6% of all bacterial 16S rRNA sequences published to date. A set of four species-specific real-time PCR primer pairs were also designed, capable of detecting less than 100 genome copies of A. baumannii, E. coli, K. pneumoniae, and P. aeruginosa. All primers were tested for specificity in vitro against 50 species of Gram-positive and -negative bacteria. Additionally, the species-specific primers were tested against a panel of 200 clinical isolates of each species, randomly selected from a large repository of clinical isolates from diverse areas and sources. A comparison of culture and real-time PCR demonstrated 100% concordance. The primers were incorporated into a rapid assay capable of positive identification from plate or broth cultures in less than 90 minutes. Furthermore, our data demonstrate that current targets, such as the uidA gene in E.coli, are not suitable as species-specific genes due to sequence variation. The assay described herein is rapid, cost-effective and accurate, and can be easily incorporated into any research laboratory capable of real-time PCR.

  14. IDENTIFICATION OF BACTERIAL DNA MARKERS FOR THE DETECTION OF HUMAN FECAL POLLUTION IN WATER

    Science.gov (United States)

    We used genome fragment enrichment and bioinformatics to identify several microbial DNA sequences with high potential for use as markers in PCR assays for detection of human fecal contamination in water. Following competitive solution-phase hybridization of total DNA from human a...

  15. Direct detection of single-nucleotide polymorphisms in bacterial DNA by SNPtrap

    DEFF Research Database (Denmark)

    Grønlund, Hugo Ahlm; Moen, Birgitte; Hoorfar, Jeffrey

    2011-01-01

    A major challenge with single-nucleotide polymorphism (SNP) fingerprinting of bacteria and higher organisms is the combination of genome-wide screenings with the potential of multiplexing and accurate SNP detection. Single-nucleotide extension by the minisequencing principle represents a technology...

  16. Detection of bacterial DNA in blood samples from febrile patients: underestimated infection or emerging contamination?

    NARCIS (Netherlands)

    Peters, Remco P. H.; Mohammadi, Tamimount; Vandenbroucke-Grauls, Christina M. J. E.; Danner, Sven A.; van Agtmael, Michiel A.; Savelkoul, Paul H. M.

    2004-01-01

    We applied real-time broad-range polymerase chain reaction (PCR) to detect bacteraemia in blood from febrile patients. Interpretation of amplification results in relation to clinical data and blood culture outcome was complex, although the reproducibility of the PCR results was good. Sequencing

  17. Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness.

    Science.gov (United States)

    Ho, Zheng Jie Marc; Zhao, Xiahong; Cook, Alex R; Loh, Jin Phang; Ng, Sock Hoon; Tan, Boon Huan; Lee, Vernon J

    2015-07-01

    Although it is known that febrile respiratory illnesses (FRI) may be caused by multiple respiratory pathogens, there are no population-level studies describing its impact on clinical disease. Between May 2009 and October 2012, 7733 FRI patients and controls in the Singapore military had clinical data and nasal wash samples collected prospectively and sent for PCR testing. Patients with one pathogen detected (mono-pathogen) were compared with those with two pathogens (dual pathogen) for differences in basic demographics and clinical presentation. In total, 45.8% had one pathogen detected, 20.2% had two pathogens detected, 30.9% had no pathogens detected, and 3.1% had more than two pathogens. Multiple pathogens were associated with recruits, those with asthma and non-smokers. Influenza A (80.0%), influenza B (73.0%) and mycoplasma (70.6%) were most commonly associated with mono-infections, while adenovirus was most commonly associated with dual infections (62.9%). Influenza A paired with S. pneumoniae had higher proportions of chills and rigors than their respective mono-pathogens (P = 0.03, P = 0.009). H. influenzae paired with either enterovirus or parainfluenzae had higher proportions of cough with phlegm than their respective mono-pathogens. Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. A substantial number of FRI patients have multiple pathogens detected. Observed clinical differences between patients of dual pathogen and mono-pathogen indicate the likely presence of complex microbial interactions between the various pathogens. © 2015 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

  18. Detection of bacterial species involved in perimplantitis concerned with cultural and RT-PCR

    Directory of Open Access Journals (Sweden)

    Marcello Gatti

    2010-06-01

    Full Text Available Dental implants offer new treatment options for edentulous either partially or completely, now represent a viable alternative to conventional fixed protheses. Dental implants are colonized by a flora dominated by Gram-positive facultative aerobic, while in patients with bone loss and formation of pockets peri-implant diseases was found a significant difference in the composition of microflora, bacteria, Gram-negative anaerobes in particular Fusobacterium spp., Treponema denticola (Spirochetes, Tannerella forsythensis, Aggregatibacter actinomycetemcomitans, Prevotella intermedia as interim black-pigmented bacteria, Porphyromonas gingivalis, often in high concentrations. Aims. The purpose of this study was to identify those at risk of perimplantitis using 2 techniques: RT-PCR examination of trade and culture. The results were compared taking into consideration the advantages and disadvantages of both methods. Materials and methods.We studied 24 patients (14 women and 10 men, aged, women between 43 and 76 years, with an average of 63.8 + / - 10.9 years, men between 45 and 88 years with a average of 64.3 years + / - 12.5 years. Was performed a double levy of sub-gingival plaque at multiple sites that had an implant CAL (clinical attachment level> 4mm in order to assess the microbiological identification with the two techniques: Examining culture and Real-Time PCR of Commerce ( Gum-Sunstar that identifies 4 bacterial species: A. actinomycetemcomitans (A.a., P.gingivalis (P.g., T.forsythensis (T.f., and T.denticola (T.d.. Results. All patients studied were positive to both tests with charger high: the consideration of tenure, with CFU / ml > 105, was positive in 66.6% of samples by:T.f., and P.g., in 12.5% for A.a., while T.d. not been sought by examining culture, the RT-PCR was positive, with high loads, in 95.8% of samples for T.f., in 79.1% for P.g., in 12.5% for A.a. and 20.8% for T.d.The test crop showed the presence of even P.intermedia in 91

  19. Optimization of quantitative polymerase chain reactions for detection and quantification of eight periodontal bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Decat Ellen

    2012-12-01

    Full Text Available Abstract Background The aim of this study was to optimize quantitative (real-time polymerase chain reaction (qPCR assays for 8 major periodontal pathogens, i.e. Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Parvimonas micros, Porphyromonas gingivalis, Prevotella intermedia, Tanerella forsythia and Treponema denticola, and of the caries pathogen Streptococcus mutans. Results Eighteen different primer pairs were analyzed in silico regarding specificity (using BLAST analysis and the presence of secondary structures at primer binding sites (using mFOLD. The most specific and efficiently binding primer pairs, according to these analyses, were selected for qPCR-analysis to determine amplification efficiency, limit of quantification and intra-run reproducibility. For the selected primer pairs, one for each species, the specificity was confirmed by assessing amplification of DNA extracts from isolates of closely related species. For these primer pairs, the intercycler portability was evaluated on 3 different thermal cyclers (the Applied Biosystems 7300, the Bio-Rad iQ5 and the Roche Light Cycler 480. For all assays on the different cyclers, a good correlation of the standard series was obtained (i.e. r2 ≥ 0.98, but quantification limits varied among cyclers. The overall best quantification limit was obtained by using a 2 μl sample in a final volume of 10 μl on the Light Cycler 480. Conclusions In conclusion, the proposed assays allow to quantify the bacterial loads of S. mutans, 6 periodontal pathogenic species and the genus Fusobacterium.This can be of use in assessing periodontal risk, determination of the optimal periodontal therapy and evaluation of this treatment.

  20. Polymerase Chain Reaction–Electrospray–Time-of-Flight Mass Spectrometry Versus Culture for Bacterial Detection in Septic Arthritis and Osteoarthritis

    Science.gov (United States)

    Palmer, Michael P.; Melton-Kreft, Rachael; Nistico, Laura; Hiller, N. Louisa; Kim, Leon H.J.; Altman, Gregory T.; Altman, Daniel T.; Sotereanos, Nicholas G.; Hu, Fen Z.

    2016-01-01

    Background: Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. Aims: The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. Patients and Methods: Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction–electrospray ionization–time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content. Patients were grouped by diagnosis into one of two cohorts, those with clinical suspicion of septic arthritis (n = 44) and those undergoing primary arthroplasty of the knee for OA (n = 21). In all cases where discrepant culture and MDx results were obtained, we performed species-specific 16S rRNA fluorescence in situ hybridization (FISH) as a confirmatory test. Results: MDx testing identified bacteria in 50% of the suspected septic arthritis cases and 29% of the arthroplasty cases, whereas culture detected bacteria in only 16% of the former and 0% of the latter group. The overall difference in detection rates for culture and MDx was very highly significant, p-value = 2.384 × 10−7. All of the culture-positive cases were typed as Staphylococcus aureus. Two of the septic arthritis cases were polymicrobial as was one of the OA cases by MDx. FISH testing of the specimens with discordant results supported the MDx findings in 91% (19/21) of the cases, including one case where culture detected S. aureus and MDx detected Streptococcus agalactiae. Conclusions: MDx were more sensitive than culture, as confirmed by FISH. FISH only identifies bacteria that are embedded or infiltrated within the tissue and is thus not susceptible to contamination. Not all

  1. Polymerase Chain Reaction-Electrospray-Time-of-Flight Mass Spectrometry Versus Culture for Bacterial Detection in Septic Arthritis and Osteoarthritis.

    Science.gov (United States)

    Palmer, Michael P; Melton-Kreft, Rachael; Nistico, Laura; Hiller, N Louisa; Kim, Leon H J; Altman, Gregory T; Altman, Daniel T; Sotereanos, Nicholas G; Hu, Fen Z; De Meo, Patrick J; Ehrlich, Garth D

    2016-12-01

    Preliminary studies have identified known bacterial pathogens in the knees of patients with osteoarthritis (OA) before arthroplasty. The current study was designed to determine the incidence and types of bacteria present in the synovial fluid of native knee joints from adult patients with diagnoses of septic arthritis and OA. Patients were enrolled between October 2010 and January 2013. Synovial fluid samples from the affected knee were collected and evaluated with both traditional microbial culture and polymerase chain reaction-electrospray ionization-time-of-flight mass spectrometry (molecular diagnostics [MDx]) to prospectively characterize the microbial content. Patients were grouped by diagnosis into one of two cohorts, those with clinical suspicion of septic arthritis (n = 44) and those undergoing primary arthroplasty of the knee for OA (n = 21). In all cases where discrepant culture and MDx results were obtained, we performed species-specific 16S rRNA fluorescence in situ hybridization (FISH) as a confirmatory test. MDx testing identified bacteria in 50% of the suspected septic arthritis cases and 29% of the arthroplasty cases, whereas culture detected bacteria in only 16% of the former and 0% of the latter group. The overall difference in detection rates for culture and MDx was very highly significant, p-value = 2.384 × 10 -7 . All of the culture-positive cases were typed as Staphylococcus aureus. Two of the septic arthritis cases were polymicrobial as was one of the OA cases by MDx. FISH testing of the specimens with discordant results supported the MDx findings in 91% (19/21) of the cases, including one case where culture detected S. aureus and MDx detected Streptococcus agalactiae. MDx were more sensitive than culture, as confirmed by FISH. FISH only identifies bacteria that are embedded or infiltrated within the tissue and is thus not susceptible to contamination. Not all suspected cases of septic arthritis contain bacteria, but a

  2. Agreement between microscopic examination and bacterial culture of bile samples for detection of bactibilia in dogs and cats with hepatobiliary disease.

    Science.gov (United States)

    Pashmakova, Medora B; Piccione, Julie; Bishop, Micah A; Nelson, Whitney R; Lawhon, Sara D

    2017-05-01

    OBJECTIVE To evaluate the agreement between results of microscopic examination and bacterial culture of bile samples from dogs and cats with hepatobiliary disease for detection of bactibilia. DESIGN Cross-sectional study. ANIMALS 31 dogs and 21 cats with hepatobiliary disease for which subsequent microscopic examination and bacterial culture of bile samples was performed from 2004 through 2014. PROCEDURES Electronic medical records of included dogs and cats were reviewed to extract data regarding diagnosis, antimicrobials administered, and results of microscopic examination and bacterial culture of bile samples. Agreement between these 2 diagnostic tests was assessed by calculation of the Cohen κ value. RESULTS 17 (33%) dogs and cats had bactibilia identified by microscopic examination of bile samples, and 11 (21%) had bactibilia identified via bacterial culture. Agreement between these 2 tests was substantial (percentage agreement [positive and negative results], 85%; κ = 0.62; 95% confidence interval, 0.38 to 0.89) and improved to almost perfect when calculated for only animals that received no antimicrobials within 24 hours prior to sample collection (percentage agreement, 94%; κ = 0.84; 95% confidence interval, 0.61 to 1.00). CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that agreement between microscopic examination and bacterial culture of bile samples for detection of bactibilia is optimized when dogs and cats are not receiving antimicrobials at the time of sample collection. Concurrent bacterial culture and microscopic examination of bile samples are recommended for all cats and dogs evaluated for hepatobiliary disease.

  3. Microbial Diagnostic Microarrays for the Detection and Typing of Food- and Water-Borne (Bacterial Pathogens

    Directory of Open Access Journals (Sweden)

    Tanja Kostić

    2011-10-01

    Full Text Available Reliable and sensitive pathogen detection in clinical and environmental (including food and water samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i specificity; (ii sensitivity; (iii multiplexing potential; (iv robustness; (v speed; (vi automation potential; and (vii low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples.

  4. Molecular detection of bacterial and parasitic pathogens in hard ticks from Portugal.

    Science.gov (United States)

    Maia, Carla; Ferreira, Andreia; Nunes, Mónica; Vieira, Maria Luísa; Campino, Lenea; Cardoso, Luís

    2014-06-01

    Ticks are important vector arthropods of human and animal pathogens. As information about agents of disease circulating in vectors in Portugal is limited, the aim of the present study was to detect bacteria and parasites with veterinary and zoonotic importance in ticks collected from dogs, cats, and field vegetation. A total of 925 ticks, comprising 888 (96.0%) adults, 8 (0.9%) nymphs, and 29 (3.1%) larvae, were collected in 4 geographic areas (districts) of Portugal. Among those, 620 (67.0%) were removed from naturally infested dogs, 42 (4.5%) from cats, and 263 (28.4%) were questing ticks obtained from field vegetation. Rhipicephalus sanguineus was the predominant tick species, and the only one collected from dogs and vegetation, while all Ixodes ricinus specimens (n=6) were recovered from cats. Rickettsia massiliae and Rickettsia conorii were identified in 35 ticks collected from cats and dogs and in 3 ticks collected from dogs. Among ticks collected from cats or dogs, 4 Rh. sanguineus specimens were detected with Hepatozoon felis, 3 with Anaplasma platys, 2 with Hepatozoon canis, one with Anaplasma phagocytophilum, one with Babesia vogeli, one with Borrelia burgdorferi sensu lato and one with Cercopithifilaria spp. Rickettsia helvetica was detected in one I. ricinus tick collected from a cat. To the best of our knowledge, this was the first time that Cercopithifilaria spp., Ba. vogeli, H. canis, and H. felis have been detected in ticks from Portugal. The wide range of tick-borne pathogens identified, some of zoonotic concern, suggests a risk for the emergence of tick-borne diseases in domestic animals and humans in Portugal. Further studies on these and other tick-borne agents should be performed to better understand their epidemiological and clinical importance, and to support the implementation of effective control measures. Copyright © 2014 Elsevier GmbH. All rights reserved.

  5. An improved haemolytic plaque assay for the detection of cells secreting antibody to bacterial antigens

    DEFF Research Database (Denmark)

    Barington, T; Heilmann, C

    1992-01-01

    -polysaccharide AbSC of the IgG isotype, the increase was as high as 7.4-11.8 times. Evidence is presented that the pronounced improvement in the detection of the latter is due to the presence of aggregating anti-IgG antibody from the beginning of the assay. It is proposed that in the case of low affinity of anti...

  6. Related antimicrobial resistance genes detected in different bacterial species co-isolated from swine fecal samples.

    Science.gov (United States)

    Frye, Jonathan G; Lindsey, Rebecca L; Meinersmann, Richard J; Berrang, Mark E; Jackson, Charlene R; Englen, Mark D; Turpin, Jennifer B; Fedorka-Cray, Paula J

    2011-06-01

    A potential factor leading to the spread of antimicrobial resistance (AR) in bacteria is the horizontal transfer of resistance genes between bacteria in animals or their environment. To investigate this, swine fecal samples were collected on-farm and cultured for Escherichia coli, Salmonella enterica, Campylobacter spp., and Enterococcus spp. which are all commonly found in swine. Forty-nine of the samples from which all four bacteria were recovered were selected yielding a total of 196 isolates for analysis. Isolates were tested for antimicrobial susceptibility followed by hybridization to a DNA microarray designed to detect 775 AR-related genes. E. coli and Salmonella isolated from the same fecal sample had the most AR genes in common among the four bacteria. Genes detected encoded resistance to aminoglycosides (aac(3), aadA1, aadB, and strAB), β-lactams (ampC, ampR, and bla(TEM)), chloramphenicols (cat and floR), sulfanillic acid (sul1/sulI), tetracyclines (tet(A), tet(D), tet(C), tet(G), and tet(R)), and trimethoprim (dfrA1 and dfh). Campylobacter coli and Enterococcus isolated from the same sample frequently had tet(O) and aphA-3 genes detected in common. Almost half (47%) of E. coli and Salmonella isolated from the same fecal sample shared resistance genes at a significant level (χ², p genes between these bacteria or there may be a common source of AR genes in the swine environment for E. coli and Salmonella.

  7. Improved sensitivity for molecular detection of bacterial and Candida infections in blood.

    Science.gov (United States)

    Bacconi, Andrea; Richmond, Gregory S; Baroldi, Michelle A; Laffler, Thomas G; Blyn, Lawrence B; Carolan, Heather E; Frinder, Mark R; Toleno, Donna M; Metzgar, David; Gutierrez, Jose R; Massire, Christian; Rounds, Megan; Kennel, Natalie J; Rothman, Richard E; Peterson, Stephen; Carroll, Karen C; Wakefield, Teresa; Ecker, David J; Sampath, Rangarajan

    2014-09-01

    The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  8. Development of internally controlled duplex real-time NASBA diagnostics assays for the detection of microorganisms associated with bacterial meningitis.

    Science.gov (United States)

    Clancy, Eoin; Coughlan, Helena; Higgins, Owen; Boo, Teck Wee; Cormican, Martin; Barrett, Louise; Smith, Terry J; Reddington, Kate; Barry, Thomas

    2016-08-01

    Three duplex molecular beacon based real-time Nucleic Acid Sequence Based Amplification (NASBA) assays have been designed and experimentally validated targeting RNA transcripts for the detection and identification of Haemophilus influenzae, Neisseria meningitidis and Streptococcus pneumoniae respectively. Each real-time NASBA diagnostics assay includes an endogenous non-competitive Internal Amplification Control (IAC) to amplify the splice variant 1 mRNA of the Homo sapiens TBP gene from human total RNA. All three duplex real-time NASBA diagnostics assays were determined to be 100% specific for the target species tested for. Also the Limits of Detection (LODs) for the H. influenzae, N. meningitidis and S. pneumoniae duplex real-time NASBA assays were 55.36, 0.99, and 57.24 Cell Equivalents (CE) respectively. These robust duplex real-time NASBA diagnostics assays have the potential to be used in a clinical setting for the rapid (bacterial meningitis in humans. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Detection of bacterial infection of agave plants by laser-induced fluorescence

    Science.gov (United States)

    Cervantes-Martinez, Jesus; Flores-Hernandez, Ricardo; Rodriguez-Garay, Benjamin; Santacruz-Ruvalcaba, Fernando

    2002-05-01

    Greenhouse-grown plants of Agave tequilana Weber var. azul were inoculated with Erwinia carotovora, the causal agent of stem soft rot. We investigated the laser-induced fluorescence (LIF) of agave plants to determine whether LIF can be used as a noninvasive sensing tool for pathological studies. The LIF technique was also investigated as a means of detecting the effect of the polyamine biosynthesis inhibitor beta-hydroxyethylhydrazine as a bactericide against the pathogenic bacterium Erwinia carotovora. A He-Ne laser at 632.8 nm was used as the excitation source, and in vivo fluorescence emission spectra were recorded in the 660-790-range. Fluorescence maxima were at 690 and 740 nm. The infected plants that were untreated with the bactericide showed a definite increase in fluorescence intensity at both maxima within the first three days after infection. Beginning on the fifth day, a steady decrease in fluorescence intensity was observed, with a greater effect at 740 than at 690 nm. After 30 days there was no fluorescence. The infected plants that had been treated with the bactericide showed no significant change in fluorescence compared with that of the uninfected plants. The ratio of fluorescence intensities was determined to be F 690 nm/F 740 nm for all treatments. These studies indicate that LIF measurements of agave plants may be used for the early detection of certain types of disease and for determining the effect of a bactericide on bacteria. The results also showed that fluorescence intensity ratios can be used as a reliable indicator of the progress of disease.

  10. Detection of bacterial endotoxin in food: New planar interdigital sensors based approach

    KAUST Repository

    Abdul Rahman, Mohd Syaifudin

    2013-02-01

    Food poisoning caused by endotoxins or Lipopolysaccharide (LPS) are associated with Gram-negative bacteria. Two major food-borne pathogens, Escherichia coli and Salmonella are examples of Gram-negative bacteria which cause a large number of outbreaks of food poisoning. New types of planar interdigital sensors have been fabricated with different coating materials to assess their response to endotoxins. A carboxyl-functional polymer, APTES (3-Aminopropyltriethoxysilane) and Thionine were chosen to be coated onto FR4 interdigital sensors. The chosen coating materials have carboxylic or amine functional groups, which were optimized to be stable in water. All coated sensors were immobilized with PmB (Polymyxin B) which has specific binding properties to LPS. The sensors were tested with different concentrations of LPS O111:B4, ranging from 0.1 to 1000 μg/ml. Analyses of sensors\\' performance were based on the impedance spectroscopy method. The impedance spectra were modeled using a constant phase-element (CPE) equivalent circuit, and a principal component analysis (PCA) was used for data classification. Sensor coated with APTES has shown better selectivity for LPS detection. The experiments were repeated by coating APTES and immobilizing PmB to a new improve designed of novel interdigital sensors (thin film silicon based sensors). These sensors were observed to have better sensitivity and selectivity to the target biomolecules of LPS. Further experiments were conducted to study the effect of different coating thickness on sensor sensitivity, selectivity and stability. Different food samples contaminated with endotoxin were also tested to verify that the interdigital sensing approach is able to be used for endotoxin detection. © 2012 Elsevier Ltd. All rights reserved.

  11. Remote detection of human toxicants in real time using a human-optimized, bioluminescent bacterial luciferase gene cassette bioreporter

    Science.gov (United States)

    Close, Dan; Webb, James; Ripp, Steven; Patterson, Stacey; Sayler, Gary

    2012-06-01

    Traditionally, human toxicant bioavailability screening has been forced to proceed in either a high throughput fashion using prokaryotic or lower eukaryotic targets with minimal applicability to humans, or in a more expensive, lower throughput manner that uses fluorescent or bioluminescent human cells to directly provide human bioavailability data. While these efforts are often sufficient for basic scientific research, they prevent the rapid and remote identification of potentially toxic chemicals required for modern biosecurity applications. To merge the advantages of high throughput, low cost screening regimens with the direct bioavailability assessment of human cell line use, we re-engineered the bioluminescent bacterial luciferase gene cassette to function autonomously (without exogenous stimulation) within human cells. Optimized cassette expression provides for fully endogenous bioluminescent production, allowing continuous, real time monitoring of the bioavailability and toxicology of various compounds in an automated fashion. To access the functionality of this system, two sets of bioluminescent human cells were developed. The first was programed to suspend bioluminescent production upon toxicological challenge to mimic the non-specific detection of a toxicant. The second induced bioluminescence upon detection of a specific compound to demonstrate autonomous remote target identification. These cells were capable of responding to μM concentrations of the toxicant n-decanal, and allowed for continuous monitoring of cellular health throughout the treatment process. Induced bioluminescence was generated through treatment with doxycycline and was detectable upon dosage at a 100 ng/ml concentration. These results demonstrate that leveraging autonomous bioluminescence allows for low-cost, high throughput direct assessment of toxicant bioavailability.

  12. Optimizing a portable biosensor system for bacterial detection in milk based mix for ice cream

    Directory of Open Access Journals (Sweden)

    A. Biscotti

    2018-04-01

    Full Text Available One of the primary focuses of the food industry is providing products compliant with safety standards. The microbiological analysis helps in the identification of the presence of pathogen microorganisms in the food. The analysis with Agar Plate is the classic method. This approach guarantees a high accuracy, but it needs a long detection time (twenty-four to forty-eight hours, beyond high costs and skilled technician. In recent times have been proposed many different methods to have a faster response, and between them there is the impedance method. One of its features is that it is fast, in fact it requires between three to fourteen hours to obtain a reliable measurement. The system is accurate, and suitable to be executed automatically. To test this method has been used UHT Ice Cream Mix. A known volume of mix has been inoculated with increasing percentage of cultures of E. coli. The measurement of the impedance of the inoculated mix has been done by an electronic board designed for the application, and by applying a sinusoidal voltage to the test tube. The signal was digitally generated by the microprocessor, and supplied externally through a D.A. converter. The signal was then filtered to delete from its spectrum the high frequency components typical of the digitally generated signals. The data obtained from impedance instrument showed a reliable correspondence with those from the plate count. By working in less time compared to traditional methods, this tool is well suited for in-situ preliminary analysis in commercial and professional foodservice environment.

  13. Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP) Assay for the Detection of Bacterial Meningitis Pathogens.

    Science.gov (United States)

    Higgins, Owen; Clancy, Eoin; Cormican, Martin; Boo, Teck Wee; Cunney, Robert; Smith, Terry J

    2018-02-09

    Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD) and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae , Neisseria meningitidis and Haemophilus influenzae . Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae , N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.

  14. Evaluation of an Internally Controlled Multiplex Tth Endonuclease Cleavage Loop-Mediated Isothermal Amplification (TEC-LAMP Assay for the Detection of Bacterial Meningitis Pathogens

    Directory of Open Access Journals (Sweden)

    Owen Higgins

    2018-02-01

    Full Text Available Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have developed novel real-time multiplex LAMP technology, TEC-LAMP, using Tth endonuclease IV and a unique LAMP primer/probe. This study evaluates the analytical specificity, limit of detection (LOD and clinical application of an internally controlled multiplex TEC-LAMP assay for detection of leading bacterial meningitis pathogens: Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae. Analytical specificities were established by testing 168 bacterial strains, and LODs were determined using Probit analysis. The TEC-LAMP assay was 100% specific, with LODs for S. pneumoniae, N. meningitidis and H. influenzae of 39.5, 17.3 and 25.9 genome copies per reaction, respectively. Clinical performance was evaluated by testing 65 archived PCR-positive samples. Compared to singleplex real-time PCR, the multiplex TEC-LAMP assay demonstrated diagnostic sensitivity and specificity of 92.3% and 100%, respectively. This is the first report of a single-tube internally controlled multiplex LAMP assay for bacterial meningitis pathogen detection, and the first report of Tth endonuclease IV incorporation into nucleic acid amplification diagnostic technology.

  15. Detection of marine and freshwater bacterioplankton in immersed victims: Post-mortem bacterial invasion does not readily occur.

    Science.gov (United States)

    Kakizaki, Eiji; Kozawa, Shuji; Imamura, Nahoko; Uchiyama, Taketo; Nishida, Sho; Sakai, Masahiro; Yukawa, Nobuhiro

    2011-09-10

    We previously applied our method of detecting marine or freshwater bacterioplankton (bacteria) in the blood of immersed victims as a marker of drowning. However, we did not confirm the absence of post-mortem bacterial invasion during immersion. Here we examined the nature of bacterioplankton in blood samples from 21 immersed and 4 non-immersed cadavers. We found only freshwater bacterioplankton in the blood of two victims that were retrieved from the sea or an estuary inhabited by marine bacterioplankton even though one victim was highly putrefied. The results of diatom testing suggested that these two victims had drowned in fresh or brackish water with low salinity and then flowed out to the estuary or the sea. Two others were submerged in water, but representative bacterioplankton were undetectable in their blood although one victim was highly putrefied. Autopsy findings and the results of diatom tests did not indicate that the cause of death was drowning. As in previous studies, we identified freshwater bacterioplankton in the blood of seven other victims that had drowned in freshwater, marine bacterioplankton in the blood of four victims that had drowned in seawater and none in four victims found on land that had died by means other than drowning. Bacterioplankton in the blood of drowned victims appears to reflect the type of water aspirated and blood does not become easily contaminated with bacteria post-mortem even in decomposed bodies. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  16. Use of PCR-DHPLC with fluorescence detection for the characterization of the bacterial diversity during cassava (Manihot esculenta Crantz) fermentation.

    Science.gov (United States)

    Kodama, C S; Cuadros-Orellana, S; Bandeira, C H M M; Graças, D A; Santos, A S; Silva, A

    2014-02-28

    Denaturing high-performance liquid chromatography (DHPLC) has been described as a suitable method to study DNA polymorphisms. Here, cassava (Manihot esculenta Crantz) fermentation liquor was examined using DHPLC analysis to characterize the bacterial diversity during the fermentation process. GC-clamped amplicons corresponding to a variable region of the bacterial community 16S rDNA were synthesized using polymerase chain reaction (PCR) and then resolved on a base-composition basis using preparative DHPLC. Eluate fractions were collected at random and used as a source of whole community DNA that could be used to determine the bacterial diversity. As a first approach, GC-clamps were removed from the eluted DNA fragments using PCR to avoid the possible bias these clamps could cause during the construction of clone libraries. As a second approach, a clone library of each eluate sample was constructed, preserving the GC-clamps of the DNA fragments. The first approach generated 132 bacterial rDNA sequences with an average size of 200 bp, 45% of which had similarity to unculturable or non-classified bacteria. The second approach produced 194 sequences identified as Proteobacteria (48%), uncultured or non-classified environmental bacteria (40%) and Firmicutes (12%). We detected a remarkably greater bacterial diversity using the first approach than the second approach. The DHPLC-PCR method allowed for the fast and non-laborious detection of a vast bacterial diversity that was associated with cassava fermentation, and we conclude that it is a promising alternative for the characterization of the overall microbial diversity in complex samples.

  17. A multi-channel bioluminescent bacterial biosensor for the on-line detection of metals and toxicity. Part I: design and optimization of bioluminescent bacterial strains

    Energy Technology Data Exchange (ETDEWEB)

    Charrier, Thomas; Durand, Marie-Jose; Jouanneau, Sulivan; Thouand, Gerald [UMR CNRS 6144 GEPEA, CBAC, Nantes University, PRES UNAM, Campus de la Courtaisiere-IUT, La Roche-sur-Yon cedex (France); Dion, Michel [UMR CNRS 6204, Nantes University, PRES UNAM, Biotechnologie, Biocatalyse, Bioregulation, 2, Rue de la Houssiniere, BP 92208, Nantes cedex 3 (France); Pernetti, Mimma; Poncelet, Denis [ONIRIS-ENITIAA, UMR CNRS GEPEA, Rue de la Geraudiere, BP 82225, Nantes cedex 3 (France)

    2011-05-15

    This study describes the construction of inducible bioluminescent strains via genetic engineering along with their characterization and optimization in the detection of heavy metals. Firstly, a preliminary comparative study enabled us to select a suitable carbon substrate from pyruvate, glucose, citrate, diluted Luria-Bertani, and acetate. The latter carbon source provided the best induction ratios for comparison. Results showed that the three constructed inducible strains, Escherichia coli DH1 pBzntlux, pBarslux, and pBcoplux, were usable when conducting a bioassay after a 14-h overnight culture at 30 C. Utilizing these sensors gave a range of 12 detected heavy metals including several cross-detections. Detection limits for each metal were often close to and sometimes lower than the European standards for water pollution. Finally, in order to maintain sensitive bacteria within the future biosensor-measuring cell, the agarose immobilization matrix was compared to polyvinyl alcohol (PVA). Agarose was selected because the detection limits of the bioluminescent strains were not affected, in contrast to PVA. Specific detection and cross-detection ranges determined in this study will form the basis of a multiple metals detection system by the new multi-channel Lumisens3 biosensor. (orig.)

  18. Infection of Bacterial Endosymbionts in Insects: A Comparative Study of Two Techniques viz PCR and FISH for Detection and Localization of Symbionts in Whitefly, Bemisia tabaci.

    Directory of Open Access Journals (Sweden)

    Harpreet Singh Raina

    Full Text Available Bacterial endosymbionts have been associated with arthropods and large number of the insect species show interaction with such bacteria. Different approaches have been used to understand such symbiont- host interactions. The whitefly, Bemisia tabaci, a highly invasive agricultural pest, harbors as many as seven different bacterial endosymbionts. These bacterial endosymbionts are known to provide various nutritional, physiological, environmental and evolutionary benefits to its insect host. In this study, we have tried to compare two techniques, Polymerase chain reaction (PCR and Flourescence in situ Hybridisation (FISH commonly used for identification and localization of bacterial endosymbionts in B. tabaci as it harbors one of the highest numbers of endosymbionts which have helped it in becoming a successful global invasive agricultural pest. The amplified PCR products were observed as bands on agarose gel by electrophoresis while the FISH samples were mounted on slides and observed under confocal microscope. Analysis of results obtained by these two techniques revealed the advantages of FISH over PCR. On a short note, performing FISH, using LNA probes proved to be more sensitive and informative for identification as well as localization of bacterial endosymbionts in B. tabaci than relying on PCR. This study would help in designing more efficient experiments based on much reliable detection procedure and studying the role of endosymbionts in insects.

  19. Molecular detection of Candidatus Scalindua pacifica and environmental responses of sediment anammox bacterial community in the Bohai Sea, China.

    Directory of Open Access Journals (Sweden)

    Hongyue Dang

    Full Text Available The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named "Ca. Scalindua pacifica". Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds, alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these

  20. Molecular Detection of Candidatus Scalindua pacifica and Environmental Responses of Sediment Anammox Bacterial Community in the Bohai Sea, China

    Science.gov (United States)

    Dang, Hongyue; Zhou, Haixia; Zhang, Zhinan; Yu, Zishan; Hua, Er; Liu, Xiaoshou; Jiao, Nianzhi

    2013-01-01

    The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named “Ca. Scalindua pacifica”. Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were

  1. Development of Real-Time PCR Methods for the Detection of Bacterial Meningitis Pathogens without DNA Extraction.

    Directory of Open Access Journals (Sweden)

    Jeni Vuong

    Full Text Available Neisseria meningitidis (Nm, Haemophilus influenzae (Hi, and Streptococcus pneumoniae (Sp are the lead causes of bacterial meningitis. Detection of these pathogens from clinical specimens using traditional real-time PCR (rt-PCR requires DNA extraction to remove the PCR inhibitors prior to testing, which is time consuming and labor intensive. In this study, five species-specific (Nm-sodC and -ctrA, Hi-hpd#1 and -hpd#3 and Sp-lytA and six serogroup-specific rt-PCR tests (A, B, C, W, X, Y targeting Nm capsular genes were evaluated in the two direct rt-PCR methods using PerfeCTa and 5x Omni that do not require DNA extraction. The sensitivity and specify of the two direct rt-PCR methods were compared to TaqMan traditional rt-PCR, the current standard rt-PCR method for the detection of meningitis pathogens. The LLD for all 11 rt-PCR tests ranged from 6,227 to 272,229 CFU/ml for TaqMan, 1,824-135,982 for 5x Omni, and 168-6,836 CFU/ml for PerfeCTa. The diagnostic sensitivity using TaqMan ranged from 89.2%-99.6%, except for NmB-csb, which was 69.7%. For 5x Omni, the sensitivity varied from 67.1% to 99.8%, with three tests below 90%. The sensitivity of these tests using PerfeCTa varied from 89.4% to 99.8%. The specificity ranges of the 11 tests were 98.0-99.9%, 97.5-99.9%, and 92.9-99.9% for TaqMan, 5x Omni, and PerfeCTa, respectively. PerfeCTa direct rt-PCR demonstrated similar or better sensitivity compared to 5x Omni direct rt-PCR or TaqMan traditional rt-PCR. Since the direct rt-PCR method does not require DNA extraction, it reduces the time and cost for processing CSF specimens, increases testing throughput, decreases the risk of cross-contamination, and conserves precious CSF. The direct rt-PCR method will be beneficial to laboratories with high testing volume.

  2. Locked Nucleic Acid Flow Cytometry-fluorescence in situ Hybridization (LNA flow-FISH): A Method for Bacterial Small RNA Detection

    Science.gov (United States)

    2012-01-10

    Friedrich, U. & Lenke, J. Improved Enumeration of Lactic Acid Bacteria in Mesophilic Dairy Starter Cultures by Using Multiplex Quantitative Real...messenger RNA using locked nucleic acid probes. Anal. Biochem. 390, 109-114 (2009). 13. Waters, L. & Storz, G. Regulatory RNAs in bacteria . Cell. 136, 615...Video Article Locked Nucleic Acid Flow Cytometry-fluorescence in situ Hybridization (LNA flow-FISH): a Method for Bacterial Small RNA Detection Kelly

  3. Single-frequency, dual-GNSS versus dual-frequency, single-GNSS: a low-cost and high-grade receivers GPS-BDS RTK analysis

    Science.gov (United States)

    Odolinski, Robert; Teunissen, Peter J. G.

    2016-11-01

    The concept of single-frequency, dual-system (SF-DS) real-time kinematic (RTK) positioning has become feasible since, for instance, the Chinese BeiDou Navigation Satellite System (BDS) has become operational in the Asia-Pacific region. The goal of the present contribution is to investigate the single-epoch RTK performance of such a dual-system and compare it to a dual-frequency, single-system (DF-SS). As the SF-DS we investigate the L1 GPS + B1 BDS model, and for DF-SS we take L1, L2 GPS and B1, B2 BDS, respectively. Two different locations in the Asia-Pacific region are analysed with varying visibility of the BDS constellation, namely Perth in Australia and Dunedin in New Zealand. To emphasize the benefits of such a model we also look into using low-cost ublox single-frequency receivers and compare such SF-DS RTK performance to that of a DF-SS, based on much more expensive survey-grade receivers. In this contribution a formal and empirical analysis is given. It will be shown that with the SF-DS higher elevation cut-off angles than the conventional 10° or 15° can be used. The experiment with low-cost receivers for the SF-DS reveals (for the first time) that it has the potential to achieve comparable ambiguity resolution performance to that of a DF-SS (L1, L2 GPS), based on the survey-grade receivers.

  4. Real-time qPCR improves meningitis pathogen detection in invasive bacterial-vaccine preventable disease surveillance in Fiji

    OpenAIRE

    Dunne, Eileen M.; Mantanitobua, Silivia; Singh, Shalini P.; Reyburn, Rita; Tuivaga, Evelyn; Rafai, Eric; Tikoduadua, Lisi; Porter, Barbara; Satzke, Catherine; Strachan, Janet E.; Fox, Kimberly K.; Jenkins, Kylie M.; Jenney, Adam; Baro, Silo; Mulholland, E. Kim

    2016-01-01

    As part of the World Health Organization Invasive Bacterial-Vaccine Preventable Diseases (IB-VPD) surveillance in Suva, Fiji, cerebrospinal fluid (CSF) samples from suspected meningitis patients of all ages were examined by traditional methods (culture, Gram stain, and latex agglutination for bacterial antigen) and qPCR for Streptococcus pneumoniae, Neisseria meningitidis, and Haemophilus influenzae. Of 266 samples tested, pathogens were identified in 47 (17.7%). S. pneumoniae was the most co...

