Relevant bibliographies by topics / Pathogen enrichment

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Pathogen enrichment'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Pathogen enrichment"

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MURAKAMI, TAKU. "Filter-Based Pathogen Enrichment Technology for Detection of Multiple Viable Foodborne Pathogens in 1 Day." Journal of Food Protection 75, no. 9 (September 1, 2012): 1603–10. http://dx.doi.org/10.4315/0362-028x.jfp-12-039.

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Conventional foodborne pathogen assays currently used in the food industry often require long culture enrichments to increase pathogen levels so they can be detected. Even using sensitive real-time PCR assays, culture enrichment at least overnight is necessary especially for detection of pathogens with slow growth rates such as Listeria monocytogenes. To eliminate this cumbersome enrichment step and detect minute amounts of pathogens within 1 day, filter-based pathogen enrichment technology was developed utilizing a unique combination of glass fiber depth filter and porous filter aid materials to efficiently separate pathogens from food homogenates and avoid filter clogging by food particles. After pathogen immobilization in depth filters, only viable pathogens were selectively collected in a small volume of growth medium via microbial multiplication and migration; nonviable pathogens remained inside the filters. By assaying viable pathogens using real-time PCRs, multiple species of foodborne pathogens were detected, including L. monocytogenes, Salmonella enterica, and Escherichia coli O157:H7, at around 1 CFU/ml or 1 CFU/g in various food samples. This filter-based pathogen enrichment technology is a unique bacterial enrichment alternative to the conventional culture enrichment step and can significantly shorten the time necessary to obtain assay results.
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Lee, Justin S., Ryan S. Mackie, Thomas Harrison, Basir Shariat, Trey Kind, Timo Kehl, Martin Löchelt, Christina Boucher, and Sue VandeWoude. "Targeted Enrichment for Pathogen Detection and Characterization in Three Felid Species." Journal of Clinical Microbiology 55, no. 6 (March 22, 2017): 1658–70. http://dx.doi.org/10.1128/jcm.01463-16.

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ABSTRACT Traditional diagnostic assays often lack sensitivity and can be difficult to multiplex across many pathogens. Next-generation sequencing (NGS) can overcome some of these problems but has limited application in the detection of low-copy-number pathogens in complex samples. Targeted genome capture (TGC) utilizes oligonucleotide probes to enrich specific nucleic acids in heterogeneous extracts and can therefore increase the proportion of NGS reads for low-abundance targets. While earlier studies have demonstrated the utility of this technology for detection of novel pathogens in human clinical samples, the capacity and practicality of TGC-NGS in a veterinary diagnostic setting have not yet been evaluated. Here we report the use of TGC-NGS assays for the detection and characterization of diverse feline pathogen taxa. We detected 31 pathogens comprising nine pathogen taxa in 28 felid samples analyzed. This included 20 pathogens detected via traditional PCR and 11 additional pathogens that had not been previously detected in the same samples. Most of the pathogens detected were sequenced at sufficient breadth and depth to confidently classify them at the species or subspecies level. Target nucleic acids were enriched from a low of 58-fold to 56 million-fold relative to host nucleic acids. Despite the promising performance of these assays, a number of pathogens detected by conventional PCR or serology were not isolated by TGC-NGS, suggesting that further validation is required before this technology can be used in lieu of quality-controlled standard assays. We conclude that TGC-NGS offers great potential as a broad multiplex pathogen characterization assay in veterinary diagnostic and research settings.
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HUANG, SHISHI, TAY BOON HUI, HYUN-GYUN YUK, and QIANWANG ZHENG. "Development of an Effective Two-Step Enrichment Process to Enhance Bax System Detection of Healthy and Injured Salmonella Enteritidis in Liquid Whole Egg and Egg Yolk." Journal of Food Protection 83, no. 3 (February 14, 2020): 397–404. http://dx.doi.org/10.4315/0362-028x.jfp-19-280.

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ABSTRACT The BAX system for pathogen detection has been highly accurate in a variety of food products. However, false-negative results have been reported for the detection of pathogens in liquid egg products because of failed pathogen resuscitation and the existence of inhibitory components. In this study, a short-time enrichment step was used to simultaneously resuscitate the target cells to the detection level and to dilute the inhibitory components to reduce detection interference. The MP medium (BAX system) enabled faster multiplication of healthy Salmonella cells than did buffered peptone water (BPW) in tested liquid whole egg and egg yolk. However, MP failed to resuscitate heat-injured cells even after 24 h of incubation. Therefore, MP was replaced with BPW as the enrichment broth for the BAX system. However, the use of BPW for a one-step enrichment was not effective for removal of PCR inhibitors in egg yolk, and unstable detection results were obtained. To improve detection accuracy, a second step of enrichment with brain heart infusion was added. This two-step enrichment process shortened the enrichment time to 14 h and greatly increased the number of samples in which the pathogen was detected during the same enrichment time, especially in the liquid egg yolk samples. The validation study revealed 100% diagnostic accuracy of the two-step enrichment process plus the BAX system. These results indicate that a two-step enrichment process added to the BAX system can improve the detection of pathogenic Salmonella in liquid egg products. HIGHLIGHTS
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Kim, Hyochin, and Arun K. Bhunia. "SEL, a Selective Enrichment Broth for Simultaneous Growth of Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes." Applied and Environmental Microbiology 74, no. 15 (June 6, 2008): 4853–66. http://dx.doi.org/10.1128/aem.02756-07.

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ABSTRACT Multipathogen detection on a single-assay platform not only reduces the cost for testing but also provides data on the presence of pathogens in a single experiment. To achieve this detection, a multipathogen selective enrichment medium is essential to allow the concurrent growth of pathogens. SEL broth was formulated to allow the simultaneous growth of Salmonella enterica, Escherichia coli O157:H7, and Listeria monocytogenes. The results were compared to those obtained with the respective individual selective enrichment broths, Rappaport-Vassiliadis (RV) for S. enterica, modified E. coli broth with 20 mg of novobiocin/liter for E. coli O157:H7, and Fraser broth for L. monocytogenes, and a currently used universal preenrichment broth (UPB). The growth of each pathogen in SEL inoculated at 101 or 103 CFU/ml was superior to that in the respective individual enrichment broth, except in the case of RV, in which Salmonella cells inoculated at both concentrations grew equally well. In mixed-culture experiments with cells of the three species present in equal concentrations or at a 1:10:1,000 ratio, the overall growth was proportional to the initial inoculation levels; however, the growth of L. monocytogenes was markedly suppressed when cells of this species were present at lower concentrations than those of the other two species. Further, SEL was able to resuscitate acid- and cold-stressed cells, and recovery was comparable to that in nonselective tryptic soy broth containing 6% yeast extract but superior to that in the respective individual selective broths. SEL promoted the growth of all three pathogens in a mixture in ready-to-eat salami and in turkey meat samples. Moreover, each pathogen was readily detected by a pathogen-specific immunochromatographic lateral-flow or multiplex PCR assay. Even though the growth of each pathogen in SEL was comparable to that in UPB, SEL inhibited greater numbers of nontarget organisms than did UPB. In summary, SEL was demonstrated to be a promising new multiplex selective enrichment broth for the detection of the three most prominent food-borne pathogens by antibody- or nucleic acid-based methods.
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Furtwängler, Anja, Judith Neukamm, Lisa Böhme, Ella Reiter, Melanie Vollstedt, Natasha Arora, Pushpendra Singh, et al. "Comparison of target enrichment strategies for ancient pathogen DNA." BioTechniques 69, no. 6 (December 2020): 455–59. http://dx.doi.org/10.2144/btn-2020-0100.

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In ancient DNA research, the degraded nature of the samples generally results in poor yields of highly fragmented DNA; targeted DNA enrichment is thus required to maximize research outcomes. The three commonly used methods – array-based hybridization capture and in-solution capture using either RNA or DNA baits – have different characteristics that may influence the capture efficiency, specificity and reproducibility. Here we compare their performance in enriching pathogen DNA of Mycobacterium leprae and Treponema pallidum from 11 ancient and 19 modern samples. We find that in-solution approaches are the most effective method in ancient and modern samples of both pathogens and that RNA baits usually perform better than DNA baits.
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ZHAO, TONG, and MICHAEL P. DOYLE. "Evaluation of Universal Preenrichment Broth for Growth of Heat-Injured Pathogens." Journal of Food Protection 64, no. 11 (November 1, 2001): 1751–55. http://dx.doi.org/10.4315/0362-028x-64.11.1751.

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Universal preenrichment broth (UPB) was developed to enable enrichment of injured foodborne pathogens of different genera simultaneously in lieu of having to undergo separate simultaneous enrichment cultures for subsequent detection or isolation of each pathogen. Enrichment conditions in UPB for growth of injured pathogens to populations that will enable pathogen detection by rapid immuno-based or polymerase chain reaction (PCR)-based assays have not been defined. Hence, studies were done to determine recovery and growth rates of heat-injured Escherichia coli O157:H7, Salmonella enterica ser. Typhimurium, Salmonella enterica ser. Enteritidis, and Listeria monocytogenes in UPB. Bacterial cells were heat injured in tryptic phosphate broth at 57.2°C and inoculated at populations of ca. 0.17 to 63 injured cells per ml with raw ground beef, fresh chicken, lettuce, and environmental sponge samples. Enrichment cultures were sampled at 1, 2, 3, 4, 5, 6, and 24 h at 37°C postinoculation, and pathogens were enumerated on appropriate selective media. Results revealed that recovery and growth of pathogens during the first 6 h of enrichment were not sufficient to ensure adequate numbers of bacteria (>103 CFU/ml) for detection by most immunoassays or PCR assays. Cells often required 3 to 4 h for recovery before growth was initiated. Salmonella Typhimurium, Salmonella Enteritidis, E. coli O157:H7, or L. monocytogenes cell populations in enrichment cultures with ground beef or lettuce at 6 h were 0.5 to 2.9 log10 CFU/ml. At 24 h of incubation, cell counts of enrichment samples for the three pathogens from all food and environmental sponge samples ranged from 4.0 to 8.3 log10 CFU/ml. Enrichment in UPB at 37°C of foods or environmental sponge samples containing heat-injured cells of Salmonella Typhimurium, Salmonella Enteritidis, E. coli O157:H7, or L. monocytogenes reliably provides at 24 h of incubation—but not at 6 h—sufficient cell populations for detection by rapid immunoassay or PCR assay procedures that can detect at least 4 log10 CFU/ml. These results raise questions regarding the sensitivity of rapid detection methods that employ an abbreviated enrichment protocol of 6 h or less.
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Parichehr, Moezi, Kargar Mohammad, Doosti Abbas, and Khoshneviszadeh Mehdi. "Developing a multiplex real-time PCR with a new pre-enrichment to simultaneously detect four foodborne bacteria in milk." Future Microbiology 14, no. 10 (July 2019): 885–98. http://dx.doi.org/10.2217/fmb-2019-0044.

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Aim: The aim of this study is to formulate a new single nonselective pre-enrichment medium (ELSS) that can support the concurrent growth of four major foodborne pathogens containing E. coli O157: H7, L. monocytogenes, S. aureus and S. enterica serovar Entertidis to develop a multiplex TaqMan Real-time PCR (mRT-PCR). Methods: The mRT-PCR with a new pre-enrichment was carried out for simultaneous detection and quantification of these foodborne bacteria. Results: By using mRT-PCR after 16 h pre-enrichment in ELSS, the detection limit of each pathogen was 1 CFU/25 ml contaminated milk, as well as inclusivity and exclusivity reached 100%. Conclusion: The mRT-PCR assay with pre-enrichment step is a fast and reliable technique for detecting single or multiple pathogens in food products.
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Hayashi, Masahiro, Tatsuya Natori, Sayoko Kubota-Hayashi, Machiko Miyata, Kiyofumi Ohkusu, Keiko Kawamoto, Hisao Kurazono, Souichi Makino, and Takayuki Ezaki. "A New Protocol to Detect Multiple Foodborne Pathogens with PCR Dipstick DNA Chromatography after a Six-Hour Enrichment Culture in a Broad-Range Food Pathogen Enrichment Broth." BioMed Research International 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/295050.

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A quick foodborne pathogen screening method after six-hour enrichment culture with a broad-range food pathogen enrichment broth is described. Pathogenic factors ofSalmonella enterica,Shigellaspp., enteroinvasiveEscherichia coli, and enterohemorrhagicE. coliare amplified with a cocktail primer and rapid polymerase chain reaction (PCR), which finishes amplification in 30 min. The PCR amplicon was differentiated with a dipstick DNA chromatography assay in 5–10 min. Starting from a four- to six-hour enrichment culture, this assay was finished within 45 min. Detection sensitivity of this protocol was less than 2.5 CFU/25 g forS. entericaand 3.3 CFU/25 g for enterohemorrhagicE. coliin spiked ground meat experiments.
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TORTORELLO, M. L., K. F. REINEKE, D. S. STEWART, and R. B. RAYBOURNE. "Comparison of Methods for Determining the Presence of Escherichia coli O157:H7 in Apple Juice." Journal of Food Protection 61, no. 11 (November 1, 1998): 1425–30. http://dx.doi.org/10.4315/0362-028x-61.11.1425.

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Six methods were compared for detection of three strains of Escherichia coli O157:H7 in enrichments of inoculated apple juice. Juice was inoculated at levels varying from 0.1 to 100 CFU/ml and centrifuged after ovemight storage at 4°C, and pellets were incubated at 37°C in nonselective enrichment broth. At hourly intervals between 5 and 10 h and at 24 h, the enrichments were tested for E. coli O157:H7 by direct fluorescent antibody (DFA), antibody-direct epifluorescent filter technique (Ab-DEFT), direct selective plating on sorbitol MacConkey agar (SMA), immunomagnetic separation coupled to either selective plating (IMS-SMA) or the polymerase chain reaction (IMS-PCR), and flow cytometry (FC). The most consistent detection of 0.1 CFU/ml of the slowest growing strain of the pathogen was provided by the IMS-SMA and IMS-PCR after 8 h of enrichment. The time required for detection at the level of 0.1 CFU/ml for each assay was Ab-DEFT, 11 h; IMS-PCR, 16 h; FC, 24 h; IMS-SMA, 32 h; and SMA, 48 h. Absolute detection limits (without enrichment) were: IMS-PCR, 103 CFU/ml; Ab-DEFT and IMS-SMA, 104 CFU/ml; SMA, 105 CFU/ml; and DFA, 106 CFU/ml. Recovery of the pathogen (10 CFU/ml) in apple juice after 28 days of 4°C storage was possible by means of an 8-h enrichment and Ab-DEFT, IMS-PCR, or IMS-SMA.
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Hahm, Byoung-Kwon, Hyochin Kim, Atul K. Singh, and Arun K. Bhunia. "Pathogen enrichment device (PED) enables one-step growth, enrichment and separation of pathogen from food matrices for detection using bioanalytical platforms." Journal of Microbiological Methods 117 (October 2015): 64–73. http://dx.doi.org/10.1016/j.mimet.2015.07.016.