  5. Detection of denitrification genes by in situ rolling circle amplification - fluorescence in situ hybridization (in situ RCA-FISH) to link metabolic potential with identity inside bacterial cells

    DEFF Research Database (Denmark)

    Hoshino, Tatsuhiko; Schramm, Andreas

    2010-01-01

    A target-primed in situ rolling circle amplification (in situ RCA) protocol was developed for detection of single-copy genes inside bacterial cells and optimized with Pseudomonas stutzeri, targeting nitrite and nitrous oxide reductase genes (nirS and nosZ). Two padlock probes were designed per gene...... as Candidatus Accumulibacter phosphatis by combining in situ RCA-FISH with 16S rRNA-targeted FISH. While not suitable for quantification because of its low detection frequency, in situ RCA-FISH will allow to link metabolic potential with 16S rRNA (gene)-based identification of single microbial cells....

  6. Near real-time PPP-based monitoring of the ionosphere using dual-frequency GPS/BDS/Galileo data

    Science.gov (United States)

    Liu, Zhinmin; Li, Yangyang; Li, Fei; Guo, Jinyun

    2018-03-01

    Ionosphere delay is very important to GNSS observations, since it is one of the main error sources which have to be mitigated even eliminated in order to determine reliable and precise positions. The ionosphere is a dispersive medium to radio signal, so the value of the group delay or phase advance of GNSS radio signal depends on the signal frequency. Ground-based GNSS stations have been used for ionosphere monitoring and modeling for a long time. In this paper we will introduce a novel approach suitable for single-receiver operation based on the precise point positioning (PPP) technique. One of the main characteristic is that only carrier-phase observations are used to avoid particular effects of pseudorange observations. The technique consists of introducing ionosphere ambiguity parameters obtained from PPP filter into the geometry-free combination of observations to estimate ionospheric delays. Observational data from stations that are capable of tracking the GPS/BDS/GALILEO from the International GNSS Service (IGS) Multi-GNSS Experiments (MGEX) network are processed. For the purpose of performance validation, ionospheric delays series derived from the novel approach are compared with the global ionospheric map (GIM) from Ionospheric Associate Analysis Centers (IAACs). The results are encouraging and offer potential solutions to the near real-time ionosphere monitoring.

  7. Detection of herpes simplex-1 and -2 and varicella zoster virus by quantitative real-time polymerase chain reaction in corneas from patients with bacterial keratitis.

    Science.gov (United States)

    Nascimento, Heloisa; Watanabe, Aripuanã; Vieira, Ana Carolina Cabreira; Pelegrini, Andrea; Yu, Maria Cecília; Bispo, Paulo José Martins; Granato, Celso Francisco Hernandes; Höfling-Lima, Ana Luisa

    2017-01-01

    Bacterial keratitis occurs worldwide, and despite recent developments, it remains a potentially blinding condition. This study assesses the presence of herpes simplex virus (HSV-1 and -2) and varicella zoster virus (VZV) by quantitative real-time polymerase chain reaction (qPCR) in corneal scrapings from patients with bacterial keratitis. A total of 65 patients with clinical diagnoses of infectious corneal ulcers prospectively underwent clinical eye examinations. Corneal scrapings were investigated by Gram staining, Giemsa staining, culture, and qPCR (the study group). Risk factors and epidemiological data were recorded. The control group comprising 25 eyes with typical herpes dendritic keratitis was also analyzed by qPCR. From the study group (n=65), nine patients (13.8%) had negative smears, cultures, and qPCR findings. Fifty-six (86.2%) patients had positive cultures: 51 for bacteria, 4 for fungi, and 1 for amoebae. Of the patients who had positive bacterial cultures, qPCR identified 10 patients who were also positive for virus: one for VZV and nine for HSV-1. Of the 25 patients in the control group, 21 tested positive for HSV-1 by qPCR analysis. Herpes may be present in patients with bacterial corneal ulcers, and qPCR may be useful in its detection.

  8. Survey of childhood empyema in Asia: Implications for detecting the unmeasured burden of culture-negative bacterial disease

    Directory of Open Access Journals (Sweden)

    Shen Xuzhuang

    2008-07-01

    Full Text Available Abstract Background Parapneumonic empyema continues to be a disease of significant morbidity and mortality among children despite recent advances in medical management. To date, only a limited number of studies have assessed the burden of empyema in Asia. Methods We surveyed medical records of four representative large pediatric hospitals in China, Korea, Taiwan and Vietnam using ICD-10 diagnostic codes to identify children Results During the study period, we identified 1,379 children diagnosed with empyema or pleural effusion (China, n = 461; Korea, n = 134; Taiwan, n = 119; Vietnam, n = 665. Diagnoses of pleural effusion (n = 1,074 were 3.5 times more common than of empyema (n = 305, although the relative proportions of empyema and pleural effusion noted in hospital records varied widely between the four sites, most likely because of marked differences in coding practices. Although pleural effusions were reported more often than empyema, children with empyema were more likely to have a cultured pathogen. In addition, we found that median age and gender distribution of children with these conditions were similar across the four countries. Among 1,379 empyema and pleural effusion specimens, 401 (29% were culture positive. Staphylococcus aureus (n = 126 was the most common organism isolated, followed by Streptococcus pneumoniae (n = 83, Pseudomonas aeruginosa (n = 37 and Klebsiella (n = 35 and Acinetobacter species (n = 34. Conclusion The age and gender distribution of empyema and pleural effusion in children in these countries are similar to the US and Western Europe. S. pneumoniae was the second leading bacterial cause of empyema and pleural effusion among Asian children. The high proportion of culture-negative specimens among patients with pleural effusion or empyema suggests that culture may not be a sufficiently sensitive diagnostic method to determine etiology in the majority of cases. Future prospective studies in different countries would

  9. Bacterial Keratitis

    Science.gov (United States)

    ... Español Eye Health / Eye Health A-Z Bacterial Keratitis Sections What Is Bacterial Keratitis? Bacterial Keratitis Symptoms ... Lens Care Bacterial Keratitis Treatment What Is Bacterial Keratitis? Leer en Español: ¿Qué Es la Queratitis Bacteriana? ...

  10. Nanomaterial-based sensors for detection of foodborne bacterial pathogens and toxins as well as pork adulteration in meat products

    Directory of Open Access Journals (Sweden)

    B. Stephen Inbaraj

    2016-01-01

    Full Text Available Food safety draws considerable attention in the modern pace of the world owing to rapid-changing food recipes and food habits. Foodborne illnesses associated with pathogens, toxins, and other contaminants pose serious threat to human health. Besides, a large amount of money is spent on both analyses and control measures, which causes significant loss to the food industry. Conventional detection methods for bacterial pathogens and toxins are time consuming and laborious, requiring certain sophisticated instruments and trained personnel. In recent years, nanotechnology has emerged as a promising field for solving food safety issues in terms of detecting contaminants, enabling controlled release of preservatives to extend the shelf life of foods, and improving food-packaging strategies. Nanomaterials including metal oxide and metal nanoparticles, carbon nanotubes, and quantum dots are gaining a prominent role in the design of sensors and biosensors for food analysis. In this review, various nanomaterial-based sensors reported in the literature for detection of several foodborne bacterial pathogens and toxins are summarized highlighting their principles, advantages, and limitations in terms of simplicity, sensitivity, and multiplexing capability. In addition, the application through a noncross-linking method without the need for any surface modification is also presented for detection of pork adulteration in meat products.

  11. Comparison of bacterial culture and qPCR testing of rectal and pen floor samples as diagnostic approaches to detect enterotoxic Escherichia coli in nursery pigs

    DEFF Research Database (Denmark)

    Weber, N. R.; Nielsen, J. P.; Hjulsager, Charlotte Kristiane

    2017-01-01

    Enterotoxigenic E. coli (ETEC) are a major cause of diarrhoea in weaned pigs. The objective of this study was to evaluate the agreement at pen level among three different diagnostic approaches for the detection of ETEC in groups of nursery pigs with diarrhoea. The diagnostic approaches used were......: bacterial culturing of faecal samples from three pigs (per pen) with clinical diarrhoea and subsequent testing for virulence genes in E. coli isolates; bacterial culturing of pen floor samples and subsequent testing for virulence genes in E. coli isolates; qPCR testing of pen floor samples in order...... to determine the quantity of F18 and F4 genes. The study was carried out in three Danish pig herds and included 31 pens with a pen-level diarrhoea prevalence of > 25%, as well as samples from 93 diarrhoeic nursery pigs from these pens. All E. coli isolates were analysed by PCR and classified as ETEC when genes...

  12. PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens

    DEFF Research Database (Denmark)

    Zankari, Ea; Allesøe, Rosa Lundbye; Joensen, Katrine Grimstrup

    2017-01-01

    Background Antibiotic resistance is a major health problem, as drugs that were once highly effective no longer cure bacterial infections. WGS has previously been shown to be an alternative method for detecting horizontally acquired antimicrobial resistance genes. However, suitable bioinformatics...... methods that can provide easily interpretable, accurate and fast results for antimicrobial resistance associated with chromosomal point mutations are still lacking. Methods Phenotypic antimicrobial susceptibility tests were performed on 150 isolates covering three different bacterial species: Salmonella...... were compared with phenotypic antimicrobial susceptibility testing results. Results A total of 685 different phenotypic tests associated with chromosomal resistance to quinolones, polymyxin, rifampicin, macrolides and tetracyclines resulted in 98.4% concordance. Eleven cases of disagreement between...

  13. DETECTION OF BACTERIAL CYTOTOXIC ACTIVITIES FROM WATER-DAMAGED CEILING TILE MATERIAL FOLLOWING INCUBATION ON BLOOD AGAR

    Science.gov (United States)

    Samples of ceiling tiles with high levels of bacteria exhibited cytotoxic activities on a HEP-2 tissue culture assay. Ceiling tiles containing low levels of bacterial colonization did not show cytotoxic activities on the HEP-2 tissue culture assay. Using a spread plate procedure ...

  14. Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

    OpenAIRE

    Weir Jerry P; Schmeisser Falko

    2007-01-01

    Abstract Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC) technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2) BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. Whi...

  15. Eight-plex PCR and liquid-array detection of bacterial and viral pathogens in cerebrospinal fluid from patients with suspected meningitis

    DEFF Research Database (Denmark)

    Bøving, Mette Kusk; Pedersen, Lisbeth Nørum; Møller, Jens Kjølseth

    2009-01-01

    We here report on the development of a novel multiplex PCR with product detection in a Luminex 100 suspension array system. The assay covers the nine most important bacterial and viral pathogens found in Danish meningitis patients. The microorganisms include Neisseria meningitidis, Streptococcus...... and culture of cerebrospinal fluid (CSF) samples in a routine diagnostic setting, and results can be available within 1 workday. The method is suitable for use for the initial screening and identification of nine important microorganisms in CSF samples from patients with suspected meningitis. Compared...

  16. Detection of bacterial DNA in cerebrospinal fluid by an assay for simultaneous detection of Neisseria meningitidis, Haemophilus influenzae, and streptococci using a seminested PCR strategy.

    OpenAIRE

    Rådström, P; Bäckman, A; Qian, N; Kragsbjerg, P; Påhlson, C; Olcén, P

    1994-01-01

    Primers specific to conserved and variable regions in the 16S rRNA sequence were selected from the partially sequenced 16S rRNA genes of Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S. agalactiae, and Staphylococcus epidermidis. The PCR assay was divided into two DNA amplifications. The first resulted in a general bacterial amplicon, and the second resulted in a species-specific amplicon. The high specificity of the PCR assay was documented after testing bacteria ...

  17. Direct bacterial loop-mediated isothermal amplification detection on the pathogenic features of the nosocomial pathogen - Methicillin resistant Staphylococcus aureus strains with respiratory origins.

    Science.gov (United States)

    Lin, Qun; Xu, Pusheng; Li, Jiaowu; Chen, Yin; Feng, Jieyi

    2017-08-01

    Loop-mediated isothermal amplification based detection assays using bacterial culture or colony for direct detection of methicillin resistant Staphylococcus aureus(MRSA) had been developed and evaluated, followed by its extensive application on a large scale of clinical MRSA isolated from respiratory origins, including nasal swabs and sputums. Six primers, including outer primers, inner primers and loop primers, were specifically designed for recognizing eight distinct sequences on four targets: 16SrRNA, femA, mecA and orfX. Twenty-seven reference strains were used to develop, evaluate and optimize this assay. Then, a total of 532 clinical MRSA isolates were employed for each detected targets. And the results were determined through both visual observation of the color change by naked eye and electrophoresis. The specific of each primer had been confirmed, and the optimal amplification was obtained under 65 °C for 40 min. The limit of detections (LOD) of bacteria culture LAMP assays were determined to be 10 4  CFU/ml for 16S rRNA, femA, as well as orfX and 10 5  CFU/ml for mecA, respectively. The established novel assays on MRSA detection may provide new strategies for rapid detection of foodborne pathogens. Copyright © 2017. Published by Elsevier Ltd.

  18. An Extended ADOP for Performance Evaluation of Single-Frequency Single-Epoch Positioning by BDS/GPS in Asia-Pacific Region

    Directory of Open Access Journals (Sweden)

    Xin Liu

    2017-09-01

    Full Text Available Single-Frequency Single-Epoch (SFSE high-precision positioning has always been the hot spot of Global Navigation Satellite System (GNSS, and ambiguity dilution of precision (ADOP is a well-known scalar measure for success rate of ambiguity resolution. Traditional ADOP expression is complicated, thus the SFSE extended ADOP (E-ADOP, with the newly defined Summation-Multiplication Ratio of Weight (SMRW and two theorems for short baseline, was developed. This simplifies the ADOP expression; gives a clearer insight into the influences of SMRW and number of satellites on E-ADOP; and makes theoretical analysis of E-ADOP more convenient than that of ADOP, and through that the E-ADOP value can be predicted more accurately than through the ADOP expression for ADOP value. E-ADOP reveals that number of satellites and SMRW or high-elevation satellite are important for ADOP and, through E-ADOP, we studied which factor is dominant to control ADOP in different conditions and make ADOP different between BeiDou Navigation Satellite System (BDS, Global Positioning System (GPS, and BDS/GPS. Based on experimental results of SFSE positioning with different baselines, some conclusions are made: (1 ADOP decreases when new satellites are added mainly because the number of satellites becomes larger; (2 when the number of satellites is constant, ADOP is mainly affected by SMRW; (3 in contrast to systems where the satellites with low-elevation are the majority or where low- and high-elevation satellites are equally distributed, in systems where the high-elevation satellites are the majority, the SMRW mainly makes ADOP smaller, even if there are fewer satellites than in the two previous cases, and the difference in numbers of satellites can be expanded as the proportion of high-elevation satellites becomes larger; and (4 ADOP of BDS is smaller than ADOP of GPS mainly because of its SMRW.

  19. A rapid two-step algorithm detects and identifies clinical macrolide and beta-lactam antibiotic resistance in clinical bacterial isolates.

    Science.gov (United States)

    Lu, Xuedong; Nie, Shuping; Xia, Chengjing; Huang, Lie; He, Ying; Wu, Runxiang; Zhang, Li

    2014-07-01

    Aiming to identify macrolide and beta-lactam resistance in clinical bacterial isolates rapidly and accurately, a two-step algorithm was developed based on detection of eight antibiotic resistance genes. Targeting at genes linked to bacterial macrolide (msrA, ermA, ermB, and ermC) and beta-lactam (blaTEM, blaSHV, blaCTX-M-1, blaCTX-M-9) antibiotic resistances, this method includes a multiplex real-time PCR, a melting temperature profile analysis as well as a liquid bead microarray assay. Liquid bead microarray assay is applied only when indistinguishable Tm profile is observed. The clinical validity of this method was assessed on clinical bacterial isolates. Among the total 580 isolates that were determined by our diagnostic method, 75% of them were identified by the multiplex real-time PCR with melting temperature analysis alone, while the remaining 25% required both multiplex real-time PCR with melting temperature analysis and liquid bead microarray assay for identification. Compared with the traditional phenotypic antibiotic susceptibility test, an overall agreement of 81.2% (kappa=0.614, 95% CI=0.550-0.679) was observed, with a sensitivity and specificity of 87.7% and 73% respectively. Besides, the average test turnaround time is 3.9h, which is much shorter in comparison with more than 24h for the traditional phenotypic tests. Having the advantages of the shorter operating time and comparable high sensitivity and specificity with the traditional phenotypic test, our two-step algorithm provides an efficient tool for rapid determination of macrolide and beta-lactam antibiotic resistances in clinical bacterial isolates. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Modulation of population density and size of silver nanoparticles embedded in bacterial cellulose via ammonia exposure: visual detection of volatile compounds in a piece of plasmonic nanopaper

    Science.gov (United States)

    Heli, B.; Morales-Narváez, E.; Golmohammadi, H.; Ajji, A.; Merkoçi, A.

    2016-04-01

    The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and from amber to a grey or taupe colour upon fish or meat spoilage exposure. These phenomena are proposed as a simple visual detection of volatile compounds in a flexible, transparent, permeable and stable single-use nanoplasmonic membrane, which opens the way to innovative approaches and capabilities in gas sensing and smart packaging.The localized surface plasmon resonance exhibited by noble metal nanoparticles can be sensitively tuned by varying their size and interparticle distances. We report that corrosive vapour (ammonia) exposure dramatically reduces the population density of silver nanoparticles (AgNPs) embedded within bacterial cellulose, leading to a larger distance between the remaining nanoparticles and a decrease in the UV-Vis absorbance associated with the AgNP plasmonic properties. We also found that the size distribution of AgNPs embedded in bacterial cellulose undergoes a reduction in the presence of volatile compounds released during food spoilage, modulating the studied nanoplasmonic properties. In fact, such a plasmonic nanopaper exhibits a change in colour from amber to light amber upon the explored corrosive vapour exposure and

  1. A multiplex PCR/LDR assay for simultaneous detection and identification of the NIAID category B bacterial food and water-borne pathogens.

    Science.gov (United States)

    Rundell, Mark S; Pingle, Maneesh; Das, Sanchita; Hussain, Aashiq; Ocheretina, Oksana; Charles, Macarthur; Larone, Davise H; Spitzer, Eric D; Golightly, Linnie; Barany, Francis

    2014-06-01

    Enteric pathogens that cause gastroenteritis remain a major global health concern. The goal of this study was to develop a multiplex PCR/ligation detection reaction (LDR) assay for the detection of all NIAID category B bacterial food and water-borne pathogens directly from stool specimens. To validate the PCR/LDR assay, clinical isolates of Campylobacter spp., Vibrio spp., Shigella spp., Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and diarrheagenic Escherichia coli were tested. The sensitivity and specificity of the assay were assessed using a large number of seeded culture-negative stool specimens and a smaller set of clinical specimens from Haiti. The overall sensitivity ranged from 91% to 100% (median 100%) depending on the species. For the majority of organisms, the sensitivity was 100%. The overall specificity based on initial testing ranged from 98% to 100% depending on the species. After additional testing of discordant samples, the lowest specificity was 99.4%. PCR/LDR detected additional category B agents (particularly diarrheagenic E. coli) in 11/40 specimens from Haiti that were culture-positive for V. cholerae and in approximately 1% of routine culture-negative stool specimens from a hospital in New York. This study demonstrated the ability of the PCR/LDR assay to detect a large comprehensive panel of category B enteric bacterial pathogens as well as mixed infections. This type of assay has the potential to provide earlier warnings of possible public health threats and more accurate surveillance of food and water-borne pathogens. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. Identification of a novel calcium binding motif based on the detection of sequence insertions in the animal peroxidase domain of bacterial proteins.

    Directory of Open Access Journals (Sweden)

    Saray Santamaría-Hernando

    Full Text Available Proteins of the animal heme peroxidase (ANP superfamily differ greatly in size since they have either one or two catalytic domains that match profile PS50292. The orf PP_2561 of Pseudomonas putida KT2440 that we have called PepA encodes a two-domain ANP. The alignment of these domains with those of PepA homologues revealed a variable number of insertions with the consensus G-x-D-G-x-x-[GN]-[TN]-x-D-D. This motif has also been detected in the structure of pseudopilin (pdb 3G20, where it was found to be involved in Ca(2+ coordination although a sequence analysis did not reveal the presence of any known calcium binding motifs in this protein. Isothermal titration calorimetry revealed that a peptide containing this consensus motif bound specifically calcium ions with affinities ranging between 33-79 µM depending on the pH. Microcalorimetric titrations of the purified N-terminal ANP-like domain of PepA revealed Ca(2+ binding with a K(D of 12 µM and stoichiometry of 1.25 calcium ions per protein monomer. This domain exhibited peroxidase activity after its reconstitution with heme. These data led to the definition of a novel calcium binding motif that we have termed PERCAL and which was abundantly present in animal peroxidase-like domains of bacterial proteins. Bacterial heme peroxidases thus possess two different types of calcium binding motifs, namely PERCAL and the related hemolysin type calcium binding motif, with the latter being located outside the catalytic domains and in their C-terminal end. A phylogenetic tree of ANP-like catalytic domains of bacterial proteins with PERCAL motifs, including single domain peroxidases, was divided into two major clusters, representing domains with and without PERCAL motif containing insertions. We have verified that the recently reported classification of bacterial heme peroxidases in two families (cd09819 and cd09821 is unrelated to these insertions. Sequences matching PERCAL were detected in all kingdoms of

  3. On-chip electrical detection of parallel loop-mediated isothermal amplification with DG-BioFETs for the detection of foodborne bacterial pathogens

    Science.gov (United States)

    The use of field effect transistors (FETs) as the transduction element for the detection of DNA amplification reactions will enable portable and inexpensive nucleic acid analysis. Transistors used as biological sensors,or BioFETs, minimize the cost and size of detection platforms by leveraging fabri...

  4. Delayed phagocytosis and bacterial killing in Chediak-Higashi syndrome neutrophils detected by a fluorochrome assay: ultrastructural aspects

    Directory of Open Access Journals (Sweden)

    Raquel Bellinati-Pires

    1992-12-01

    Full Text Available The few studies already published about phagocyte functions in Chediak-Higashi syndrome (CHS has stated that neutrophils present slow rate of bacterial killing but normally ingest microorganisms. In the present study, both phagocytosis and killing of Staphylococcus aureus were verified to be in neutrophils from two patients with CHS when these functions were simultaneously evaluated by a fluorochrome phagocytosis assay. Electron microscopic examination showed morphologic differences among neutophils from CHS patients and normal neutrophils regarding the cytoplasmic structures and the aspects of the phagolysosomes. It was noteworthy the presence of giant phagolysosomes enclosing bacteria in active proliferation commonly observed in CHS neutrophils after 45 min of phagocytosis, wich corresponded with the impaired bactericidal activity of these leukocytes. The present results suggest that phagocytosis may also be defective in CHS, and point out to the sensitivity of the fluorochrome phagocytosis assay and its application in clinical laboratories.

  5. Bacterial meningitis

    NARCIS (Netherlands)

    Roos, Karen L.; van de Beek, Diederik

    2010-01-01

    Bacterial meningitis is a neurological emergency. Empiric antimicrobial and adjunctive therapy should be initiated as soon as a single set of blood cultures has been obtained. Clinical signs suggestive of bacterial meningitis include fever, headache, meningismus, vomiting, photophobia, and an

  6. RT-qPCR with chimeric dU stem-loop primer is efficient for the detection of bacterial small RNAs.

    Science.gov (United States)

    Wu, Yangfan; Xing, Xuejiao; You, Ting; Liang, Rubing; Liu, Jianhua

    2017-06-01

    Small non-coding RNAs are considered be involved in the regulation of multiple cellular processes. Quantitative reverse transcription PCR (RT-qPCR) is widely used in the detection of eukaryotic microRNA, and the stem-loop primers can improve the specificity and efficiency of reverse transcription. However, the loop structure of primers probably influence the next quantitative amplification due to the base stacking and steric hindrance. Here, we designed a chimeric stem-loop primer with a deoxyuracil (dU) base located near the RNA matching part. After the reverse transcription, uracil-DNA glycosylase (UDG) treatment was used to remove the dU base and destroy the stem-loop structure of RT product. Enzymatic assay confirmed that the recombinant UDG could efficiently eliminate the dU base in the oligonucleotide. Transcriptions of two small RNAs (TFF and ryeA) in Escherichia coli were detected by RT-qPCR with different primers. Results showed that the use of the chimeric dU stem-loop primer and UDG treatment could enhance the detection specificity and sensitivity about 1.1- to 3.4-fold, compared to those with traditional stem-loop primer and linear primer. Total RNA of 1-10 pg was enough for efficient detection with the chimeric stem-loop primers. In a word, this strategy could promote the RT-qPCR detection efficiency on the transcription of bacterial small RNAs even in trace samples and can facilitate the detection of exiguous change in cellular metabolism.

  7. A comprehensive analysis of the microbial communities of healthy and diseased marine macroalgae and the detection of known and potential bacterial pathogens

    Directory of Open Access Journals (Sweden)

    Torsten eThomas

    2015-02-01

    Full Text Available Microorganisms are increasingly being recognized as the causative agents in the diseases of marine higher organisms, such as corals, sponges and macroalgae. Delisea pulchra is a common, temperate red macroalga, which suffers from a bleaching disease. Two bacterial strains, Nautella italica R11 and Phaeobacter gallaeciensis LSS9, have been shown in vitro to cause bleaching symptoms, but previous work has failed to detect them during a natural bleaching event. To provide a link between in vitro observations and natural occurrences of the disease, we employ here deep-sequencing of the 16S rRNA gene to comprehensively analyze the community composition of healthy and diseased D. pulchra samples from two separate locations. We observed operational taxonomic units (OTUs with 100% identity and coverage to the 16S RNA gene sequence of both in vitro pathogens, but only the OTU with similarity to strain LSS9 showed a statistically significant higher abundance in diseased samples. Our analysis also reveals the existence of other bacterial groups within the families Rhodobacteraceae and Flavobacteriaceae that strongly contribute to difference between diseased and healthy samples and thus these groups potentially contain novel macroalgal pathogens and/or saprophytes. Together our results provide evidence for the ecological relevance of one kind of in vitro pathogen, but also highlight the possibility that multiple opportunistic pathogens are involved in the bleaching disease of D. pulchra.

  8. Flow Cytometry Detection of Bacterial Cell Entrapment within the Chitosan Hydrogel and Antibacterial Property of Extracted Chitosan

    Directory of Open Access Journals (Sweden)

    Nafise Sadat Majidi

    2016-09-01

    Full Text Available Background:   Chitosan is unbranched polysaccharide composed of D-glucosamine and N-acetyl-D-glucosamine. Chitosan, derived from shrimp shell, has broad antimicrobial properties against Gram-negative, Gram-positive bacteria and fungi. Methods:  Chitosan was extracted from shrimp shell and studied for cell entrapment and anti-bacterial properties. The hydrogel chitosan was used as the beads for cell entrapment and chitosan beads were designed to deliver cells and nutrients. These data confirmed with flow cytometric analyses.                 Results:   Experimental results exhibited that internal diffusion through the chitosan matrix was the main mechanism for whole gelation by TPP (Tri-polyphosphate. The minimum inhibitory concentration (MIC for chitosan against Staphylococcus aureus and Escherichia coli was 16 and 32 μg/ml respectively. Conclusion:  Despite the antimicrobial properties of chitosan, trapped bacteria in the gel network were alive and were chelated indicating that their access to the outside was limited.

  9. Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

    Directory of Open Access Journals (Sweden)

    Weir Jerry P

    2007-05-01

    Full Text Available Abstract Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2 BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. While the BAC mutagenesis procedure is a powerful method to generate HSV-2 recombinants, particularly in the absence of selective marker in eukaryotic culture, the mutagenesis procedure is still difficult and cumbersome. Results Here we describe the incorporation of a phage lambda recombination system into an allele replacement vector. This strategy enables any DNA fragment containing the phage attL recombination sites to be efficiently inserted into the attR sites of the allele replacement vector using phage lambda clonase. We also describe how the incorporation of EGFP into the allele replacement vector can facilitate the selection of the desired cross-over recombinant BACs when the allele replacement reaction is a viral gene deletion. Finally, we incorporate the lambda phage recombination sites directly into an HSV-2 BAC vector for direct recombination of gene cassettes using the phage lambda clonase-driven recombination reaction. Conclusion Together, these improvements to the techniques of HSV BAC mutagenesis will facilitate the construction of recombinant herpes simplex viruses and viral vectors.

  10. Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes.

    Science.gov (United States)

    Schmeisser, Falko; Weir, Jerry P

    2007-05-14

    Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC) technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2) BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. While the BAC mutagenesis procedure is a powerful method to generate HSV-2 recombinants, particularly in the absence of selective marker in eukaryotic culture, the mutagenesis procedure is still difficult and cumbersome. Here we describe the incorporation of a phage lambda recombination system into an allele replacement vector. This strategy enables any DNA fragment containing the phage attL recombination sites to be efficiently inserted into the attR sites of the allele replacement vector using phage lambda clonase. We also describe how the incorporation of EGFP into the allele replacement vector can facilitate the selection of the desired cross-over recombinant BACs when the allele replacement reaction is a viral gene deletion. Finally, we incorporate the lambda phage recombination sites directly into an HSV-2 BAC vector for direct recombination of gene cassettes using the phage lambda clonase-driven recombination reaction. Together, these improvements to the techniques of HSV BAC mutagenesis will facilitate the construction of recombinant herpes simplex viruses and viral vectors.

  11. Detection of Ca2+-dependent acid phosphatase activity identifies neuronal integrity in damaged rat central nervous system after application of bacterial melanin

    Directory of Open Access Journals (Sweden)

    Tigran R Petrosyan

    2016-01-01

    Full Text Available The study aims to confirm the neuroregenerative effects of bacterial melanin (BM on central nervous system injury using a special staining method based on the detection of Ca2+-dependent acid phosphatase activity. Twenty-four rats were randomly assigned to undergo either unilateral destruction of sensorimotor cortex (group I; n = 12 or unilateral rubrospinal tract transection at the cervical level (C3–4 (group II; n = 12. In each group, six rats were randomly selected after surgery to undergo intramuscular injection of BM solution (BM subgroup and the remaining six rats were intramuscularly injected with saline (saline subgroup. Neurological testing confirmed that BM accelerated the recovery of motor function in rats from both BM and saline subgroups. Two months after surgery, Ca2+-dependent acid phosphatase activity detection in combination with Chilingarian's calcium adenoside triphosphate method revealed that BM stimulated the sprouting of fibers and dilated the capillaries in the brain and spinal cord. These results suggest that BM can promote the recovery of motor function of rats with central nervous system injury; and detection of Ca2+-dependent acid phosphatase activity is a fast and easy method used to study the regeneration-promoting effects of BM on the injured central nervous system.

  12. Isolation of identical nitrilase genes from multiple bacterial strains and real-time PCR detection of the genes from soils provides evidence of horizontal gene transfer.

    Science.gov (United States)

    Coffey, Lee; Clarke, Adrienne; Duggan, Patrick; Tambling, Karen; Horgan, Serenia; Dowling, David; O'Reilly, Catherine

    2009-10-01

    Bacterial enzymes capable of nitrile hydrolysis have significant industrial potential. Microbacterium sp. AJ115, Rhodococcus erythropolis AJ270 and AJ300 were isolated from the same location in England and harbour identical nitrile hydratase/amidase gene clusters. Strain AJ270 has been well studied due to its nitrile hydratase and amidase activity. R. erythropolis ITCBP was isolated from Denmark and carries a very similar nitrile hydratase/amidase gene cluster. In this study, an identical nitrilase gene (nit1) was isolated from the four strains, and the nitrilase from strain AJ270 cloned and expressed in Escherichia coli. Analysis of the recombinant nitrilase has shown it to be functional with activity demonstrated towards phenylacetonitrile. A real-time PCR TaqMan assay was developed that allowed nit1 detection directly from soil enrichment cultures without DNA extraction, with nit1 detected in all samples tested. Real-time PCR screening of isolates from these soils resulted in the isolation of nit1 and also very similar nitrilase gene nit2 from a number of Burkholderia sp. The genes nit1 and nit2 have also been detected in many bacteria of different genera but are unstable in these isolates. It is likely that the genes were acquired by horizontal gene transfer and may be wide-spread in the environment.

  13. Detection of antibiotic resistance genes β-lactamics in bacterial strains isolated from Umbilical Cord Blood Units for transplant

    Directory of Open Access Journals (Sweden)

    J.M. Bello-López

    2017-01-01

    Conclusions: The genotype detection encoding antibiotic resistance in isolates of UCBU clearly indicates the potential risk of sepsis difficult to eradicate in the patient, if present in a UCBU available for transplant. Additionally, the existence of these genes reveals horizontal transfer events of genetic material between bacteria. So the importance to realize this studies before transplant.

  14. A novel gold nanoparticle-DNA aptamer-based plasmonic chip for rapid and sensitive detection of bacterial pathogens

    DEFF Research Database (Denmark)

    Sun, Yi; Phuoc Long, Truong; Wolff, Anders

    2016-01-01

    Gold nanoparticles (AuNPs)-based biosensors are emerging technologies for rapid detection of pathogens. However, it is very challenging to develop chip-based AuNP-biosensors for whole cells. This paper describes a novel AuNPs-DNA aptamer-based plasmonic assay which allows DNA aptamers to be detac...

  15. Comparison of the EntericBio multiplex PCR system with routine culture for detection of bacterial enteric pathogens.

    LENUS (Irish Health Repository)

    O'Leary, James

    2009-11-01

    The EntericBio system uses a multiplex PCR assay for the simultaneous detection of Campylobacter spp., Salmonella enterica, Shigella spp., and Escherichia coli O157 from feces. It combines overnight broth enrichment with PCR amplification and detection by hybridization. An evaluation of this system was conducted by comparing the results obtained with the system with those obtained by routine culture, supplemented with alternative PCR detection methods. In a study of 773 samples, routine culture and the EntericBio system yielded 94.6 and 92.4% negative results, respectively. Forty-two samples had positive results by culture, and all of these were positive with the EntericBio system. This system detected an additional 17 positive samples (Campylobacter spp., n = 12; Shigella spp., n = 1; E. coli O157, n = 4), but the results for 5 samples (Campylobacter spp., n = 2; Shigella spp., n = 1; E. coli O157, n = 2) could not be confirmed. The target for Shigella spp. detected by the EntericBio system is the ipaH gene, and the molecular indication of the presence of Shigella spp. was investigated by sequence analysis, which confirmed that the ipaH gene was present in a Klebsiella pneumoniae isolate from the patient. The sensitivity, specificity, positive predictive value, and negative predictive value were 100%, 99.3%, 91.5%, and 100%, respectively. Turnaround times were significantly reduced with the EntericBio system, and a result was available between 24 and 32 h after receipt of the sample in the laboratory. In addition, the amount of laboratory waste was significantly reduced by use of this system. In summary, the EntericBio system proved convenient to use, more sensitive than the conventional culture used in this study, and highly specific; and it generated results significantly faster than routine culture for the pathogens tested.

  16. 6q deletion detected by fluorescence in situ hybridization using bacterial artificial chromosome in chronic lymphocytic leukemia.

    Science.gov (United States)

    Dalsass, Alessia; Mestichelli, Francesca; Ruggieri, Miriana; Gaspari, Paola; Pezzoni, Valerio; Vagnoni, Davide; Angelini, Mario; Angelini, Stefano; Bigazzi, Catia; Falcioni, Sadia; Troiani, Emanuela; Alesiani, Francesco; Catarini, Massimo; Attolico, Immacolata; Scortechini, Ilaria; Discepoli, Giancarlo; Galieni, Piero

    2013-07-01

    Deletions of the long arm of chromosome 6 are known to occur at relatively low frequency (3-6%) in chronic lymphocytic leukemia (CLL), and they are more frequently observed in 6q21. Few data have been reported regarding other bands on 6q involved by cytogenetic alterations in CLL. The cytogenetic study was performed in nuclei and metaphases obtained after stimulation with a combination of CpG-oligonucleotide DSP30 and interleukin-2. Four bacterial artificial chromosome (BAC) clones mapping regions in bands 6q16, 6q23, 6q25, 6q27 were used as probes for fluorescence in situ hybridization in 107 CLL cases in order to analyze the occurrence and localization of 6q aberrations. We identified 11 cases (10.2%) with 6q deletion of 107 patients studied with CLL. The trends of survival curves and the treatment-free intervals (TFI) of patients with deletion suggest a better outcome than the other cytogenetic risk groups. We observed two subgroups with 6q deletion as the sole anomaly: two cases with 6q16 deletion, and three cases with 6q25.2-27 deletion. There were differences of age, stage, and TFI between both subgroups. By using BAC probes, we observed that 6q deletion has a higher frequency in CLL and is linked with a good prognosis. In addition, it was observed that the deletion in 6q16 appears to be the most frequent and, if present as the only abnormality, it could be associated with a most widespread disease. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  17. Rapid detection and identification of viral and bacterial fish pathogens using a DNA array‐based multiplex assay

    DEFF Research Database (Denmark)

    Lievens, B.; Frans, I.; Heusdens, C.

    2011-01-01

    Fish diseases can be caused by a variety of diverse organisms, including bacteria, fungi, viruses and protozoa, and pose a universal threat to the ornamental fish industry and aquaculture. The lack of rapid, accurate and reliable means by which fish pathogens can be detected and identified has been...... one of the main limitations in fish pathogen diagnosis and fish disease management and has consequently stimulated the search for alternative diagnostic techniques. Here, we describe a method based on multiplex and broad‐range PCR amplification combined with DNA array hybridization...... for the simultaneous detection and identification of all cyprinid herpesviruses (CyHV‐1, CyHV‐2 and CyHV‐3) and some of the most important fish pathogenic Flavobacterium species, including F. branchiophilum, F. columnare and F. psychrophilum. For virus identification, the DNA polymerase and helicase genes were...

  18. A novel gold nanoparticle-DNA aptamer-based plasmonic chip for rapid and sensitive detection of bacterial pathogens

    DEFF Research Database (Denmark)

    Sun, Yi; Phuoc Long, Truong; Wolff, Anders

    2016-01-01

    Gold nanoparticles (AuNPs)-based biosensors are emerging technologies for rapid detection of pathogens. However, it is very challenging to develop chip-based AuNP-biosensors for whole cells. This paper describes a novel AuNPs-DNA aptamer-based plasmonic assay which allows DNA aptamers to be detac......Gold nanoparticles (AuNPs)-based biosensors are emerging technologies for rapid detection of pathogens. However, it is very challenging to develop chip-based AuNP-biosensors for whole cells. This paper describes a novel AuNPs-DNA aptamer-based plasmonic assay which allows DNA aptamers...... to be detached from AuNPs when interacting with bacteria. The new strategy greatly increases the sensitivity and specificity of chip-based whole-cell biosensing....