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Dissertations / Theses on the topic "Pathogen enrichment"

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Bernardo, Letizia. "IDENTIFICATION AND CHARACTERIZATION OF PROTEINS INVOLVED IN BIOTIC STRESS RESISTANCE OF CEREALS." Doctoral thesis, Università degli studi di Padova, 2010. http://hdl.handle.net/11577/3426966.

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Leaf rust is one of the most important diseases of barley (Hordeum vulgare) and is caused by the biotrophic fungal pathogen Puccinia hordei. The rust fungi penetrate barley leaves through stomata and colonize cells of the mesophyll, then growing systemically through the leaf vascular tissue. The leaf rust resistance gene Rph15 is of outstanding interest for resistance breeding because it confers resistance to over 350 Puccinia hordei isolates collected from around the world (Weerasena et al. 2004). Plant-pathogen interactions activate many cellular signalling processes and, most likely, changes on protein accumulation and phosphorylation pattern of proteins play a pivotal role in plant responses to biotic stress. In this work, a proteomic approach was undertaken to study changes in total proteins accumulation and protein phosphorylation pattern in response to the leaf rust pathogen infection in two barley near isogenic lines, Bowman and Rph15, which differ for the introgression of the leaf rust resistance gene Rph15. Two infection time points, 24 hours and four days, were considered for the analysis. No statistically significant differences were identified at the early time point, 24 hours post infection, for total and phosphorylated proteins. At four days after inoculation, total protein analysis led to the identification of twenty-one protein spots significantly up or down regulated with a fold-change equal or higher than two following pathogen infection. Most of down-regulated proteins were found in the Rph15 near-isogenic line while no significantly differential protein abundance was recovered in the susceptible line. Nineteen out of 21 protein spots were characterized by LC-MS/MS analysis and found to be involved in photosynthesis, sugar metabolism, energy balance and defence. Phosphoproteomics analysis was performed at four day after inoculation. A phosphoprotein enrichment methodology based on MOAC (metal oxide affinity chromatography) was optimized for subsequent 2DE analyses.
La ruggine fogliare è una delle malattie più importanti della coltura dell'orzo (Hordeum vulgare) ed è causata dal patogeno fungino biotrofo Puccinia hordei. Il fungo penetra attraverso gli stomi delle foglie dell’orzo e colonizza le cellule del mesofillo, crescendo poi per via sistemica nei tessuti vascolari della foglia. Il gene Rph15 di orzo è di considerevole importanza per il miglioramento genetico della resistenza in quanto conferisce resistenza a più di 350 isolati di P. hordei provenienti da tutto il mondo (Weerasena et al. 2004). L’interazione pianta-patogeno attiva numerosi processi di signalling cellulare e, molto probabilmente, l’accumulo delle proteine e i cambiamenti nel pattern di fosforilazione delle proteine giocano un ruolo centrale nella risposta della pianta in seguito a stress biotico. In questo lavoro, un approccio di tipo proteomico è stato intrapreso per studiare i cambiamenti nei pattern proteici totali e delle proteine fosforilate in seguito a risposta alla ruggine fogliare in due linee quasi isogeniche di orzo, Bowman e la linea Rph15, che differiscono per l’ introgressione del gene Rph15. Due tempi di infezione, 24 ore e quattro giorni, sono stati presi in considerazione per le analisi. Nessuna differenza statisticamente significativa è stata individuate nel primo tempo di infezione precoce, a 24 ore dopo l’inoculo, sia per quanto riguarda le proteine totali che per le proteine fosforilate. A 4 giorni dall’infezione, l’ analisi delle proteine totali ha consentito di identificare ventuno spot proteici significativamente up o down regolati in risposta all’ infezione con un fold-change almeno di 2. La maggior parte delle proteine down-regolate sono state trovate nel campione infettato della linea isogenica contenente il gene di resistenza Rph15, mentre non è stata riscontrata alcuna differenza statisticamente significativa nel pattern proteico della linea isogenica suscettibile. Diciannove dei 21 spot proteici sono stati caratterizzati mediante analisi LC-MS/MS e identificati essere implicati in processi come fotosintesi, metabolismo degli zuccheri, bilancio energetico e risposte di difesa. L’analisi del fosfoproteoma è stata condotta a quattro giorni dopo l’inoculo. Una tecnica di arricchimento in fosfoproteine basata su MOAC (cromatografia di affinità mediante ossidi metallici) che è stata ottimizzata per la successiva analisi 2DE.
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Jani, Mehul. "Genomic Island Discovery through Enrichment of Statistical Modeling with Biological Information." Thesis, University of North Texas, 2018. https://digital.library.unt.edu/ark:/67531/metadc1248417/.

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Horizontal gene transfer enables acquisition and dissemination of novel traits including antibiotic resistance and virulence among bacteria. Frequently such traits are gained through the acquisition of clusters of functionally related genes, often referred to as genomic islands (GIs). Quantifying horizontal flow of GIs and assessing their contributions to the emergence and evolution of novel metabolic traits in bacterial organisms are central to understanding the evolution of bacteria in general and the evolution of pathogenicity and antibiotic resistance in particular, a focus of this dissertation study. Methods for GI detection have also evolved with advances in sequencing and bioinformatics, however, comprehensive assessment of these methods has been lacking. This motivated us to assess the performance of current methods for identifying islands on broad datasets of well-characterized bacterial genomes and synthetic genomes, and leverage this information to develop a novel approach that circumvents the limitations of the current state-of-the-art in GI detection. The main findings from our assessment studies were 1) the methods have complementary strengths, 2) a gene-clustering method utilizing codon usage bias as the discriminant criterion, namely, JS-CB, is most efficient in localizing genomic islands, specifically the well-studied SCCmec resistance island in methicillin resistant Staphylococcus aureus (MRSA) genomes, and 3) in general, the bottom up, gene by gene analysis methods, are inherently limited in their ability to decipher large structures such as GIs as single entities within bacterial genomes. We adapted a top-down approach based on recursive segmentation and agglomerative clustering and developed a GI prediction tool, GEMINI, which combined compositional features with segment context information to localize GIs in the Liverpool epidemic strain of Pseudomonas aeruginosa. Application of GEMINI to the genome of P. aeruginosa LESB58 demonstrated its ability to delineate experimentally verified GIs in the LESB58 genome. GEMINI identified several novel islands including pathogenicity islands and revealed the mosaic structure of several LESB58 harbored GIs. A new GI identification approach, CAFE, with broad applicability was developed. CAFE incorporates biological information encoded in a genome within the statistical framework of segmentation and clustering to more robustly localize GIs in the genome. CAFE identifies genomic islands lacking markers by virtue of their association with genomic islands with markers originating from the same source. This is made possible by performing marker enrichment and phyletic pattern analyses within the integrated framework of recursive segmentation and clustering. CAFE compared favorably with frequently used methods for genomic island detection on synthetic test datasets and on a test-set of known islands from 15 well-characterized bacterial species. These tools can be readily adapted for cataloging GIs in just sequenced, yet uncharacterized genomes.
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Penczykowski, Rachel M. "Interactions between ecosystems and disease in the plankton of freshwater lakes." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/50368.