  19. Simultaneous detection of major blackleg and soft rot bacterial pathogens in potato by multiplex polymerase chain reaction‡

    Science.gov (United States)

    Potrykus, M; Sledz, W; Golanowska, M; Slawiak, M; Binek, A; Motyka, A; Zoledowska, S; Czajkowski, R; Lojkowska, E

    2014-01-01

    A multiplex polymerase chain reaction (PCR) assay for simultaneous, fast and reliable detection of the main soft rot and blackleg potato pathogens in Europe has been developed. It utilises three pairs of primers and enables detection of three groups of pectinolytic bacteria frequently found in potato, namely: Pectobacterium atrosepticum, Pectobacterium carotovorum subsp. carotovorum together with Pectobacterium wasabiae and Dickeya spp. in a multiplex PCR assay. In studies with axenic cultures of bacteria, the multiplex assay was specific as it gave positive results only with strains of the target species and negative results with 18 non-target species of bacteria that can possibly coexist with pectinolytic bacteria in a potato ecosystem. The developed assay could detect as little as 0.01 ng µL–1 of Dickeya sp. genomic DNA, and down to 0.1 ng µL–1 of P. atrosepticum and P. carotovorum subsp. carotovorum genomic DNA in vitro. In the presence of competitor genomic DNA, isolated from Pseudomonas fluorescens cells, the sensitivity of the multiplex PCR decreased tenfold for P. atrosepticum and Dickeya sp., while no change was observed for P. carotovorum subsp. carotovorum and P. wasabiae. In spiked potato haulm and tuber samples, the threshold level for target bacteria was 101 cfu mL–1 plant extract (102 cfu g–1 plant tissue), 102 cfu mL–1 plant extract (103 cfu g–1 plant tissue), 103 cfu mL–1 plant extract (104 cfu g–1 plant tissue), for Dickeya spp., P. atrosepticum and P. carotovorum subsp. carotovorum/P. wasabiae, respectively. Most of all, this assay allowed reliable detection and identification of soft rot and blackleg pathogens in naturally infected symptomatic and asymptomatic potato stem and progeny tuber samples collected from potato fields all over Poland. PMID:25506085

  20. Detection of entero viruses and hepatitis A in treated wastewater and Correlation between viral and bacterial contamination

    International Nuclear Information System (INIS)

    Dridi, Soumaya

    2010-01-01

    The main human viruses likely to contaminate waste water are Non-enveloped viruses able to resist in the environment, so essentially the viruses presenting an enteric cycle of multiplication. Many of these viruses, namely entero virus, hepatitis Avirus are excreted in the saddles of patients or of carriers and meet in waste water. To fight against the viral risk it is necessary to have a methodology allowing the control and the surveillance of virological and Hydric contamination. For the revealing of enteric virus, the reference technique remains the isolation on cellular culture. However, the disadvantage of this technique is the fact that it is difficult for certain viruses. Thus, the rise of molecular biology allowed the focusing of reliable and significant methods for detection of the enteric viruses in the environmental takings. The aim of this work was to detect hepatitis A virus and entero virus in waste water. A total of 20 samples were concentrated then precipitated by Polyethylene glycol 6000 according to the method of EPA. Extraction and purification of the viral ARN are made by the Kit QIAmp Viral RNA (Qiagen). The analysis of nucleic acids extracted by RT-PCR allowed to detect Entero virus with a 15 pour cent frequency (3/20) and 10 pour cent (2/20) for the hepatitis A virus.

  1. Detection of the Causal Agent of Bacterial Wilt, Ralstonia solanacearum in the Seeds of Solanaceae by PCR

    Directory of Open Access Journals (Sweden)

    Jung-Hee Cho

    2011-08-01

    Full Text Available Ralstonia solanacearum, a causal agent of bacterium wilt is very difficult to control once the disease becomes endemic. Thus, Ralstonia solanacearum is a plant quarantine bacterium in many countries including Korea. In this study, we developed PCR assays, which can detect Ralstonia solanacearum from the Solanaceae seeds. Primers RS-JH-F and RS-JH-R amplified specifically a 401 bp fragment only from Ralstonia solanacearum race 1 and race 3. The nested PCR primers, RS-JH-F-ne and RS-JH-R-ne that were designed inside of 1st PCR amplicon amplified specifically a 131 bp fragment only from Ralstonia solanacearum race 1 and race 3. The primers did not amplify any non-specific DNA from the seed extracts of the Solanaceae including tomato and pepper. When detection sensitivity were compared using the Solanaceae seeds inoculated with target bacteria artificially, the nested PCR method developed in this study 100 times more sensitive than ELISA and selective medium. Therefore, we believe that the PCR assays developed in this work is very useful to detect Ralstonia solanacearum in the Solanaceae seeds.

  2. A multi-channel bioluminescent bacterial biosensor for the on-line detection of metals and toxicity. Part II: technical development and proof of concept of the biosensor

    Energy Technology Data Exchange (ETDEWEB)

    Charrier, Thomas; Thouand, Gerald [UMR CNRS 6144 GEPEA, CBAC, Nantes University, PRES UNAM, Campus de la Courtaisiere-IUT, La Roche-sur-Yon cedex (France); Chapeau, Cyrille [Biolumine, Biokar Diagnostic, Rue des Quarante Mines ZAC de Ther-Allonne, Beauvais Cedex (France); Bendria, Loubna; Daniel, Philippe [UMR CNRS 6087 LPEC, Universite du Maine, Av Olivier Messiaen, Le Mans cedex 9 (France); Picart, Pascal [UMR CNRS 6613 IAM-LAUM, Ecole Nationale des Ingenieurs du Mans, Universite du Maine, Le Mans Cedex 9 (France)

    2011-05-15

    This research study deals with the on-line detection of heavy metals and toxicity within the context of environmental pollution monitoring. It describes the construction and the proof of concept of a multi-channel bioluminescent bacterial biosensor in immobilized phase: Lumisens3. This new versatile device, designed for the non-stop analysis of water pollution, enables the insertion of any bioluminescent strains (inducible or constitutive), immobilized in a multi-well removable card. The technical design of Lumisens3 has benefited from both a classical and a robust approach and includes four main parts: (1) a dedicated removable card contains 64 wells, 3 mm in depth, arranged in eight grooves within which bacteria are immobilized, (2) this card is incubated on a Pelletier block with a CCD cooled camera on top for bioluminescence monitoring, (3) a fluidic network feeds the card with the sample to be analyzed and finally (4) a dedicated computer interface, BIOLUX 1.0, controls all the elements of the biosensor, allowing it to operate autonomously. The proof of concept of this biosensor was performed using a set of four bioluminescent bacteria (Escherichia coli DH1 pBzntlux, pBarslux, pBcoplux, and E. coli XL1 pBfiluxCDABE) in the on-line detection of CdCl{sub 2} 0.5 {mu}M and As{sub 2}O{sub 3} 5 {mu}M from an influent. When considering metals individually, the ''fingerprints'' from the biosensor were as expected. However, when metals were mixed together, cross reaction and synergistic effects were detected. This biosensor allowed us to demonstrate the simultaneous on-line cross detection of one or several heavy metals as well as the measurement of the overall toxicity of the sample. (orig.)

  3. PCR-based detection of bacterial DNA after antimicrobial treatment is indicative of persistent, viable bacteria in the chinchilla model of otitis media.

    Science.gov (United States)

    Post, J C; Aul, J J; White, G J; Wadowsky, R M; Zavoral, T; Tabari, R; Kerber, B; Doyle, W J; Ehrlich, G D

    1996-01-01

    Bacterial deoxyribonucleic acid (DNA) has been previously detected by polymerase chain reactions (PCR) in a significant percentage of culturally-sterile pediatric middle-ear effusions. The current study was designed to determine whether this represents the existence of viable bacteria or the persistence of residual DNA in the middle-ear cleft. The middle-ear cavities of two sets of chinchillas were inoculated with either: 1) 100 colony-forming units (CFU) of live Haemophilus influenzae, 2.2 x 10(6) CFU of pasteurized Moraxella catarrhalis, and 1000 ng of DNA (>10(8) genomic equivalents) from Streptococcus pneumoniae; or 2) 100 CFU of live S pneumoniae, 2.2 x 10(6) CFU of pasteurized M catarrhalis and 1000 ng of purified DNA from H influenzae. Animals were treated with ampicillin for 5 days beginning on day 3. A single-point longitudinal study design was used for sampling to eliminate the possibility of contamination. No DNA was detectable from the heat-killed bacteria or the purified DNA after day 3. However, DNA from the live bacteria persisted through day 21, even though all specimens were culture-negative following the initiation of antimicrobial therapy. These findings indicate that purified DNA and DNA from intact but nonviable bacteria do not persist in the middle-ear cleft in the presence of an effusion, even following high copy inoculation. In contrast, antibiotic-treated bacteria persist in some viable state for weeks as evidenced by the differential ability of the PCR-based assay systems to detect the live bacteria, but not detect the heat-killed organisms.

  4. Application of a bacterial whole cell biosensor for the rapid detection of cytotoxicity in heavy metal contaminated seawater.

    Science.gov (United States)

    Cui, Zhisong; Luan, Xiao; Jiang, Huichao; Li, Qian; Xu, Guangfei; Sun, Chengjun; Zheng, Li; Song, Yizhi; Davison, Paul A; Huang, Wei E

    2018-06-01

    A toxicity biosensor Acinetobacter baylyi Tox2 was constructed with the host strain A. baylyi ADP1 harboring a new and medium-copy-number plasmid pWH1274_lux, and was applied to detect the cytotoxicity of heavy metal contaminated seawater. The gene cassette luxCDABE was controlled by constitutively expressed promoter P tet on pWH1274_lux and the bioluminescence intensity of the biosensor reduces in proportional to the concentrations of toxic compounds. A. baylyi Tox2 exhibits tolerance to salinity, hence it is applicable to seawater samples. A. baylyi Tox2 and Mugilogobius chulae were exposed to different concentrations of heavy metals (Hg 2+ , Zn 2+ , Cu 2+ , and Cd 2+ ) in artificial seawater for performance comparison and Pearson correlation analysis showed a significant correlation (p cytotoxicity detection of heavy metal contaminated seawater. Furthermore, A. baylyi Tox2 was used to evaluate cytotoxicity of field-collected seawater samples. The results indicate that there was a significant correlation between the luminescence inhibition ratio (IR) of A. baylyi Tox2 and heavy metal concentrations detected by ICP-MS in the samples. Two seawater samples, which contained a high concentration of total heavy metals, exhibited stronger cytotoxicity than the samples containing low concentrations of heavy metals. In conclusion, A. baylyi Tox2 can be used as an alternative tool to aquatic animals for the evaluation of the cytotoxicity of heavy metal contamination in the marine environment. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Evaluation of an expanded microarray for detecting antibiotic resistance genes in a broad range of gram-negative bacterial pathogens.

    Science.gov (United States)

    Card, Roderick; Zhang, Jiancheng; Das, Priya; Cook, Charlotte; Woodford, Neil; Anjum, Muna F

    2013-01-01

    A microarray capable of detecting genes for resistance to 75 clinically relevant antibiotics encompassing 19 different antimicrobial classes was tested on 132 Gram-negative bacteria. Microarray-positive results correlated >91% with antimicrobial resistance phenotypes, assessed using British Society for Antimicrobial Chemotherapy clinical breakpoints; the overall test specificity was >83%. Microarray-positive results without a corresponding resistance phenotype matched 94% with PCR results, indicating accurate detection of genes present in the respective bacteria by microarray when expression was low or absent and, hence, undetectable by susceptibility testing. The low sensitivity and negative predictive values of the microarray results for identifying resistance to some antimicrobial resistance classes are likely due to the limited number of resistance genes present on the current microarray for those antimicrobial agents or to mutation-based resistance mechanisms. With regular updates, this microarray can be used for clinical diagnostics to help accurate therapeutic options to be taken following infection with multiple-antibiotic-resistant Gram-negative bacteria and prevent treatment failure.

  6. Optimization and evaluation of Flexicult® Vet for detection, identification and antimicrobial susceptibility testing of bacterial uropathogens in small animal veterinary practice.

    Science.gov (United States)

    Guardabassi, Luca; Hedberg, Sandra; Jessen, Lisbeth Rem; Damborg, Peter

    2015-10-26

    Urinary tract infection (UTI) is a common reason for antimicrobial prescription in dogs and cats. The objective of this study was to optimize and evaluate a culture-based point-of-care test for detection, identification and antimicrobial susceptibility testing of bacterial uro-pathogens in veterinary practice. Seventy-two urine samples from dogs and cats with suspected UTI presenting to seven veterinary facilities were used by clinical staff and an investigator to estimate sensitivity and specificity of Flexicult Vet A compared to laboratory reference standards for culture and susceptibility testing. Subsequently, the test was modified by inclusion of an oxacillin-containing compartment for detection of methicillin-resistant staphylococci. The performance of the modified product (Flexicult Vet B) for susceptibility testing was evaluated in vitro using a collection of 110 clinical isolates. Bacteriuria was reported by the laboratory in 25 (35 %) samples from the field study. The sensitivity and specificity of Flexicult Vet A for detection of bacteriuria were 83 and 100 %, respectively. Bacterial species were correctly identified in 53 and 100 % of the positive samples by clinical staff and the investigator, respectively. The susceptibility results were interpreted correctly by clinical staff for 70 % of the 94 drug-strain combinations. Higher percentages of correct interpretation were observed when the results were interpreted by the investigator in both the field (76 %) and the in vitro study (94 %). The most frequent errors were false resistance to β-lactams (ampicillin, amoxicillin-clavulanate and cephalotin) in Escherichia coli for Flexicult Vet A, and false amoxicillin-clavulanate resistance in E. coli and false ampicillin susceptibility in Staphylococcus pseudintermedius for Flexicult Vet B. The latter error can be prevented by categorizing staphylococcal strains growing in the oxacillin compartment as resistant to all β-lactams. Despite the

  7. Rapid on-site TLC-SERS detection of four antidiabetes drugs used as adulterants in botanical dietary supplements.

    Science.gov (United States)

    Zhu, Qingxia; Cao, Yongbing; Cao, Yingying; Chai, Yifeng; Lu, Feng

    2014-03-01

    A novel facile method has been established for rapid on-site detection of antidiabetes chemicals used to adulterate botanical dietary supplements (BDS) for diabetes. Analytes and components of pharmaceutical matrices were separated by thin-layer chromatography (TLC) then surface-enhanced Raman spectroscopy (SERS) was used for qualitative identification of trace substances on the HPTLC plate. Optimization and standardization of the experimental conditions, for example the method used for preparation of silver colloids, the mobile phase, and the concentration of colloidal silver, resulted in a very robust and highly sensitive method which enabled successful detection when the amount of adulteration was as low as 0.001 % (w/w). The method was also highly selective, enabling successful identification of some chemicals in extremely complex herbal matrices. The established TLC-SERS method was used for analysis of real BDS used to treat diabetes, and the results obtained were verified by liquid chromatography-triple quadrupole mass spectrometry (LC-MS-MS). The study showed that TLC-SERS could be used for effective separation and detection of four chemicals used to adulterate BDS, and would have good prospects for on-site qualitative screening of BDS for adulterants.

  8. Smart Device-Supported BDS/GNSS Real-Time Kinematic Positioning for Sub-Meter-Level Accuracy in Urban Location-Based Services.

    Science.gov (United States)

    Wang, Liang; Li, Zishen; Zhao, Jiaojiao; Zhou, Kai; Wang, Zhiyu; Yuan, Hong

    2016-12-21

    Using mobile smart devices to provide urban location-based services (LBS) with sub-meter-level accuracy (around 0.5 m) is a major application field for future global navigation satellite system (GNSS) development. Real-time kinematic (RTK) positioning, which is a widely used GNSS-based positioning approach, can improve the accuracy from about 10-20 m (achieved by the standard positioning services) to about 3-5 cm based on the geodetic receivers. In using the smart devices to achieve positioning with sub-meter-level accuracy, a feasible solution of combining the low-cost GNSS module and the smart device is proposed in this work and a user-side GNSS RTK positioning software was developed from scratch based on the Android platform. Its real-time positioning performance was validated by BeiDou Navigation Satellite System/Global Positioning System (BDS/GPS) combined RTK positioning under the conditions of a static and kinematic (the velocity of the rover was 50-80 km/h) mode in a real urban environment with a SAMSUNG Galaxy A7 smartphone. The results show that the fixed-rates of ambiguity resolution (the proportion of epochs of ambiguities fixed) for BDS/GPS combined RTK in the static and kinematic tests were about 97% and 90%, respectively, and the average positioning accuracies (RMS) were better than 0.15 m (horizontal) and 0.25 m (vertical) for the static test, and 0.30 m (horizontal) and 0.45 m (vertical) for the kinematic test.

  9. Smart Device-Supported BDS/GNSS Real-Time Kinematic Positioning for Sub-Meter-Level Accuracy in Urban Location-Based Services

    Directory of Open Access Journals (Sweden)

    Liang Wang

    2016-12-01

    Full Text Available Using mobile smart devices to provide urban location-based services (LBS with sub-meter-level accuracy (around 0.5 m is a major application field for future global navigation satellite system (GNSS development. Real-time kinematic (RTK positioning, which is a widely used GNSS-based positioning approach, can improve the accuracy from about 10–20 m (achieved by the standard positioning services to about 3–5 cm based on the geodetic receivers. In using the smart devices to achieve positioning with sub-meter-level accuracy, a feasible solution of combining the low-cost GNSS module and the smart device is proposed in this work and a user-side GNSS RTK positioning software was developed from scratch based on the Android platform. Its real-time positioning performance was validated by BeiDou Navigation Satellite System/Global Positioning System (BDS/GPS combined RTK positioning under the conditions of a static and kinematic (the velocity of the rover was 50–80 km/h mode in a real urban environment with a SAMSUNG Galaxy A7 smartphone. The results show that the fixed-rates of ambiguity resolution (the proportion of epochs of ambiguities fixed for BDS/GPS combined RTK in the static and kinematic tests were about 97% and 90%, respectively, and the average positioning accuracies (RMS were better than 0.15 m (horizontal and 0.25 m (vertical for the static test, and 0.30 m (horizontal and 0.45 m (vertical for the kinematic test.

  10. Characterization and purification of a bacterial chlorogenic acid esterase detected during the extraction of chlorogenic acid from arbuscular mycorrhizal tomato roots.

    Science.gov (United States)

    Negrel, Jonathan; Javelle, Francine; Morandi, Dominique; Lucchi, Géraldine

    2016-12-01

    A Gram-negative bacterium able to grow using chlorogenic acid (5-caffeoylquinic acid) as sole carbon source has been isolated from the roots of tomato plants inoculated with the arbuscular mycorrhizal fungus Rhizophagus irregularis. An intracellular esterase exhibiting very high affinity (K m  = 2 μM) for chlorogenic acid has been extracted and purified by FPLC from the chlorogenate-grown cultures of this bacterium. The molecular mass of the purified esterase determined by SDS-PAGE was 61 kDa and its isoelectric point determined by chromatofocusing was 7.75. The esterase hydrolysed chlorogenic acid analogues (caffeoylshikimate, and the 4- and 3-caffeoylquinic acid isomers), feruloyl esterases substrates (methyl caffeate and methyl ferulate), and even caffeoyl-CoA in vitro but all of them were less active than chlorogenic acid, demonstrating that the esterase is a genuine chlorogenic acid esterase. It was also induced when the bacterial strain was cultured in the presence of hydroxycinnamic acids (caffeic, p-coumaric or ferulic acid) as sole carbon source, but not in the presence of simple phenolics such as catechol or protocatechuic acid, nor in the presence of organic acids such as succinic or quinic acids. The purified esterase was remarkably stable in the presence of methanol, rapid formation of methyl caffeate occurring when its activity was measured in aqueous solutions containing 10-60% methanol. Our results therefore show that this bacterial chlorogenase can catalyse the transesterification reaction previously detected during the methanolic extraction of chlorogenic acid from arbuscular mycorrhizal tomato roots. Data are presented suggesting that colonisation by Rhizophagus irregularis could increase chlorogenic acid exudation from tomato roots, especially in nutrient-deprived plants, and thus favour the growth of chlorogenate-metabolizing bacteria on the root surface or in the mycorhizosphere. Copyright © 2016 Elsevier Masson SAS. All rights

  11. Detection and differentiation of bacterial spores in a mineral matrix by Fourier transform infrared spectroscopy (FTIR and chemometrical data treatment

    Directory of Open Access Journals (Sweden)

    Brandes Ammann Andrea

    2011-07-01

    Full Text Available Abstract Background Fourier transform infrared spectroscopy (FTIR has been used as analytical tool in chemistry for many years. In addition, FTIR can also be applied as a rapid and non-invasive method to detect and identify microorganisms. The specific and fingerprint-like spectra allow - under optimal conditions - discrimination down to the species level. The aim of this study was to develop a fast and reproducible non-molecular method to differentiate pure samples of Bacillus spores originating from different species as well as to identify spores in a simple matrix, such as the clay mineral, bentonite. Results We investigated spores from pure cultures of seven different Bacillus species by FTIR in reflection or transmission mode followed by chemometrical data treatment. All species investigated (B. atrophaeus, B. brevis, B. circulans, B. lentus, B. megaterium, B. subtilis, B. thuringiensis are typical aerobic soil-borne spore formers. Additionally, a solid matrix (bentonite and mixtures of benonite with spores of B. megaterium at various wt/wt ratios were included in the study. Both hierarchical cluster analysis and principal component analysis of the spectra along with multidimensional scaling allowed the discrimination of different species and spore-matrix-mixtures. Conclusions Our results show that FTIR spectroscopy is a fast method for species-level discrimination of Bacillus spores. Spores were still detectable in the presence of the clay mineral bentonite. Even a tenfold excess of bentonite (corresponding to 2.1 × 1010 colony forming units per gram of mineral matrix still resulted in an unambiguous identification of B. megaterium spores.

  12. Bacterial Proteasomes.

    Science.gov (United States)

    Jastrab, Jordan B; Darwin, K Heran

    2015-01-01

    Interest in bacterial proteasomes was sparked by the discovery that proteasomal degradation is required for the pathogenesis of Mycobacterium tuberculosis, one of the world's deadliest pathogens. Although bacterial proteasomes are structurally similar to their eukaryotic and archaeal homologs, there are key differences in their mechanisms of assembly, activation, and substrate targeting for degradation. In this article, we compare and contrast bacterial proteasomes with their archaeal and eukaryotic counterparts, and we discuss recent advances in our understanding of how bacterial proteasomes function to influence microbial physiology.

  13. Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation : Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site

    NARCIS (Netherlands)

    Hendrickx, B; Junca, H; Vosahlova, J; Lindner, A; Ruegg, [No Value; Bucheli-Witschel, M; Faber, F; Egli, T; Mau, M; Schlomann, M; Brennerova, M; Brenner, [No Value; Pieper, DH; Top, EM; Dejonghe, W; Bastiaens, L; Springael, D

    Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for metacleavage of the aromatic ring. The new primer sets

  14. The Role of Multiplex Polymerase Chain Reaction in Detecting Etiological Causes of Bacterial Prostatitis Associated Benign Prostatic Hyperplasia

    Directory of Open Access Journals (Sweden)

    Bramastha Rosadi

    2015-01-01

    Full Text Available Background: Benign Prostatic Hyperplasia (BPH has been correlated with chronic prostatitis according recent study. Chronic pelvic pain is the chief complain of BPH followed by prostatitis. The gold standard of the etiological diagnosis is urine culture, but the negativity rate is still high. Multiplex polymerase chain reaction (PCR as a diagnostic tool in search of etiological causes could identify microorganism on DNA level. This research aims to find out the role of multiplex polymerase chain reaction as diagnostic tools on prostatitis patients. Material and Method: A total of 12 samples collected during the TURP procedure in Sanglah General Hospital Denpasar – Bali from February until May 2015. All of the samples has been diagnosed prostatitis clinically and perform urine culture test. The prostate specimen taken was sent to the Pathological anatomy for histopathology diagnostic and underwent multiplex PCR for etiologic diagnostic. Result: 12 samples have been declared as prostatitis based on histopathology examination, and then were analyzed using multiplex PCR. 10 samples were positive (6 were E. coli, 2 were C. trachomatis, the rest were N. gonorrhea and P. aeruginosa. The urine culture revealed 9 positive, within the result 6 were E. coli, and the others were P. aeruginosa, M. morganii and A. haemolyticus. Conclusion: In prostatitis patient, the etiological diagnostic was important. Multiplex PCR as diagnostic tools could detect the microorganism on a negative urine culture. The combination of the urine culture test and multiplex PCR revealed a better result on etiologic diagnosis which leads to a better management of the disease. 

  15. Finding New Enzymes from Bacterial Physiology: A Successful Approach Illustrated by the Detection of Novel Oxidases in Marinomonas mediterranea

    Science.gov (United States)

    Sanchez-Amat, Antonio; Solano, Francisco; Lucas-Elío, Patricia

    2010-01-01

    The identification and study of marine microorganisms with unique physiological traits can be a very powerful tool discovering novel enzymes of possible biotechnological interest. This approach can complement the enormous amount of data concerning gene diversity in marine environments offered by metagenomic analysis, and can help to place the activities associated with those sequences in the context of microbial cellular metabolism and physiology. Accordingly, the detection and isolation of microorganisms that may be a good source of enzymes is of great importance. Marinomonas mediterranea, for example, has proven to be one such useful microorganism. This Gram-negative marine bacterium was first selected because of the unusually high amounts of melanins synthesized in media containing the amino acid l-tyrosine. The study of its molecular biology has allowed the cloning of several genes encoding oxidases of biotechnological interest, particularly in white and red biotechnology. Characterization of the operon encoding the tyrosinase responsible for melanin synthesis revealed that a second gene in that operon encodes a protein, PpoB2, which is involved in copper transfer to tyrosinase. This finding made PpoB2 the first protein in the COG5486 group to which a physiological role has been assigned. Another enzyme of interest described in M. mediterranea is a multicopper oxidase encoding a membrane-associated enzyme that shows oxidative activity on a wide range of substrates typical of both laccases and tyrosinases. Finally, an enzyme very specific for l-lysine, which oxidises this amino acid in epsilon position and that has received a new EC number (1.4.3.20), has also been described for M. mediterranea. Overall, the studies carried out on this bacterium illustrate the power of exploring the physiology of selected microorganisms to discover novel enzymes of biotechnological relevance. PMID:20411113

  16. Bacterial adhesion

    NARCIS (Netherlands)

    Loosdrecht, van M.C.M.

    1988-01-01

    As mentioned in the introduction of this thesis bacterial adhesion has been studied from a variety of (mostly practice oriented) starting points. This has resulted in a range of widely divergent approaches. In order to elucidate general principles in bacterial adhesion phenomena, we felt it

  17. Stable Carbon Isotope Fractionation during Bacterial Acetylene Fermentation: Potential for Life Detection in Hydrocarbon-Rich Volatiles of Icy Planet(oid)s.

    Science.gov (United States)

    Miller, Laurence G; Baesman, Shaun M; Oremland, Ronald S

    2015-11-01

    We report the first study of stable carbon isotope fractionation during microbial fermentation of acetylene (C2H2) in sediments, sediment enrichments, and bacterial cultures. Kinetic isotope effects (KIEs) averaged 3.7 ± 0.5‰ for slurries prepared with sediment collected at an intertidal mudflat in San Francisco Bay and 2.7 ± 0.2‰ for a pure culture of Pelobacter sp. isolated from these sediments. A similar KIE of 1.8 ± 0.7‰ was obtained for methanogenic enrichments derived from sediment collected at freshwater Searsville Lake, California. However, C2H2 uptake by a highly enriched mixed culture (strain SV7) obtained from Searsville Lake sediments resulted in a larger KIE of 9.0 ± 0.7‰. These are modest KIEs when compared with fractionation observed during oxidation of C1 compounds such as methane and methyl halides but are comparable to results obtained with other C2 compounds. These observations may be useful in distinguishing biologically active processes operating at distant locales in the Solar System where C2H2 is present. These locales include the surface of Saturn's largest moon Titan and the vaporous water- and hydrocarbon-rich jets emanating from Enceladus. Acetylene-Fermentation-Isotope fractionation-Enceladus-Life detection.

  18. Detection of multi-tomato leaf diseases (late blight, target and bacterial spots) in different stages by using a spectral-based sensor.

    Science.gov (United States)

    Lu, Jinzhu; Ehsani, Reza; Shi, Yeyin; de Castro, Ana Isabel; Wang, Shuang

    2018-02-12

    Several diseases have threatened tomato production in Florida, resulting in large losses, especially in fresh markets. In this study, a high-resolution portable spectral sensor was used to investigate the feasibility of detecting multi-diseased tomato leaves in different stages, including early or asymptomatic stages. One healthy leaf and three diseased tomato leaves (late blight, target and bacterial spots) were defined into four stages (healthy, asymptomatic, early stage and late stage) and collected from a field. Fifty-seven spectral vegetation indices (SVIs) were calculated in accordance with methods published in previous studies and established in this study. Principal component analysis was conducted to evaluate SVIs. Results revealed six principal components (PCs) whose eigenvalues were greater than 1. SVIs with weight coefficients ranking from 1 to 30 in each selected PC were applied to a K-nearest neighbour for classification. Amongst the examined leaves, the healthy ones had the highest accuracy (100%) and the lowest error rate (0) because of their uniform tissues. Late stage leaves could be distinguished more easily than the two other disease categories caused by similar symptoms on the multi-diseased leaves. Further work may incorporate the proposed technique into an image system that can be operated to monitor multi-diseased tomato plants in fields.

  19. Diagnosis of bacterial infection

    African Journals Online (AJOL)

    rapid and easy-to-use test for bacterial infections. Clearly, this is a very ... detect antigens or specific antibodies, e.g. group A streptococcal antigen testing can be employed to reduce antibiotic use. Culture-based tests are often ... White blood cell count 12 000 cells/mm³; or the presence of >10% ...

  20. Multicenter evaluation of the BD max enteric bacterial panel PCR assay for rapid detection of Salmonella spp., Shigella spp., Campylobacter spp. (C. jejuni and C. coli), and Shiga toxin 1 and 2 genes.

    Science.gov (United States)

    Harrington, S M; Buchan, B W; Doern, C; Fader, R; Ferraro, M J; Pillai, D R; Rychert, J; Doyle, L; Lainesse, A; Karchmer, T; Mortensen, J E

    2015-05-01

    Diarrhea due to enteric bacterial pathogens causes significant morbidity and mortality in the United States and worldwide. However, bacterial pathogens may be infrequently identified. Currently, culture and enzyme immunoassays (EIAs) are the primary methods used by clinical laboratories to detect enteric bacterial pathogens. We conducted a multicenter evaluation of the BD Max enteric bacterial panel (EBP) PCR assay in comparison to culture for the detection of Salmonella spp., Shigella spp., Campylobacter jejuni, and Campylobacter coli and an EIA for Shiga toxins 1 and 2. A total of 4,242 preserved or unpreserved stool specimens, including 3,457 specimens collected prospectively and 785 frozen, retrospective samples, were evaluated. Compared to culture or EIA, the positive percent agreement (PPA) and negative percent agreement (NPA) values for the BD Max EBP assay for all specimens combined were as follows: 97.1% and 99.2% for Salmonella spp., 99.1% and 99.7% for Shigella spp., 97.2% and 98.4% for C. jejuni and C. coli, and 97.4% and 99.3% for Shiga toxins, respectively. Discrepant results for prospective samples were resolved with alternate PCR assays and bidirectional sequencing of amplicons. Following discrepant analysis, PPA and NPA values were as follows: 97.3% and 99.8% for Salmonella spp., 99.2% and 100% for Shigella spp., 97.5% and 99.0% for C. jejuni and C. coli, and 100% and 99.7% for Shiga toxins, respectively. No differences in detection were observed for samples preserved in Cary-Blair medium and unpreserved samples. In this large, multicenter study, the BD Max EBP assay showed superior sensitivity compared to conventional methods and excellent specificity for the detection of enteric bacterial pathogens in stool specimens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. Bacterial Vaginosis

    Science.gov (United States)

    ... Archive STDs Home Page Bacterial Vaginosis (BV) Chlamydia Gonorrhea Genital Herpes Hepatitis HIV/AIDS & STDs Human Papillomavirus ( ... of getting other STDs, such as chlamydia and gonorrhea . These bacteria can sometimes cause pelvic inflammatory disease ( ...

  2. Triple-Frequency Code-Phase Combination Determination: A Comparison with the Hatch-Melbourne-Wübbena Combination Using BDS Signals

    Directory of Open Access Journals (Sweden)

    Chenlong Deng

    2018-02-01

    Full Text Available Considering the influence of the ionosphere, troposphere, and other systematic errors on double-differenced ambiguity resolution (AR, we present an optimal triple-frequency code-phase combination determination method driven by both the model and the real data. The new method makes full use of triple-frequency code measurements (especially the low-noise of the code on the B3 signal to minimize the total noise level and achieve the largest AR success rate (model-driven under different ionosphere residual situations (data-driven, thus speeding up the AR by directly rounding. With the triple-frequency Beidou Navigation Satellite System (BDS data collected at five stations from a continuously-operating reference station network in Guangdong Province of China, different testing scenarios are defined (a medium baseline, whose distance is between 20 km and 50 km; a medium-long baseline, whose distance is between 50 km and 100 km; and a long baseline, whose distance is larger than 100 km. The efficiency of the optimal code-phase combination on the AR success rate was compared with that of the geometry-free and ionosphere-free (GIF combination and the Hatch-Melbourne-Wübbena (HMW combination. Results show that the optimal combinations can always achieve better results than the HMW combination with B2 and B3 signals, especially when the satellite elevation angle is larger than 45°. For the wide-lane AR which aims to obtain decimeter-level kinematic positioning service, the standard deviation (STD of ambiguity residuals for the suboptimal combination are only about 0.2 cycles, and the AR success rate by directly rounding can be up to 99%. Compared with the HMW combinations using B1 and B2 signals and using B1 and B3 signals, the suboptimal combination achieves the best results in all baselines, with an overall improvement of about 40% and 20%, respectively. Additionally, the STD difference between the optimal and the GIF code-phase combinations decreases

  3. Metagenomic Diagnosis of Bacterial Infections

    Science.gov (United States)

    Nakamura, Shota; Maeda, Norihiro; Miron, Ionut Mihai; Yoh, Myonsun; Izutsu, Kaori; Kataoka, Chidoh; Honda, Takeshi; Yasunaga, Teruo; Nakaya, Takaaki; Kawai, Jun; Hayashizaki, Yoshihide; Horii, Toshihiro

    2008-01-01

    To test the ability of high-throughput DNA sequencing to detect bacterial pathogens, we used it on DNA from a patient’s feces during and after diarrheal illness. Sequences showing best matches for Campylobacter jejuni were detected only in the illness sample. Various bacteria may be detectable with this metagenomic approach. PMID:18976571

  4. Evaluation of the Limulus amoebocyte lysate test in conjunction with a gram negative bacterial plate count for detecting irradiation of chicken

    International Nuclear Information System (INIS)

    Scotter, S.L.; Wood, R.; McWeeny, D.J.

    1990-01-01

    A study to evaluate the potential of the Limulus amoebocyte lysate (LAL) test in conjunction with a Gram negative bacterial (GNB) plate count for detecting the irradiation of chicken is described. Preliminary studies demonstrated that chickens irradiated at an absorbed dose of 2.5 kGy could be differentiated from unirradiated birds by measuring levels of endotoxin and of numbers of GNB on chicken skin. Irradiated birds were found to have endotoxin levels similar to those found in unirradiated birds but significantly lower numbers of GNB. In a limited study the test was found to be applicable to birds from different processors. The effect of temperature abuse on the microbiological profile, and thus the efficacy of the test, was also investigated. After temperature abuse, the irradiated birds were identifiable at worst up to 3 days after irradiation treatment at the 2.5 kGy level and at best some 13 days after irradiation. Temperature abuse at 15 0 C resulted in rapid recovery of surviving micro-organisms which made differentiation of irradiated and unirradiated birds using this test unreliable. The microbiological quality of the bird prior to irradiation treatment also affected the test as large numbers of GNB present on the bird prior to irradiation treatment resulted in larger numbers of survivors. In addition, monitoring the developing flora after irradiation treatment amd during subsequent chilled storage also aided differentiation of irradiated and unirradiated birds. Large numbers of yeast and Gram positive cocci were isolated from irradiated carcasses whereas Gram negative oxidative rods were the predominant spoilage flora on unirradiated birds. (author)

  5. Evaluation of the Limulus amoebocyte lysate test in conjunction with a gram negative bacterial plate count for detecting irradiation of chicken

    Energy Technology Data Exchange (ETDEWEB)

    Scotter, S.L.; Wood, R.; McWeeny, D.J. (Ministry of Agriculture, Fisheries and Food, Norwich (UK). Food Science Lab.)

    1990-01-01

    A study to evaluate the potential of the Limulus amoebocyte lysate (LAL) test in conjunction with a Gram negative bacterial (GNB) plate count for detecting the irradiation of chicken is described. Preliminary studies demonstrated that chickens irradiated at an absorbed dose of 2.5 kGy could be differentiated from unirradiated birds by measuring levels of endotoxin and of numbers of GNB on chicken skin. Irradiated birds were found to have endotoxin levels similar to those found in unirradiated birds but significantly lower numbers of GNB. In a limited study the test was found to be applicable to birds from different processors. The effect of temperature abuse on the microbiological profile, and thus the efficacy of the test, was also investigated. After temperature abuse, the irradiated birds were identifiable at worst up to 3 days after irradiation treatment at the 2.5 kGy level and at best some 13 days after irradiation. Temperature abuse at 15{sup 0}C resulted in rapid recovery of surviving micro-organisms which made differentiation of irradiated and unirradiated birds using this test unreliable. The microbiological quality of the bird prior to irradiation treatment also affected the test as large numbers of GNB present on the bird prior to irradiation treatment resulted in larger numbers of survivors. In addition, monitoring the developing flora after irradiation treatment amd during subsequent chilled storage also aided differentiation of irradiated and unirradiated birds. Large numbers of yeast and Gram positive cocci were isolated from irradiated carcasses whereas Gram negative oxidative rods were the predominant spoilage flora on unirradiated birds. (author).

  6. Multicenter Evaluation of the ePlex Respiratory Pathogen Panel for the Detection of Viral and Bacterial Respiratory Tract Pathogens in Nasopharyngeal Swabs.

    Science.gov (United States)

    Babady, N Esther; England, Matthew R; Jurcic Smith, Kristen L; He, Taojun; Wijetunge, Dona Saumya; Tang, Yi-Wei; Chamberland, Robin R; Menegus, Marilyn; Swierkosz, Ella M; Jerris, Robert C; Greene, Wallace

    2018-02-01

    The performance of the new ePlex Respiratory Pathogen (RP) panel (GenMark Diagnostics) for the simultaneous detection of 19 viruses (influenza A virus; influenza A H1 virus; influenza A 2009 H1 virus; influenza A H3 virus; influenza B virus; adenovirus; coronaviruses [HKU1, OC43, NL63, and 229E]; human rhinovirus/enterovirus; human metapneumovirus; parainfluenza viruses 1, 2, 3, and 4; and respiratory syncytial virus [RSV] [RSV subtype A and RSV subtype B]) and 2 bacteria ( Mycoplasma pneumoniae and Chlamydia pneumoniae ) was evaluated. Prospectively and retrospectively collected nasopharyngeal swab (NPS) specimens ( n = 2,908) were evaluated by using the ePlex RP panel, with the bioMérieux/BioFire FilmArray Respiratory Panel (BioFire RP) as the comparator method. Discordance analysis was performed by using target-specific PCRs and bidirectional sequencing. The reproducibility of the assay was evaluated by using reproducibility panels comprised of 6 pathogens. The overall agreement between the ePlex RP and BioFire RP results was >95% for all targets. Positive percent agreement with the BioFire RP result for viruses ranged from 85.1% (95% confidence interval [CI], 80.2% to 88.9%) to 95.1% (95% CI, 89.0% to 97.9%), while negative percent agreement values ranged from 99.5% (95% CI, 99.1% to 99.7%) to 99.8% (95% CI, 99.5% to 99.9%). Additional testing of discordant targets (12%; 349/2,908) confirmed the results of ePlex RP for 38% (131/349) of samples tested. Reproducibility was 100% for all targets tested, with the exception of adenovirus, for which reproducibilities were 91.6% at low virus concentrations and 100% at moderate virus concentrations. The ePlex RP panel offers a new, rapid, and sensitive "sample-to-answer" multiplex panel for the detection of the most common viral and bacterial respiratory pathogens. Copyright © 2018 Babady et al.

  7. BACTERIAL CONSORTIUM

    Directory of Open Access Journals (Sweden)

    Payel Sarkar

    2013-01-01

    Full Text Available Petroleum aromatic hydrocarbons like benzen e, toluene, ethyl benzene and xylene, together known as BTEX, has almost the same chemical structure. These aromatic hydrocarbons are released as pollutants in th e environment. This work was taken up to develop a solvent tolerant bacterial cons ortium that could degrade BTEX compounds as they all share a common chemical structure. We have isolated almost 60 different types of bacterial strains from different petroleum contaminated sites. Of these 60 bacterial strains almost 20 microorganisms were screene d on the basis of capability to tolerate high concentration of BTEX. Ten differe nt consortia were prepared and the compatibility of the bacterial strains within the consortia was checked by gram staining and BTEX tolerance level. Four successful mi crobial consortia were selected in which all the bacterial strains concomitantly grew in presence of high concentration of BTEX (10% of toluene, 10% of benzene 5% ethyl benzene and 1% xylene. Consortium #2 showed the highest growth rate in pr esence of BTEX. Degradation of BTEX by consortium #2 was monitored for 5 days by gradual decrease in the volume of the solvents. The maximum reduction observed wa s 85% in 5 days. Gas chromatography results also reveal that could completely degrade benzene and ethyl benzene within 48 hours. Almost 90% degradation of toluene and xylene in 48 hours was exhibited by consortium #2. It could also tolerate and degrade many industrial solvents such as chloroform, DMSO, acetonitrile having a wide range of log P values (0.03–3.1. Degradation of aromatic hydrocarbon like BTEX by a solvent tolerant bacterial consortium is greatly significant as it could degrade high concentration of pollutants compared to a bacterium and also reduces the time span of degradation.

  8. Evaluation of a fluorescence-labelled oligonucleotide tide probe targeting 23S rRNA for in situ detection of Salmonella serovars in paraffin-embedded tissue sections and their rapid identification in bacterial smears

    DEFF Research Database (Denmark)

    Nordentoft, Steen; Christensen, H.; Wegener, Henrik Caspar

    1997-01-01

    A method for the detection of Salmonella based on fluorescence in situ hybridization (FISH) has been developed and applied for the direct detection of Salmonella in pure cultures and in formalin-fixed, paraffin-embedded tissue sections. On the basis of the 23S rRNA gene sequences representing all...... with the probe. The probe did not hybridize to serovars from subspecies IIIa (S. arizonae) or to S. bongori. No cross-reaction to 64 other strains of the family Enterobacteriaceae or 18 other bacterial strains outside this family was observed. The probe was tested with sections of formalin-fixed, paraffin...

  9. Detection of carboxylesterase and esterase activity in culturable gut bacterial flora isolated from diamondback moth, Plutella xylostella (Linnaeus, from India and its possible role in indoxacarb degradation

    Directory of Open Access Journals (Sweden)

    Shanivarsanthe Leelesh Ramya

    2016-06-01

    Full Text Available Abstract Diamondback moth (DBM, Plutella xylostella (Linnaeus, is a notorious pest of brassica crops worldwide and is resistant to all groups of insecticides. The insect system harbors diverse groups of microbiota, which in turn helps in enzymatic degradation of xenobiotic-like insecticides. The present study aimed to determine the diversity of gut microflora in DBM, quantify esterase activity and elucidate their possible role in degradation of indoxacarb. We screened 11 geographic populations of DBM in India and analyzed them for bacterial diversity. The culturable gut bacterial flora underwent molecular characterization with 16S rRNA. We obtained 25 bacterial isolates from larvae (n = 13 and adults (n = 12 of DBM. In larval gut isolates, gammaproteobacteria was the most abundant (76%, followed by bacilli (15.4%. Molecular characterization placed adult gut bacterial strains into three major classes based on abundance: gammaproteobacteria (66%, bacilli (16.7% and flavobacteria (16.7%. Esterase activity from 19 gut bacterial isolates ranged from 0.072 to 2.32 µmol/min/mg protein. Esterase bands were observed in 15 bacterial strains and the banding pattern differed in Bacillus cereus – KC985225 and Pantoea agglomerans – KC985229. The bands were characterized as carboxylesterase with profenofos used as an inhibitor. Minimal media study showed that B. cereus degraded indoxacarb up to 20%, so it could use indoxacarb for metabolism and growth. Furthermore, esterase activity was greater with minimal media than control media: 1.87 versus 0.26 µmol/min/mg protein. Apart from the insect esterases, bacterial carboxylesterase may aid in the degradation of insecticides in DBM.

  10. Biological Threats Detection Technologies

    International Nuclear Information System (INIS)

    Bartoszcze, M.

    2007-01-01

    Among many decisive factors, which can have the influence on the possibility of decreases the results of use biological agents should be mentioned obligatory: rapid detection and identification of biological factor used, the proper preventive treatment and the medical management. The aims of identification: to identify the factor used, to estimate the area of contamination, to evaluate the possible countermeasure efforts (antibiotics, disinfectants) and to assess the effectiveness of the decontamination efforts (decontamination of the persons, equipment, buildings, environment etc.). The objects of identification are: bacteria and bacteria's spores, viruses, toxins and genetically modified factors. The present technologies are divided into: based on PCR techniques (ABI PRISM, APSIS, BIOVERIS, RAPID), immuno (BADD, RAMP, SMART) PCR and immuno techniques (APDS, LUMINEX) and others (BDS2, LUNASCAN, MALDI). The selected technologies assigned to field conditions, mobile and stationary laboratories will be presented.(author)

  11. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    Bacterial ecology is concerned with the interactions between bacteria and their biological and nonbiological environments and with the role of bacteria in biogeochemical element cycling. Many fundamental properties of bacteria are consequences of their small size. Thus, they can efficiently exploit...

  12. Bacterial meningitis

    NARCIS (Netherlands)

    Heckenberg, Sebastiaan G. B.; Brouwer, Matthijs C.; van de Beek, Diederik

    2014-01-01

    Bacterial meningitis is a neurologic emergency. Vaccination against common pathogens has decreased the burden of disease. Early diagnosis and rapid initiation of empiric antimicrobial and adjunctive therapy are vital. Therapy should be initiated as soon as blood cultures have been obtained,

  13. Bacterial lipases

    NARCIS (Netherlands)

    Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation,

  14. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    , the production and oxidation of methane, nitrate reduction and fixation of atmospheric nitrogen are exclusively carried out by different groups of bacteria. Some bacterial species – ‘extremophiles’ – thrive in extreme environments in which no eukaryotic organisms can survive with respect to temperature, salinity...

  15. Bacterial Vaginosis

    Science.gov (United States)

    ... that coats the walls of the vagina Vaginal discharge with an unpleasant or fishlike odor Vaginal pain or itching Burning during urination Doctors are unsure of the incubation period for bacterial vaginosis. How Is the Diagnosis Made? Your child’s pediatrician can make the diagnosis ...

  16. Bacterial stress

    Indian Academy of Sciences (India)

    First page Back Continue Last page Graphics. Bacterial stress. Physicochemical and chemical parameters: temperature, pressure, pH, salt concentration, oxygen, irradiation. Nutritional depravation: nutrient starvation, water shortage. Toxic compounds: Antibiotics, heavy metals, toxins, mutagens. Interactions with other cells: ...

  17. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    reduce or delay bacterial biofilm formation of a range of urinary tract infectious E.coli and Klebsiella isolates. Several other proteinaceous coatings were also found to display anti-adhesive properties, possibly providing a measure for controlling the colonization of implant materials. Several other...... components. These substances may both mediate and stabilize the bacterial biofilm. Finally, several adhesive structures were examined, and a novel physiological biofilm phenotype in E.coli biofilms was characterized, namely cell chain formation. The autotransporter protein, antigen 43, was implicated...

  18. Bacterial lipases

    OpenAIRE

    Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

    1994-01-01

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation, meaning a sharp increase in lipase activity observed when the substrate starts to form an emulsion, thereby presenting to the enzyme an interfacial area. As a consequence, the kinetics of a lipase rea...

  19. Bacterial mitosis

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Borch, Jonas; Dam, Mette

    2003-01-01

    Bacterial DNA segregation takes place in an active and ordered fashion. In the case of Escherichia coli plasmid R1, the partitioning system (par) separates paired plasmid copies and moves them to opposite cell poles. Here we address the mechanism by which the three components of the R1 par system...... movement is powered by insertional polymerization of ParM. Consistently, we find that segregating plasmids are positioned at the ends of extending ParM filaments. Thus, the process of R1 plasmid segregation in E. coli appears to be mechanistically analogous to the actin-based motility operating...

  20. Detection of Androgenic-Mutagenic Compounds and Potential Autochthonous Bacterial Communities during In Situ Bioremediation of Post-methanated Distillery Sludge

    Directory of Open Access Journals (Sweden)

    Ram Chandra

    2017-05-01

    Full Text Available Sugarcane-molasses-based post-methanated distillery waste is well known for its toxicity, causing adverse effects on aquatic flora and fauna. Here, it has been demonstrated that there is an abundant mixture of androgenic and mutagenic compounds both in distillery sludge and leachate. Gas chromatography-mass spectrometry (GC-MS analysis showed dodecanoic acid, octadecanoic acid, n-pentadecanoic acid, hexadecanoic acid, β-sitosterol, stigmasterol, β-sitosterol trimethyl ether, heptacosane, dotriacontane, lanosta-8, 24-dien-3-one, 1-methylene-3-methyl butanol, 1-phenyl-1-propanol, 5-methyl-2-(1-methylethyl cyclohexanol, and 2-ethylthio-10-hydroxy-9-methoxy-1,4 anthraquinone as major organic pollutants along with heavy metals (all mg kg-1: Fe (2403, Zn (210.15, Mn (126.30, Cu (73.62, Cr (21.825, Pb (16.33 and Ni (13.425. In a simultaneous analysis of bacterial communities using the restriction fragment length polymorphism (RFLP method the dominance of Bacillus sp. followed by Enterococcus sp. as autochthonous bacterial communities growing in this extremely toxic environment was shown, indicating a primary community for bioremediation. A toxicity evaluation showed a reduction of toxicity in degraded samples of sludge and leachate, confirming the role of autochthonous bacterial communities in the bioremediation of distillery waste in situ.

  1. Gram stain method shows better sensitivity than clinical criteria for detection of bacterial vaginosis in surveillance of pregnant, low-income women in a clinical setting.

    Science.gov (United States)

    Tam, M T; Yungbluth, M; Myles, T

    1998-01-01

    OBJECTIVE: The purpose of the study is to determine whether the Gram stain method is superior to the clinical criteria for the diagnosis of bacterial vaginosis in low-income pregnant women seen in a resident clinic setting. The clinical criteria is the current diagnostic method employed to diagnose bacterial vaginosis. STUDY DESIGN: In this study, 51 pregnant women with vaginal discharge were prospectively evaluated. All were screened using the clinical criteria, Gram stain method, and culture of the discharge. The modified scoring system instituted by Nugent et al. (J Clin Microbiol 29:297-301, 1991) was employed in reading the Gram stain smears. The clinical criteria were then compared with the Gram stain method. Isolation of moderate to many Gardnerella vaginalis growth by culture was used as the confirmatory finding. RESULTS: Sensitivity of the Gram stain method (91%) was significantly higher than that of the clinical criteria (46%), (sign test P = 0.0023, Gram stain method also has both a low false-negative (4%) and high negative predictive value (96%), making it an ideal diagnostic test. CONCLUSION: The Gram stain method is a rapid and cost-effective test that is also highly reproducible and readily available in many laboratories. These features make the Gram stain method a more desirable screening procedure for bacterial vaginosis in a clinic population. PMID:9894174

  2. Implementation of immunomagnetic separation (IMS) for the enrichment and automated detection of bacterial contaminants in flow through lab on the chip technology

    DEFF Research Database (Denmark)

    Ahmed, Shakil

    Due to an increased public concern for food safety and quality, food processing industries have an urgent need for fast and reliable contaminant detection technologies. Conventional pathogen detection methods are time consuming, cost intensive, require skilled laboratory workers and are inappropr...... and detect pathogens in food, feed or beverage industries in real-time and has the potential to offer significant advantages compared to conventional systems.......Due to an increased public concern for food safety and quality, food processing industries have an urgent need for fast and reliable contaminant detection technologies. Conventional pathogen detection methods are time consuming, cost intensive, require skilled laboratory workers...

  3. [Acute bacterial meningitis with soluble antigen detected by latex particle agglutination tests at the Sourô-Sanou University Hospital of Bobo-Dioulasso (Burkina Faso)].

    Science.gov (United States)

    Ouédraogo, S M; Yaméogo, T M; Kyelem, C G; Poda, G E A; Ouédraogo, N F; Millogo, A; Ouédraogo, A; Ouédraogo-Traoré, A; Drabo, Y J

    2012-01-01

    Acute bacterial meningitis constitutes a major public health problem in Burkina Faso, in part because of its high lethality rate, estimated in 2004 at 17.5%. Failure to confirm suspected cases of meningitis results in overestimating reported cases and incorrectly treating false positives. The latex particle agglutination test is a diagnostic alternative that overcomes these limitations. Determine the bacteriological and therapeutic profile as well as the course of cases of acute meningitis confirmed by the latex agglutination test at Sourô-Sanou University Hospital. This prospective longitudinal study took place over a one-year period (2008 to 2009). Data were collected from clinical and laboratory records. The diagnosis of meningitis was confirmed by testing for specific soluble antigens in the spinal fluid. We used the Pastorex(™) Meningitis Kit for that purpose. The threshold of significance selected for our study was 0.05. In all, 457 samples of spinal fluid from patients with suspected acute bacterial meningitis were analyzed and the latex test was performed in 438 of these samples: 154 (35.2%) were positive. The average age of our cases confirmed by the latex test was 13.2 ± 4.2 years old. This test confirmed more cases than any other method of identification. The therapeutic strategy used from one to four treatment agents. Streptococcus pneumoniae was the most virulent and the most lethal pathogen, with a 64.7% lethality rate. The earliness of the consultation and the treatment of the bacterial meningitis seem to have a positive effect on the course of disease.

  4. BDS thin film damage competition

    Energy Technology Data Exchange (ETDEWEB)

    Stolz, C J; Thomas, M D; Griffin, A J

    2008-10-24

    A laser damage competition was held at the 2008 Boulder Damage Symposium in order to determine the current status of thin film laser resistance within the private, academic, and government sectors. This damage competition allows a direct comparison of the current state-of-the-art of high laser resistance coatings since they are all tested using the same damage test setup and the same protocol. A normal incidence high reflector multilayer coating was selected at a wavelength of 1064 nm. The substrates were provided by the submitters. A double blind test assured sample and submitter anonymity so only a summary of the results are presented here. In addition to the laser resistance results, details of deposition processes, coating materials, and layer count will also be shared.

  5. Diagnosis and prevalence of bacterial vaginosis.

    Directory of Open Access Journals (Sweden)

    Saharan S

    1993-04-01

    Full Text Available A prospective study of 80 women was undertaken to estimate the prevalence of bacterial vaginosis, and to compare two methods of diagnosing the condition. Bacterial Vaginosis was detected by both Gram stain and compound criteria in 30 women. The prevalence was 37.5%. Gram stain provides a simple and inexpensive method for laboratory confirmation of bacterial vaginosis where facilities for using the compound criteria are not available.

  6. Comparison of in-house and commercial real time-PCR based carbapenemase gene detection methods in Enterobacteriaceae and non-fermenting gram-negative bacterial isolates.

    Science.gov (United States)

    Smiljanic, M; Kaase, M; Ahmad-Nejad, P; Ghebremedhin, B

    2017-07-10

    Carbapenemase-producing gram-negative bacteria are increasing globally and have been associated with outbreaks in hospital settings. Thus, the accurate detection of these bacteria in infections is mandatory for administering the adequate therapy and infection control measures. This study aimed to establish and evaluate a multiplex real-time PCR assay for the simultaneous detection of carbapenemase gene variants in gram-negative rods and to compare the performance with a commercial RT-PCR assay (Check-Direct CPE). 116 carbapenem-resistant Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii isolates were genotyped for carbapenemase genes by PCR and sequencing. The defined isolates were used for the validation of the in-house RT-PCR by use of designed primer pairs and probes. Among the carbapenem-resistant isolates the genes bla KPC , bla VIM , bla NDM or bla OXA were detected. Both RT-PCR assays detected all bla KPC , bla VIM and bla NDM in the isolates. The in-house RT-PCR detected 53 of 67 (79.0%) whereas the commercial assay detected only 29 (43.3%) of the OXA genes. The in-house sufficiently distinguished the most prevalent OXA types (23-like and 48-like) in the melting curve analysis and direct detection of the genes from positive blood culture vials. The Check-Direct CPE and the in-house RT-PCR assay detected the carbapenem resistance from solid culture isolates. Moreover, the in-house assay enabled the identification of carbapenemase genes directly from positive blood-culture vials. However, we observed insufficient detection of various OXA genes in both assays. Nevertheless, the in-house RT-PCR detected the majority of the OXA type genes in Enterobacteriaceae and A. baumannii.

  7. BACTERIAL PLASMIDS

    Directory of Open Access Journals (Sweden)

    Marina Dinic

    2007-12-01

    Full Text Available Plasmids, extrachromosomal DNA, were identified in bacteria pertaining to family of Enterobacteriacae for the very first time. After that, they were discovered in almost every single observed strain. The structure of plasmids is made of circular double chain DNA molecules which are replicated autonomously in a host cell. Their length may vary from few up to several hundred kilobase (kb. Among the bacteria, plasmids are mostly transferred horizontally by conjugation process. Plasmid replication process can be divided into three stages: initiation, elongation, and termination. The process involves DNA helicase I, DNA gyrase, DNA polymerase III, endonuclease, and ligase.Plasmids contain genes essential for plasmid function and their preservation in a host cell (the beginning and the control of replication. Some of them possess genes whichcontrol plasmid stability. There is a common opinion that plasmids are unnecessary fora growth of bacterial population and their vital functions; thus, in many cases they can be taken up or kicked out with no lethal effects to a plasmid host cell. However,there are numerous biological functions of bacteria related to plasmids. Plasmids identification and classification are based upon their genetic features which are presented permanently in all of them, and these are: abilities to preserve themselves in a host cell and to control a replication process. In this way, plasmids classification among incompatibility groups is performed. The method of replicon typing, which is based on genotype and not on phenotype characteristics, has the same results as in compatibility grouping.

  8. Bacterial Cryoprotectants

    Indian Academy of Sciences (India)

    some tips to scientists striving to find a way to control food- borne pathogens that survive at low temperatures. ... cryoprotectant was first demonstrated in the food borne patho- gen Listeria monocytogenes. This organism ... culture plate, whereas no growth was detected under similar conditions without betaine. They also ...

  9. Application of denaturing gradient gel electrophoresis for detection of bacterial and yeast communities along a salinity gradient in the estuary of the Cachoeira River in Brazil.

    Science.gov (United States)

    Rodrigues, C S P; Souza, S S; Rezende, R P; Silva, A; Andrioli, J L; Costa, H; Fontana, R; Dias, J C T

    2013-05-21

    An estuary is a transition zone between freshwater and marine ecosystems, resulting in dilution of seawater. Estuaries are also considered environments of intense biological activity related to the processes of nutrient cycling. The aim of this study was to evaluate the microbial community composition along a salinity gradient in the estuary of the Cachoeira River, located in southern Bahia, Brazil. The analysis of bacterial and yeast communities was performed by determining the denaturing gradient gel electrophoresis band richness. Formation of zones with similar profiles of bands was observed, and the increasing richness at the intermediate zone demonstrated a clear spatial distinction of communities depending on salinity. In addition, the dissolved oxygen content, temperature, pH, salinity, and dissolved inorganic nutrient contents (NH3(+), NO2(-), NO3(-), PO4(-)) were determined. Nutrients were distributed in similar patterns, with decreasing concentrations as the salinity increases.

  10. Radiology of bacterial pneumonia

    Energy Technology Data Exchange (ETDEWEB)

    Vilar, Jose E-mail: vilar_jlu@gva.es; Domingo, Maria Luisa; Soto, Cristina; Cogollos, Jonathan

    2004-08-01

    Bacterial pneumonia is commonly encountered in clinical practice. Radiology plays a prominent role in the evaluation of pneumonia. Chest radiography is the most commonly used imaging tool in pneumonias due to its availability and excellent cost benefit ratio. CT should be used in unresolved cases or when complications of pneumonia are suspected. The main applications of radiology in pneumonia are oriented to detection, characterisation and follow-up, especially regarding complications. The classical classification of pneumonias into lobar and bronchial pneumonia has been abandoned for a more clinical classification. Thus, bacterial pneumonias are typified into three main groups: Community acquired pneumonia (CAD), Aspiration pneumonia and Nosocomial pneumonia (NP).The usual pattern of CAD is that of the previously called lobar pneumonia; an air-space consolidation limited to one lobe or segment. Nevertheless, the radiographic patterns of CAD may be variable and are often related to the causative agent. Aspiration pneumonia generally involves the lower lobes with bilateral multicentric opacities. Nosocomial Pneumonia (NP) occurs in hospitalised patients. The importance of NP is related to its high mortality and, thus, the need to obtain a prompt diagnosis. The role of imaging in NP is limited but decisive. The most valuable information is when the chest radiographs are negative and rule out pneumonia. The radiographic patterns of NP are very variable, most commonly showing diffuse multifocal involvement and pleural effusion. Imaging plays also an important role in the detection and evaluation of complications of bacterial pneumonias. In many of these cases, especially in hospitalised patients, chest CT must be obtained in order to better depict these associate findings.

  11. Radiology of bacterial pneumonia

    International Nuclear Information System (INIS)

    Vilar, Jose; Domingo, Maria Luisa; Soto, Cristina; Cogollos, Jonathan

    2004-01-01

    Bacterial pneumonia is commonly encountered in clinical practice. Radiology plays a prominent role in the evaluation of pneumonia. Chest radiography is the most commonly used imaging tool in pneumonias due to its availability and excellent cost benefit ratio. CT should be used in unresolved cases or when complications of pneumonia are suspected. The main applications of radiology in pneumonia are oriented to detection, characterisation and follow-up, especially regarding complications. The classical classification of pneumonias into lobar and bronchial pneumonia has been abandoned for a more clinical classification. Thus, bacterial pneumonias are typified into three main groups: Community acquired pneumonia (CAD), Aspiration pneumonia and Nosocomial pneumonia (NP).The usual pattern of CAD is that of the previously called lobar pneumonia; an air-space consolidation limited to one lobe or segment. Nevertheless, the radiographic patterns of CAD may be variable and are often related to the causative agent. Aspiration pneumonia generally involves the lower lobes with bilateral multicentric opacities. Nosocomial Pneumonia (NP) occurs in hospitalised patients. The importance of NP is related to its high mortality and, thus, the need to obtain a prompt diagnosis. The role of imaging in NP is limited but decisive. The most valuable information is when the chest radiographs are negative and rule out pneumonia. The radiographic patterns of NP are very variable, most commonly showing diffuse multifocal involvement and pleural effusion. Imaging plays also an important role in the detection and evaluation of complications of bacterial pneumonias. In many of these cases, especially in hospitalised patients, chest CT must be obtained in order to better depict these associate findings

  12. Biosensors of bacterial cells.

    Science.gov (United States)

    Burlage, Robert S; Tillmann, Joshua

    2017-07-01

    Biosensors are devices which utilize both an electrical component (transducer) and a biological component to study an environment. They are typically used to examine biological structures, organisms and processes. The field of biosensors has now become so large and varied that the technology can often seem impenetrable. Yet the principles which underlie the technology are uncomplicated, even if the details of the mechanisms are elusive. In this review we confine our analysis to relatively current advancements in biosensors for the detection of whole bacterial cells. This includes biosensors which rely on an added labeled component and biosensors which do not have a labeled component and instead detect the binding event or bound structure on the transducer. Methods to concentrate the bacteria prior to biosensor analysis are also described. The variety of biosensor types and their actual and potential uses are described. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. An accurate, specific, sensitive, high-throughput method based on a microsphere immunoassay for multiplex detection of three viruses and bacterial fruit blotch bacterium in cucurbits.

    Science.gov (United States)

    Charlermroj, Ratthaphol; Makornwattana, Manlika; Himananto, Orawan; Seepiban, Channarong; Phuengwas, Sudtida; Warin, Nuchnard; Gajanandana, Oraprapai; Karoonuthaisiri, Nitsara

    2017-09-01

    To employ a microsphere immunoassay (MIA) to simultaneously detect multiple plant pathogens (potyviruses, Watermelon silver mottle virus, Melon yellow spot virus, and Acidovorax avenae subsp. citrulli) in actual plant samples, several factors need to be optimized and rigorously validated. Here, a simple extraction method using a single extraction buffer was successfully selected to detect the four pathogens in various cucurbit samples (cucumber, cantaloupe, melon, and watermelon). The extraction method and assay performance were validated with inoculated and field cucurbit samples. The MIA showed 98-99% relative accuracy, 97-100% relative specificity and 92-100% relative sensitivity when compared to commercial ELISA kits and reverse transcription PCR. In addition, the MIA was also able to accurately detect multiple-infected field samples. The results demonstrate that one common extraction method for all tested cucurbit samples could be applied to detect multiple pathogens; avoiding the need for multiple protocols to be employed. This multiplex method can therefore be instrumental for high-throughput screening of multiple plant pathogens with many advantages such as a shorter assay time (2.5h) with single assay format, a lower cost of detection ($5 vs $19.7 for 4 pathogens/sample) and less labor requirement. Its multiplex capacity can also be expanded to detect up to 50 different pathogens upon the availability of specific antibodies. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. A TaqMan-based real time PCR assay for specific detection and quantification of Xylella fastidiosa strains causing bacterial leaf scorch in oleander.

    Science.gov (United States)

    Guan, Wei; Shao, Jonathan; Singh, Raghuwinder; Davis, Robert E; Zhao, Tingchang; Huang, Qi

    2013-02-15

    A TaqMan-based real-time PCR assay was developed for specific detection of strains of X. fastidiosa causing oleander leaf scorch. The assay uses primers WG-OLS-F1 and WG-OLS-R1 and the fluorescent probe WG-OLS-P1, designed based on unique sequences found only in the genome of oleander strain Ann1. The assay is specific, allowing detection of only oleander-infecting strains, not other strains of X. fastidiosa nor other plant-associated bacteria tested. The assay is also sensitive, with a detection limit of 10.4fg DNA of X. fastidiosa per reaction in vitro and in planta. The assay can also be applied to detect low numbers of X. fastidiosa in insect samples, or further developed into a multiplex real-time PCR assay to simultaneously detect and distinguish diverse strains of X. fastidiosa that may occupy the same hosts or insect vectors. Specific and sensitive detection and quantification of oleander strains of X. fastidiosa should be useful for disease diagnosis, epidemiological studies, management of oleander leaf scorch disease, and resistance screening for oleander shrubs. Published by Elsevier B.V.

  15. Multi-GNSS real-time precise positioning service and Initial assessment of BDS-3 (G Division Outstanding ECS Award Lecture)

    Science.gov (United States)

    Li, Xingxing; Ge, Maaorong; Li, Xin; Zhang, Xiuaohong; Wu, Mingkui; Wickert, Jens; Schuh, Harald

    2017-04-01

    The rapid development of multi-constellation GNSSs (Global Navigation Satellite Systems, e.g., BeiDou, Galileo, GLONASS, GPS) and the IGS (International GNSS Service) Multi-GNSS Experiment (MGEX) bring great opportunities and challenges for real-time precise positioning service. In this contribution, we present a GPS+GLONASS+BeiDou+Galileo four-system model to fully exploit the observations of all these four navigation satellite systems for real-time precise orbit determination, clock estimation and positioning. Meanwhile, an efficient multi-GNSS real-time precise positioning service system is designed and demonstrated by using the Multi-GNSS Experiment (MGEX) and International GNSS Service (IGS) data streams including stations all over the world. The addition of the BeiDou, Galileo and GLONASS systems to the standard GPS-only processing, reduces the convergence time almost by 70%, while the positioning accuracy is improved by about 25%. The successful launch of five new-generation satellites of the Chinese BeiDou Navigation Satellite System (BDS-3) marks a significant step in expanding BeiDou into a navigation system with global coverage. We present an initial characterization and performance assessment for these new-generation BeiDou-3 satellites and their signals. The characteristics of the B1C, B1I, B2a, B2b and B3I signals are evaluated in terms of observed carrier-to-noise density ratio, pseudorange multipath and noise, triple-frequency carrier phase ionosphere-free and geometry-free combination, and double-differenced carrier phase and code residuals. With respect to BeiDou-2 satellites, the analysis of code multipath shows that the elevation-dependent code biases, which have been previously identified to exist in the code observations of BeiDou-2 satellites, seem to be not obvious for all the available signals of new-generation BeiDou-3 satellites. This will significantly benefit precise applications that resolve wide-lane ambiguity based on Melbourne

  16. Bacterial contamination of blood products.

    Science.gov (United States)

    Palavecino, Elizabeth; Jacobs, Michael; Yomtovian, Roslyn

    2004-11-01

    The occurrence of a septic reaction resulting from bacterial contamination of blood products, particularly with room-temperature stored platelets, is the most common transfusion-associated infectious risk in the United States. Bacterial contamination of blood products was first identified more than 60 years ago; yet, strategies to resolve this problem have proved daunting despite ongoing awareness and increasing concern especially in the last few years. With the recent US Food and Drug Administration (FDA) approval of culture methods for quality control testing of platelet units and the promulgation of accreditation standards by the College of American Pathologists and American Association of Blood Banks to detect bacterially contaminated platelet units and to prevent transfusion of these units, blood banks and transfusion services have finally started to address this problem, in a more standardized manner. Furthermore, as new methods of interdicting, inactivating and detecting bacterially contaminated blood products emerge, it is hoped that the problem of bacterial contamination of blood products will be overcome.

  17. Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR.

    Science.gov (United States)

    Dalla-Costa, Libera M; Morello, Luis G; Conte, Danieli; Pereira, Luciane A; Palmeiro, Jussara K; Ambrosio, Altair; Cardozo, Dayane; Krieger, Marco A; Raboni, Sonia M

    2017-09-01

    Sepsis is the leading cause of death in intensive care units (ICUs) worldwide and its diagnosis remains a challenge. Blood culturing is the gold standard technique for blood stream infection (BSI) identification. Molecular tests to detect pathogens in whole blood enable early use of antimicrobials and affect clinical outcomes. Here, using real-time PCR, we evaluated DNA extraction using seven manual and three automated commercially available systems with whole blood samples artificially contaminated with Escherichia coli, Staphylococcus aureus, and Candida albicans, microorganisms commonly associated with BSI. Overall, the commercial kits evaluated presented several technical limitations including long turnaround time and low DNA yield and purity. The performance of the kits was comparable for detection of high microorganism loads (10 6 CFU/mL). However, the detection of lower concentrations was variable, despite the addition of pre-processing treatment to kits without such steps. Of the evaluated kits, the UMD-Universal CE IVD kit generated a higher quantity of DNA with greater nucleic acid purity and afforded the detection of the lowest microbial load in the samples. The inclusion of pre-processing steps with the kit seems to be critical for the detection of microorganism DNA directly from whole blood. In conclusion, future application of molecular techniques will require overcoming major challenges such as the detection of low levels of microorganism nucleic acids amidst the large quantity of human DNA present in samples or differences in the cellular structures of etiological agents that can also prevent high-quality DNA yields. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Stable carbon isotope fractionation during bacterial acetylene fermentation: Potential for life detection in hydrocarbon-rich volatiles of icy planet(oid)s

    Science.gov (United States)

    Miller, Laurence; Baesman, Shaun; Oremland, Ron

    2015-01-01

    We report the first study of stable carbon isotope fractionation during microbial fermentation of acetylene (C2H2) in sediments, sediment enrichments, and bacterial cultures. Kinetic isotope effects (KIEs) averaged 3.7 ± 0.5‰ for slurries prepared with sediment collected at an intertidal mudflat in San Francisco Bay and 2.7 ± 0.2‰ for a pure culture of Pelobacter sp. isolated from these sediments. A similar KIE of 1.8 ± 0.7‰ was obtained for methanogenic enrichments derived from sediment collected at freshwater Searsville Lake, California. However, C2H2 uptake by a highly enriched mixed culture (strain SV7) obtained from Searsville Lake sediments resulted in a larger KIE of 9.0 ± 0.7‰. These are modest KIEs when compared with fractionation observed during oxidation of C1 compounds such as methane and methyl halides but are comparable to results obtained with other C2compounds. These observations may be useful in distinguishing biologically active processes operating at distant locales in the Solar System where C2H2 is present. These locales include the surface of Saturn's largest moon Titan and the vaporous water- and hydrocarbon-rich jets emanating from Enceladus.

  19. A bacterial community analysis using reverse transcription (RT) PCR which detects the bacteria with high activity in a wastewater treatment reactor

    Science.gov (United States)

    This research used reverse transcription polymerase chain reaction (RT-PCR) method to help detect active bacteria in a single-tank deammonification reactor combining partial nitritation and anammox. The single-tank aerobic deammonification reactor effectively removed the ammonia in anaerobically di...

  20. Comprehensive Evaluation of the MBT STAR-BL Module for Simultaneous Bacterial Identification and β-Lactamase-Mediated Resistance Detection in Gram-Negative Rods from Cultured Isolates and Positive Blood Cultures.

    Science.gov (United States)

    Lee, Annie W T; Lam, Johnson K S; Lam, Ricky K W; Ng, Wan H; Lee, Ella N L; Lee, Vicky T Y; Sze, Po P; Rajwani, Rahim; Fung, Kitty S C; To, Wing K; Lee, Rodney A; Tsang, Dominic N C; Siu, Gilman K H

    2018-01-01

    Objective: This study evaluated the capability of a MALDI Biotyper system equipped with the newly introduced MBT STAR-BL module to simultaneously perform species identification and β-lactamase-mediated resistance detection in bacteremia -causing bacteria isolated from cultured isolates and patient-derived blood cultures (BCs). Methods: Two hundred retrospective cultured isolates and 153 prospective BCs containing Gram-negative rods (GNR) were collected and subjected to direct bacterial identification, followed by the measurement of β-lactamase activities against ampicillin, piperacillin, cefotaxime, ceftazidime, and meropenem using the MBT STAR-BL module. The results and turnaround times were compared with those of routine microbiological processing. All strains were also characterized by beta-lactamase PCR and sequencing. Results: Using the saponin-based extraction method, MALDI-TOF MS correctly identified bacteria in 116/134 (86.6%) monomicrobial BCs. The detection sensitivities for β-lactamase activities against ampicillin, piperacillin, third-generation cephalosporin and meropenem were 91.3, 100, 97.9, and 100% for cultured isolates, and 80.4, 100, 68.8, and 40% for monomicrobial BCs ( n = 134) respectively. The overall specificities ranged from 91.5 to 100%. Furthermore, the MBT STAR-BL and conventional drug susceptibility test results were concordant in 14/19 (73.7%) polymicrobial cultures. Reducing the logRQ cut-off value from 0.4 to 0.2 increased the direct detection sensitivities for β-lactamase activities against ampicillin, cefotaxime and meropenem in BCs to 85.7, 87.5, and 100% respectively. The MBT STAR-BL test enabled the reporting of β-lactamase-producing GNR at 14.16 and 47.64 h before the interim and final reports of routine BCs processing, respectively, were available. Conclusion: The MALDI Biotyper system equipped with the MBT STAR-BL module enables the simultaneous rapid identification of bacterial species and

  1. Evaluation of the NanoCHIP® Gastrointestinal Panel (GIP Test for Simultaneous Detection of Parasitic and Bacterial Enteric Pathogens in Fecal Specimens.

    Directory of Open Access Journals (Sweden)

    Shifra Ken Dror

    Full Text Available Infectious gastroenteritis is a global health problem associated with high morbidity and mortality rates. Rapid and accurate diagnosis is crucial to allow appropriate and timely treatment. Current laboratory stool testing has a long turnaround time (TAT and demands highly qualified personnel and multiple techniques. The need for high throughput and the number of possible enteric pathogens compels the implementation of a molecular approach which uses multiplex technology, without compromising performance requirements. In this work we evaluated the feasibility of the NanoCHIP® Gastrointestinal Panel (GIP (Savyon Diagnostics, Ashdod, IL, a molecular microarray-based screening test, to be used in the routine workflow of our laboratory, a big outpatient microbiology laboratory. The NanoCHIP® GIP test provides simultaneous detection of nine major enteric bacteria and parasites: Campylobacter spp., Salmonella spp., Shigella spp., Giardia sp., Cryptosporidium spp., Entamoeba histolytica, Entamoeba dispar, Dientamoeba fragilis, and Blastocystis spp. The required high-throughput was obtained by the NanoCHIP® detection system together with the MagNA Pure 96 DNA purification system (Roche Diagnostics Ltd., Switzerland. This combined system has demonstrated a higher sensitivity and detection yield compared to the conventional methods in both, retrospective and prospective samples. The identification of multiple parasites and bacteria in a single test also enabled increased efficiency of detecting mixed infections, as well as reduced hands-on time and work load. In conclusion, the combination of these two automated systems is a proper response to the laboratory needs in terms of improving laboratory workflow, turn-around-time, minimizing human errors and can be efficiently integrated in the routine work of the laboratory.

  2. Screening for bacterial DNA in the hard tick Hyalomma marginatum (Ixodidae from Socotra Island (Yemen: detection of Francisella-like endosymbiont

    Directory of Open Access Journals (Sweden)

    M. Montagna

    2012-12-01

    Full Text Available Thirty-four adult ticks collected from livestock on Socotra Island (Yemen were identified as Hyalomma marginatum using traditional morphological characteristics. Morphological identification was confirmed for all the collected specimens using a molecular approach targeting a fragment of the mitochondrial gene 12S rRNA. All the specimens were examined for the presence of tick-borne pathogens and the tick endosymbiont Candidatus Midichloria mitochondrii using polymerase chain reaction. Three specimens out of the 34 analyzed tested positive to the presence of Francisella spp. leading to the first detection of these bacteria in H. marginatum on Socotra Island. The phylogenetic analyses conducted on a 660 bp fragment of the ribosomal gene 16S rRNA of Francisella spp. (including F. philomiragia as outgroup, the four subspecies of F. tularensis and the Francisella-like endosymbiont of ticks confirm that the newly detected Francisella strains cluster into the Francisella-like endosymbionts of ticks. Interestingly, the detected Francisella-like endosymbiont, shows a different genotype to that previously isolated from H. marginatum collected in Bulgaria. No specimen was positive for the presence of Rickettsia spp., Coxiella burnetii, Borrelia burgdorferi or M. mitochondrii.

  3. Detection of Acidovorax valerianellae, the causing agent of bacterial leaf spots in corn salad [Valerianella locusta (L.) Laterr.], in corn salad seeds.