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I investigated effects of environmental change on disease, and effects of disease on ecosystems, using a freshwater zooplankton host and its fungal parasite. This research involved lake surveys, manipulative experiments, and mathematical models. My results indicate that ecosystem characteristics such as habitat structure, nutrient availability, and quality of a host’s resources (here, phytoplankton) can affect the spread of disease. For example, a survey of epidemics in lakes revealed direct and indirect links between habitat structure and epidemic size, where indirect connections were mediated by non-host species. Then, in a mesocosm experiment in a lake, manipulations of habitat structure and nutrient availability interactively affected the spread of disease, and nutrient enrichment increased densities of infected hosts. In a separate laboratory experiment, poor quality resources were shown to decrease parasite transmission rate by altering host foraging behavior. My experimental results also suggest that disease can affect ecosystems through effects on host densities and host traits. In the mesocosm experiment, the parasite indirectly increased abundance of algal resources by decreasing densities of the zooplankton host. Disease in the experimental zooplankton populations also impacted nutrient stoichiometry of algae, which could entail a parasite-mediated shift in food quality for grazers such as the host. Additionally, I showed that infection dramatically reduces host feeding rate, and used a dynamic epidemiological model to illustrate how this parasite-mediated trait change could affect densities of resources and hosts, as well as the spread of disease. I discuss the implications of these ecosystem–disease interactions in light of ongoing changes to habitat and nutrient regimes in freshwater ecosystems.
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Trindade, Maria Theresa. "Detection of pathogenic bacteria and fecal enterococci in recreational water with an evanescent wave fiber optic biosensor." [Tampa, Fla] : University of South Florida, 2005. http://purl.fcla.edu/usf/dc/et/SFE0001443.

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Panji, Sumir. "Identification of bacterial pathogenic gene classes subject to diversifying selection." Thesis, University of the Western Cape, 2009. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_5842_1297942831.

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Availability of genome sequences for numerous bacterial species comprising of different bacterial strains allows elucidation of species and strain specific adaptations that facilitate their survival in widely fluctuating micro-environments and enhance their pathogenic potential. Different bacterial species use different strategies in their pathogenesis and the pathogenic potential of a bacterial species is dependent on its genomic complement of virulence factors. A bacterial virulence factor, within the context of this study, is defined as any endogenous protein product encoded by a gene that aids in the adhesion, invasion, colonization, persistence and pathogenesis of a bacterium within a host. Anecdotal evidence suggests that bacterial virulence genes are undergoing diversifying evolution to counteract the rapid adaptability of its host&rsquo
s immune defences. Genome sequences of pathogenic bacterial species and strains provide unique opportunities to study the action of diversifying selection operating on different classes of bacterial genes.

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Nyarko, Esmond Boafo. "Improved Recovery And Rapid Identification Of Strains, Mixed Strains, Mixed Species, And Various Physiological States Of Foodborne Pathogens Using Infrared Spectroscopy." ScholarWorks @ UVM, 2014. http://scholarworks.uvm.edu/graddis/276.

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Challenges encountered in pathogen identification and detection include the genetic heterogeneity of strains within species of some foodborne pathogens, isolation of injured cells, mixed strains or mixed species contamination of foods, and differentiation between viable and dead cells. The first objective of this research was to evaluate an isolation medium that was based on time-delayed release (5 to 6 h) of selective agents in tablet format to a modified Listeria recovery enrichment broth (mLRB) medium for enhanced and rapid recovery of injured Listeria. The second objective involved the use of Fourier transform infrared (FT-IR) spectroscopy and chemometric analysis for the differentiation of: Listeria monocytogenes epidemic clones (ECs); viable versus heat-killed populations; different mixed strains and mixed species of Listeria; and different injury treatments and repair in Listeria populations. Nitrite- or acid-injured Listeria at approximately 10 CFU/ml were recovered in mLRB medium, and cell populations enumerated at various times (12 to 48 h) of incubation at 37oC. Analysis of variance revealed that acid-injured Listeria populations in mLRBS6 (mLRB plus the selective agents at 6 h) were significantly higher (P < 0.05) than those in mLRBS0 (mLRB plus the selective agents at 0 h) at 24 h; however, the differences in populations on these two media were not significant for nitrite-injured Listeria. Cell populations of four strains of Listeria recovered in mLRBTD (mLRB plus the time-delayed release tablets of the selective agents) were significantly higher than when those strains were enriched in the U.S. Food and Drug Administration (FDA), International Organization for Standardization (ISO), and U.S. Department of Agriculture (USDA) broths at 24 h. Comparison between artificially contaminated milk and meat samples with a four-strain cocktail of Listeria resulted in cell populations that were significantly higher (P < 0.05) on mLRBTD for contaminated meat than on mLRBTD for contaminated milk at 24 h. FT-IR spectroscopy in the mid-infrared region (4000 to 600 cm-1) and chemometrics was successfully applied to discriminate L. monocytogenes strains belonging to the same EC (ECII or ECIV) (100% accurate spectral classification), intact and heat-killed populations of each EC strain (100% accurate spectral classification), and spectral wavenumbers 1650 to 1390 cm-1 were used to differentiate heat-killed from intact populations. FT-IR spectroscopy and chemometrics in the wavelength region 1800 to 900 cm-1 could successfully discriminate different mixed strains of L. monocytogenes (98.15% accurate spectral classification) and different mixed species of L. monocytogenes and L. innocua (92.06% accurate spectral classification) from individual strains; Wavelength range 1800 to 900 cm-1 was successfully used to discriminate between intact, acid-injured, and heat-injured Listeria, with repaired cells from acid and heat treatments clustering closer to intact cells (93.33% of spectra accurately classified). Delayed-addition of selective agents to broth medium improves recovery of injured Listeria by allowing repair time, could minimize contamination through manual addition of selective agents, and saves analyst time; FT-IR spectroscopy is a highly discriminatory and reproducible technique that can be used for the differentiation of strains and various physiological states of Listeria.
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Marimuthu, Saranya. "Development of quantitative RNA sequencing methods to understand RNA variant diversity." Thesis, 2021. https://etd.iisc.ac.in/handle/2005/5548.