    Science.gov (United States)

    Thiele, K; Smalla, K; Kropf, S; Rabenstein, F

    2012-02-01

      The black leaf spot disease on corn salad caused by the bacterium Acidovorax valerianellae has been observed in Europe for several years and causes economic losses in corn salad cropping. Contaminated seeds or infested soil are considered as the major infection sources. The use of healthy seed material is the only way to prevent disease outbreaks. Therefore, a sensitive diagnostic method for seed testing should be developed.   Using a triple antibody sandwich ELISA with a high-specific monoclonal antibody, a quick and reliable detection method for contamination of seed lots with the pathogen was developed. This method allowed to detect contaminated seed lots as well as contamination with A. valerianellae in single seeds. Furthermore, the occurrence and distribution of the pathogen could be shown in symptomatic corn salad leaves and in naturally infested seeds by transmission electron microscopy and immunogold labelling for the first time.   Our results confirm the seed transmission of this corn salad disease. Pathogen load and distribution vary between positively tested seed lots.   With this method, not only routine testing of seed material to eliminate contaminated seed lots from production is possible but also the control of sanitation procedures to reduce contamination. © 2011 The Authors. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

  4. Optimization and evaluation of Flexicult(®) Vet for detection, identification and antimicrobial susceptibility testing of bacterial uropathogens in small animal veterinary practice

    DEFF Research Database (Denmark)

    Guardabassi, Luca; Hedberg, Sandra; Jessen, Lisbeth Rem

    2015-01-01

    -pathogens in veterinary practice. METHODS: Seventy-two urine samples from dogs and cats with suspected UTI presenting to seven veterinary facilities were used by clinical staff and an investigator to estimate sensitivity and specificity of Flexicult Vet A compared to laboratory reference standards for culture...... B (commercial name Flexicult(®) Vet) is a time- and cost-effective point-of-care test to guide antimicrobial choice and facilitate implementation of antimicrobial use guidelines for treatment of UTIs in small animals, provided that clinical staff is adequately trained to interpret the results...... and susceptibility testing. Subsequently, the test was modified by inclusion of an oxacillin-containing compartment for detection of methicillin-resistant staphylococci. The performance of the modified product (Flexicult Vet B) for susceptibility testing was evaluated in vitro using a collection of 110 clinical...

  5. Comparative evaluation of culture and PCR for the detection and determination of persistence of bacterial strains and DNAs in the Chinchilla laniger model of otitis media.

    Science.gov (United States)

    Aul, J J; Anderson, K W; Wadowsky, R M; Doyle, W J; Kingsley, L A; Post, J C; Ehrlich, G D

    1998-06-01

    This study was designed to determine the persistence of culturable bacteria versus DNA in the presence of a middle ear effusion in a chinchilla model of otitis media. Cohorts of animals were either infected with an ampicillin-resistant Haemophilus influenzae strain or injected with a tripartite inoculum consisting of freeze-thawed Streptococcus pneumoniae; pasteurized Moraxella catarrhalis; and DNA from H influenzae. The H influenzae-infected animals displayed culture positivity and polymerase chain reaction positivity through day 35. In the chinchillas infected with the low-copy number inocula of S pneumoniae, DNA was not detectable after day 1 from the co-inoculated pasteurized M catarrhalis bacteria or the purified H influenzae DNA; however, amplifiable DNA from the live low-copy number bacteria persisted through day 21 even though they were not culture-positive past day 3. These results demonstrate that DNA, and DNA from intact but nonviable bacteria, does not persist in an amplifiable form for more than a day in the presence of an effusion; however, live bacteria, while not culturable, persist in a viable state for weeks.

  6. Comparison of bacterial culture and real-time PCR for the detection of Salmonella in grow-finish pigs in Western Canada using a Bayesian approach.

    Science.gov (United States)

    Wilkins, W; Waldner, C; Rajić, A; McFall, M; Muckle, A; Mainar-Jaime, R C

    2010-11-01

    The study objective was to evaluate the accuracy of a real-time polymerase chain reaction (RT-PCR) and a culture protocol used to detect Salmonella in the faeces of grow-finish pigs using a Bayesian approach. The RT-PCR was invA-gene-based assay, while the culture protocol included pre-enrichment in buffered peptone water, selective enrichment in tetrathionate and Rappaport-Vassiliadis broths, and isolation on semi-solid (modified semi-solid RV) or solid (XLT4, Rambach) agar plates. Bayesian analysis was performed using a two-test, two-population model with dependence between culture and RT-PCR and compared to a second model with conditional independence between these two tests. Two hundred and ninety three individual faecal and 294 pooled pen samples from grow-finish pig collected from 10 farms were tested and results were divided into two groups according to herd size (five herds 400 sows). In the dependence model, RT-PCR sensitivity (Se) and specificity (Sp) were estimated to be 90% (95% probability interval 74, 97) and 99% (98, 99), respectively. Culture Se was 92% (75, 99), while culture Sp was considered 100% as all culture-positive samples were confirmed by serotyping. In the conditional independence model, RT-PCR Se and Sp, and culture Se, were 96% (93, 98), 99% (98, 100) and 97% (94, 100), respectively. The dependence model resulted in posterior estimates of Se that were lower and with broader probability intervals than the independence model, indicating that when RT-PCR and culture are evaluated relative to each other, the correlation between these tests is an important source of bias and should be adjusted for during analysis. The RT-PCR evaluated in this study performed almost comparably to culture; given the cost savings associated with using this test and more timely results, the RT-PCR may be a useful alternative to culture for screening large numbers of samples, particularly when Salmonella prevalence is low. © 2010 Blackwell Verlag GmbH.

  7. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach...... that imposes selection pressure for resistant bacteria. New approaches are urgently needed. Targeting bacterial virulence functions directly is an attractive alternative. An obvious target is bacterial adhesion. Bacterial adhesion to surfaces is the first step in colonization, invasion, and biofilm formation....... As such, adhesion represents the Achilles heel of crucial pathogenic functions. It follows that interference with adhesion can reduce bacterial virulence. Here, we illustrate this important topic with examples of techniques being developed that can inhibit bacterial adhesion. Some of these will become...

  8. Intracellular Biosynthesis of Fluorescent CdSe Quantum Dots in Bacillus subtilis: A Strategy to Construct Signaling Bacterial Probes for Visually Detecting Interaction Between Bacillus subtilis and Staphylococcus aureus.

    Science.gov (United States)

    Yan, Zheng-Yu; Ai, Xiao-Xia; Su, Yi-Long; Liu, Xin-Ying; Shan, Xiao-Hui; Wu, Sheng-Mei

    2016-02-01

    In this work, fluorescent Bacillus subtilis (B. subtilis) cells were developed as probes for imaging applications and to explore behaviorial interaction between B. subtilis and Staphylococcus aureus (S. aureus). A novel biological strategy of coupling intracellular biochemical reactions for controllable biosynthesis of CdSe quantum dots by living B. subtilis cells was demonstrated, through which highly luminant and photostable fluorescent B. subtilis cells were achieved with good uniformity. With the help of the obtained fluorescent B. subtilis cells probes, S. aureus cells responded to co-cultured B. subtilis and to aggregate. The degree of aggregation was calculated and nonlinearly fitted to a polynomial model. Systematic investigations of their interactions implied that B. subtilis cells inhibit the growth of neighboring S. aureus cells, and this inhibition was affected by both the growth stage and the amount of surrounding B. subtilis cells. Compared to traditional methods of studying bacterial interaction between two species, such as solid culture medium colony observation and imaging mass spectrometry detection, the procedures were more simple, vivid, and photostable due to the efficient fluorescence intralabeling with less influence on the cells' surface, which might provide a new paradigm for future visualization of microbial behavior.

  9. Higher atypical enteropathogenic Escherichia coli (a-EPEC) bacterial loads in children with diarrhea are associated with PCR detection of the EHEC factor for adherence 1/lymphocyte inhibitory factor A (efa1/lifa) gene.

    Science.gov (United States)

    Slinger, Robert; Lau, Kimberley; Slinger, Michael; Moldovan, Ioana; Chan, Francis

    2017-03-23

    Typical enteropathogenic Escherichia coli (t-EPEC) are known to cause diarrhea in children but it is uncertain whether atypical EPEC (a-EPEC) do, since a-EPEC lack the bundle-forming pilus (bfp) gene that encodes a key adherence factor in t-EPEC. In culture-based studies of a-EPEC, the presence of another adherence factor, called EHEC factor for adherence/lymphocyte activation inhibitor (efa1/lifA), was strongly associated with diarrhea. Since a-EPEC culture is not feasible in clinical laboratories, we designed an efa1/lifA quantitative PCR assay and examined whether the presence of efa1/lifA was associated with higher a-EPEC bacterial loads in pediatric diarrheal stool samples. Fecal samples from children with diarrhea were tested by qPCR for EPEC (presence of eae gene) and for shiga toxin genes to exclude enterohemorrhagic E. coli, which also contain the eae gene. EPEC containing samples were then tested for the bundle-forming pilus gene found in t-EPEC and efa1/lifA. The eae gene quantity in efa1/lifA-positive and negative samples was compared. Thirty-nine of 320 (12%) fecal samples tested positive for EPEC and 38/39 (97%) contained a-EPEC. The efa1/lifA gene was detected in 16/38 (42%) a-EPEC samples. The median eae concentration for efa1/lifA positive samples was significantly higher than for efa1/lifA negative samples (median 16,745 vs. 1183 copies/µL, respectively, p = 0.006). Atypical enteropathogenic E. coli-positive diarrheal stool samples containing the efa1/lifA gene had significantly higher bacterial loads than samples lacking this gene. This supports the idea that efa1/lifA contributes to diarrheal pathogenesis and suggests that, in EPEC-positive samples, efa/lifA may be a useful additional molecular biomarker.

  10. Oral bacterial DNA findings in pericardial fluid

    Directory of Open Access Journals (Sweden)

    Anne-Mari Louhelainen

    2014-11-01

    Full Text Available Background: We recently reported that large amounts of oral bacterial DNA can be found in thrombus aspirates of myocardial infarction patients. Some case reports describe bacterial findings in pericardial fluid, mostly done with conventional culturing and a few with PCR; in purulent pericarditis, nevertheless, bacterial PCR has not been used as a diagnostic method before. Objective: To find out whether bacterial DNA can be measured in the pericardial fluid and if it correlates with pathologic–anatomic findings linked to cardiovascular diseases. Methods: Twenty-two pericardial aspirates were collected aseptically prior to forensic autopsy at Tampere University Hospital during 2009–2010. Of the autopsies, 10 (45.5% were free of coronary artery disease (CAD, 7 (31.8% had mild and 5 (22.7% had severe CAD. Bacterial DNA amounts were determined using real-time quantitative PCR with specific primers and probes for all bacterial strains associated with endodontic disease (Streptococcus mitis group, Streptococcus anginosus group, Staphylococcus aureus/Staphylococcus epidermidis, Prevotella intermedia, Parvimonas micra and periodontal disease (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Treponema denticola, Fusobacterium nucleatus, and Dialister pneumosintes. Results: Of 22 cases, 14 (63.6% were positive for endodontic and 8 (36.4% for periodontal-disease-associated bacteria. Only one case was positive for bacterial culturing. There was a statistically significant association between the relative amount of bacterial DNA in the pericardial fluid and the severity of CAD (p=0.035. Conclusions: Oral bacterial DNA was detectable in pericardial fluid and an association between the severity of CAD and the total amount of bacterial DNA in pericardial fluid was found, suggesting that this kind of measurement might be useful for clinical purposes.

  11. Detecting bacterial spores in soup manufacturing

    NARCIS (Netherlands)

    van Zuijlen, A.C.M.; Oomes, S.J.C.M.; Vos, P.; Brul, S.

    2009-01-01

    Spores from mesophilic aerobic sporeforming bacteria (Bacillus) are sometimes able to survive the thermal process of commercial sterile products and sporadically cause spoilage or food poisoning. Because of an increasing demand for more fresh products, ideally the processing temperatures should be

  12. Studying bacterial multispecies biofilms

    DEFF Research Database (Denmark)

    Røder, Henriette Lyng; Sørensen, Søren Johannes; Burmølle, Mette

    2016-01-01

    , but the identity and significance of interspecies bacterial interactions is neglected in these analyses. There is therefore an urgent need for bridging the gap between metagenomic analysis and in vitro models suitable for studies of bacterial interactions.Bacterial interactions and coadaptation are important......The high prevalence and significance of multispecies biofilms have now been demonstrated in various bacterial habitats with medical, industrial, and ecological relevance. It is highly evident that several species of bacteria coexist and interact in biofilms, which highlights the need for evaluating...

  13. Estimativa da incerteza em ensaio de detecção de endotoxina bacteriana pelo método de gelificação Estimation of uncertainty in the detection of bacterial endotoxin by gel-clot method

    Directory of Open Access Journals (Sweden)

    Felipe Rebello Lourenço

    2005-12-01

    Full Text Available Desde a publicação da ISO 17025:1999, o interesse em métodos para estimativa da incerteza em ensaios qualitativos, do tipo "passa/não passa", têm ganho grande importância. Uma forma de estimar e informar a incerteza deste tipo de ensaio é o uso das probabilidades de respostas-falsas, particularmente falsos-positivos e falsos-negativos, determinados a partir do teorema de Bayes. O objetivo deste artigo é estabelecer um método para a estimativa de incerteza em ensaios de detecção de endotoxina bacteriana pelo método in vitro Limulus Amebocyte Lysate (LAL. Considerando a confirmação da sensibilidade do LAL e a validação do teste, a probabilidade de uma resposta falsa corresponde à soma da probabilidade dos resultados falso-negativos e falso-positivos. A partir dos resultados obtidos foi verificado que a etapa da confirmação da sensibilidade do LAL contribui para a incerteza de forma mais significativa (67,6% que a etapa de validação do teste (32,4%. Através de um procedimento simples, descrito neste artigo, e de dados obtidos a partir da confirmação da sensibilidade do LAL e validação do teste para um produto em questão é possível obter uma estimativa de incerteza razoável para o ensaio de detecção de endotoxinas bacterianas pelo método de gelificação.Since the publication of ISO 17025:1999, the interest in methods for estimation of the uncertainty in qualitative analysis, such as 'pass/fail', have became more important. The usual form of estimating and informing the uncertainty in this kind of analysis is the use of false-response rates, particularly false-positive and false-negative, determinated from Bayes theorem. The aim of this paper is establish a method for estimation of the uncertainty in the detection of bacterial endotoxins by in vitro Limulus Amebocyte Lysate (LAL test. Considering the confirmation of LAL sensitivity and the validation of the test, the probability of a false-response corresponds to the

  14. Detecção da resistência a antibióticos de bactérias isoladas de casos clínicos ocorridos em animais de companhia Detection of antibiotic resistance in clinical bacterial strains from pets

    Directory of Open Access Journals (Sweden)

    P. Poeta

    2008-04-01

    Full Text Available The identification of different bacterial strains and the occurrence of antibiotic resistance were investigated in several infection processes of pets as skin abscess with purulent discharge, bronco alveolar fluid, earwax, urine, mammary, and eye fluid. Streptococcus spp. and Staphylococcus spp. were the most detected in the different samples. A high frequency of antimicrobial resistance has been observed and this could reflect the wide use of antimicrobials in pets, making the effectiveness of antibiotic treatment to become more complicated.

  15. Dialkylresorcinols as bacterial signaling molecules.

    Science.gov (United States)

    Brameyer, Sophie; Kresovic, Darko; Bode, Helge B; Heermann, Ralf

    2015-01-13

    It is well recognized that bacteria communicate via small diffusible molecules, a process termed quorum sensing. The best understood quorum sensing systems are those that use acylated homoserine lactones (AHLs) for communication. The prototype of those systems consists of a LuxI-like AHL synthase and a cognate LuxR receptor that detects the signal. However, many proteobacteria possess LuxR receptors, yet lack any LuxI-type synthase, and thus these receptors are referred to as LuxR orphans or solos. In addition to the well-known AHLs, little is known about the signaling molecules that are sensed by LuxR solos. Here, we describe a novel cell-cell communication system in the insect and human pathogen Photorhabdus asymbiotica. We identified the LuxR homolog PauR to sense dialkylresorcinols (DARs) and cyclohexanediones (CHDs) instead of AHLs as signals. The DarABC synthesis pathway produces the molecules, and the entire system emerged as important for virulence. Moreover, we have analyzed more than 90 different Photorhabdus strains by HPLC/MS and showed that these DARs and CHDs are specific to the human pathogen P. asymbiotica. On the basis of genomic evidence, 116 other bacterial species are putative DAR producers, among them many human pathogens. Therefore, we discuss the possibility of DARs as novel and widespread bacterial signaling molecules and show that bacterial cell-cell communication goes far beyond AHL signaling in nature.

  16. [Spontaneous bacterial peritonitis].

    Science.gov (United States)

    Strauss, Edna; Caly, Wanda Regina

    2003-01-01

    Spontaneous bacterial peritonitis occurs in 30% of patients with ascites due to cirrhosis leading to high morbidity and mortality rates. The pathogenesis of spontaneous bacterial peritonitis is related to altered host defenses observed in end-stage liver disease, overgrowth of microorganisms, and bacterial translocation from the intestinal lumen to mesenteric lymph nodes. Clinical manifestations vary from severe to slight or absent, demanding analysis of the ascitic fluid. The diagnosis is confirmed by a number of neutrophils over 250/mm3 associated or not to bacterial growth in culture of an ascites sample. Enterobacteriae prevail and Escherichia coli has been the most frequent bacterium reported. Mortality rates decreased markedly in the last two decades due to early diagnosis and prompt antibiotic treatment. Third generation intravenous cephalosporins are effective in 70% to 95% of the cases. Recurrence of spontaneous bacterial peritonitis is common and can be prevented by the continuous use of oral norfloxacin. The development of bacterial resistance demands the search for new options in the prophylaxis of spontaneous bacterial peritonitis; probiotics are a promising new approach, but deserve further evaluation. Short-term antibiotic prophylaxis is recommended for patients with cirrhosis and ascites shortly after an acute episode of gastrointestinal bleeding.

  17. FIRST DETECTION OF THERMAL RADIOJETS IN A SAMPLE OF PROTO-BROWN DWARF CANDIDATES

    Energy Technology Data Exchange (ETDEWEB)

    Morata, Oscar [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 106, Taiwan (China); Palau, Aina; González, Ricardo F. [Centro de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, P.O. Box 3-72, 58090 Morelia, Michoacán, México (Mexico); Gregorio-Monsalvo, Itziar de [Joint ALMA Observatory (JAO), Alonso de Córdova 3107, Vitacura, Santiago (Chile); Ribas, Álvaro [European Space Astronomy Centre (ESA), P.O. Box 78, E-28691 Villanueva de la Cañada, Madrid (Spain); Perger, Manuel [Institut de Ciències de l’Espai (CSIC-IEEC), Campus UAB—Facultat de Ciències, Torre C5—parell 2, E-08193 Bellaterra, Catalunya (Spain); Bouy, Hervé; Barrado, David; Huélamo, Nuria; Morales-Calderón, María [Centro de Astrobiología, INTA-CSIC, Dpto.Astrofísica, ESAC Campus, P.O. Box 78, E-28691 Villanueva de la Cañada, Madrid (Spain); Eiroa, Carlos [Departamento de Física Teórica, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, E-28049 Madrid (Spain); Bayo, Amelia, E-mail: omorata@asiaa.sinica.edu.tw [Max Planck Institut für Astronomie, Königstuhl 17, D-69117, Heidelberg (Germany); and others

    2015-07-01

    We observed with the Jansky Very Large Array at 3.6 and 1.3 cm a sample of 11 proto-brown dwarf (BD) candidates in Taurus in a search for thermal radio jets driven by the most embedded BDs. We detected for the first time four thermal radio jets in proto-BD candidates. We compiled data from UKIDSS, 2MASS, Spitzer, WISE, and Herschel to build the spectral energy distribution (SED) of the objects in our sample, which are similar to typical Class I SEDs of young stellar objects (YSOs). The four proto-BD candidates driving thermal radio jets also roughly follow the well-known trend of centimeter luminosity against bolometric luminosity determined for YSOs, assuming they belong to Taurus, although they present some excess of radio emission compared to the known relation for YSOs. Nonetheless, we are able to reproduce the flux densities of the radio jets modeling the centimeter emission of the thermal radio jets using the same type of models applied to YSOs, but with corresponding smaller stellar wind velocities and mass-loss rates, and exploring different possible geometries of the wind or outflow from the star. Moreover, we also find that the modeled mass outflow rates for the bolometric luminosities of our objects agree reasonably well with the trends found between the mass outflow rates and bolometric luminosities of YSOs, which indicates that, despite the “excess” centimeter emission, the intrinsic properties of proto-BDs are consistent with a continuation of those of very low-mass stars to a lower mass range. Overall, our study favors the formation of BDs as a scaled-down version of low-mass stars.

  18. Hexadecane degradation by bacterial strains isolated from ...

    African Journals Online (AJOL)

    A study was undertaken to detect and monitor the degradation of hexadecane by three potential degrading bacteria (Pseudomonas putida, Rhodococcus erythroplolis and Bacillus thermoleovorans) isolated from contaminated soils in Riyadh, Saudi Arabia. The extraction of the bacterial populations from these polluted soils ...

  19. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

    2011-01-01

    defense. Antibiotics exhibit a rather limited effect on biofilms. Furthermore, antibiotics have an ‘inherent obsolescence’ because they select for development of resistance. Bacterial infections with origin in bacterial biofilms have become a serious threat in developed countries. Pseudomonas aeruginosa...... that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation......, resistance and QS inhibition as future antimicrobial targets, in particular those that would work to minimize selection pressures for the development of resistant bacteria....

  20. Bacterial surface adaptation

    Science.gov (United States)

    Utada, Andrew

    2014-03-01

    Biofilms are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. Parasitic bacterial biofilms can cause lethal infections and biofouling, but commensal bacterial biofilms, such as those found in the gut, can break down otherwise indigestible plant polysaccharides and allow us to enjoy vegetables. The first step in biofilm formation, adaptation to life on a surface, requires a working knowledge of low Reynolds number fluid physics, and the coordination of biochemical signaling, polysaccharide production, and molecular motility motors. These crucial early stages of biofilm formation are at present poorly understood. By adapting methods from soft matter physics, we dissect bacterial social behavior at the single cell level for several prototypical bacterial species, including Pseudomonas aeruginosa and Vibrio cholerae.

  1. Bacterial Meningitis in Infants

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-04-01

    Full Text Available A retrospective study of 80 infantile patients (ages 30-365 days; 47 male, 33 female with culture-proven bacterial meningitis seen over a 16 year period (1986-2001 is reported from Taiwan.

  2. Factitious Bacterial Meningitis Revisited

    Science.gov (United States)

    Peterson, E.; Thrupp, L.; Uchiyama, N.; Hawkins, B.; Wolvin, B.; Greene, G.

    1982-01-01

    Nonviable gram-negative bacilli were seen in smears of cerebrospinal fluid from eight infants in whom bacterial meningitis was ruled out. Tubes from commercial kits were the source of the factitious organisms. PMID:7153328

  3. Vimentin in Bacterial Infections

    DEFF Research Database (Denmark)

    Mak, Tim N; Brüggemann, Holger

    2016-01-01

    filaments (IFs). IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge...... about the role of IFs in bacterial infections, focusing on the type III IF protein vimentin. Recent studies have revealed the involvement of vimentin in host cell defenses, acting as ligand for several pattern recognition receptors of the innate immune system. Two main aspects of bacteria......-vimentin interactions are presented in this review: the role of vimentin in pathogen-binding on the cell surface and subsequent bacterial invasion and the interaction of cytosolic vimentin and intracellular pathogens with regards to innate immune signaling. Mechanistic insight is presented involving distinct bacterial...

  4. Labeled Antimicrobial Peptides for Detection of Microorganisms

    Science.gov (United States)

    2008-12-01

    environmental samples for presence of bacterial pollution, detection of bioagents, and food safety for the presence of spoilage and pathogenic organisms... bacterial cel1s/ml in food matrices (DeMarco and Lim, 2001; Demarco and Lim, 2002; Geng et aI., 2006). To address antibody limitations, AMPs were...detection of 103 to 104 bacterial cells/mI. Antimicrobial peptides naturally bind to the lipopolysaccharide component of bacterial cell walls as part of

  5. Volatiles in Inter-Specific Bacterial Interactions.

    Science.gov (United States)

    Tyc, Olaf; Zweers, Hans; de Boer, Wietse; Garbeva, Paolina

    2015-01-01

    The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well-described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium, and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal, and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide) were tested for their effect on three target bacteria. Here, we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.

  6. Volatiles in inter-specific bacterial interactions

    Directory of Open Access Journals (Sweden)

    Olaf eTyc

    2015-12-01

    Full Text Available The importance of volatile organic compounds for functioning of microbes is receiving increased research attention. However, to date very little is known on how inter-specific bacterial interactions effect volatiles production as most studies have been focused on volatiles produced by monocultures of well described bacterial genera. In this study we aimed to understand how inter-specific bacterial interactions affect the composition, production and activity of volatiles. Four phylogenetically different bacterial species namely: Chryseobacterium, Dyella, Janthinobacterium and Tsukamurella were selected. Earlier results had shown that pairwise combinations of these bacteria induced antimicrobial activity in agar media whereas this was not the case for monocultures. In the current study, we examined if these observations were also reflected by the production of antimicrobial volatiles. Thus, the identity and antimicrobial activity of volatiles produced by the bacteria were determined in monoculture as well in pairwise combinations. Antimicrobial activity of the volatiles was assessed against fungal, oomycetal and bacterial model organisms. Our results revealed that inter-specific bacterial interactions affected volatiles blend composition. Fungi and oomycetes showed high sensitivity to bacterial volatiles whereas the effect of volatiles on bacteria varied between no effects, growth inhibition to growth promotion depending on the volatile blend composition. In total 35 volatile compounds were detected most of which were sulfur-containing compounds. Two commonly produced sulfur-containing volatile compounds (dimethyl disulfide and dimethyl trisulfide were tested for their effect on three target bacteria. Here we display the importance of inter-specific interactions on bacterial volatiles production and their antimicrobial activities.

  7. New Application of Hyperspectral Imaging for Bacterial Cell Classification

    Science.gov (United States)

    Hyperspectral microscopy has shown potential as a method for rapid detection of foodborne pathogenic bacteria with spectral characteristics from bacterial cells. Hyperspectral microscope images (HMIs) are collected from broiler chicken isolates of Salmonella serotypes Enteritidis, Typhimurium, Infa...

  8. [Diagnosis of bacterial vaginosis].

    Science.gov (United States)

    Djukić, Slobodanka; Ćirković, Ivana; Arsić, Biljana; Garalejić, Eliana

    2013-01-01

    Bacterial vaginosis is a common, complex clinical syndrome characterized by alterations in the normal vaginal flora. When symptomatic, it is associated with a malodorous vaginal discharge and on occasion vaginal burning or itching. Under normal conditions, lactobacilli constitute 95% of the bacteria in the vagina. Bacterial vaginosis is associated with severe reduction or absence of the normal H2O2-producing lactobacilli and overgrowth of anaerobic bacteria and Gardnerella vaginalis, Atopobium vaginae, Mycoplasma hominis and Mobiluncus species. Most types of infectious disease are diagnosed by culture, by isolating an antigen or RNA/DNA from the microbe, or by serodiagnosis to determine the presence of antibodies to the microbe. Therefore, demonstration of the presence of an infectious agent is often a necessary criterion for the diagnosis of the disease. This is not the case for bacterial vaginosis, since the ultimate cause of the disease is not yet known. There are a variety of methods for the diagnosis of bacterial vaginosis but no method can at present be regarded as the best. Diagnosing bacterial vaginosis has long been based on the clinical criteria of Amsel, whereby three of four defined criteria must be satisfied. Nugent's scoring system has been further developed and includes validation of the categories of observable bacteria structures. Up-to-date molecular tests are introduced, and better understanding of vaginal microbiome, a clear definition for bacterial vaginosis, and short-term and long-term fluctuations in vaginal microflora will help to better define molecular tests within the broader clinical context.

  9. Kynetic resazurin assay (KRA) for bacterial quantification of foodborne pathogens

    Science.gov (United States)

    Arenas, Yaxal; Mandel, Arkady; Lilge, Lothar

    2012-03-01

    Fast detection of bacterial concentrations is important for the food industry and for healthcare. Early detection of infections and appropriate treatment is essential since, the delay of treatments for bacterial infections tends to be associated with higher mortality rates. In the food industry and in healthcare, standard procedures require the count of colony-forming units in order to quantify bacterial concentrations, however, this method is time consuming and reports require three days to be completed. An alternative is metabolic-colorimetric assays which provide time efficient in vitro bacterial concentrations. A colorimetric assay based on Resazurin was developed as a time kinetic assay (KRA) suitable for bacterial concentration measurements. An optimization was performed by finding excitation and emission wavelengths for fluorescent acquisition. A comparison of two non-related bacteria, foodborne pathogens Escherichia coli and Listeria monocytogenes, was performed in 96 well plates. A metabolic and clonogenic dependence was established for fluorescent kinetic signals.

  10. Bacterial Aggregates Establish at the Edges of Acute Epidermal Wounds

    DEFF Research Database (Denmark)

    Bay, Lene; Kragh, Kasper N.; Eickhardt, Steffen R.

    2018-01-01

    Objective: The bacterial composition and distribution were evaluated in acute standardized epidermal wounds and uninjured skin by a molecular in situ technology benchmarked to conventional culturing. This was done to reveal whether bacterial biofilm is present in acute wounds. Approach...... microscopy (CLSM). Results: No bacterial aggregates were detected at day 0. At day 4, coagulase-negative staphylococci (CoNS) were the sole bacteria identified by CLSM/PNA-FISH and culturing. CoNS was isolated from 78% of the wound swabs and 48% of the skin swabs. Bacterial aggregates (5–150 μm) were...... detected by PNA-FISH/CLSM in the split stratum corneum and fibrin deposits at the wound edges and in the stratum corneum and the hair follicles of the adjacent skin. The bacterial aggregates were more common (p = 0.0084) and larger (p = 0.0083) at wound edges than in the adjacent skin. Innovation...

  11. Bacterial Cell Mechanics.

    Science.gov (United States)

    Auer, George K; Weibel, Douglas B

    2017-07-25

    Cellular mechanical properties play an integral role in bacterial survival and adaptation. Historically, the bacterial cell wall and, in particular, the layer of polymeric material called the peptidoglycan were the elements to which cell mechanics could be primarily attributed. Disrupting the biochemical machinery that assembles the peptidoglycan (e.g., using the β-lactam family of antibiotics) alters the structure of this material, leads to mechanical defects, and results in cell lysis. Decades after the discovery of peptidoglycan-synthesizing enzymes, the mechanisms that underlie their positioning and regulation are still not entirely understood. In addition, recent evidence suggests a diverse group of other biochemical elements influence bacterial cell mechanics, may be regulated by new cellular mechanisms, and may be triggered in different environmental contexts to enable cell adaptation and survival. This review summarizes the contributions that different biomolecular components of the cell wall (e.g., lipopolysaccharides, wall and lipoteichoic acids, lipid bilayers, peptidoglycan, and proteins) make to Gram-negative and Gram-positive bacterial cell mechanics. We discuss the contribution of individual proteins and macromolecular complexes in cell mechanics and the tools that make it possible to quantitatively decipher the biochemical machinery that contributes to bacterial cell mechanics. Advances in this area may provide insight into new biology and influence the development of antibacterial chemotherapies.

  12. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    The aim of the study was to investigate the bacterial profile of chronic venous leg ulcers and the importance of the profile to ulcer development. Patients with persisting venous leg ulcers were included and followed for 8 weeks. Every second week, ulcer samples were collected and the bacterial...... of P. aeruginosa in venous leg ulcers can induce ulcer enlargement and/or cause delayed healing....... species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  13. Rapid on-site detection of ephedrine and its analogues used as adulterants in slimming dietary supplements by TLC-SERS.

    Science.gov (United States)

    Lv, Diya; Cao, Yan; Lou, Ziyang; Li, Shujin; Chen, Xiaofei; Chai, Yifeng; Lu, Feng

    2015-02-01

    Ephedrine and its analogues are in the list of prohibited substance in adulteration to botanical dietary supplements (BDS) for their uncontrollable stimulating side effects. However, they were always adulterated illegally in BDS to promote losing weight. In order to avoid detection, various kinds of ephedrine analogues were added rather than ephedrine itself. This has brought about great difficulties in authentication of BDS. In this study, we put forward for the first time a method which combined thin-layer chromatography (TLC) and surface-enhanced Raman scattering (SERS) to directly identify trace adulterant. Ephedrine, pseudoephedrine, methylephedrine, and norephedrine were mixed and used in this method to develop an analytical model. As a result, the four analogues were separated efficiently in TLC analysis, and trace-components and low-background SERS detection was realized. The limit of detection (LOD) of the four analogues was 0.01 mg/mL. Eight common Raman peaks (△υ = 620, 1003, 1030, 1159, 1181, 1205, 1454, 1603 cm(-1)) were extracted experimentally and statistically to characterize the common feature of ephedrine analogues. A TLC-SERS method coupled with common-peak model was adopted to examine nine practical samples, two of which were found to be adulterated with ephedrine analogues. Identification results were then confirmed by UPLC-QTOF/MS analysis. The proposed method was simple, rapid, and accurate and can also be employed to trace adulterant identification even when there are no available reference derivatives on-site or unknown types of ephedrine analogues are adulterated.

  14. Bacterial meningitis in children

    International Nuclear Information System (INIS)

    Marji, S.

    2007-01-01

    To demonstrate the epidemiology, clinical manifestations and bacteriological profile of bacterial meningitis in children beyond the neonatal period in our hospital. This was a retrospective descriptive study conducted at Prince Rashid Hospital in Irbid, Jordan. The medical records of 50 children with the diagnosis of bacterial meningitis during 4 years period, were reviewed. The main cause of infection was streptococcus pneumoniae, followed by Haemophilus influenza and Niesseria meningitides. Mortality was higher in infants and meningococcal infection, while complications were more encountered in cases of streptococcus pneumoniae. Cerebrospinal fluid culture was positive in 11 cases and Latex agglutination test in 39. There is a significant reduction of the numbers of bacterial meningitis caused by Haemophilus influenza type B species. (author)

  15. Interfering with bacterial gossip

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Tolker-Nielsen, Tim; Givskov, Michael

    2011-01-01

    Biofilm resilience poses major challenges to the development of novel antimicrobial agents. Biofilm bacteria can be considered small groups of “Special Forces” capable of infiltrating the host and destroying important components of the cellular defense system with the aim of crippling the host...... defense. Antibiotics exhibit a rather limited effect on biofilms. Furthermore, antibiotics have an ‘inherent obsolescence’ because they select for development of resistance. Bacterial infections with origin in bacterial biofilms have become a serious threat in developed countries. Pseudomonas aeruginosa...... that appropriately target bacteria in their relevant habitat with the aim of mitigating their destructive impact on patients. In this review we describe molecular mechanisms involved in “bacterial gossip” (more scientifically referred to as quorum sensing (QS) and c-di-GMP signaling), virulence, biofilm formation...

  16. Diagnosis of bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Đukić Slobodanka

    2013-01-01

    Full Text Available Bacterial vaginosis is a common, complex clinical syndrome characterized by alterations in the normal vaginal flora. When symptomatic, it is associated with a malodorous vaginal discharge and on occasion vaginal burning or itching. Under normal conditions, lactobacilli constitute 95% of the bacteria in the vagina. Bacterial vaginosis is associated with severe reduction or absence of the normal H2O2­producing lactobacilli and overgrowth of anaerobic bacteria and Gardnerella vaginalis, Atopobium vaginae, Mycoplasma hominis and Mobiluncus species. Most types of infectious disease are diagnosed by culture, by isolating an antigen or RNA/DNA from the microbe, or by serodiagnosis to determine the presence of antibodies to the microbe. Therefore, demonstration of the presence of an infectious agent is often a necessary criterion for the diagnosis of the disease. This is not the case for bacterial vaginosis, since the ultimate cause of the disease is not yet known. There are a variety of methods for the diagnosis of bacterial vaginosis but no method can at present be regarded as the best. Diagnosing bacterial vaginosis has long been based on the clinical criteria of Amsel, whereby three of four defined criteria must be satisfied. Nugent’s scoring system has been further developed and includes validation of the categories of observable bacteria structures. Up­to­date molecular tests are introduced, and better understanding of vaginal microbiome, a clear definition for bacterial vaginosis, and short­term and long­term fluctuations in vaginal microflora will help to better define molecular tests within the broader clinical context.

  17. Adult bacterial meningitis

    DEFF Research Database (Denmark)

    Meyer, C N; Samuelsson, I S; Galle, M

    2004-01-01

    Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin susceptibi......Episodes of adult bacterial meningitis (ABM) at a Danish hospital in 1991-2000 were identified from the databases of the Department of Clinical Microbiology, and compared with data from the Danish National Patient Register and the Danish National Notification System. Reduced penicillin...

  18. Bacterial blight of cotton

    Directory of Open Access Journals (Sweden)

    Aïda JALLOUL

    2015-04-01

    Full Text Available Bacterial blight of cotton (Gossypium ssp., caused by Xanthomonas citri pathovar malvacearum, is a severe disease occurring in all cotton-growing areas. The interactions between host plants and the bacteria are based on the gene-for-gene concept, representing a complex resistance gene/avr gene system. In light of the recent data, this review focuses on the understanding of these interactions with emphasis on (1 the genetic basis for plant resistance and bacterial virulence, (2 physiological mechanisms involved in the hypersensitive response to the pathogen, including hormonal signaling, the oxylipin pathway, synthesis of antimicrobial molecules and alteration of host cell structures, and (3 control of the disease.

  19. Bacterial meningitis in infants.

    Science.gov (United States)

    Ku, Lawrence C; Boggess, Kim A; Cohen-Wolkowiez, Michael

    2015-03-01

    Neonatal bacterial meningitis is uncommon but devastating. Morbidity among survivors remains high. The types and distribution of pathogens are related to gestational age, postnatal age, and geographic region. Confirming the diagnosis is difficult. Clinical signs are often subtle, lumbar punctures are frequently deferred, and cerebrospinal fluid (CSF) cultures can be compromised by prior antibiotic exposure. Infants with bacterial meningitis can have negative blood cultures and normal CSF parameters. Promising tests such as the polymerase chain reaction require further study. Prompt treatment with antibiotics is essential. Clinical trials investigating a vaccine for preventing neonatal Group B Streptococcus infections are ongoing. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Bacterial meningitis and neurological complications in adults

    Directory of Open Access Journals (Sweden)

    Parunyou Julayanont

    2016-04-01

    Full Text Available Bacterial meningitis is a leading cause of death from infectious disease worldwide. The neurological complications secondary to bacterial meningitis contribute to the high mortality rate and to disability among the survivors. Cerebrovascular complications, including infarction and hemorrhage, are common. Inflammation and increased pressure in the subarachnoid space result in cranial neuropathy. Seizures occur in either the acute or delayed phase after the infection and require early detection and treatment. Spreading of infection to other intracranial structures, including the subdural space, brain parenchyma, and ventricles, increases morbidity and mortality in survivors. Infection can also spread to the spinal canal causing spinal cord abscess, epidural abscess, polyradiculitis, and spinal cord infarction secondary to vasculitis of the spinal artery. Hypothalamic-pituitary dysfunction is also an uncommon complication after bacterial meningitis. Damage to cerebral structures contributes to cognitive and neuropsychiatric problems.  Being aware of these complications leads to early detection and treatment and improves mortality and outcomes in patients with bacterial meningitis.