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The advent of next-generation sequencing (NGS) has accelerated biological research by providing the opportunity to connect genome level sequence information to function. One key application of NGS has been analysis of gene expression and variation by implementing ways to recapitulate RNA level differences accurately. However, for studies that require accurate estimates of closely related variants or isoforms, as in case of evolutionary dynamics of viral quasispecies, each of the available sequencing platforms have critical limitations. In this thesis work, we have developed methods to eliminate three of the significant limitations of current NGS platforms. These new methods tackle (i) Inability to reconstruct individual whole viral genomes due to genome fragmentation during sequence library preparations in short-read platforms (ii) High sequencing errors associated with 1D Oxford Nanopore sequencing platform and (iii) High background levels of host RNA hampering the detection of pathogen or novel RNA species in metagenomics studies. Our three novel workflows, namely, Single RNA sequencing (sRNA-Seq), TelN proteolemerase based nanopore 2D sequencing (T2D-NanoSeq), and Direct RNA amplification (D-RAMP), are designed to resolve each of these three limitations respectively. We have demonstrated each of the workflows, benchmarked them using synthetic samples and measured their efficiency. Our first method, sRNA-Seq, can report sequences distantly separated on a single RNA molecule with > 10% recovery and 87% specificity. On the other hand, T2D-NanoSeq, has 40% efficiency in covalently linking both forward and reverse sequences of a duplex DNA that enables tandem reads of both strands which can allow us to reduce sequencing errors. Finally, our third method can generate short DNA probes against target (host) RNA molecules from a physical sample of the RNA and has demonstrated a ~5 fold decrease in the target RNA compared to non-targeted RNA. Overall, these approaches provide improved sequencing alternatives for quantitative and accurate RNA sequencing.
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Lin, Chien-Ju, and 林建汝. "Feasibility Study of Rapid Detection for Foodborne Pathogenic Bacterial by Multiple primers-PCR and PCR-enrichment." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/10614801838677193718.

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碩士
國立臺灣海洋大學
食品科學系
95
First part of this study is to develop a combination of multiple primers for the major food poisoning pathogens: Bacillus cereus、Campylobacter jejuni, Escherichia coli O157:H7, Listeria monocytogenes, Salmonella spp., Shigella spp., Staphylococcus aureus and Vibrio parahaemolyticus, and further to investigate the feasibility of applying those primer combination for rapid detection the presence of those pathogens by PCR. The second part of this study is to develop a PCR enrichment technique that can rapidly identify the presence of target pathogen at low number of cells and at a shorter period of incubation time as compared to traditional enrichment procedures. Escherichia coli O157:H7, and Vibrio parahaemolyticus were selected for this part of study. Results indicated that the production of non-specific PCR products will obstruct the interpretation of DNA electrophoretograms with multiple PCR primer combination, and thus make individual identification of those pathogens impossible. Possible approaches to resolve these inferences including categorized primer pair and combination design, Ta (annealing temperature) selection, and target pathogen grouping were suggested for further studies. In PCR enrichment experiment, results suggested that the detection limit can be reduced from 102~103 CFU/ml for traditional selective enrichment procedures to as low as a single cell for both Escherichia coli O157:H7 and Vibrio parahaemolyticus by PCR enrichment technique. Since PCR enrichment technique tends to cause non-specific signal and different primers need respective Ta, it is not suitable for applying on various pathogenic microbes. However, PCR enrichment technique will still be a potential, low costing, time saving, and sensitive methology while the problems of annealing conditions and non-specific PCR reactions are solved.
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Sousa, Ana Catarina da Silva e. "Development of rapid methods for the detection of pathogenic microorganisms, based on NAM-FISH technology." Master's thesis, 2018. http://hdl.handle.net/10773/25528.

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The access of pathogenic microorganisms to the human body can compromise the health of the individual, causing several clinical manifestations. Helicobacter pylori and Campylobacter are two important gastrointestinal pathogens. H. pylori infection is one of the most common human infections, whose treatment includes the administration of antibiotics, namely fluoroquinolones (FQ). However, there has been an increasing resistance of H. pylori to FQ, which can lead to treatment failures, making it important not only to detect the bacterium but also to define its resistance profile. Campylobacter is currently considered the leading cause of bacterial foodborne illnesses, usually associated with the consumption of raw meat. The detection of pathogenic microorganisms can be achieved by conventional culture techniques or by molecular methods, namely immunological tests or nucleic acid detection. Biomode is an innovative company that develops and commercializes rapid diagnostic methods based on Nucleic Acid Mimic (NAM) – fluorescence in situ hybridization (FISH) technology, which enables the rapid detection of microorganisms, through the hybridization of complementary fluorescent probes with specific sequences present in the target microorganism. In this context, the present work focused on two applications of NAM-FISH. In the clinical area, the main objective was the development of a method for the detection of H. pylori and its resistance to FQ. For this purpose, Peptide Nucleic Acid (PNA) and Locked Nucleic Acid (LNA)/2'OMe probes were designed for the detection of mutations that cause resistance. In order to cover the most prevalent mutations, as well as the wildtype phenotype, 5 LNA/2'OMe probes were selected. In the area of food safety, the objective was the optimization of a PNA-FISH method for Campylobacter detection in food samples. A preliminary testing of the inclusivity/exclusivity of the Campylobacter probe resulted in the detection of two non-target microorganisms, H. cinaedi and H. pamatensis. To optimize the procedure, samples of raw broiler meat inoculated artificially with C. jejuni were used. Prior to PNA -FISH, a new step was introduced in which the enriched samples are subjected to a centrifugation (10 000 g), followed by resuspension in 0.1% Triton X-100, in order to reduce the strong autofluorescence shown in samples without any treatment. The possibility of a two-step sample enrichment was also tested, however, this approach did not show advantages compared to the one-step procedure. Additionally, a robustness test, required by the AOAC International to obtain product certification, was performed, which showed that the variation of the parameters of the time and temperature of hybridization influence the performance of the method, showing that the PNA-FISH conditions must be strictly controlled. The results obtained in this study showed that the PNA-FISH method is suitable for the rapid detection of Campylobacter in food samples. With this work, it is concluded that although the two NAM-FISH based methods are a promising alternative for the detection of H. pylori and Campylobacter, they both require optimization.
O acesso de microrganismos patogénicos ao corpo humano pode comprometer a saúde do indivíduo, provocando variadas manifestações clínicas. Helicobacter pylori e Campylobacter são dois importantes patógenos gastrointestinais. A infeção por H. pylori é uma das infeções humanas mais comuns, cujo tratamento inclui a administração de antibióticos, nomeadamente fluoroquinolonas (FQ). Contudo, tem-se verificado um aumento da resistência de H. pylori a FQ, o que pode resultar em falhas no tratamento, tornando-se importante não só a deteção da bactéria, mas também a definição do seu perfil de resistência. Campylobacter é atualmente considerada a principal causa de doenças transmitidas por alimentos, encontrando-se normalmente associada ao consumo de carne crua. A deteção de microrganismos patogénicos pode ser alcançada por técnicas de cultura convencionais ou por métodos moleculares, nomeadamente testes imunológicos ou de deteção de ácidos nucleicos. A Biomode é uma empresa inovadora que desenvolve e comercializa métodos de diagnóstico rápidos baseados na tecnologia de hibridação fluorescente in situ (FISH) de ácidos nucleicos mímicos (NAM), NAM-FISH, que possibilita a deteção rápida de microrganismos, através da hibridação de sondas fluorescentes complementares com sequências específicas presentes no microrganismo alvo. Neste contexto, o presente trabalho teve como foco duas aplicações do NAM-FISH. Na área clínica, o objetivo principal foi o desenvolvimento de um método para a deteção de H. pylori e da resistência a FQ. Para tal, procedeu-se ao desenho de sondas de Peptide Nucleic Acid (PNA) e Locked Nucleic Acid (LNA)/2’OMe para a deteção de mutações causadoras da resistência. De forma a cobrir as mutações mais prevalentes, bem como o fenótipo wild-type, foram selecionadas 5 sondas de LNA/2’OMe. Na área da segurança alimentar, foi objetivo a otimização de um método de PNA-FISH para a deteção de Campylobacter em amostras alimentares. Um ensaio preliminar da inclusividade/exclusividade da sonda Campylobacter resultou na deteção de dois microrganismos não-alvo, H. cinaedi e H. pamatensis. Para a otimização do procedimento, foram utilizadas amostras de carne de frango crua, inoculadas artificialmente com C. jejuni. Antes do PNAFISH, foi introduzido um novo passo, no qual as amostras enriquecidas são sujeitas a uma centrifugação (10 000 g), seguida de ressuspensão em 0.1% Triton X-100, com o objetivo de reduzir a autofluorescência forte visualizada em amostras sem qualquer tratamento. Testou-se também a possibilidade de um enriquecimento das amostras em dois passos, no entanto, esta abordagem não demonstrou vantagens comparativamente ao procedimento em um passo. Efetuou-se ainda um teste de robustez, requerido pela AOAC International para a obtenção de certificação de produto, que revelou que a variação dos parâmetros do tempo e temperatura de hibridação influenciam a performance do método, pelo que as condições do PNA-FISH devem ser rigorosamente controladas. Os resultados obtidos neste estudo mostraram que o método PNAFISH é adequado para a rápida deteção de Campylobacter em amostras alimentares. Com este trabalho conclui-se que, embora os dois métodos baseados em NAM-FISH sejam uma opção promissora para a deteção de H. pylori e Campylobacter, ambos necessitam de otimização futura.
Mestrado em Biotecnologia
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Wilson, TK. "Development of a streamlined, selective-enrichment culture, one-tube (RT-)PCR-enzyme hybridization assay to detect bacterial fish pathogens in covertly infected farmed salmonids." Thesis, 2003. https://eprints.utas.edu.au/22118/1/whole_WilsonTeresaKaye2003_thesis.pdf.