  1. Bacterial biofilms and antibiotic resistance

    Directory of Open Access Journals (Sweden)

    Liliana Caldas-Arias

    2015-04-01

    Full Text Available Biofilms give to bacteria micro-environmental benefits; confers protection against antimicrobials. Bacteria have antibiotic resistance by conventional and unusual mechanisms leading to delayed wound healing, to increase recurrent chronic infections and nosocomial contamination of medical devices. Objective: This narrative review aims to introduce the characteristics of Bacteria-biofilms, antimicrobial resistance mechanisms and potential alternatives for prevention and control of its formation. Methods: Search strategy was performed on records: PubMed / Medline, Lilacs, Redalyc; with suppliers such as EBSCO and thesaurus MeSH and DeCS. Conclusions: Knowledge and research performance of biofilm bacteria are relevant in the search of technology for detection and measuring sensitivity to antibiotics. The identification of Bacterial-biofilms needs no-traditional microbiological diagnosis.

  2. The Bacterial Growth Curve.

    Science.gov (United States)

    Paulton, Richard J. L.

    1991-01-01

    A procedure that allows students to view an entire bacterial growth curve during a two- to three-hour student laboratory period is described. Observations of the lag phase, logarithmic phase, maximum stationary phase, and phase of decline are possible. A nonpathogenic, marine bacterium is used in the investigation. (KR)

  3. Bacterial fingerprints across Europe

    NARCIS (Netherlands)

    Glasner, Corinna

    2014-01-01

    Bacterial pathogens, such as Staphylococcus aureus and carbapenemase-producing Enterobacteriaceae (CPE), impose major threats to human health worldwide. Both have a ‘Jekyll & Hyde’ character, since they can be present as human commensals, but can also become harmful invasive pathogens especially

  4. [Bacterial biofilms and infection].

    Science.gov (United States)

    Lasa, I; Del Pozo, J L; Penadés, J R; Leiva, J

    2005-01-01

    In developed countries we tend to think of heart disease and the numerous forms of cancer as the main causes of mortality, but on a global scale infectious diseases come close, or may even be ahead: 14.9 million deaths in 2002 compared to cardiovascular diseases (16.9 million deaths) and cancer (7.1 million deaths) (WHO report 2004). The infectious agents responsible for human mortality have evolved as medical techniques and hygienic measures have changed. Modern-day acute infectious diseases caused by specialized bacterial pathogens such as diphtheria, tetanus, cholera, plague, which represented the main causes of death at the beginning of XX century, have been effectively controlled with antibiotics and vaccines. In their place, more than half of the infectious diseases that affect mildly immunocompromised patients involve bacterial species that are commensal with the human body; these can produce chronic infections, are resistant to antimicrobial agents and there is no effective vaccine against them. Examples of these infections are the otitis media, native valve endocarditis, chronic urinary infections, bacterial prostatitis, osteomyelitis and all the infections related to medical devices. Direct analysis of the surface of medical devices or of tissues that have been foci of chronic infections shows the presence of large numbers of bacteria surrounded by an exopolysaccharide matrix, which has been named the "biofilm". Inside the biofilm, bacteria grow protected from the action of the antibodies, phagocytic cells and antimicrobial treatments. In this article, we describe the role of bacterial biofilms in human persistent infections.

  5. EDITORIAL SPONTANEOUS BACTERIAL PERITONITIS ...

    African Journals Online (AJOL)

    hi-tech

    Spontaneous bacterial peritonitis (SBP) frequent]y occurs in patients with liver cirrhosis and ascites. It is defined as an infection of previously sterile ascitic fluid without any demonstrable intrabdominal source of infection. It is now internationally agreed that a polymorphonuclear (PMN) cell count in the ascitic fluid of over 250 ...

  6. Bacterial membrane proteomics.

    Science.gov (United States)

    Poetsch, Ansgar; Wolters, Dirk

    2008-10-01

    About one quarter to one third of all bacterial genes encode proteins of the inner or outer bacterial membrane. These proteins perform essential physiological functions, such as the import or export of metabolites, the homeostasis of metal ions, the extrusion of toxic substances or antibiotics, and the generation or conversion of energy. The last years have witnessed completion of a plethora of whole-genome sequences of bacteria important for biotechnology or medicine, which is the foundation for proteome and other functional genome analyses. In this review, we discuss the challenges in membrane proteome analysis, starting from sample preparation and leading to MS-data analysis and quantification. The current state of available proteomics technologies as well as their advantages and disadvantages will be described with a focus on shotgun proteomics. Then, we will briefly introduce the most abundant proteins and protein families present in bacterial membranes before bacterial membrane proteomics studies of the last years will be presented. It will be shown how these works enlarged our knowledge about the physiological adaptations that take place in bacteria during fine chemical production, bioremediation, protein overexpression, and during infections. Furthermore, several examples from literature demonstrate the suitability of membrane proteomics for the identification of antigens and different pathogenic strains, as well as the elucidation of membrane protein structure and function.

  7. Seizures Complicating Bacterial Meningitis

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-09-01

    Full Text Available The clinical data of 116 patients, 1 month to <5 years of age, admitted for bacterial meningitis, and grouped according to those with and without seizures during hospitalization, were compared in a study at Buddhist Dalin Tzu Chi General Hospital, Chang Gung Memorial Hospital and other centers in Taiwan.

  8. Bacterial Meningitis Outcome

    OpenAIRE

    J Gordon Millichap

    1995-01-01

    The neurologic, psychological, and educational outcomes of bacterial meningitis in 130 children evaluated at a mean age of 8 years, and 6 years after their meningitis, are reported from the Department of Paediatrics and Clinical Epidemiology and Biostatistics Unit, University of Melbourne, and the Royal Children’s Hospital, Victoria, Australia.

  9. Metabolic signatures of bacterial vaginosis.

    Science.gov (United States)

    Srinivasan, Sujatha; Morgan, Martin T; Fiedler, Tina L; Djukovic, Danijel; Hoffman, Noah G; Raftery, Daniel; Marrazzo, Jeanne M; Fredricks, David N

    2015-04-14

    Bacterial vaginosis (BV) is characterized by shifts in the vaginal microbiota from Lactobacillus dominant to a microbiota with diverse anaerobic bacteria. Few studies have linked specific metabolites with bacteria found in the human vagina. Here, we report dramatic differences in metabolite compositions and concentrations associated with BV using a global metabolomics approach. We further validated important metabolites using samples from a second cohort of women and a different platform to measure metabolites. In the primary study, we compared metabolite profiles in cervicovaginal lavage fluid from 40 women with BV and 20 women without BV. Vaginal bacterial representation was determined using broad-range PCR with pyrosequencing and concentrations of bacteria by quantitative PCR. We detected 279 named biochemicals; levels of 62% of metabolites were significantly different in women with BV. Unsupervised clustering of metabolites separated women with and without BV. Women with BV have metabolite profiles marked by lower concentrations of amino acids and dipeptides, concomitant with higher levels of amino acid catabolites and polyamines. Higher levels of the signaling eicosanoid 12-hydroxyeicosatetraenoic acid (12-HETE), a biomarker for inflammation, were noted in BV. Lactobacillus crispatus and Lactobacillus jensenii exhibited similar metabolite correlation patterns, which were distinct from correlation patterns exhibited by BV-associated bacteria. Several metabolites were significantly associated with clinical signs and symptoms (Amsel criteria) used to diagnose BV, and no metabolite was associated with all four clinical criteria. BV has strong metabolic signatures across multiple metabolic pathways, and these signatures are associated with the presence and concentrations of particular bacteria. Bacterial vaginosis (BV) is a common but highly enigmatic condition that is associated with adverse outcomes for women and their neonates. Small molecule metabolites in the

  10. Corticosteroids for Bacterial Keratitis

    Science.gov (United States)

    Srinivasan, Muthiah; Mascarenhas, Jeena; Rajaraman, Revathi; Ravindran, Meenakshi; Lalitha, Prajna; Glidden, David V.; Ray, Kathryn J.; Hong, Kevin C.; Oldenburg, Catherine E.; Lee, Salena M.; Zegans, Michael E.; McLeod, Stephen D.; Lietman, Thomas M.; Acharya, Nisha R.

    2013-01-01

    Objective To determine whether there is a benefit in clinical outcomes with the use of topical corticosteroids as adjunctive therapy in the treatment of bacterial corneal ulcers. Methods Randomized, placebo-controlled, double-masked, multicenter clinical trial comparing prednisolone sodium phosphate, 1.0%, to placebo as adjunctive therapy for the treatment of bacterial corneal ulcers. Eligible patients had a culture-positive bacterial corneal ulcer and received topical moxifloxacin for at least 48 hours before randomization. Main Outcome Measures The primary outcome was best spectacle-corrected visual acuity (BSCVA) at 3 months from enrollment. Secondary outcomes included infiltrate/scar size, reepithelialization, and corneal perforation. Results Between September 1, 2006, and February 22, 2010, 1769 patients were screened for the trial and 500 patients were enrolled. No significant difference was observed in the 3-month BSCVA (−0.009 logarithm of the minimum angle of resolution [logMAR]; 95% CI, −0.085 to 0.068; P = .82), infiltrate/scar size (P = .40), time to reepithelialization (P = .44), or corneal perforation (P > .99). A significant effect of corticosteroids was observed in subgroups of baseline BSCVA (P = .03) and ulcer location (P = .04). At 3 months, patients with vision of counting fingers or worse at baseline had 0.17 logMAR better visual acuity with corticosteroids (95% CI, −0.31 to −0.02; P = .03) compared with placebo, and patients with ulcers that were completely central at baseline had 0.20 logMAR better visual acuity with corticosteroids (−0.37 to −0.04; P = .02). Conclusions We found no overall difference in 3-month BSCVA and no safety concerns with adjunctive corticosteroid therapy for bacterial corneal ulcers. Application to Clinical Practice Adjunctive topical corticosteroid use does not improve 3-month vision in patients with bacterial corneal ulcers. PMID:21987582

  11. Role of lipids in bacterial radioresistance

    International Nuclear Information System (INIS)

    Abushady, M.R.; Fawkia, M.E.; Tawfik, Z.S.

    1992-01-01

    The radioresistance of three bacterial isolates was determined. S. aureus was the most sensitive one (D 1 0 value 0.14 KGy), B. coagulans was moderate resistant (D 1 0 value 3.3 KGy) and the most resistant one was B.megaterium (D 1 0 value 3.7 KGy). Total lipids and lipid patterns of these bacteria were determined and the role of lipids in radioresistance was investigated. Least amount of total lipids was detected in the most sensitive organism (S. aureus). The increase in the bacterial content of total lipids was concomitant with high degrees of radioresistance. The most resistant organism (B. megaterium was characterized by high content of methyl esters of fatty acids, phosphatidylcholine and phosphatidylethanolamine, followed by appreciable amounts in the moderate resistant (B. coagulans) and the least amounts were detected in the most sensitive organism (S.aureus).6 fig., 3 tab

  12. Particle surface area and bacterial activity in recirculating aquaculture systems

    DEFF Research Database (Denmark)

    Pedersen, Per Bovbjerg; von Ahnen, Mathis; Fernandes, Paulo

    2017-01-01

    Suspended particles in recirculating aquaculture systems (RAS) provide surface area that can be colonized by bacteria. More particles accumulate as the intensity of recirculation increases thus potentially increasing the bacterial carrying capacity of the systems. Applying a recent, rapid, cultur...... for determining bacterial activity might provide a means for future monitoring and assessment of microbial water quality in aquaculture farming systems......Suspended particles in recirculating aquaculture systems (RAS) provide surface area that can be colonized by bacteria. More particles accumulate as the intensity of recirculation increases thus potentially increasing the bacterial carrying capacity of the systems. Applying a recent, rapid, culture......-independent fluorometric detection method (Bactiquant®) for measuring bacterial activity, the current study explored the relationship between total particle surface area (TSA, derived from the size distribution of particles >5 μm) and bacterial activity in freshwater RAS operated at increasing intensity of recirculation...

  13. Methods to classify bacterial pathogens in cystic fibrosis

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Nielsen, Xiaohui Chen; Johansen, Ulla

    2011-01-01

    Many bacteria can be detected in CF sputum, pathogenic and commensal. Modified Koch's criteria for identification of established and emerging CF pathogens are therefore described. Methods are described to isolate bacteria and to detect bacterial biofilms in sputum or lung tissue from CF patients ...

  14. Bacterial Cell Wall Components

    Science.gov (United States)

    Ginsberg, Cynthia; Brown, Stephanie; Walker, Suzanne

    Bacterial cell-surface polysaccharides cells are surrounded by a variety of cell-surface structures that allow them to thrive in extreme environments. Components of the cell envelope and extracellular matrix are responsible for providing the cells with structural support, mediating intercellular communication, allowing the cells to move or to adhere to surfaces, protecting the cells from attack by antibiotics or the immune system, and facilitating the uptake of nutrients. Some of the most important cell wall components are polysaccharide structures. This review discusses the occurrence, structure, function, and biosynthesis of the most prevalent bacterial cell surface polysaccharides: peptidoglycan, lipopolysaccharide, arabinogalactan, and lipoarabinomannan, and capsular and extracellular polysaccharides. The roles of these polysaccharides in medicine, both as drug targets and as therapeutic agents, are also described.

  15. Bacterial meningitis in Nottingham.

    OpenAIRE

    Ispahani, P.

    1983-01-01

    Records of 171 cases of bacterial meningitis admitted to Nottingham hospitals from January 1974 to June 1980 were reviewed. The distribution of organisms producing meningitis and the factors influencing mortality in different age groups were assessed. Neisseria meningitidis, Haemophilus influenzae and Streptococcus pneumoniae accounted for 69% of all proven cases. The overall mortality was 26% being lowest in patients with meningococcal meningitis (0%) and highest in those with pneumococcal m...

  16. Neglected bacterial zoonoses.

    Science.gov (United States)

    Chikeka, I; Dumler, J S

    2015-05-01

    Bacterial zoonoses comprise a group of diseases in humans or animals acquired by direct contact with or by oral consumption of contaminated animal materials, or via arthropod vectors. Among neglected infections, bacterial zoonoses are among the most neglected given emerging data on incidence and prevalence as causes of acute febrile illness, even in areas where recognized neglected tropical diseases occur frequently. Although many other bacterial infections could also be considered in this neglected category, five distinct infections stand out because they are globally distributed, are acute febrile diseases, have high rates of morbidity and case fatality, and are reported as commonly as malaria, typhoid or dengue virus infections in carefully designed studies in which broad-spectrum diagnoses are actively sought. This review will focus attention on leptospirosis, relapsing fever borreliosis and rickettsioses, including scrub typhus, murine typhus and spotted fever group rickettsiosis. Of greatest interest is the lack of distinguishing clinical features among these infections when in humans, which confounds diagnosis where laboratory confirmation is lacking, and in regions where clinical diagnosis is often attributed to one of several perceived more common threats. As diseases such as malaria come under improved control, the real impact of these common and under-recognized infections will become evident, as will the requirement for the strategies and allocation of resources for their control. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  17. Bacterial growth kinetics

    International Nuclear Information System (INIS)

    Boonkitticharoen, V.; Ehrhardt, J.C.; Kirchner, P.T.

    1989-01-01

    Quantitative measurement of bacterial growth may be made using a radioassay technique. This method measures, by scintillation counting, the 14 CO 2 derived from the bacterial metabolism of a 14 C-labeled substrate. Mathematical growth models may serve as reliable tools for estimation of the generation rate constant (or slope of the growth curve) and provide a basis for evaluating assay performance. Two models, i.e., exponential and logistic, are proposed. Both models yielded an accurate fit to the data from radioactive measurement of bacterial growth. The exponential model yielded high precision values of the generation rate constant, with an average relative standard deviation of 1.2%. Under most conditions the assay demonstrated no changes in the slopes of growth curves when the number of bacteria per inoculation was changed. However, the radiometric assay by scintillation method had a growth-inhibiting effect on a few strains of bacteria. The source of this problem was thought to be hypersensitivity to trace amounts of toluene remaining on the detector

  18. High level bacterial contamination of secondary school students' mobile phones.

    Science.gov (United States)

    Kõljalg, Siiri; Mändar, Rando; Sõber, Tiina; Rööp, Tiiu; Mändar, Reet

    2017-06-01

    While contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. Our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones. Altogether 27 mobile phones were studied. The contact plate method and microbial identification using MALDI-TOF mass spectrometer were used for culture studies. Quantitative PCR reaction for detection of universal 16S rRNA, Enterococcus faecalis 16S rRNA and Escherichia coli allantoin permease were performed, and the presence of tetracycline ( tet A, tet B, tet M), erythromycin ( erm B) and sulphonamide ( sul 1) resistance genes was assessed. We found a high median bacterial count on secondary school students' mobile phones (10.5 CFU/cm 2 ) and a median of 17,032 bacterial 16S rRNA gene copies per phone. Potentially pathogenic microbes ( Staphylococcus aureus , Acinetobacter spp. , Pseudomonas spp., Bacillus cereus and Neisseria flavescens ) were found among dominant microbes more often on phones with higher percentage of E. faecalis in total bacterial 16S rRNA. No differences in contamination level or dominating bacterial species between phone owner's gender and between phone types (touch screen/keypad) were found. No antibiotic resistance genes were detected on mobile phone surfaces. Quantitative study methods revealed high level bacterial contamination of secondary school students' mobile phones.

  19. Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica

    Directory of Open Access Journals (Sweden)

    Neus eGarcias-Bonet

    2012-09-01

    Full Text Available Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes and leaves by DGGE. A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ and δ subclasses and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

  20. Effect of disopyramide on bacterial diversity in drinking water

    Science.gov (United States)

    Wu, Qing; Zhao, Xiaofei; Tian, Qi; Wang, Lei; Zhao, Xinhua

    2018-02-01

    Disopyramide was detected in drinking water by LC-MS/MS and the microbial diversity was investigated by PCR and high-throughput sequencing. The results showed that bacteria community structure in drinking water changed a lot when added different concentrations of disopyramide. The results of Shannon index showed that the total number and abundance of bacterial community species in drinking water samples decreased significantly after the addition of disopyramide. However, the number and abundance of community structure did not change with the concentration of disopyramide. Disopyramide inhibits the activity of bacterial community in drinking water and also can reduce the bacterial community diversity in drinking water.

  1. Simultaneous detection of Neisseria meningitidis, Haemophilus influenzae and Streptococcus sp. by polymerase chain reaction for the diagnosis of bacterial meningits Detecção simultânea da Neisseria meningitidis, Haemophilus influenzae e Streptococcus sp. pela reação em cadeia da polimerase no diagnóstico das meningites bacterianas

    Directory of Open Access Journals (Sweden)

    Luciane Failace

    2005-12-01

    Full Text Available The simultaneous detection of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus sp. was assessed by polymerase chain reaction (PCR for the diagnosis of bacterial meningitis, as well as the applicability of PCR as a routine test. A cohort study was carried out with 182 children (2 months to 12 years of age with suspicion of bacterial meningitis. Routine tests identified the etiologic agent in 65/84 children whose clinical status and laboratory findings suggested the presence of bacterial meningitis. Bacterial meningitis was ruled out in 98 children. In 19 children, the etiologic diagnosis was not possible using standard methods; in 14 of these patients, the etiologic agent was identified by PCR (N. meningitidis=12; H. influenzae=1; Streptococcus sp.=1. The sensitivity of PCR was 88.1%; specificity, 99.0%; positive predictive value, 98.7%; and negative predictive, 90.1%. PCR is a useful complementary diagnostic technique, especially when Gram stain, culture, or antigenic detection are negative or inconclusive.Avaliamos o desempenho da reação em cadeia da polimerase (PCR para detecção simultânea da Neisseria meningitidis, Haemophilus influenzae e Streptococcus sp. no diagnóstico das meningites bacterianas e sua aplicabilidade na rotina diagnóstica. Foi realizado um estudo de coorte com 182 crianças apresentando suspeita de meningite bacteriana. Em 84, havia alterações clínicas e laboratoriais sugestivas de meningite bacteriana. Destas, 65 tiveram o agente etiológico identificado pelos métodos laboratoriais de rotina e 19 ficaram sem diagnóstico etiológico. Em 98 pacientes foi excluído o diagnóstico de meningite bacteriana. Analisando o desempenho da PCR encontramos sensibilidade de 88,1%, especificidade de 99,0% e valores preditivos positivo e negativo de 98,7% e 90,1% respectivamente. Nos 19 pacientes com meningite bacteriana mas sem diagnóstico etiológico a PCR detectou microrganismos em 14, sendo 12 N

  2. Study On Application Of Molecular Techniques (RAPD-PCR And RAMP-PCR) To Detect Mutation In Rice Breeding

    International Nuclear Information System (INIS)

    Hoang Thi My Linh; Phan, D. T. Son; Nguyen Thi Vang; Nguyen, T. T. Hien; Le XuanTham

    2007-01-01

    The project was carried out in 2007 with the purpose of consideration for using the two simple and inexpensive molecular techniques to estimate changes in DNA of rice mutant after gamma irradiation. Three rice cultivars: Basmati370, Tam Thom (TT1), IR64 and three gamma irradiated mutants BDS, TDS and VND 95-20 respectively, were used. Suitable DNA extraction procedure was obtained. PCR optimization was conducted on three important factors including: amount of MgCl 2 , DNA concentration and annealing temperature. 2.5 mM of MgCl 2 for RAPD-PCR and 3.75 mM for RAMP-PCR were found the best. 40 ng DNA provided a good amplification for RAMP-PCR; this figure was 50 ng for RAPD-PCR. Annealing temperatures were determined at 36 o C for RAPD primer and at 55±3 o C for Microsatellite primer. Final results showed that, both RAPD-PCR and RAMP-PCR could detect changes in DNA of rice mutants after gamma irradiation compared to their parents. Percentage of DNA changes determined by RAPD-PCR and RAMP-PCR on Basmati370 and its mutant BDS were 11.49% and 21.2% respectively; These on TT1 and TDS were 8.98% and 15.4%; and on IR64 and VND 95-20 were 3.45% and 4.95%. (author)

  3. Bacterial Degradation of Pesticides

    DEFF Research Database (Denmark)

    Knudsen, Berith Elkær

    This PhD project was carried out as part of the Microbial Remediation of Contaminated Soil and Water Resources (MIRESOWA) project, funded by the Danish Council for Strategic Research (grant number 2104-08-0012). The environment is contaminated with various xenobiotic compounds e.g. pesticides......D student, to construct fungal-bacterial consortia in order to potentially stimulate pesticide degradation thereby increasing the chance of successful bioaugmentation. The results of the project are reported in three article manuscripts, included in this thesis. In manuscript I, the mineralization of 2...

  4. Bacterial mitotic machineries

    DEFF Research Database (Denmark)

    Gerdes, Kenn; Møller-Jensen, Jakob; Ebersbach, Gitte

    2004-01-01

    Here, we review recent progress that yields fundamental new insight into the molecular mechanisms behind plasmid and chromosome segregation in prokaryotic cells. In particular, we describe how prokaryotic actin homologs form mitotic machineries that segregate DNA before cell division. Thus, the Par......M protein of plasmid R1 forms F actin-like filaments that separate and move plasmid DNA from mid-cell to the cell poles. Evidence from three different laboratories indicate that the morphogenetic MreB protein may be involved in segregation of the bacterial chromosome....

  5. Changes in bacterial meningitis.

    OpenAIRE

    Carter, P E; Barclay, S M; Galloway, W H; Cole, G F

    1990-01-01

    In 1964, one of us (WHG) undertook a retrospective study of bacterial meningitis in childhood in the north east of Scotland during the period 1946-61. We have recently carried out a similar review of cases occurring during 1971-86, to compare the incidence, mortality, and bacteriological patterns. During the earlier period 285 cases occurred, a total incidence of 16.9/100,000 children per year. In the later period 274 children were affected, an annual incidence of 17.8/100,000. The overall mo...

  6. Bacterial Dissemination to the Brain in Sepsis.

    Science.gov (United States)

    Singer, Benjamin H; Dickson, Robert P; Denstaedt, Scott J; Newstead, Michael W; Kim, Kwi; Falkowski, Nicole R; Erb-Downward, John R; Schmidt, Thomas M; Huffnagle, Gary B; Standiford, Theodore J

    2018-03-15

    Sepsis causes brain dysfunction and neuroinflammation. It is unknown whether neuroinflammation in sepsis is initiated by dissemination of bacteria to the brain and sustained by persistent infection, or whether neuroinflammation is a sterile process resulting solely from circulating inflammatory mediators. To determine if gut bacteria translocate to the brain during sepsis, and are associated with neuroinflammation. Murine sepsis was induced using cecal ligation and puncture, and sepsis survivor mice were compared with sham and unoperated control animals. Brain tissue of patients who died of sepsis was compared with patients who died of noninfectious causes. Bacterial taxa were characterized by 16S ribosomal RNA gene sequencing in both murine and human brain specimens; compared among sepsis and nonsepsis groups; and correlated with levels of S100A8, a marker of neuroinflammation using permutational multivariate ANOVA. Viable gut-associated bacteria were enriched in the brains of mice 5 days after surviving abdominal sepsis (P < 0.01), and undetectable by 14 days. The community structure of brain-associated bacteria correlated with severity of neuroinflammation (P < 0.001). Furthermore, bacterial taxa detected in brains of humans who die of sepsis were distinct from those who died of noninfectious causes (P < 0.001) and correlated with S100A8/A9 expression (P < 0.05). Although bacterial translocation is associated with acute neuroinflammation in murine sepsis, bacterial translocation did not result in chronic cerebral infection. Postmortem analysis of patients who die of sepsis suggests a role for bacteria in acute brain dysfunction in sepsis. Further work is needed to determine if modifying gut-associated bacterial communities modulates brain dysfunction after sepsis.

  7. Bacterial diversity of symptomatic primary endodontic infection by clonal analysis

    Directory of Open Access Journals (Sweden)

    Letícia Maria Menezes NÓBREGA

    Full Text Available Abstract The aim of this study was to explore the bacterial diversity of 10 root canals with acute apical abscess using clonal analysis. Samples were collected from 10 patients and submitted to bacterial DNA isolation, 16S rRNA gene amplification, cloning, and sequencing. A bacterial genomic library was constructed and bacterial diversity was estimated. The mean number of taxa per canal was 15, ranging from 11 to 21. A total of 689 clones were analyzed and 76 phylotypes identified, of which 47 (61.84% were different species and 29 (38.15% were taxa reported as yet-uncultivable or as yet-uncharacterized species. Prevotella spp., Fusobacterium nucleatum, Filifactor alocis, and Peptostreptococcus stomatis were the most frequently detected species, followed by Dialister invisus, Phocaeicola abscessus, the uncharacterized Lachnospiraceae oral clone, Porphyromonas spp., and Parvimonas micra. Eight phyla were detected and the most frequently identified taxa belonged to the phylum Firmicutes (43.5%, followed by Bacteroidetes (22.5% and Proteobacteria (13.2%. No species was detected in all studied samples and some species were identified in only one case. It was concluded that acute primary endodontic infection is characterized by wide bacterial diversity and a high intersubject variability was observed. Anaerobic Gram-negative bacteria belonging to the phylum Firmicutes, followed by Bacteroidetes, were the most frequently detected microorganisms.

  8. Animal Models of Bacterial Keratitis

    Science.gov (United States)

    Marquart, Mary E.

    2011-01-01

    Bacterial keratitis is a disease of the cornea characterized by pain, redness, inflammation, and opacity. Common causes of this disease are Pseudomonas aeruginosa and Staphylococcus aureus. Animal models of keratitis have been used to elucidate both the bacterial factors and the host inflammatory response involved in the disease. Reviewed herein are animal models of bacterial keratitis and some of the key findings in the last several decades. PMID:21274270

  9. Radionuclide scintigraphy of bacterial nephritis

    Energy Technology Data Exchange (ETDEWEB)

    Conway, J.J.; Weiss, S.C.; Shkolnik, A.; Yogev, R.; Firlit, C.; Traisman, E.S.

    1984-01-01

    Pyelonephritis is a leading cause of renal failure and is expected to cost as much as three billion dollars in 1984. The diagnosis of urinary tract infection is usually not difficult. However, localization of the infection within the renal parenchyma as opposed to the collecting system is much more difficult. Flank pain, fever, bacteiuria and evidence of parenchymal involvement by intravenous urography may be absent or unrecognized particularly in the infant. Ultrasound and Nuclear Medicine are advocated as better methods to define parenchymal involvement. Such definition is important in the consideration of treatment since parenchymal involvement of the kidney carries a much more ominous potential outcome than infection restricted to within the collecting system. 38 children with a clinical diagnosis of urinary tract infection were studied. 26 of the patients demonstrated abnormal renal parenchymal findings with Gallium-67 Citrate or Tc-99m Glucoheptonate scintigraphy. Intravenous urography was notably ineffective with only 5 of the 20 interpreted as abnormal due to parenchymal disease or decreased function. 11 were entirely normal while only 5 demonstrated scars or hydronephrosis. Only 10 of 17 patients demonstrated intranvesicoureteral reflux on x-ray or nuclear cystography. Ultrasound depicted 6 of 20 patients as having parenchymal abnormalities. Seven were normal. Nonspecific findings such as dilitation of the renal pelvis or renal enlargement was noted in 11 of the 20 patients. Radionuclide Scintigraphy is the most efficacious modality to detect since acute bacterial nephritis.

  10. Bacterial acquisition in juveniles of several broadcast spawning coral species.

    Directory of Open Access Journals (Sweden)

    Koty H Sharp

    Full Text Available Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  11. Bacterial acquisition in juveniles of several broadcast spawning coral species.

    Science.gov (United States)

    Sharp, Koty H; Ritchie, Kim B; Schupp, Peter J; Ritson-Williams, Raphael; Paul, Valerie J

    2010-05-28

    Coral animals harbor diverse microorganisms in their tissues, including archaea, bacteria, viruses, and zooxanthellae. The extent to which coral-bacterial associations are specific and the mechanisms for their maintenance across generations in the environment are unknown. The high diversity of bacteria in adult coral colonies has made it challenging to identify species-specific patterns. Localization of bacteria in gametes and larvae of corals presents an opportunity for determining when bacterial-coral associations are initiated and whether they are dynamic throughout early development. This study focuses on the early onset of bacterial associations in the mass spawning corals Montastraea annularis, M. franksi, M. faveolata, Acropora palmata, A. cervicornis, Diploria strigosa, and A. humilis. The presence of bacteria and timing of bacterial colonization was evaluated in gametes, swimming planulae, and newly settled polyps by fluorescence in situ hybridization (FISH) using general eubacterial probes and laser-scanning confocal microscopy. The coral species investigated in this study do not appear to transmit bacteria via their gametes, and bacteria are not detectable in or on the corals until after settlement and metamorphosis. This study suggests that mass-spawning corals do not acquire, or are not colonized by, detectable numbers of bacteria until after larval settlement and development of the juvenile polyp. This timing lays the groundwork for developing and testing new hypotheses regarding general regulatory mechanisms that control bacterial colonization and infection of corals, and how interactions among bacteria and juvenile polyps influence the structure of bacterial assemblages in corals.

  12. Aerotaxis in Bacterial Turbulence

    Science.gov (United States)

    Fernandez, Vicente; Bisson, Antoine; Bitton, Cindy; Waisbord, Nicolas; Smriga, Steven; Rusconi, Roberto; Stocker, Roman

    2012-11-01

    Concentrated suspensions of motile bacteria exhibit correlated dynamics on spatial scales much larger than an individual bacterium. The resulting flows, visually similar to turbulence, can increase mixing and decrease viscosity. However, it remains unclear to what degree the collective dynamics depend on the motile behavior of bacteria at the individual level. Using a new microfluidic device to create controlled horizontal oxygen gradients, we studied the two dimensional behavior of dense suspensions of Bacillus subtilis. This system makes it possible to assess the interplay between the coherent large-scale motions of the suspension, oxygen transport, and the directional response of cells to oxygen gradients (aerotaxis). At the same time, this device has enabled us to examine the onset of bacterial turbulence and its influence on the propagation of the diffusing oxygen front, as the bacteria begin in a dormant state and transition to swimming when exposed to oxygen.

  13. Bacterial intermediate filaments

    DEFF Research Database (Denmark)

    Charbon, Godefroid; Cabeen, M.; Jacobs-Wagner, C.

    2009-01-01

    Crescentin, which is the founding member of a rapidly growing family of bacterial cytoskeletal proteins, was previously proposed to resemble eukaryotic intermediate filament (IF) proteins based on structural prediction and in vitro polymerization properties. Here, we demonstrate that crescentin...... also shares in vivo properties of assembly and dynamics with IF proteins by forming stable filamentous structures that continuously incorporate subunits along their length and that grow in a nonpolar fashion. De novo assembly of crescentin is biphasic and involves a cell size-dependent mechanism...... a new function for MreB and providing a parallel to the role of actin in IF assembly and organization in metazoan cells. Additionally, analysis of an MreB localization mutant suggests that cell wall insertion during cell elongation normally occurs along two helices of opposite handedness, each...

  14. Bacterial polyhydroxyalkanoates: Still fabulous?

    Science.gov (United States)

    Możejko-Ciesielska, Justyna; Kiewisz, Robert

    2016-11-01

    Bacterial polyhydroxyalkanoates (PHA) are polyesters accumulated as carbon and energy storage materials under limited growth conditions in the presence of excess carbon sources. They have been developed as biomaterials with unique properties for the past many years being considered as a potential substitute for conventional non-degradable plastics. Due to the increasing concern towards global climate change, depleting petroleum resource and problems with an utilization of a growing number of synthetic plastics, PHAs have gained much more attention from industry and research. These environmentally friendly microbial polymers have great potential in biomedical, agricultural, and industrial applications. However, their production on a large scale is still limited. This paper describes the backgrounds of PHAs and discussed the current state of knowledge on the polyhydroxyalkanoates. Ability of bacteria to convert different carbon sources to PHAs, the opportunities and challenges of their introduction to global market as valuable renewable products have been also discussed. Copyright © 2016 Elsevier GmbH. All rights reserved.

  15. Bacterial proteases and virulence

    DEFF Research Database (Denmark)

    Frees, Dorte; Brøndsted, Lone; Ingmer, Hanne

    2013-01-01

    with the proteases either encoded within the same polypeptide or on separate subunits. In contrast, substrate recognition by extracellular proteases is less selective and therefore these enzymes are generally expressed as zymogens to prevent premature proteolytic activity that would be detrimental to the cell......Bacterial pathogens rely on proteolysis for variety of purposes during the infection process. In the cytosol, the main proteolytic players are the conserved Clp and Lon proteases that directly contribute to virulence through the timely degradation of virulence regulators and indirectly by providing...... signalling to short-circuit host cell processes. Common to both intra- and extracellular proteases is the tight control of their proteolytic activities. In general, substrate recognition by the intracellular proteases is highly selective which is, in part, attributed to the chaperone activity associated...

  16. Detection of bacterial and viral pathogens in hospitalized children with acute respiratory illness and determination of different socio demographic factors as important cause of the disease in Odisha, India

    Directory of Open Access Journals (Sweden)

    Bhagyalaxmi Biswal

    2017-10-01

    Full Text Available The paper an attempt has been made to analysis the status of acute respiratory tract infection among children in India. In the present study we aimed to present first time the detection of viruses, bacteria and mix infection of viruses and bacteria in hospitalized children with ARI and also to analyze the influence of socioeconomic status of parent in two divergent geographical settings of Odisha. Hospitalized children with ARI aged <5 were recruited from July 2014 to June 2015. Nasopharyngeal/Oropharyngial swabs were collected for detection of common respiratory viruses by reverse transcriptase chain reaction (RT-PCR. Bacteria were isolated by routine culture methods. Bivitiate analysis including chi square was used as test of significance. The analysis revealed 150 (56% were detected with ≥1 bacteria, 40 (15% with ≥ 1virus, 22 (8.2% with ≥ 2 bacteria and 20 (7-4% with both bacteria and virus. Most frequently detected pathogens were Klebsiella pneumonae (18.3%, Sptrptococcus pneumonae (12.7%, Parainfluenza A (36.6% and Influenza- A18 (30%. Incidences of pathogens were detected more among children <1 year, Gender discrimination in the form of dietary neglect of the female children has also been noted mostly in case of tribal patients. The present study had identified low socioeconomic status, poor housing conditions, illiterate mothers, birth weight, tobacco smoking families and nutritional status as important determinants for ARI. Interventions to improve these modifiable risk factors can significantly reduce the ARI burden among children especially in tribal population.

  17. QTLs for Resistance to Major Rice Diseases Exacerbated by Global Warming: Brown Spot, Bacterial Seedling Rot, and Bacterial Grain Rot.

    Science.gov (United States)

    Mizobuchi, Ritsuko; Fukuoka, Shuichi; Tsushima, Seiya; Yano, Masahiro; Sato, Hiroyuki

    2016-12-01

    In rice (Oryza sativa L.), damage from diseases such as brown spot, caused by Bipolaris oryzae, and bacterial seedling rot and bacterial grain rot, caused by Burkholderia glumae, has increased under global warming because the optimal temperature ranges for growth of these pathogens are relatively high (around 30 °C). Therefore, the need for cultivars carrying genes for resistance to these diseases is increasing to ensure sustainable rice production. In contrast to the situation for other important rice diseases such as blast and bacterial blight, no genes for complete resistance to brown spot, bacterial seedling rot or bacterial grain rot have yet been discovered. Thus, rice breeders have to use partial resistance, which is largely influenced by environmental conditions. Recent progress in molecular genetics and improvement of evaluation methods for disease resistance have facilitated detection of quantitative trait loci (QTLs) associated with resistance. In this review, we summarize the results of worldwide screening for cultivars with resistance to brown spot, bacterial seedling rot and bacterial grain rot and we discuss the identification of QTLs conferring resistance to these diseases in order to provide useful information for rice breeding programs.

  18. Spectrophotometric Analysis of Bacterial Contamination in Water

    Science.gov (United States)

    Spence, Sarah

    2010-10-01

    Bacterial contamination in water is a hazard everywhere from wells in third world countries to reclaimed water on the International Space Station. Traditional lab techniques detect bacteria in approximately 48 hours, while optical techniques can detect bacteria in as little as six hours. The Beer-Lambert Law states that absorption of light is directly correlated to the concentration of a solute in a solution. By passing light through a sample of contaminated broth, the transmittance and in turn the absorption of the solution can be observed. The transmittance data alone follows the inverse of the bacterial growth curve. A sharp drop in transmittance represents the exponential growth phase of bacteria. This drop is observed between six and eight hours following the inoculation of the laboratory samples with Escherichia coli, using both a standard lab monochrometer as well as a device designed for this study. The Optical Bacteria Detection (OBD) was designed to be effective and inexpensive, with a limited use of consumables and minimum waste generation. The OBD device uses a phototransistor as a sensor and an LED with wavelength of approximately 500 nm. Data from the monochrometer shows the sudden decrease in transmittance is most pronounced at this wavelength. The OBD can be tuned to test for other bacteria, such as Salmonella and Vibrio fisheri by changing the wavelength of the LED light source.

  19. Light scattering application for bacterial cell monitoring during cultivation process

    Science.gov (United States)

    Kotsyumbas, Igor Ya.; Kushnir, Igor M.; Bilyy, Rostyslav O.; Yarynovska, Ivanna H.; Getman, Vasyl'B.; Bilyi, Alexander I.

    2007-07-01

    Monitoring of bacterial cell numbers is of great importance not only in microbiological industry but also for control of liquids contamination in the food and pharmaceutical industries. Here we describe a novel low-cost and highly efficient technology for bacterial cell monitoring during cultivation process. The technology incorporates previously developed monitoring device and algorithm of its action. The devise analyses light scattered by suspended bacterial cells. Current stage utilizes monochromatic coherent light and detects amplitudes and durations of scattered light impulses, it does not require any labeling of bacterial cell. The system is calibrated using highly purificated bacteria-free water as standard. Liquid medial are diluted and analyzed by the proposed technology to determine presence of bacteria. Detection is done for a range of particle size from 0.1 to 10 μm, and thus particles size distribution is determined. We analyzed a set of different bacterial suspensions and also their changes in quantity and size distribution during cultivation. Based on the obtained results we conclude that proposed technology can be very effective for bacteria monitoring during cultivation process, providing benefits of low simplicity and low cost of analysis with simultaneous high detection precision.

  20. Bacteriële meningitis

    NARCIS (Netherlands)

    Brouwer, M. C.; van de Beek, D.

    2012-01-01

    Bacterial meningitis is a severe disease which affects 35.000 Europeans each year and has a mortality rate of about 20%. During the past 25 years the epidemiology of bacterial meningitis has changed significantly due to the implementation of vaccination against Haemophilus influenzae, Neisseria

  1. Bacterial meningitis in immunocompromised patients

    NARCIS (Netherlands)

    van Veen, K.E.B.

    2018-01-01

    Bacterial meningitis is an acute infection of the meninges, in The Netherlands most commonly caused by Streptococcus pneumoniae and Neisseria meningitides. Risk factors for acquiring bacterial meningitis include a decreased function of the immune system. The aim of this thesis was to study

  2. Fungal corneal ulcer and bacterial orbital cellulitis occur as complications of bacterial endophthalmitis after cataract surgery in an immunocompetent patient.

    Science.gov (United States)

    Kim, Eun Chul; Kim, Man Soo; Kang, Nam Yeo

    2013-03-01

    To report a case of fungal corneal ulcer and bacterial orbital cellulitis as complications of bacterial endophthalmitis following cataract surgery. A 51-year-old man underwent anterior chamber irrigation and aspiration in the left eye one day after cataract surgery because of bacterial endophthalmitis. Marked lid swelling with purulent discharge was developed after 5 days. Slit lamp examination showed generalized corneal ulcer and pus in the total anterior chamber. A computerized tomography scan showed left retrobulbar fat stranding with thickened optic disc. Streptococcus pneumonia was cultured from corneal scraping, vireous, and subconjunctival pus. The patient improved gradually with antibiotics treatments, but the corneal ulcer did not fully recover 2 months after cataract surgery. Candida albicans was detected in repetitive corneal culture. After antifungal and antibacterial therapy, the corneal epithelium had healed, but phthisis bulbi had developed. Fungal corneal ulcer and bacterial orbital cellulitis can occur as complications of endophthalmitis in an immunocompetent patient.

  3. Identification of bacteriology and risk factor analysis of asymptomatic bacterial colonization in pacemaker replacement patients.

    Directory of Open Access Journals (Sweden)

    Xian-Ming Chu

    Full Text Available Recent researches revealed that asymptomatic bacterial colonization on PMs might be ubiquitous and increase the risk of clinical PM infection. Early diagnosis of patients with asymptomatic bacterial colonization could provide opportunity for targeted preventive measures.The present study explores the incidence of bacterial colonization of generator pockets in pacemaker replacement patients without signs of infection, and to analyze risk factors for asymptomatic bacterial colonization.From June 2011 to December 2013, 118 patients underwent pacemaker replacement or upgrade. Identification of bacteria was carried out by bacterial culture and 16S rRNA sequencing. Clinical risk characteristics were analyzed.The total bacterial positive rate was 37.3% (44 cases, and the coagulase-negative Staphylococcus aureus detection rate was the highest. Twenty two (18.6% patients had positive bacterial culture results, of which 50% had coagulase-negative staphylococcus. The bacterial DNA detection rate was 36.4 % (43 cases. Positive bacterial DNA results from pocket tissues and the surface of the devices were 22.0% and 29.7%, respectively. During follow-up (median, 27.0 months, three patients (6.8%, 3/44 became symptomatic with the same genus of microorganism, S. aureus (n=2 and S. epidermidis (n=1. Multivariable logistic regression analysis showed that history of bacterial infection, use of antibiotics, application of antiplatelet drugs, replacement frequency were independent risk factors for asymptomatic bacterial colonization.There was a high incidence of asymptomatic bacterial colonization in pacemaker patients with independent risk factors. Bacterial culture combined genetic testing could improve the detection rate.

  4. Molecular approaches for bacterial azoreductases

    Directory of Open Access Journals (Sweden)

    Montira Leelakriangsak

    2013-12-01

    Full Text Available Azo dyes are the dominant types of synthetic dyes, widely used in textiles, foods, leather, printing, tattooing, cosmetics, and pharmaceutical industries. Many microorganisms are able to decolorize azo dyes, and there is increasing interest in biological waste treatment methods. Bacterial azoreductases can cleave azo linkages (-N=N- in azo dyes, forming aromatic amines. This review mainly focuses on employing molecular approaches, including gene manipulation and recombinant strains, to study bacterial azoreductases. The construction of the recombinant protein by cloning and the overexpression of azoreductase is described. The mechanisms and function of bacterial azoreductases can be studied by other molecular techniques discussed in this review, such as RT-PCR, southern blot analysis, western blot analysis, zymography, and muta-genesis in order to understand bacterial azoreductase properties, function and application. In addition, understanding the regulation of azoreductase gene expression will lead to the systematic use of gene manipulation in bacterial strains for new strategies in future waste remediation technologies.

  5. Carbon nanotubes as in vivo bacterial probes

    Science.gov (United States)

    Bardhan, Neelkanth M.; Ghosh, Debadyuti; Belcher, Angela M.

    2014-09-01

    With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F‧-positive and F‧-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F‧-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections.

  6. Microbial ecology of bacterially mediated PCB biodegradation

    International Nuclear Information System (INIS)

    Pettigrew, C.A. Jr.

    1989-01-01

    The roles of plasmid mediated and consortia mediated polychlorinated biphenyl (PCB) biodegradation by bacterial populations isolated from PCB contaminated freshwater sediments were investigated. PCB degrading bacteria were isolated by DNA:DNA colony hybridization, batch enrichments, and chemostat enrichment. Analysis of substrate removal and metabolite production were done using chlorinated biphenyl spray plates, reverse phase high pressure liquid chromatography, Cl - detection, and 14 C-labeled substrate mineralization methods. A bacterial consortium, designated LPS10, involved in a concerted metabolic attack on chlorinated biphenyls, was shown to mineralize 4-chlorobiphenyl (4CB) and 4,4'-dichlorobiphenyl (4,4' CB). The LPS10 consortium was isolated by both batch and chemostat enrichment using 4CB and biphenyl (BP) as sole carbon source and was found to have tree bacterial isolates that predominated; these included: Pseudomonas, testosteroni LPS10A which mediated the breakdown of 4CB and 4,4' CB to the putative meta-cleavage product and subsequently to 4-chlorobenzoic acid (4CBA), an isolate tentatively identified as an Arthrobacter sp. LPS10B which mediated 4CBA degradation, and Pseudomonas putida by A LPS10C whose role in the consortium has not been determined

  7. Exploiting Quorum Sensing To Confuse Bacterial Pathogens

    Science.gov (United States)

    LaSarre, Breah

    2013-01-01

    SUMMARY Cell-cell communication, or quorum sensing, is a widespread phenomenon in bacteria that is used to coordinate gene expression among local populations. Its use by bacterial pathogens to regulate genes that promote invasion, defense, and spread has been particularly well documented. With the ongoing emergence of antibiotic-resistant pathogens, there is a current need for development of alternative therapeutic strategies. An antivirulence approach by which quorum sensing is impeded has caught on as a viable means to manipulate bacterial processes, especially pathogenic traits that are harmful to human and animal health and agricultural productivity. The identification and development of chemical compounds and enzymes that facilitate quorum-sensing inhibition (QSI) by targeting signaling molecules, signal biogenesis, or signal detection are reviewed here. Overall, the evidence suggests that QSI therapy may be efficacious against some, but not necessarily all, bacterial pathogens, and several failures and ongoing concerns that may steer future studies in productive directions are discussed. Nevertheless, various QSI successes have rightfully perpetuated excitement surrounding new potential therapies, and this review highlights promising QSI leads in disrupting pathogenesis in both plants and animals. PMID:23471618

  8. [Mondini dysplasia: recurrent bacterial meningitis in adolescence].

    Science.gov (United States)

    Vargas-Dĭaz, J; Garófalo-Gómez, N; Rodríguez, U; Parra, M; Barroso-García, E; Novoa-López, L; Rojas-Massipe, E; Sardiñas-Hernández, N L

    Episodes of recurrent bacterial meningitis can occur in patients due to either congenital or acquired disorders. Congenital deformity of the bony labyrinth can be linked to a fistulous tract communicating it with the intracranial subarachnoid space. Mondini deformity is a frequent malformation in congenitally deaf patients. We report the case of an adolescent with a history of being unable to hear in one ear who, from the age of 10 years, began to suffer repeated bacterial meningoencephalitis with microbiological recovery of Streptococcus pneumoniae on three occasions. The type of germ recovered in the cerebrospinal fluid (CSF) and the history of congenital deafness that was detected when the patient was 3 years old were the diagnostic clues to the possible anomaly of the inner ear with a CSF fistula. The clinically proven CSF rhinorrhea contributed to the diagnosis of an ear anomaly with a fistula. Computerised axial tomography and magnetic resonance studies of the petrous portion of the temporal bone revealed the malformation that was later found and closed during the surgical intervention on the affected ear. The clinical absence of rhinorrhea, a year's progression without new infections after operating on the patient and post-surgery imaging studies were all proof that the fistula had closed. Mondini dysplasia with CSF fistula must be included as a possible diagnosis when faced with a patient with recurrent bacterial meningoencephalitis. Imaging studies, especially magnetic resonance, enable the clinician to check the diagnosis and the CSF fistula can be closed with ear surgery.

  9. Zoonotic bacterial meningitis in human adults

    NARCIS (Netherlands)

    van Samkar, Anusha; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2016-01-01

    To describe the epidemiology, etiology, clinical characteristics, treatment, outcome, and prevention of zoonotic bacterial meningitis in human adults. We identified 16 zoonotic bacteria causing meningitis in adults. Zoonotic bacterial meningitis is uncommon compared to bacterial meningitis caused by

  10. Evolution of Bacterial Suicide

    Science.gov (United States)

    Tchernookov, Martin; Nemenman, Ilya

    2013-03-01

    While active, controlled cellular suicide (autolysis) in bacteria is commonly observed, it has been hard to argue that autolysis can be beneficial to an individual who commits it. We propose a theoretical model that predicts that bacterial autolysis is evolutionarily advantageous to an individualand would fixate in physically structured environments for stationary phase colonies. We perform spatially resolved agent-based simulations of the model, which predict that lower mixing in the environment results in fixation of a higher autolysis rate from a single mutated cell, regardless of the colony's genetic diversity. We argue that quorum sensing will fixate as well, even if initially rare, if it is coupled to controlling the autolysis rate. The model does not predict a strong additional competitive advantage for cells where autolysis is controlled by quorum sensing systems that distinguish self from nonself. These predictions are broadly supported by recent experimental results in B. subtilisand S. pneumoniae. Research partially supported by the James S McDonnell Foundation grant No. 220020321 and by HFSP grant No. RGY0084/2011.

  11. Electromagnetism of Bacterial Growth

    Science.gov (United States)

    Ainiwaer, Ailiyasi

    2011-10-01

    There has been increasing concern from the public about personal health due to the significant rise in the daily use of electrical devices such as cell phones, radios, computers, GPS, video games and television. All of these devices create electromagnetic (EM) fields, which are simply magnetic and electric fields surrounding the appliances that simultaneously affect the human bio-system. Although these can affect the human system, obstacles can easily shield or weaken the electrical fields; however, magnetic fields cannot be weakened and can pass through walls, human bodies and most other objects. The present study was conducted to examine the possible effects of bacteria when exposed to magnetic fields. The results indicate that a strong causal relationship is not clear, since different magnetic fields affect the bacteria differently, with some causing an increase in bacterial cells, and others causing a decrease in the same cells. This phenomenon has yet to be explained, but the current study attempts to offer a mathematical explanation for this occurrence. The researchers added cultures to the magnetic fields to examine any effects to ion transportation. Researchers discovered ions such as potassium and sodium are affected by the magnetic field. A formula is presented in the analysis section to explain this effect.

  12. Bacterial vaginosis, alterations in vaginal flora and HIV genital ...

    African Journals Online (AJOL)

    Bacterial vaginosis, alterations in vaginal flora and HIV genital shedding among HIV-1-infected women in Mozambique. ... We compared women with detectable cervical HIV viral load (≥40 copies/ml) with women with undetectable cervical HIV. Results. We enrolled 106 women. Women with abnormal vaginal flora ...

  13. Monitoring bacterial faecal contamination in waters using multiplex ...

    African Journals Online (AJOL)

    Monitoring of sanitary quality or faecal pollution in water is currently based on quantifying some bacterial indicators such as Escherichia coli and faecal enterococci. Using a multiplex real-time PCR assay for faecal enterococci and Bacteroides spp., the detection of faecal contamination in non-treated water can be done in a ...

  14. Bacterial indicators of faecal pollution of water supplies and public ...

    African Journals Online (AJOL)

    Bacterial indicators of faecal pollution of water supplies and their significance to public health are reviewed in this paper, to highlight their levels of general acceptability and suitability as safeguards against health hazards associated with water supplies. Regular bacteriological analysis with the sole aim of detecting faecal ...

  15. Bacterial growth on macrophyte leachate and fate of bacterial production

    International Nuclear Information System (INIS)

    Findlay, S.; Carlough, L.; Crocker, M.T.; Gill, H.K.; Meyer, J.L.; Smith, P.J.

    1986-01-01

    The role bacteria play in transferring organic carbon to other trophic levels in aquatic ecosystems depends on the efficiency with which they convert dissolved organic [ 14 C]-labelled carbon into bacterial biomass and on the ability of consumers to graze bacteria. The authors have measured the conversion efficiency for bacteria growing on macrophyte-derived dissolved organic carbon and estimated the amount of bacterial production removed by grazing. Bacteria converted this DOC into new tissue with an efficiency of 53%, substantially higher than the apparent conversion efficiency of macrophyte-derived particulate organic carbon or other types of DOC. Two estimates of grazing indicate that the decline in bacterial numbers after the bloom was probably due to grazing by flagellates. These results show the significance of the bacterial link between DOC and other trophic levels

  16. Adjunctive Therapies for Bacterial Keratitis.

    Science.gov (United States)

    Dakhil, Turki Abdulaziz Bin; Stone, Donald U; Gritz, David C

    2017-01-01

    Bacterial keratitis is the most common type among all types of infectious keratitis. Currently, antibiotics are the main-stay of treatment. The objective of this systematic review is to review published clinical studies which discuss the adjunctive treatment of bacterial keratitis to guide clinical decision-making. We reviewed the role of a variety of medications and surgeries which can help in managing bacterial keratitis complications, which include as thinning, perforation, and impaired wound healing. We have included appropriate animal and laboratory studies, case reports and case series, and randomized clinical trials regarding each therapy.

  17. Fluoroquinolones as imaging agents for bacterial infection.

    Science.gov (United States)

    Naqvi, Syed Ali Raza; Drlica, Karl

    2017-10-31

    Diagnosis of deep-seated bacterial infection is difficult, as neither standard anatomical imaging nor radiolabeled, autologous leukocytes distinguish sterile inflammation from infection. Two recent imaging efforts are receiving attention: (1) radioactive derivatives of sorbitol show good specificity with Gram-negative bacterial infections, and (2) success in combining anatomical and functional imaging for cancer diagnosis has rekindled interest in 99m Tc-fluoroquinolone-based imaging. With the latter, computed tomography (CT) would be combined with single-photon-emission-computed tomography (SPECT) to detect 99m Tc-fluoroquinolone-bacterial interactions. The present minireview provides a framework for advancing fluoroquinolone-based imaging by identifying gaps in our understanding of the process. One issue is the reliance of 99m Tc labeling on the reduction of sodium pertechnetate, which can lead to colloid formation and loss of specificity. Specificity problems may be reduced by altering the quinolone structure (for example, switching from ciprofloxacin to sitafloxacin). Another issue is the uncharacterized nature of 99m Tc-ciprofloxacin binding to, or sequestration in, bacteria: specific interactions with DNA gyrase, an intracellular fluoroquinolone target, are unlikely. Labeling with 68 Ga rather than 99m Tc enables detection by positron emission tomography, but with similar biological uncertainties. Replacing the C6-F of the fluoroquinolone with 18 F provides an alternative to pertechnetate and gallium that may lead to imaging based on drug interactions with gyrase. Gyrase-based imaging requires knowledge of fluoroquinolone action, which we update. We conclude that quinolone-based probes show promise for the diagnosis of infection, but improvements in specificity and sensitivity are needed. These improvements include the optimization of the quinolone structure; such chemistry efforts can be accelerated by refining microbiological assays.

  18. Role of the chronic bacterial infection in urinary bladder carcinogenesis

    International Nuclear Information System (INIS)

    Higgy, N.A.

    1985-01-01

    The purpose of this thesis was to determine whether or not bacterial infection of the urinary bladder had a role in urinary bladder carcinogenesis. To investigate this proposition, four separate studies were conducted. The first study developed an experimental animal model where bacterial infection of the urinary bladder could be introduced and maintained for a period in excess of one year. The method of infection, inoculation of bacteria (Escherichia coli type 04) subserosally into the vesical wall, successfully caused persistent infection in the majority of animals. In the second study the temporal effects of bacterial infection on the induction of urothelial ornithine decarboxylase (ODC) and 3 H-thymidine uptake and DNA synthesis were examined. Bacterial infection of the urinary bladder induced urothelial ODC with a peak in enzyme activity 6 hr after infection. 3 H-Thymidine uptake and DNA synthesis peaked 48 hr after infection and coincided with the urothelial hyperplasia that occurred in response to the infection. In the third study the specific bladder carcinogen N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) was given to rats concurrent with the urinary bacterial infection. In the fourth study rats were administered sodium nitrate and either dibutylamine or piperazine in the drinking water. The infected group developed bladder tumors while none were detected in the non-infected rats. From these studies it may be concluded that bacterial infection may have a significant role in the process of urinary bladder carcinogenesis

  19. Procalcitonin as Predictor of Bacterial Infection in Meconium Aspiration Syndrome.

    Science.gov (United States)

    K, Mahendiran; Batra, Prerna; Faridi, M M A; Singh, N P

    2017-12-29

     There is a lack of definite consensus on indications for initiating antibiotics in neonates with meconium aspiration syndrome (MAS), instigating researchers to search for a biomarker that can help differentiate MAS from MAS with bacterial infection.  Our primary objective was to compare serum procalcitonin (PCT) levels in full-term vigorous neonates having MAS with or without bacterial infection.  Seventy term vigorous neonates with diagnosis of MAS were enrolled. Blood samples were taken for sepsis screen, C-reactive protein (CRP), PCT, and blood culture at 6 ± 2 hours of respiratory distress. Neonates were categorized into group 1 (MAS without bacterial infection) and group 2 (MAS with bacterial infection) based on blood culture. The duration of our study was 18 months.  Mean ± standard deviation PCT level was 2.52 ± 3.99 in group 1 and 2.71 ± 4.22 in group 2, which was comparable. At cutoff of 0.1 ng/mL, PCT had a sensitivity of 90% and specificity of 8% in detecting bacterial infection. Mean total leukocyte count, absolute neutrophil count, immature to total leucocyte ratio, microerythrocyte sedimentation rate, and CRP were comparable.  Though PCT is an early and reliable marker of neonatal infection, the levels were increased in neonates with MAS irrespective of the presence of bacterial infection. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  20. Networked Chemoreceptors Benefit Bacterial Chemotaxis Performance

    Directory of Open Access Journals (Sweden)

    Vered Frank

    2016-12-01

    Full Text Available Motile bacteria use large receptor arrays to detect and follow chemical gradients in their environment. Extended receptor arrays, composed of networked signaling complexes, promote cooperative stimulus control of their associated signaling kinases. Here, we used structural lesions at the communication interface between core complexes to create an Escherichia coli strain with functional but dispersed signaling complexes. This strain allowed us to directly study how networking of signaling complexes affects chemotactic signaling and gradient-tracking performance. We demonstrate that networking of receptor complexes provides bacterial cells with about 10-fold-heightened detection sensitivity to attractants while maintaining a wide dynamic range over which receptor adaptational modifications can tune response sensitivity. These advantages proved especially critical for chemotaxis toward an attractant source under conditions in which bacteria are unable to alter the attractant gradient.

  1. Comparison of Established Diagnostic Methodologies and a Novel Bacterial smpB Real-Time PCR Assay for Specific Detection of Haemophilus influenzae Isolates Associated with Respiratory Tract Infections.

    Science.gov (United States)

    Reddington, Kate; Schwenk, Stefan; Tuite, Nina; Platt, Gareth; Davar, Danesh; Coughlan, Helena; Personne, Yoann; Gant, Vanya; Enne, Virve I; Zumla, Alimuddin; Barry, Thomas

    2015-09-01

    Haemophilus influenzae is a significant causative agent of respiratory tract infections (RTI) worldwide. The development of a rapid H. influenzae diagnostic assay that would allow for the implementation of infection control measures and also improve antimicrobial stewardship for patients is required. A number of nucleic acid diagnostics approaches that detect H. influenzae in RTIs have been described in the literature; however, there are reported specificity and sensitivity limitations for these assays. In this study, a novel real-time PCR diagnostic assay targeting the smpB gene was designed to detect all serogroups of H. influenzae. The assay was validated using a panel of well-characterized Haemophilus spp. Subsequently, 44 Haemophilus clinical isolates were collected, and 36 isolates were identified as H. influenzae using a gold standard methodology that combined the results of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fucK diagnostic assay. Using the novel smpB diagnostic assay, 100% concordance was observed with the gold standard, demonstrating a sensitivity of 100% (95% confidence interval [CI], 90.26% to 100.00%) and a specificity of 100% (95% CI, 63.06% to 100.00%) when used on clinical isolates. To demonstrate the clinical utility of the diagnostic assay presented, a panel of lower RTI samples (n = 98) were blindly tested with the gold standard and smpB diagnostic assays. The results generated were concordant for 94/98 samples tested, demonstrating a sensitivity of 90.91% (95% CI, 78.33% to 97.47%) and a specificity of 100% (95% CI, 93.40% to 100.00%) for the novel smpB assay when used directly on respiratory specimens. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  2. Herpesviral-bacterial coinfection in periapical pathosis.

    Science.gov (United States)

    Sabeti, Mohammad; Slots, Jørgen

    2004-02-01

    Two members of the herpesvirus family, human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV), seem to be important putative pathogens of human periodontitis and symptomatic periapical lesions, causing pathosis either by inducing immunosuppression with a subsequent risk of aggressive bacterial infections or by infecting of periodontal cells directly. This study aimed to relate periapical occurrence of HCMV, EBV, and herpes simplex virus active infections to clinical characteristics of periapical lesions and periapical bacterial flora. Microbial samples were collected from 34 periapical lesions in conjunction with periapical surgery. Part of the periapical specimen was frozen for virologic examination, and another part was transferred to anaerobic transport medium for bacteriologic examination. RNA was isolated by means of a guanidinium isothiocyanate-acid phenol procedure, and cDNA was produced using herpesvirus-specific primers and reverse-transcription polymerase chain reaction amplification. Bacteriologic examination was performed according to established anaerobic culture methods. Of the 34 periapical lesions studied, 20 showed both HCMV and EBV, seven showed only HCMV, one showed only EBV, and six showed neither HCMV nor EBV. Herpes simplex virus was detected in two lesions. Higher occurrence of herpesvirus was detected in large versus small periapical lesions (p aggressive types of periapical pathosis in humans.

  3. Bacterial communities in petroleum oil in stockpiles.

    Science.gov (United States)

    Yoshida, Nobuyuki; Yagi, Kazuhiro; Sato, Daisuke; Watanabe, Noriko; Kuroishi, Takeshi; Nishimoto, Kana; Yanagida, Akira; Katsuragi, Tohoru; Kanagawa, Takahiro; Kurane, Ryuichiro; Tani, Yoshiki

    2005-02-01

    Bacterial communities in crude-oil samples from Japanese oil stockpiles were investigated by 16S rRNA gene cloning, followed by denaturing gradient gel electrophoresis (DGGE) analysis. 16S rRNA genes were successfully amplified by PCR after isooctane treatment from three kinds of crude-oil sample collected at four oil stockpiles in Japan. DGGE profiles showed that bacteria related to Ochrobactrum anthropi, Burkholderia cepacia, Stenotrophomonas maltophilia, Propionibacterium acnes, and Brevundimonas diminuta were frequently detected in most crude-oil samples. The bacterial communities differed in the sampling time and layer. Among the predominant bacteria detected in the crude oil, only three species were found for bacteria isolated on agar plates and were related to Burkholderia, Stenotrophomonas, and Propionibacterium, while Ochrobactrum sp. could not be isolated although this species seemed to be the most abundant bacterium in crude oil from the DGGE profiles. Using an archaea-specific primer set, methanogens were found in crude-oil sludge but not in crude-oil samples, indicating that methanogens might be involved in sludge formation in oil stockpiles.

  4. Detection of wetwood by ultrasonics

    Science.gov (United States)

    Mohammed F. Kabir; Theodor D. Leininger; Philip A. Araman; Matthew F. Winn

    2006-01-01

    Wetwood, or bacterially infected wood, is a severe processing problem and causes serious drying defects in lumber. The detection of wetwood is, therefore, important for proper processing and quality wood products. An investigation has been carried out to detect wetwood of cherrybark oak (Quercus pagoda Raf.), water oak (Quercus nigra...

  5. Bacterial community survey of sediments at Naracoorte Caves, Australia

    Directory of Open Access Journals (Sweden)

    Ball Andrew S.

    2012-07-01

    Full Text Available Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits and Strawhaven Cave was used as control (no tourist access. Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces. The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.

  6. Bacterial sepsis and chemokines.

    Science.gov (United States)

    Kobayashi, Makiko; Tsuda, Yasuhiro; Yoshida, Tsuyoshi; Takeuchi, Dan; Utsunomiya, Tokuichiro; Takahashi, Hitoshi; Suzuki, Fujio

    2006-01-01

    Bacterial sepsis causes a high mortality rate when it occurs in patients with compromised host defenses. Severely burned patients, typical immunocompromised hosts, are extremely susceptible to infections from various pathogens, and a local wound infection frequently escalates into sepsis. In these patients, Staphylococcus aureus, Enterococcus faecalis and Pseudomonas aeruginosa are familiar pathogens that cause opportunistic infections. Also, polymicrobial sepsis frequently occurs in these patients. In this review, therefore, the roles of chemokines in thermally injured patients infected with these 3 pathogens and polymicrobial sepsis will be discussed. These infections in thermally injured patients may be controlled immunologically, because immunocompetent hosts are resistant to infections with these pathogens. Classically activated macrophages (M1Mphi) are major effector cells for host innate immune responses against these infections. However, M1Mphi are not generated in thermally injured patients whose alternatively activated macrophages (M2Mphi) predominate. M2Mphi appear in patients early after severe burn injuries. M2Mphi inhibit M1Mphi generation through the secretion of CCL17 and IL-10. As a modulator of Mphi, two different subsets of neutrophils (PMN-I, PMN-II) are described. PMN-I direct the polarization of resident Mphi into M1Mphi through the production of CCL3. M2Mphi are induced from resident Mphi by CCL2 released from PMN-II. Therefore, as an inhibitor of CCL2, glycyrrhizin protects individuals infected with S. aureus. Sepsis stemming from P. aeruginosa wound infection is also influenced by CCL2 released from immature myeloid cells. A large number of immature myeloid cells appear in association with burn injuries. Host resistance to S. aureus, E. faecalis, P. aeruginosa or polymicrobial infections may be improved in thermally injured patients through the induction of M1Mphi, elimination of CCL2 and/or depletion of M2Mphi induced by CCL2.

  7. Bacterial Communities: Interactions to Scale

    Directory of Open Access Journals (Sweden)

    Reed M. Stubbendieck

    2016-08-01

    Full Text Available In the environment, bacteria live in complex multispecies communities. These communities span in scale from small, multicellular aggregates to billions or trillions of cells within the gastrointestinal tract of animals. The dynamics of bacterial communities are determined by pairwise interactions that occur between different species in the community. Though interactions occur between a few cells at a time, the outcomes of these interchanges have ramifications that ripple through many orders of magnitude, and ultimately affect the macroscopic world including the health of host organisms. In this review we cover how bacterial competition influences the structures of bacterial communities. We also emphasize methods and insights garnered from culture-dependent pairwise interaction studies, metagenomic analyses, and modeling experiments. Finally, we argue that the integration of multiple approaches will be instrumental to future understanding of the underlying dynamics of bacterial communities.

  8. Bacterial flora of sturgeon fingerling

    International Nuclear Information System (INIS)

    Arani, A.S.; Mosahab, R.

    2008-01-01

    The study on microbial populations is a suitable tool to understand and apply control methods to improve the sanitary level of production in fish breeding and rearing centers, ensure health of sturgeon fingerlings at the time of their release into the rivers and also in the conversation and restoration of these valuable stocks in the Caspian Sea, Iran. A laboratory research based on Austin methods (Austin, B., Austin, D.A. 1993) was conducted for bacterial study on 3 sturgeon species naming A. persicus, A. stellatus and A. nudiventris during different growth stages. Bacterial flora of Acinetobacter, Moraxella, Aeromonas, Vibrio, Edwardsiella, Staphylococcus, Proteus, Yersinia, Pseudomonas and Plesiomonas were determined. The factors which may induce changes in bacterial populations during different stages of fife are the followings: quality of water in rearing ponds, different conditions for growth stages, suitable time for colonization of bacterial flora in rearing pond, water temperature increase in fingerlings size and feeding condition. (author)

  9. Subdural Empyema in Bacterial Meningitis

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2013-01-01

    Full Text Available Researchers at the University of Amsterdam, the Netherlands, evaluated the occurrence, treatment, and outcome of subdural empyema as a complication of community-acquired bacterial meningitis in 28 (2.7% adults.

  10. The role of small intestinal bacterial overgrowth in Parkinson's disease.

    Science.gov (United States)

    Fasano, Alfonso; Bove, Francesco; Gabrielli, Maurizio; Petracca, Martina; Zocco, Maria Assunta; Ragazzoni, Enzo; Barbaro, Federico; Piano, Carla; Fortuna, Serena; Tortora, Annalisa; Di Giacopo, Raffaella; Campanale, Mariachiara; Gigante, Giovanni; Lauritano, Ernesto Cristiano; Navarra, Pierluigi; Marconi, Stefano; Gasbarrini, Antonio; Bentivoglio, Anna Rita

    2013-08-01

    Parkinson's disease is associated with gastrointestinal motility abnormalities favoring the occurrence of local infections. The aim of this study was to investigate whether small intestinal bacterial overgrowth contributes to the pathophysiology of motor fluctuations. Thirty-three patients and 30 controls underwent glucose, lactulose, and urea breath tests to detect small intestinal bacterial overgrowth and Helicobacter pylori infection. Patients also underwent ultrasonography to evaluate gastric emptying. The clinical status and plasma concentration of levodopa were assessed after an acute drug challenge with a standard dose of levodopa, and motor complications were assessed by Unified Parkinson's Disease Rating Scale-IV and by 1-week diaries of motor conditions. Patients with small intestinal bacterial overgrowth were treated with rifaximin and were clinically and instrumentally reevaluated 1 and 6 months later. The prevalence of small intestinal bacterial overgrowth was significantly higher in patients than in controls (54.5% vs. 20.0%; P = .01), whereas the prevalence of Helicobacter pylori infection was not (33.3% vs. 26.7%). Compared with patients without any infection, the prevalence of unpredictable fluctuations was significantly higher in patients with both infections (8.3% vs. 87.5%; P = .008). Gastric half-emptying time was significantly longer in patients than in healthy controls but did not differ in patients based on their infective status. Compared with patients without isolated small intestinal bacterial overgrowth, patients with isolated small intestinal bacterial overgrowth had longer off time daily and more episodes of delayed-on and no-on. The eradication of small intestinal bacterial overgrowth resulted in improvement in motor fluctuations without affecting the pharmacokinetics of levodopa. The relapse rate of small intestinal bacterial overgrowth at 6 months was 43%. © 2013 Movement Disorder Society. Copyright © 2013 Movement

  11. Significant relationship between soil bacterial community structure and incidence of bacterial wilt disease under continuous cropping system.

    Science.gov (United States)

    She, Siyuan; Niu, Jiaojiao; Zhang, Chao; Xiao, Yunhua; Chen, Wu; Dai, Linjian; Liu, Xueduan; Yin, Huaqun

    2017-03-01

    Soil bacteria are very important in biogeochemical cycles and play significant role in soil-borne disease suppression. Although continuous cropping is responsible for soil-borne disease enrichment, its effect on tobacco plant health and how soil bacterial communities change are yet to be elucidated. In this study, soil bacterial communities across tobacco continuous cropping time-series fields were investigated through high-throughput sequencing of 16S ribosomal RNA genes. The results showed that long-term continuous cropping could significantly alter soil microbial communities. Bacterial diversity indices and evenness indices decreased over the monoculture span and obvious variations for community structures across the three time-scale tobacco fields were detected. Compared with the first year, the abundances of Arthrobacter and Lysobacter showed a significant decrease. Besides, the abundance of the pathogen Ralstonia spp. accumulated over the monoculture span and was significantly correlated with tobacco bacterial wilt disease rate. Moreover, Pearson's correlation demonstrated that the abundance of Arthrobacter and Lysobacter, which are considered to be beneficial bacteria had significant negative correlation with tobacco bacterial wilt disease. Therefore, after long-term continuous cropping, tobacco bacterial wilt disease could be ascribed to the alteration of the composition as well as the structure of the soil microbial community.

  12. Correlation Between the Clinical Diagnosis of Bacterial Vaginosis and the Results of a Proline Aminopeptidase Assay

    Directory of Open Access Journals (Sweden)

    George H. Nelson

    1994-01-01

    Full Text Available Objective: The object of this study was to develop a simple and inexpensive test for detection of bacterial vaginosis (BV in pregnant patients and to test its accuracy in a clinic population.

  13. Arsenic uptake in bacterial calcite

    Energy Technology Data Exchange (ETDEWEB)

    Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew G.; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

    2018-02-01

    Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and Xray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

  14. Arsenic uptake in bacterial calcite

    Science.gov (United States)

    Catelani, Tiziano; Perito, Brunella; Bellucci, Francesco; Lee, Sang Soo; Fenter, Paul; Newville, Matthew; Rimondi, Valentina; Pratesi, Giovanni; Costagliola, Pilario

    2018-02-01

    Bio-mediated processes for arsenic (As) uptake in calcite were investigated by means of X-ray Diffraction (XRD) and X-ray Absorption Spectroscopy (XAS) coupled with X-ray Fluorescence measurements. The environmental bacterial strain Bacillus licheniformis BD5, sampled at the Bullicame Hot Springs (Viterbo, Central Italy), was used to synthesize calcite from As-enriched growth media. Both liquid and solid cultures were applied to simulate planktonic and biofilm community environments, respectively. Bacterial calcite samples cultured in liquid media had an As enrichment factor (Kd) 50 times higher than that from solid media. The XRD analysis revealed an elongation of the crystal lattice along the c axis (by 0.03 Å) for biogenic calcite, which likely resulted from the substitution of larger arsenate for carbonate in the crystal. The XAS data also showed a clear difference in the oxidation state of sorbed As between bacterial and abiotic calcite. Abiotic chemical processes yielded predominantly As(V) uptake whereas bacterial precipitation processes led to the uptake of both As(III) and As(V). The presence of As(III) in bacterial calcite is proposed to result from subsequent reduction of arsenate to arsenite by bacterial activities. To the best of our knowledge, this is the first experimental observation of the incorporation of As(III) in the calcite crystal lattice, revealing a critical role of biochemical processes for the As cycling in nature.

  15. Current knowledge of bacterial vaginosis

    Directory of Open Access Journals (Sweden)

    Đukić Slobodanka

    2011-01-01

    Full Text Available Bacterial vaginosis, earlier termed nonspecific vaginitis (anaerobic vaginosis because of the absence of recognized pathogens, is most common vaginal syndrome of women of childbearing age affecting 15-30%. This syndrome, whose aetiology and pathogenesis remains unknown, is characterized by significant changes in the vaginal ecosystem. These changes consist of a decrease in the number of lactobacilli and a large increase in the number of anaerobic organisms. The bacteria adhere to desquamated epithelial cells with a distinctive appearance of clue cells The main complaints of women with symptomatic bacterial vaginosis include vaginal discharge and odour. However, a significant number of all women who have bacterial vaginosis deny symptoms. Bacterial vaginosis is associated with a number of gynaecologic and obstetric complications including cervicitis, cervical neoplasia, pelvic inflammatory disease, postoperative infections, and preterm labour. The diagnosis is most frequently made based on vaginal smear stained according to Gram (Nugent scoring method. Metronidazole and clindamycin are the drugs of choice for treatment of women with bacterial vaginosis. Which women should undergo treatment? According to the prevailing attitude, it should include women with symptoms. Symptomatic women with frequent relapses of bacterial vaginosisas, as a rule, have poor response to the applied therapy. To achieve better efficiency in the treatment of such women, it is necessary to have more extensive understanding of all factors in the pathogenesis of the syndrome.

  16. Bacterial migration through punctured surgical gloves under real surgical conditions

    Directory of Open Access Journals (Sweden)

    Heidecke Claus-Dieter

    2010-07-01

    Full Text Available Abstract Background The aim of this study was to confirm recent results from a previous study focussing on the development of a method to measure the bacterial translocation through puncture holes in surgical gloves under real surgical conditions. Methods An established method was applied to detect bacterial migration from the operating site through the punctured glove. Biogel™ double-gloving surgical gloves were used during visceral surgeries over a 6-month period. A modified Gaschen-bag method was used to retrieve organisms from the inner glove, and thus-obtained bacteria were compared with micro-organisms detected by an intra-operative swab. Results In 20 consecutive procedures, 194 gloves (98 outer gloves, 96 inner gloves were examined. The rate of micro-perforations of the outer surgical glove was 10% with a median wearing time of 100 minutes (range: 20-175 minutes. Perforations occurred in 81% on the non-dominant hand, with the index finger most frequently (25% punctured. In six cases, bacterial migration could be demonstrated microbiologically. In 5% (5/98 of outer gloves and in 1% (1/96 of the inner gloves, bacterial migration through micro-perforations was observed. For gloves with detected micro-perforations (n = 10 outer layers, the calculated migration was 50% (n = 5. The minimum wearing time was 62 minutes, with a calculated median wearing time of 71 minutes. Conclusions This study confirms previous results that bacterial migration through unnoticed micro-perforations in surgical gloves does occur under real practical surgical conditions. Undetected perforation of surgical gloves occurs frequently. Bacterial migration from the patient through micro-perforations on the hand of surgeons was confirmed, limiting the protective barrier function of gloves if worn over longer periods.