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A new system which offers a low-cost and high performance means for detecting four bacterial pathogens Aeromonas salmonicida, Tenacibaculum maritimum, Lactococcus garvieae and Yersinia ruckeri in covertly infected farmed salmonid fish has been developed. The system couples Selective Enrichment Culture (SEC), Polymerase Chain Reaction (PCR) and Enzyme Hybridization Assay (EHA) technologies to provide streamlined high-throughput sample processing suitable for large scale surveillance and monitoring programs. The SEC media used for the technology were those developed by T.Wilson and J.Carson for the Cooperative Research Centre (CRC) for Aquaculture Ltd, except for the A. salmonicida medium which was developed using information obtained during the CRC project and by performing Minimum Inhibitory Concentration (MIG) assays with 32 antimicrobial agents that were not previously tested. Laboratory sensitivity of the A. salmonicida medium was 100% as determined by Most Probable Number (MPN) analysis and specificity of the medium was 97%. Bacterial DNA and RNA were extracted from the SEC media using guanidinium isothiocyanate (GuSCN) and Whatman Polyfiltronics GF/B 96-well Uni-filter plates. Sensitivity of the system as determined by PCR was between 1 and 16 CFU per 200 μI of selective-enrichment medium for DNA and between 1 and 9 CFU per 200 μI of selective-enrichment medium for RNA. The use of vacuum filtration and the 96-well glass microfibre filter plate allowed for rapid high-throughput and inexpensive extraction. Due to the high sensitivity of PCR, the technology is prone to false-positive results due to amplicon carry-over. To help prevent the occurrence of these erroneous results the photochemical IP-10 was added to the procedure. IP-10 inactivates PCR amplicons rendering them incapable of re-amplification in subsequent PCR reactions. Nucleolink ™ PCR-enzyme hybridization strips were used to perform sensitive streamlined (RT)PCR-EHA. For each bacterium 4 fg of pure target DNA or RNA was detected. With this system only one tube per sample from cDNA to EHA was required, decreasing the cost and time involved in sample transfer and decreasing the risk of cross-contamination between samples. In laboratory trials the final SEC-(RT-)PCR-EHA system proved to be very sensitive with 1-16 CFU from selective-enrichment culture detected. Specificity of the system was >99%. The system was also rapid with the 96-well nucleic acid extraction to EHA results achieved in as little as 8 hours. Test validation with field samples was achieved by determining test specificity and sensitivity from an epidemiological perspective. During this testing the sensitivity and specificity of the system matched that obtained using purified nucleic acids in the laboratory. Validation was conducted using a total of 10 fish trials using fish from different environments and from different sample sources. The system described here uses two types of technology, PCR and RT-PCR. The SEC-PCR-EHA system detects genomic DNA from the target pathogen, demonstrating evidence of infection, past or present and is ideal for use in surveillance programs and for quarantine. The SEC-RT-PCR-EHA system detects ribosomal RNA from the target pathogens. This system gives a more accurate indication of the presence of live bacteria and therefore of live covert infection and is useful when monitoring changes in the disease status of a population of fish over a short period of time. The system was developed using inexpensive materials instead of proprietary products, and disposable equipment usage was minimised in an effort to keep the system low-cost. The sensitivity of the system was maximised to ensure the detection of covertly infected fish and specificity of the system was as good as the PCR primers would allow. The system utilises 96-well technology to minimise the volume of reagents and to enable streamlined sample processing using a multichannel pipette. In summary, a low-cost, high-performance and streamlined highthroughput sampling system has been developed.
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Books on the topic "Pathogen enrichment"

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McKinney, Mark William. The application of "deletion enrichment" strategy for the isolation of DNA sequences unique to pathogenic clostridia. [s.l: The Author], 1991.

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Book chapters on the topic "Pathogen enrichment"

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Prasad, Priya. "Loss of Function of Sth1, The Catalytic Component of RSC (Remodel the Structure of Chromatin) Complex Grossly Alter the Chromatin Architecture." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 168–75. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_17.

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AbstractChromatin architecture has a profound effect on the gene expression in eukaryotes. It is constantly modulated in the cells in response to different stress condition and during the normal physiological process in the cell. The chromatin is also modulated during the cell growth and division, where several proteins involved during the cell cycle are synthesized, and hence the gene expression profile and chromatin state of an actively dividing cell differ from that of a resting cell in G0 state. Candida albicans, which is a harmless commensal in human host and an opportunistic fungal pathogen also show dynamic chromatin architecture, and this is facilitated by the several epigenetic determinants, which modulate the chromatin architecture. In this context, RSC (Remodel the structure of chromatin) complex in C. albicans is previously shown to be crucial for cell viability and to carry out several DNA templated events, like kinetochore function and cohesion enrichment. To correlate the role of RSC in kinetochore function with the chromatin architecture at centromeric and non-centromeric region, here we have shown that the chromatin at non-CEN7 regions shows lesser occupancy of nucleosomes in absence of Sth1 protein (catalytic component of RSC complex), which is due to the reduced binding but not due to the reduced expression of the histones.
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Penyalver, R., E. Bertolini, A. Olmos, A. García, M. Cambra, and M. M. López. "Detection of Pseudomonas savastanoi pv. savastanoi (Pss) on Asymptomatic Olive Plant Tissues by Enrichment-PCR." In Plant Pathogenic Bacteria, 421–24. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-010-0003-1_94.