  17. Molecular analysis of bacterial pathogens in otitis media with effusion.

    Science.gov (United States)

    Post, J C; Preston, R A; Aul, J J; Larkins-Pettigrew, M; Rydquist-White, J; Anderson, K W; Wadowsky, R M; Reagan, D R; Walker, E S; Kingsley, L A; Magit, A E; Ehrlich, G D

    To determine if the polymerase chain reaction (PCR) can detect bacterial DNA in pediatric middle ear effusions that are sterile by standard cultural methods. Single-center, blinded, comparative study of diagnostic assays. The PCR-based detection systems for Moraxella catarrhalis, Haemophilus influenzae, and Streptococcus pneumoniae were designed and validated using a battery of DNAs obtained from cultured bacteria. Chronic middle ear effusion specimens were collected and comparatively analyzed by culture and the PCR. Tertiary care pediatric hospital. A total of 97 middle ear effusions were collected from pediatric outpatients at Children's Hospital of Pittsburgh (Pa) during myringotomy and tube placement for chronic otitis media with effusion (duration > 3 months). All patients had failed multiple courses of antimicrobial therapy and were diagnosed by a combination of validated otoscopy and tympanograms. Differences in the percentage of positive test results between PCR-based assays and culture for M catarrhalis, H influenzae, and S pneumoniae. Of the 97 specimens of otitis media with effusion, 28 (28.9%) tested positive by both culture and PCR for M catarrhalis, H influenzae, or S pneumoniae. An additional 47 specimens (48%) were PCR positive/culture negative for these three bacterial species. Thus, 75 (77.3%) of the 97 specimens tested PCR positive for one or more of the three test organisms. The minimum number of bacterial genomic equivalents present in the average culture-negative ear was estimated to be greater than 10(4) based on dilutional experiments. The PCR-based assay systems can detect the presence of bacterial DNA in a significant percentage of culturally sterile middle ear effusions. While this finding is not proof of an active bacterial infectious process, the large number of bacterial genomic equivalents present in the ears is suggestive of an active process.

  18. [Implementation of in vitro culture of Mycobacterium ulcerans from clinical samples versus detection of acid-fast bachilli and bacterial genome in Abidjan, Côte d'Ivoire].

    Science.gov (United States)

    Coulibaly, B; Coulibaly-N'Golo, M-D G; Ekaza, E; Aka, N; N'Guessan, K R; Baudryard, A; Assandé, J-M; Trébissou, N; Guédé-Guina, F; Dosso, M

    2010-02-01

    Mycobacterium ulcerans infections are a public health problem in Céte d'Ivoire. The etiological diagnosis of this disease made by culture remains a big concern due to the slowness and difficulties encountered. This detection by culture of M. ulcerans represents a big interest as it allows obtaining the circulating strains for research. The purpose of this study was to determine on a routine basis in a poorly equipped laboratory, in vitro culture of M. ulcerans from exudates of skin ulcerations and from biopsy of patients with suspected Buruli ulcer. A particular attention was paid to the conditioning of the sample forwarded to the laboratory and inoculation in Lowenstein-Jensen medium supplemented with glycerol. The results of the three methods for the analysis showed 26.7, 57.4 and 17.8% positive rate respectively in the microscopy examination by nested PCR and by culture. In all the analysis, the positive rate from biopsy is higher than that obtained from exudates. The overall contamination rate by invasion of the three tubes of culture by fungi is 15.8 with 14.3 and 19.4% respectively,from exudates and biopsies. All positive samples in Ziehl-Neelsen staining and in culture were also positive by nested PCR. The nested PCR confirmed the positive strains found in culture, which were responsible for skin ulcerations. After culture, only one strain was nPCR negative. This strain was identified as Mycobacterium Gordonae. Our culture conditions showed that M. ulcerans was not the only strain identified and that other strains were present in the culture. We can conclude that the culture of M. ulcerans, in spite of the growth difficulties of the bacterium can be performed in laboratory in developing countries despite the lack of reagent and consumables. The implementation of this culture is the only way to determine sensitivity tests in vitro and in vivo in order to treat patients with Buruli ulcer.

  19. Bacterial Biosensors for Measuring Availability of Environmental Pollutants

    Directory of Open Access Journals (Sweden)

    Jan Roelof van der Meer

    2008-07-01

    Full Text Available Traditionally, pollution risk assessment is based on the measurement of a pollutant’s total concentration in a sample. The toxicity of a given pollutant in the environment, however, is tightly linked to its bioavailability, which may differ significantly from the total amount. Physico-chemical and biological parameters strongly influence pollutant fate in terms of leaching, sequestration and biodegradation. Bacterial sensorreporters, which consist of living micro-organisms genetically engineered to produce specific output in response to target chemicals, offer an interesting alternative to monitoring approaches. Bacterial sensor-reporters detect bioavailable and/or bioaccessible compound fractions in samples. Currently, a variety of environmental pollutants can be targeted by specific biosensor-reporters. Although most of such strains are still confined to the lab, several recent reports have demonstrated utility of bacterial sensing-reporting in the field, with method detection limits in the nanomolar range. This review illustrates the general design principles for bacterial sensor-reporters, presents an overview of the existing biosensor-reporter strains with emphasis on organic compound detection. A specific focus throughout is on the concepts of bioavailability and bioaccessibility, and how bacteria-based sensing-reporting systems can help to improve our basic understanding of the different processes at work.

  20. Bacterial Prostatitis: Bacterial Virulence, Clinical Outcomes, and New Directions.

    Science.gov (United States)

    Krieger, John N; Thumbikat, Praveen

    2016-02-01

    Four prostatitis syndromes are recognized clinically: acute bacterial prostatitis, chronic bacterial prostatitis, chronic prostatitis/chronic pelvic pain syndrome, and asymptomatic prostatitis. Because Escherichia coli represents the most common cause of bacterial prostatitis, we investigated the importance of bacterial virulence factors and antimicrobial resistance in E. coli strains causing prostatitis and the potential association of these characteristics with clinical outcomes. A structured literature review revealed that we have limited understanding of the virulence-associated characteristics of E. coli causing acute prostatitis. Therefore, we completed a comprehensive microbiological and molecular investigation of a unique strain collection isolated from healthy young men. We also considered new data from an animal model system suggesting certain E. coli might prove important in the etiology of chronic prostatitis/chronic pelvic pain syndrome. Our human data suggest that E. coli needs multiple pathogenicity-associated traits to overcome anatomic and immune responses in healthy young men without urological risk factors. The phylogenetic background and accumulation of an exceptional repertoire of extraintestinal pathogenic virulence-associated genes indicate that these E. coli strains belong to a highly virulent subset of uropathogenic variants. In contrast, antibiotic resistance confers little added advantage to E. coli strains in these healthy outpatients. Our animal model data also suggest that certain pathogenic E. coli may be important in the etiology of chronic prostatitis/chronic pelvic pain syndrome through mechanisms that are dependent on the host genetic background and the virulence of the bacterial strain.

  1. The Human Vaginal Bacterial Biota and Bacterial Vaginosis

    Directory of Open Access Journals (Sweden)

    Sujatha Srinivasan

    2008-01-01

    Full Text Available The bacterial biota of the human vagina can have a profound impact on the health of women and their neonates. Changes in the vaginal microbiota have been associated with several adverse health outcomes including premature birth, pelvic inflammatory disease, and acquisition of HIV infection. Cultivation-independent molecular methods have provided new insights regarding bacterial diversity in this important niche, particularly in women with the common condition bacterial vaginosis (BV. PCR methods have shown that women with BV have complex communities of vaginal bacteria that include many fastidious species, particularly from the phyla Bacteroidetes and Actinobacteria. Healthy women are mostly colonized with lactobacilli such as Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus iners, though a variety of other bacteria may be present. The microbiology of BV is heterogeneous. The presence of Gardnerella vaginalis and Atopobium vaginae coating the vaginal epithelium in some subjects with BV suggests that biofilms may contribute to this condition.

  2. Community-acquired bacterial meningitis.

    Science.gov (United States)

    Costerus, Joost M; Brouwer, Matthijs C; Bijlsma, Merijn W; van de Beek, Diederik

    2017-02-01

    Bacterial meningitis is a medical emergency and is associated with a high disease burden. We reviewed recent progress in the management of patients with community-acquired bacterial meningitis. The worldwide burden of disease of bacterial meningitis remains high, despite the decreasing incidence following introduction of routine vaccination campaigns. Delay in diagnosis and treatment remain major concerns in the management of acute bacterial meningitis. European Society of Clinical Microbiology and Infectious Diseases guidelines strive for a door-to-antibiotic-time less than 1 h. Polymerase chain reaction (PCR) has emerged as an important diagnostic tool to identify the causative organism. Point-of-care tests using fast multiplex PCR have been developed, but additional value has not been proven. Although anecdotal observations advocate pressure-based management, a randomized controlled trial will need to be performed first to determine efficacy and safety of such an aggressive treatment approach. Adjunctive dexamethasone remains the only adjunctive therapy with proven efficacy. The incidence of bacterial meningitis has been decreasing after the implementation of effective vaccines. Treatment should be administered as soon as possible and time to treatment should not exceed 1 h.

  3. Biodegradation of petroleum oil by certain bacterial strains

    International Nuclear Information System (INIS)

    Zakaria, A.E.M.

    1998-01-01

    Balaeam base oil was chosen as a model oil in the present study through which some abiotic treatments were implemented aiming at attenuating its naphthenic and aromatic contents; such as the adsorptive technique and the gamma-irradiation technique . In an attempt to apply the biodegrading bacteria as oil pollutant bio indicators upon coastal water samples, a correlation between hydrocarbon concentration and the relative enumeration of the bacterial oil degraders was detected for some litter locations along the mediterranean Sea shore west and east Delta, Suez canal. and suez gulf. 24 petroleum utilizing bacterial isolates were isolated from El-Zayteia port (suez) and identified by morphological, physiological and environmental examination . the biodegradation capacity of the isolates towards the chosen model oil and its separate components was studied in comparison with the standard isolate pseudomonas aeruginosa. Further, the role of the bacterial plasmids taking part in the biodegradation process was investigated as well

  4. Bacterial communities in batch and continuous-flow wetlands treating the herbicide S-metolachlor

    International Nuclear Information System (INIS)

    Elsayed, O.F.; Maillard, E.; Vuilleumier, S.; Imfeld, G.

    2014-01-01

    Knowledge of wetland bacterial communities in the context of pesticide contamination and hydrological regime is scarce. We investigated the bacterial composition in constructed wetlands receiving Mercantor Gold ® contaminated water (960 g L −1 of the herbicide S-metolachlor, > 80% of the S-enantiomer) operated under continuous-flow or batch modes to evaluate the impact of the hydraulic regime. In the continuous-flow wetland, S-metolachlor mass removal was > 40%, whereas in the batch wetland, almost complete removal of S-metolachlor (93–97%) was observed. Detection of ethanesulfonic and oxanilic acid degradation products further indicated S-metolachlor biodegradation in the two wetlands. The dominant bacterial populations were characterised by terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing. The bacterial profiles evolved during the first 35 days of the experiment, starting from a composition similar to that of inlet water, with the use of nitrate and to a lesser extent sulphate and manganese as terminal electron acceptors for microbial metabolism. Proteobacteria were the most abundant phylum, with Beta-, Alpha- and Gammaproteobacteria representing 26%, 19% and 17% respectively of total bacterial abundance. Bacterial composition in wetland water changed gradually over time in continuous-flow wetland and more abruptly in the batch wetland. Differences in overall bacterial water structure in the two systems were modest but significant (p = 0.008), and S-metolachlor, nitrate, and total inorganic carbon concentrations correlated with changes in the bacterial profiles. Together, the results highlight that bacterial composition profiles and their dynamics may be used as bioindicators of herbicide exposure and hydraulic disturbances in wetland systems. - Highlights: • We evaluated the bacterial composition in wetlands treating S-metolachlor • Hydraulic regime impacted biogeochemical processes and S-metolachlor removal

  5. Precise, High-throughput Analysis of Bacterial Growth.

    Science.gov (United States)

    Kurokawa, Masaomi; Ying, Bei-Wen

    2017-09-19

    Bacterial growth is a central concept in the development of modern microbial physiology, as well as in the investigation of cellular dynamics at the systems level. Recent studies have reported correlations between bacterial growth and genome-wide events, such as genome reduction and transcriptome reorganization. Correctly analyzing bacterial growth is crucial for understanding the growth-dependent coordination of gene functions and cellular components. Accordingly, the precise quantitative evaluation of bacterial growth in a high-throughput manner is required. Emerging technological developments offer new experimental tools that allow updates of the methods used for studying bacterial growth. The protocol introduced here employs a microplate reader with a highly optimized experimental procedure for the reproducible and precise evaluation of bacterial growth. This protocol was used to evaluate the growth of several previously described Escherichia coli strains. The main steps of the protocol are as follows: the preparation of a large number of cell stocks in small vials for repeated tests with reproducible results, the use of 96-well plates for high-throughput growth evaluation, and the manual calculation of two major parameters (i.e., maximal growth rate and population density) representing the growth dynamics. In comparison to the traditional colony-forming unit (CFU) assay, which counts the cells that are cultured in glass tubes over time on agar plates, the present method is more efficient and provides more detailed temporal records of growth changes, but has a stricter detection limit at low population densities. In summary, the described method is advantageous for the precise and reproducible high-throughput analysis of bacterial growth, which can be used to draw conceptual conclusions or to make theoretical observations.

  6. Abdominal radiation causes bacterial translocation

    International Nuclear Information System (INIS)

    Guzman-Stein, G.; Bonsack, M.; Liberty, J.; Delaney, J.P.

    1989-01-01

    The purpose of this study was to determine if a single dose of radiation to the rat abdomen leads to bacterial translocation into the mesenteric lymph nodes (MLN). A second issue addressed was whether translocation correlates with anatomic damage to the mucosa. The radiated group (1100 cGy) which received anesthesia also was compared with a control group and a third group which received anesthesia alone but no abdominal radiation. Abdominal radiation lead to 100% positive cultures of MLN between 12 hr and 4 days postradiation. Bacterial translocation was almost nonexistent in the control and anesthesia group. Signs of inflammation and ulceration of the intestinal mucosa were not seen until Day 3 postradiation. Mucosal damage was maximal by Day 4. Bacterial translocation onto the MLN after a single dose of abdominal radiation was not apparently dependent on anatomical, histologic damage of the mucosa

  7. Bacterial Degradation of Aromatic Compounds

    Directory of Open Access Journals (Sweden)

    Qing X. Li

    2009-01-01

    Full Text Available Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.

  8. Soil bacterial communities associated with natural and commercial Cyclopia spp.

    Science.gov (United States)

    Postma, Anneke; Slabbert, Etienne; Postma, Ferdinand; Jacobs, Karin

    2016-03-01

    The commercially important plants in the genus Cyclopia spp. are indigenous to the Cape Floristic Region of South Africa and are used to manufacture an herbal tea known as honeybush tea. Growing in the low nutrient fynbos soils, these plants are highly dependent on symbiotic interactions with soil microorganisms for nutrient acquisition. The aim of this study was to investigate the soil bacterial communities associated with two commercially important Cyclopia species, namely C. subternata and C. longifolia. Specific interest was the differences between rhizosphere and bulk soil collected from natural sites and commercially grown plants. Samples were collected on two occasions to include a dry summer and wet winter season. Results showed that the dominant bacterial taxa associated with these plants included Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria. Commercial and natural as well as rhizosphere and bulk soil samples were highly similar in bacterial diversity and species richness. Significant differences were detected in bacterial community structures and co-occurrence patterns between the wet and dry seasons. The results of this study improved our knowledge on what effect commercial Cyclopia plantations and seasonal changes can have on soil bacterial communities within the endemic fynbos biome. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Bacterial computing with engineered populations.

    Science.gov (United States)

    Amos, Martyn; Axmann, Ilka Maria; Blüthgen, Nils; de la Cruz, Fernando; Jaramillo, Alfonso; Rodriguez-Paton, Alfonso; Simmel, Friedrich

    2015-07-28

    We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output and cell-cell interfacing, as well as extensive analysis. In this overview paper, we describe our approach to each of these, and suggest possible areas for future research. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  10. The physical basis of bacterial quorum communication

    CERN Document Server

    2015-01-01

    This book aims to educate physical scientists and quantitatively-oriented biologists on the application of physical experimentation and analysis, together with appropriate modeling, to understanding and interpreting microbial chemical communication and especially quorum sensing (QS). Quorum sensing describes a chemical communication behavior that is nearly universal among bacteria. Individual cells release a diffusible small molecule (an autoinducer) into their environment. A high concentration of this autoinducer serves as a signal of high population density, triggering new patterns of gene expression throughout the population. However QS is often much more complex than simple census-taking. Many QS bacteria produce and detect multiple autoinducers, which generate quorum signal cross talk with each other and with other bacterial species. QS gene regulatory networks operate in physically complex environments and respond to a range of inputs in addition to autoinducer signals. While many individual QS systems ...

  11. Counterimmunoelectrophoresis in the diagnosis of bacterial meningitis

    DEFF Research Database (Denmark)

    Colding, H; Lind, I

    1977-01-01

    was performed with antisera to Neisseria meningitidis (groups A, B and C), Streptococcus pneumoniae (omni-serum and pools A to 1), and Haemophilus influenzae type b. Antigen was detected in 57% (72/126) of specimens in which cultures revealed these three kinds of microorganisms in CSF and in 12% (17....... influenzae type b. Specific diagnosis was achieved in 60% (170/283) of the specimens studied and could be extablished within 1 h in 85% (145/170) by the combined results of microscopy and CIE. Ten specimens, nine of which showed a reaction with antiserum to N. meningitidis group A, were positive by CIE only......./139) of the culture-negative specimens. CSF specimens from 21 patients with bacterial meningitis caused by other species were all negative in CIE, except four, three of which contained Escherichia coli antigen reacting with antiserum to N. meningitidis group B and one E. coli antigen reacting with antiserum to H...

  12. Biotechnological applications of bacterial cellulases

    Czech Academy of Sciences Publication Activity Database

    Menéndez, E.; García-Fraile, Paula; Rivas, R.

    2015-01-01

    Roč. 2, č. 3 (2015), s. 163-182 ISSN 2306-5354 R&D Projects: GA MŠk(CZ) EE2.3.30.0003 Institutional support: RVO:61388971 Keywords : Biotechnological applications * Bacterial cellulases * Cellulose degradation Subject RIV: EE - Microbiology, Virology

  13. Disease notes - Bacterial root rot

    Science.gov (United States)

    Bacterial root rot initiated by lactic acid bacteria, particularly Leuconostoc, occurs every year in Idaho sugarbeet fields. Hot fall weather seems to make the problem worse. Although Leuconostoc initiates the rot, other bacteria and yeast frequently invade the tissue as well. The acetic acid bac...

  14. bacterial flora and antibiotic sensitivity

    African Journals Online (AJOL)

    Purulent pelvic collections are common pathologies observed in contemporary gynaecological practice. They may originate from chronic pelvic inflammatory disease, from abortions or following normal deliveries. This study was designed to compare the bacterial flora in purulent pelvic collections obtained from HIV infected ...

  15. Community-acquired bacterial meningitis

    NARCIS (Netherlands)

    van de Beek, Diederik; Brouwer, Matthijs; Hasbun, Rodrigo; Koedel, Uwe; Whitney, Cynthia G.; Wijdicks, Eelco

    2016-01-01

    Meningitis is an inflammation of the meninges and subarachnoid space that can also involve the brain cortex and parenchyma. It can be acquired spontaneously in the community - community-acquired bacterial meningitis - or in the hospital as a complication of invasive procedures or head trauma

  16. Molecular mechanisms underlying bacterial persisters

    DEFF Research Database (Denmark)

    Maisonneuve, Etienne; Gerdes, Kenn

    2014-01-01

    All bacteria form persisters, cells that are multidrug tolerant and therefore able to survive antibiotic treatment. Due to the low frequencies of persisters in growing bacterial cultures and the complex underlying molecular mechanisms, the phenomenon has been challenging to study. However, recent...

  17. Biotechnological applications of bacterial cellulases

    Directory of Open Access Journals (Sweden)

    Esther Menendez

    2015-08-01

    Full Text Available Cellulases have numerous applications in several industries, including biofuel production, food and feed industry, brewing, pulp and paper, textile, laundry, and agriculture.Cellulose-degrading bacteria are widely spread in nature, being isolated from quite different environments. Cellulose degradation is the result of a synergic process between an endoglucanase, an exoglucanase and a,β-glucosidase. Bacterial endoglucanases degrade ß-1,4-glucan linkages of cellulose amorphous zones, meanwhile exoglucanases cleave the remaining oligosaccharide chains, originating cellobiose, which is hydrolyzed by ß-glucanases. Bacterial cellulases (EC 3.2.1.4 are comprised in fourteen Glycosil Hydrolase families. Several advantages, such as higher growth rates and genetic versatility, emphasize the suitability and advantages of bacterial cellulases over other sources for this group of enzymes. This review summarizes the main known cellulolytic bacteria and the best strategies to optimize their cellulase production, focusing on endoglucanases, as well as it reviews the main biotechnological applications of bacterial cellulases in several industries, medicine and agriculture.

  18. [Bacterial vaginosis and spontaneous preterm birth].

    Science.gov (United States)

    Brabant, G

    2016-12-01

    To determine if bacterial vaginosis is a marker for risk of spontaneous preterm delivery and if its detection and treatment can reduce this risk. Consultation of the database Pubmed/Medline, Science Direct, and international guidelines of medical societies. Bacterial vaginosis (BV) is a dysbiosis resulting in an imbalance in the vaginal flora through the multiplication of anaerobic bacteria and jointly of a disappearance of well-known protective Lactobacilli. His diagnosis is based on clinical Amsel criteria and/or a Gram stain with establishment of the Nugent score. The prevalence of the BV extraordinarily varies according to ethnic and/or geographical origin (4-58 %), in France, it is close to 7 % in the first trimester of pregnancy (EL2). The link between BV and spontaneous premature delivery is low with an odds ratio between 1.5 and 2 in the most recent studies (EL3). Metronidazole or clindamycin is effective to treat BV (EL3). It is recommended to prescribe one of these antibiotics in the case of symptomatic BV (Professional Consensus). The testing associated with the treatment of BV in the global population showed no benefit in the prevention of the risk of spontaneous preterm delivery (EL2). Concerning low-risk asymptomatic population (defined by the absence of antecedent of premature delivery), it has been failed profit to track and treat the BV in the prevention of the risk of spontaneous preterm delivery (EL1). Concerning the high-risk population (defined by a history of preterm delivery), it has been failed profit to track and treat the VB in the prevention of the risk of spontaneous preterm delivery (EL3). However, in the sub population of patients with a history of preterm delivery occurred in a context of materno-fetal bacterial infection, there may be a benefit to detect and treat early and systematically genital infection, and in particular the BV (Professional Consensus). The screening and treatment of BV during pregnancy in asymptomatic low

  19. Engineering Bacterial Thiosulfate and Tetrathionate Sensors for Detecting Gut Inflammation

    Science.gov (United States)

    2017-04-03

    of environments. Materials and Methods Bioinformatics analysis A full alignment based on the phosphonate-bd Pfam family (PF12974) was downloaded from...2006) TorT, a member of a new periplasmic binding protein family, triggers induction of the Tor respiratory system upon trimethylamine N-oxide

  20. Detection of meta- and ortho-cleavage dioxygenases in bacterial ...

    African Journals Online (AJOL)

    DR. MIKE HORSFALL

    was defined as the initial rate of indigo formation or enzyme specific activity normalized to the protein content of the sample. ... One unit of activity was defined as the amount of enzyme catalyzing the oxidation of 1 mmol NADH min .... degrade hydrocarbons. These can easily allow the formation of new mixed metabolic ...

  1. Detection of meta - and ortho -cleavage dioxygenases in bacterial ...

    African Journals Online (AJOL)

    In contrast, isolates S-5, Sea-8, W-6, W-15 and Pla-1 showed activity with the enzyme catalyzing the second step in the phenol degradation meta-cleavage pathway, catechol-2,3-dioxygenase. On the basis of our previous and present analysis, the investigated isolates are considered to have a good potential for application ...

  2. Detection and Characterization of Bacterial Proteinases Using Zymography.

    Science.gov (United States)

    Madanan, Madathiparambil G; Mechoor, Ambili

    2017-01-01

    Proteinases play a crucial role in invasion and pathogenesis of bacteria, especially the extracellular and membrane-bound forms. Analysis of these proteinases demands the isolation by retaining the enzymatic activity. The isolation procedures maintaining the native structure of the enzyme in its soluble form are also of extreme importance. The qualitative analyses of these proteinases are carried out by electrophoresis and zymography. Enzymatic characterization based on the effect of inhibitors and activators on gelatinase activity also can be assessed using this zymography. The membrane-bound proteinases can be isolated in their native and soluble form, still retaining the activity using 6-aminocaproic acid and sodium deoxycholate; the procedure of which is explained in this chapter.

  3. Detection of bacterial toxins by lateral flow immunoassay

    Science.gov (United States)

    Foodborne bacteria sicken over 48 million Americans each year, causing more than 200,000 hospitalizations and over 3,000 deaths. The majority of food producers operate with strict sanitation and hygiene controls throughout production to minimize the risk of product contamination. Additional consume...

  4. Detection of postcardiotomy bacterial pericarditis with gallium-67 citrate

    Energy Technology Data Exchange (ETDEWEB)

    Zuckier, L.S.; Weissmann, H.S.; Goldman, M.J.; Brodman, R.; Kamholz, S.L.; Freeman, L.M.

    1986-04-01

    A 46-year-old man who had undergone apical cardiac aneurysmectomy with a ventriculotomy graft and implanted automatic cardioverter-defibrillator electrodes, presented with fever, left-sided pleuritic chest pain, and a draining sinus. A Ga-67 scan was performed to aid in determining whether the infection was limited to the chest wall or if it had penetrated deeper to the cardiac structures. Uptake of gallium within the cardiac region, in association with minimal rib uptake of Tc-99m MDP, strongly supported the existence of infection within the pericardium. CT scan demonstrated a pericardial collection which under CT-guided aspiration proved to be purulent. Definitive surgical drainage was performed, and the patient was discharged 4 weeks postoperatively. Ga-67 imaging can provide an accurate and relatively rapid means of localizing infection in the postcardiotomy patient. A thorough bibliography of pericardial gallium uptake is provided.

  5. Methods to classify bacterial pathogens in cystic fibrosis

    DEFF Research Database (Denmark)

    Bjarnsholt, Thomas; Nielsen, Xiaohui Chen; Johansen, Ulla

    2011-01-01

    Many bacteria can be detected in CF sputum, pathogenic and commensal. Modified Koch's criteria for identification of established and emerging CF pathogens are therefore described. Methods are described to isolate bacteria and to detect bacterial biofilms in sputum or lung tissue from CF patients...... by means of conventional culturing and staining techniques and by the PNA FISH technique. Additionally, the confocal scanning laser microscopy technique is described for studying biofilms in vitro in a flow cell system. The recA-gene PCR and the RFLP-based identification methods are described...... for identification of isolates from the Burkholderia complex to the species level. DNA typing by PFGE, which can be used for any bacterial pathogen, is described as it is employed for Pseudomonas aeruginosa. A commercially available ELISA method is described for measuring IgG antibodies against P. aeruginosa in CF...

  6. MICROBIOLOGICAL DIAGNOSTICS OF THE MENINGOCOCCAL INFECTION AND PURULENT BACTERIAL MENINGITIS

    Directory of Open Access Journals (Sweden)

    L. A. Kraeva

    2011-01-01

    Full Text Available Abstract. In the review modern data on taxonomy, biological features and clinical significance of agent of meningococcal infection and bacterial purulent meningitis are presented. Methods of laboratory diagnostics as well as recommendations about use of high-quality culture media and diagnostic kits for isolation and identification of microorganisms are described. Modern techniques to detect sensitivity of bacteria to antibiotics are proposed.

  7. Bacterial cells with improved tolerance to polyamines

    DEFF Research Database (Denmark)

    2017-01-01

    Provided are bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as polyamines, and methods of preparing and using such bacterial cells for production of polyamines and other compounds....

  8. Bacterial cells with improved tolerance to polyols

    DEFF Research Database (Denmark)

    2017-01-01

    The present invention relates to bacterial cells genetically modified to improve their tolerance to certain commodity chemicals, such as diols and other polyols, and to methods of preparing and using such bacterial cells for production of polyols and other compounds....

  9. Adjunctive Corticosteroids in Adults with Bacterial Meningitis

    NARCIS (Netherlands)

    van de Beek, Diederik; de Gans, Jan

    2005-01-01

    Bacterial meningitis is a complex disorder in which neurologic injury is caused, in part, by the causative organism and, in part, by the host's own inflammatory response. In studies of experimental bacterial meningitis, adjuvant treatment with corticosteroids, specifically dexamethasone, has

  10. Endocarditis in adults with bacterial meningitis

    NARCIS (Netherlands)

    Lucas, Marjolein J.; Brouwer, Matthijs C.; van der Ende, Arie; van de Beek, Diederik

    2013-01-01

    Endocarditis may precede or complicate bacterial meningitis, but the incidence and impact of endocarditis in bacterial meningitis are unknown. We assessed the incidence and clinical characteristics of patients with meningitis and endocarditis from a nationwide cohort study of adults with

  11. Dexamethasone in adults with bacterial meningitis

    NARCIS (Netherlands)

    de Gans, Jan; van de Beek, Diederik

    2002-01-01

    Background: Mortality and morbidity rates are high among adults with acute bacterial meningitis, especially those with pneumococcal meningitis. In studies of bacterial meningitis in animals, adjuvant treatment with corticosteroids has beneficial effects. Methods: We conducted a prospective,

  12. Cognitive outcome in adults after bacterial meningitis

    NARCIS (Netherlands)

    Hoogman, Martine; van de Beek, Diederik; Weisfelt, Martijn; de Gans, Jan; Schmand, Ben

    2007-01-01

    OBJECTIVE: To evaluate cognitive outcome in adult survivors of bacterial meningitis. METHODS: Data from three prospective multicentre studies were pooled and reanalysed, involving 155 adults surviving bacterial meningitis (79 after pneumococcal and 76 after meningococcal meningitis) and 72 healthy

  13. Cognitive outcome in adults after bacterial meningitis.

    NARCIS (Netherlands)

    Hoogman, M.; Beek, D. van de; Weisfelt, M.; Gans, J. de; Schmand, B.A.

    2007-01-01

    OBJECTIVE: To evaluate cognitive outcome in adult survivors of bacterial meningitis. METHODS: Data from three prospective multicentre studies were pooled and reanalysed, involving 155 adults surviving bacterial meningitis (79 after pneumococcal and 76 after meningococcal meningitis) and 72 healthy

  14. Antimicrobial susceptibility in community-acquired bacterial ...

    African Journals Online (AJOL)

    Objectives: To determine the antimicrobial susceptibility patterns of Streptococcus pneumoniae and Haemophilus influenzae, two bacterial pathogens commonly associated with communityacquired pneumonia. Design: Cross-sectional study. Setting: Bacterial isolates were obtained from adults suspected to have ...

  15. (PCR) in the diagnosis of bacterial infections

    African Journals Online (AJOL)

    ... bacterial infections that can be diagnosed using the technique which include among others; Tuberculosis (TB), whooping cough, brain abscesses and spinal infection, otitis media with effusion, Mycoplasmal pneumonia, endophthalmitis and bacterial meningitis. Keywords: Polymerase chain reaction, Diagnosis, Bacteria, ...

  16. Biomimetic Bacterial Identification Platform Based on Thermal Wave Transport Analysis (TWTA) through Surface-Imprinted Polymers.

    Science.gov (United States)

    Steen Redeker, Erik; Eersels, Kasper; Akkermans, Onno; Royakkers, Jeroen; Dyson, Simba; Nurekeyeva, Kunya; Ferrando, Beniamino; Cornelis, Peter; Peeters, Marloes; Wagner, Patrick; Diliën, Hanne; van Grinsven, Bart; Cleij, Thomas Jan

    2017-05-12

    This paper introduces a novel bacterial identification assay based on thermal wave analysis through surface-imprinted polymers (SIPs). Aluminum chips are coated with SIPs, serving as synthetic cell receptors that have been combined previously with the heat-transfer method (HTM) for the selective detection of bacteria. In this work, the concept of bacterial identification is extended toward the detection of nine different bacterial species. In addition, a novel sensing approach, thermal wave transport analysis (TWTA), is introduced, which analyzes the propagation of a thermal wave through a functional interface. The results presented here demonstrate that bacterial rebinding to the SIP layer resulted in a measurable phase shift in the propagated wave, which is most pronounced at a frequency of 0.03 Hz. In this way, the sensor is able to selectively distinguish between the different bacterial species used in this study. Furthermore, a dose-response curve was constructed to determine a limit of detection of 1 × 10 4 CFU mL -1 , indicating that TWTA is advantageous over HTM in terms of sensitivity and response time. Additionally, the limit of selectivity of the sensor was tested in a mixed bacterial solution, containing the target species in the presence of a 99-fold excess of competitor species. Finally, a first application for the sensor in terms of infection diagnosis is presented, revealing that the platform is able to detect bacteria in clinically relevant concentrations as low as 3 × 10 4 CFU mL -1 in spiked urine samples.

  17. Radiometric assay of bacterial growth: analysis of factors determining system performance and optimization of assay technique

    International Nuclear Information System (INIS)

    Boonkitticharoen, V.; Ehrhardt, J.C.; Kirchner, P.T.

    1987-01-01

    A quantitative technique for the measurement of 14 CO 2 released from a bacterial culture was evaluated. The technique uses liquid scintillation counting to record 14 CO 2 accumulation on a fluor-impregnated filter paper within a double-chambered scintillation vial that also houses the bacterial growth medium. We have successfully identified and corrected the major causes for a variably low detection efficiency, and also established the optimum mixture of reagents for the detection system. Incorporation of Triton X-100 into the scintillation fluid used for the detector reduced the variability between identical assays in a single batch from 50% to 5%, and, in conjunction with an increase in the scintillator concentration, raised the counting efficiency from 30% to 70-88%. The response of the improved detector is linear over a wide range of count-rates. Another significant modification was the interchange of growth and detector chambers. Overall, a 40-fold increase in count-rate during the exponential phase of bacterial growth was obtained by improving 14 CO 2 detection efficiency, increasing the rate of 14 CO 2 transfer from liquid to gas phases and enlarging the growth supporting capacity of the detector system. The minimum detection time for bacterial growth was shortened and the exponential phase of bacterial proliferation was lengthened by at least 2 hr. High counting efficiency, precision, and linearity make the improved detector a sensitive and reliable tool for radiometry of bacterial growth and metabolism

  18. Direct molecular testing to assess the incidence of meningococcal and other bacterial causes of meningitis among persons reported with unspecified bacterial meningitis.

    Science.gov (United States)

    Ramautar, Arianne E; Halse, Tanya A; Arakaki, Lola; Antwi, Mike; Del Rosso, Paula; Dorsinville, Marie; Nazarian, Elizabeth; Steiner-Sichel, Linda; Lee, Lillian; Dickinson, Michelle; Wroblewski, Danielle; Dumas, Nellie; Musser, Kimberlee; Isaac, Beth; Rakeman, Jennifer; Weiss, Don

    2015-11-01

    Confirmed and probable cases of invasive Neisseria meningitidis (Nm) infection are reportable in New York City. We conducted a study to identify Nm among culture-negative reports of bacterial and viral meningitis. During the study period, 262 reports of suspected meningitis were eligible. Cerebrospinal fluid (CSF) specimens from 138 patients were obtained for testing. No Nm cases were detected. Results from real-time polymerase chain reaction and 16S on CSF specimens were concordant with hospital microbiology findings in 80%; however, other pathogenic organisms were detected in 14 culture-negative specimens. New York City's surveillance system appears to be effective at capturing cases of Nm meningitis. Nucleic acid testing is useful for detecting the presence of bacterial DNA when antibiotic therapy precedes lumbar puncture or bacterial cultures are negative. It remains unanswered whether culture-negative cases of Nm bacteremia are being missed by reportable disease surveillance. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Significance of human beta-defensins in the epithelial lining fluid of patients with chronic lower respiratory tract infections.

    Science.gov (United States)

    Yanagi, S; Ashitani, J; Imai, K; Kyoraku, Y; Sano, A; Matsumoto, N; Nakazato, M

    2007-01-01

    Human beta-defensins (hBDs) are the most abundant antimicrobial peptides in epithelial cells, and function in the host immune system. Respiratory epithelial cells express hBDs to inhibit bacterial proliferation during respiratory tract infections. The aim of this study was to investigate the release of hBDs into the respiratory tract and their benefit as a host defence system in chronic Pseudomonas aeruginosa infections. The levels of four hBD peptides (hBD-1-hBD-4) were measured in the bronchial epithelial lining fluid (ELF) of nine patients with chronic lower respiratory tract infection caused by P. aeruginosa. Eight patients with idiopathic pulmonary fibrosis and eight volunteers free of pulmonary disease were recruited as controls. ELF was obtained by bronchoscopic microsampling and hBD levels were measured by radioimmunoassays. The antimicrobial effects of hBDs were studied individually and in combination using an in-vitro colony count assay for P. aeruginosa. Concentrations of hBD-1 and hBD-3 tended to be higher in patients with chronic lower respiratory tract infection than in the controls. hBD-2 and hBD-4 were detected in ELF from five and four of nine patients, respectively, but the hBD levels in controls were all below the limits of detection. All patients with infection caused by mucoid P. aeruginosa had detectable hBD-2 and hBD-4 levels in ELF. In-vitro colony count assays showed a potential synergism between hBD-2 and hBD-4 in inhibiting bacterial proliferation. The findings indicate that hBDs, especially hBD-2 and hBD-4, are pathophysiologically important in infections caused by mucoid strains of P. aeruginosa.

  20. The Bacterial Sequential Markov Coalescent.

    Science.gov (United States)

    De Maio, Nicola; Wilson, Daniel J

    2017-05-01

    Bacteria can exchange and acquire new genetic material from other organisms directly and via the environment. This process, known as bacterial recombination, has a strong impact on the evolution of bacteria, for example, leading to the spread of antibiotic resistance across clades and species, and to the avoidance of clonal interference. Recombination hinders phylogenetic and transmission inference because it creates patterns of substitutions (homoplasies) inconsistent with the hypothesis of a single evolutionary tree. Bacterial recombination is typically modeled as statistically akin to gene conversion in eukaryotes, i.e. , using the coalescent with gene conversion (CGC). However, this model can be very computationally demanding as it needs to account for the correlations of evolutionary histories of even distant loci. So, with the increasing popularity of whole genome sequencing, the need has emerged for a faster approach to model and simulate bacterial genome evolution. We present a new model that approximates the coalescent with gene conversion: the bacterial sequential Markov coalescent (BSMC). Our approach is based on a similar idea to the sequential Markov coalescent (SMC)-an approximation of the coalescent with crossover recombination. However, bacterial recombination poses hurdles to a sequential Markov approximation, as it leads to strong correlations and linkage disequilibrium across very distant sites in the genome. Our BSMC overcomes these difficulties, and shows a considerable reduction in computational demand compared to the exact CGC, and very similar patterns in simulated data. We implemented our BSMC model within new simulation software FastSimBac. In addition to the decreased computational demand compared to previous bacterial genome evolution simulators, FastSimBac provides more general options for evolutionary scenarios, allowing population structure with migration, speciation, population size changes, and recombination hotspots. FastSimBac is