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Kinoshita, Eiji, Emiko Kinoshita-Kikuta, and Tohru Koike. "Phos-tag-Based Affinity Chromatography Techniques for Enrichment of the Phosphoproteome." In Protein Modifications in Pathogenic Dysregulation of Signaling, 17–30. Tokyo: Springer Japan, 2015. http://dx.doi.org/10.1007/978-4-431-55561-2_2.

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Van Vuurde, J. W., M. A. Ruissen, and H. Vruggink. "Principles and Prospects of New Serological Techniques Including Immunosorbent Immunofluorescence, Immunoaffinity Isolation and Immunosorbent Enrichment for Sensitive Detection of Phytopathogenic Bacteria." In Plant Pathogenic Bacteria, 835–42. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-009-3555-6_180.

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Shen, Cangliang, and Yifan Zhang. "Isolation of Foodborne Pathogens on Selective, Differential, and Enrichment Medium by Streak-Plating." In Food Microbiology Laboratory for the Food Science Student, 25–30. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-26197-8_4.

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López, M. M., M. T. Gorris, P. Llop, J. Cubero, B. Vicedo, and M. Cambra. "Selective Enrichment Improves Isolation, Serological and Molecular Detection of Plant Pathogenic Bacteria." In Developments in Plant Pathology, 117–21. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-009-0043-1_25.

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Speicher, David J., Jalees A. Nasir, Peng Zhou, and Danielle E. Anderson. "Whole-Genome Sequencing of Pathogens in : A Target-Enrichment Approach for SARS-CoV-2." In Methods in Molecular Biology, 119–37. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1518-8_8.

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Arunachalam, Kannappan, and Chunlei Shi. "Developments in rapid detection/high throughput screening techniques for identifying pathogens in food." In Advances in ensuring the microbiological safety of fresh produce, 97–136. Burleigh Dodds Science Publishing, 2023. http://dx.doi.org/10.19103/as.2023.0121.08.

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For reasons of food safety and quality assurance, rapid identification of pathogens causing spoilage and infections in food matrices is essential. Conventional approaches include enrichment of microbial pathogens in a range of non-selective and pathogen-specific selective media, followed by biochemical and phenotypic identification. In conventional culturing techniques, time-dependent detection is a major obstacle when it comes to delicate foods such as fish, dairy products and fresh produce. To overcome the limits of conventional approaches, numerous detection technologies such as molecular-, spectroscopy- and spectrometry-based methods, as well as optical phenotyping and biosensor methods are now available. This chapter provides an overview of the principles, mechanisms and applications of new and emerging technologies for microbial identification in food systems. It also provides researchers in the field of food safety and quality assurance with the known advantages and limitations of available rapid detection techniques for identifying pathogens in foods.
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Blackburn, Clive de W. "ENRICHMENT SEROLOGY | An Enhanced Cultural Technique for Detection of Food-borne Pathogens." In Encyclopedia of Food Microbiology, 589–97. Elsevier, 1999. http://dx.doi.org/10.1006/rwfm.1999.0500.

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Singh, Karuna, and Radha Chaube. "Enrichment of drug resistance genes in human pathogenic bacteria showing antimicrobial resistance." In Antimicrobial Resistance in Wastewater and Human Health, 41–60. Elsevier, 2023. http://dx.doi.org/10.1016/b978-0-323-96124-0.00008-8.

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Conference papers on the topic "Pathogen enrichment"

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Manzanas, Carlos, Xiao Jiang, John A. Lednicky, and Z. Hugh Fan. "Development of Ball-Enabled Miniaturized Valves for Sample Preparation and Microheaters for Pathogen Detection." In ASME 2020 Fluids Engineering Division Summer Meeting collocated with the ASME 2020 Heat Transfer Summer Conference and the ASME 2020 18th International Conference on Nanochannels, Microchannels, and Minichannels. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/fedsm2020-20379.

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Abstract There have been numerous Zika virus (ZIKV) outbreaks in the past few years, representing a public health problem. The recommended tests for the diagnosis of Zika infections are performed in a laboratory setting. However, diagnostics platforms at the point-of-care (POC) are highly desirable for understanding and preventing ZIKV transmission. To address this need, we have developed a testing platform that (1) can be operated in the field for pathogen detection, (2) is rapid, cost-effective, and reliable, and (3) does not require a power supply. To realize the platform, we have developed (1) a series of ball-based valves for the storage and sequential delivery of reagents and (2) microheater-enabled RNA amplification, both of which are integral components of this POC device. The multiple reagents are needed for virus lysis, RNA enrichment and purification. These ball-based are employed for fluid-control and they are actuated manually by sliding the unit and a pole under it, which can lift the balls. Nucleic acid amplification is then performed by a smart coffee mug that provides a constant temperature for reverse transcription loop mediated isothermal amplification (RT-LAMP), followed by colorimetric detection. We have demonstrated the detection of Zika virus in human urine and saliva samples using this testing platform.
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Lopes, Camila Galvão, Gabriele Campos, Jaqueline Wang, Ana Cristina Girardi, and Maria Rita Passos Bueno. "Characterization of de novo variants in exomes of individuals with autism spectrum disorder." In XIV Congresso Paulista de Neurologia. Zeppelini Editorial e Comunicação, 2023. http://dx.doi.org/10.5327/1516-3180.141s1.564.

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The main objective of this essay was to contribute to the characterization of the genetic architecture of autism spectrum disorder (ASD) based on an analysis of a Brazilian series, which is still little studied. To achieve this goal, we verified the proportion of cases of ASD caused by de novo variants in neurodevelopment genes (genes from the SFARI bank and those associated with neurodevelopment described in the DECIPHER bank). Sixty-three trios were evaluated, composed of parents and probands diagnosed with ASD treated at the Human Genome and Stem Cell Studies Center (CEGH-CEL, USP). Genealogy, clinical data, gender, age at the consultation, and parental age were collected. Whole-exome sequencing was performed through a collaboration with Mount Sinai, New York, United States (collaboration with the Autism Sequencing ConsortiumACS). Identification of De novo variants in candidate genes for ASD was performed using the LOVD program (LOVD v.3.0 – Leiden Open Variation Database). It was observed that most of the probands were boys (n = 55, 86%), and the minority had a family history of ASD (n = 4, 6%). It was also found that 40% (n = 25) of individuals had a delay in language development, and a small percentage had comorbidities such as ADHD and epilepsy (n=6, 10% and n=2, 3%, respectively). The mean parental age at the time of pregnancy was close to 30 years for both parents (29.7 and 32.5 for the mother and father, respectively). Nine de novo pathogenic or potentially pathogenic variants were identified in candidate genes: for TEA: six in SFARI genes (four pathogenic variants in NF1, TLK2, DNAH17, BRSK2 genes, and two probably pathogenic variants in ARHGAP5 and HUWE1) and three in genes of neurodevelopment of DECIPHER (Deciphering Developmental Disorders Study, 2015) (two pathogenic variants in the ERLIN2, ST3GAL3 genes and one probably pathogenic in COL11A1). When performing the gene enrichment analysis of genes with pathogenic or potentially pathogenic variants, we observed the enrichment of genes for intracellular protein transport. The clinical picture of individuals with pathogenic or potentially pathogenic variants was expected, as previously described in the literature. This study suggests that de novo variants are also an essential mechanism for the etiology of ASD in Brazil, explaining the genetic architecture of 9.5% of cases.
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Bowman, Andrew, Andrew Mack, Wondwossen A. Gebreyes, and Julie A. Funk. "Comparison of enrichment schemes for the isolation of Yersinia enterocolitica." In Fifth International Symposium on the Epidemiology and Control of Foodborn Pathogens in Pork. Iowa State University, Digital Press, 2003. http://dx.doi.org/10.31274/safepork-180809-534.

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Davies, H., Christine E. R. Dodd, S. Tötermeyer, J. Wiseman, and Ken H. Mellits. "A rapid, sensitive enrichment PCR to detect Salmonella and ETEC infections in pigs." In Eighth International Symposium on the Epidemiology and Control of Foodborne Pathogens in Pork. Iowa State University, Digital Press, 2009. http://dx.doi.org/10.31274/safepork-180809-825.

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Bernate, Ilze, and Martins Sabovics. "Research on germinated wheat grain, broccoli, alfalfa, radish and hemp seeds microbiological safety." In Research for Rural Development 2021 : annual 27th International scientific conference proceedings. Latvia University of Life Sciences and Technologies, 2021. http://dx.doi.org/10.22616/rrd.27.2021.013.

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For a long time, germinated seeds have been used in food as a healthy product with high nutritional value and as a decor for exquisite dishes today. However, there have been many foodborne outbreaks in Europe, the United States, and other parts of the world associated with pathogens contamination of sprouts. These outbreaks pose a constant challenge to the entire sprouts industry. The aim of this study was to determine the presence of Shiga toxin-producing Escherichia coli (STEC), Salmonella spp., and potentially pathogenic bacteria in germinated grains and seeds intended for industrial food production and ready for use without further processing. In this study, grains of wheat (Triticum aestivum), seeds of broccoli (Brassica oleracea), alfalfa (Medicago sativa), radish (Raphanus sativus) and hemp (Cannabis sativa) were germinated for 72 hours and were evaluated compared with ungerminated grains and seeds. The presence of E.coli was assessed by the inoculation of enrichment broth to Tryptone Bile X-glucuronide (TBX) and Eosin methylene blue (EMB) agars, and colony characterization with MALDI-TOF. E.coli was carried out in accordance with LVS ISO 16649-2:2007. The presence of STEC was determined in accordance with ISO/TS 13136:2012. Salmonella spp. detection was in accordance with ISO 6579-1:2017. As a result, E.coli, Salmonella spp., and STEC were not found in any sample. However, environmental bacteria were detected in TBX dry seeds and 12 h – soaked seeds. The presence of Enterobacteriaceae was found in all samples by colony characterization on EMB by MALDI-TOF. The results show that the sprouts and edible seeds available in Latvia could be included as healthy and relatively safe food.
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Malorny, Burkhard, Nadine Krämer, Håkan Vigre, Jeffrey Hoorfar, and Charlotta Löfström. "A novel strategy to obtain quantitative data for modelling: Combined enrichment and real-time PCR for enumeration of salmonellae from pig carcasses." In Fifth International Symposium on the Epidemiology and Control of Foodborn Pathogens in Pork. Iowa State University, Digital Press, 2011. http://dx.doi.org/10.31274/safepork-180809-578.

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Nollet, Nathalie, Dominiek Maes, Lieven De Zutter, Aart de Kruif, and Jan van Hoof. "Evaluation of different enrichment media for the isolation of Salmonella spp from faeces and lymph nodes in slaughter pigs." In Fourth International Symposium on the Epidemiology and Control of Salmonella and Other Food Borne Pathogens in Pork. Iowa State University, Digital Press, 2001. http://dx.doi.org/10.31274/safepork-180809-1183.

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Giannakou, Lydia, Athanasios-Stefanos Giannopoulos, Erasmia Rouka, Chrissi Hatzoglou, Konstantinos Gourgoulianis, and Sotirios Zarogiannis. "Investigation and functional enrichment analysis of the human gene interaction network with common gram-negative respiratory pathogens predicts possible association with lung adenocarcinoma." In ERS International Congress 2019 abstracts. European Respiratory Society, 2019. http://dx.doi.org/10.1183/13993003.congress-2019.pa5417.

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Reports on the topic "Pathogen enrichment"

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VanderGheynst, Jean, Michael Raviv, Jim Stapleton, and Dror Minz. Effect of Combined Solarization and in Solum Compost Decomposition on Soil Health. United States Department of Agriculture, October 2013. http://dx.doi.org/10.32747/2013.7594388.bard.

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In soil solarization, moist soil is covered with a transparent plastic film, resulting in passive solar heating which inactivates soil-borne pathogen/weed propagules. Although solarization is an effective alternative to soil fumigation and chemical pesticide application, it is not widely used due to its long duration, which coincides with the growing season of some crops, thereby causing a loss of income. The basis of this project was that solarization of amended soil would be utilized more widely if growers could adopt the practice without losing production. In this research we examined three factors expected to contribute to greater utilization of solarization: 1) investigation of techniques that increase soil temperature, thereby reducing the time required for solarization; 2) development and validation of predictive soil heating models to enable informed decisions regarding soil and solarization management that accommodate the crop production cycle, and 3) elucidation of the contributions of microbial activity and microbial community structure to soil heating during solarization. Laboratory studies and a field trial were performed to determine heat generation in soil amended with compost during solarization. Respiration was measured in amended soil samples prior to and following solarization as a function of soil depth. Additionally, phytotoxicity was estimated through measurement of germination and early growth of lettuce seedlings in greenhouse assays, and samples were subjected to 16S ribosomal RNA gene sequencing to characterize microbial communities. Amendment of soil with 10% (g/g) compost containing 16.9 mg CO2/g dry weight organic carbon resulted in soil temperatures that were 2oC to 4oC higher than soil alone. Approximately 85% of total organic carbon within the amended soil was exhausted during 22 days of solarization. There was no significant difference in residual respiration with soil depth down to 17.4 cm. Although freshly amended soil proved highly inhibitory to lettuce seed germination and seedling growth, phytotoxicity was not detected in solarized amended soil after 22 days of field solarization. The sequencing data obtained from field samples revealed similar microbial species richness and evenness in both solarized amended and non-amended soil. However, amendment led to enrichment of a community different from that of non-amended soil after solarization. Moreover, community structure varied by soil depth in solarized soil. Coupled with temperature data from soil during solarization, community data highlighted how thermal gradients in soil influence community structure and indicated microorganisms that may contribute to increased soil heating during solarization. Reliable predictive tools are necessary to characterize the solarization process and to minimize the opportunity cost incurred by farmers due to growing season abbreviation, however, current models do not accurately predict temperatures for soils with internal heat generation associated with the microbial breakdown of the soil amendment. To address the need for a more robust model, a first-order source term was developed to model the internal heat source during amended soil solarization. This source term was then incorporated into an existing “soil only” model and validated against data collected from amended soil field trials. The expanded model outperformed both the existing stable-soil model and a constant source term model, predicting daily peak temperatures to within 0.1°C during the critical first week of solarization. Overall the results suggest that amendment of soil with compost prior to solarization may be of value in agricultural soil disinfestations operations, however additional work is needed to determine the effects of soil type and organic matter source on efficacy. Furthermore, models can be developed to predict soil temperature during solarization, however, additional work is needed to couple heat transfer models with pathogen and weed inactivation models to better estimate solarization duration necessary for disinfestation.
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