Relevant bibliographies by topics / Pathogen tracking

Contents

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

Academic literature on the topic 'Pathogen tracking'

Author: Grafiati
Published: 25 May 2024

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Journal articles on the topic "Pathogen tracking"

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Check, Erika. "Pathogen-tracking questioned." Nature 420, no. 6915 (December 2002): 451. http://dx.doi.org/10.1038/420451b.

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COOKE, DAVID E. L. "Tracking the sudden oak death pathogen." Molecular Ecology 16, no. 18 (September 2007): 3735–36. http://dx.doi.org/10.1111/j.1365-294x.2007.03430.x.

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Hadfield, James, Colin Megill, Sidney M. Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, and Richard A. Neher. "Nextstrain: real-time tracking of pathogen evolution." Bioinformatics 34, no. 23 (May 22, 2018): 4121–23. http://dx.doi.org/10.1093/bioinformatics/bty407.

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Stroeymeyt, Nathalie, Anna V. Grasse, Alessandro Crespi, Danielle P. Mersch, Sylvia Cremer, and Laurent Keller. "Social network plasticity decreases disease transmission in a eusocial insect." Science 362, no. 6417 (November 22, 2018): 941–45. http://dx.doi.org/10.1126/science.aat4793.

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Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogen-triggered responses. We tested this hypothesis experimentally in the antLasius nigerusing a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmission-inhibitory properties of the colony’s contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups.
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Noble, Rachel T., Steven M. Allen, Angelia D. Blackwood, Weiping Chu, Sunny C. Jiang, Greg L. Lovelace, Mark D. Sobsey, Jill R. Stewart, and Douglas A. Wait. "Use of viral pathogens and indicators to differentiate between human and non-human fecal contamination in a microbial source tracking comparison study." Journal of Water and Health 1, no. 4 (December 1, 2003): 195–207. http://dx.doi.org/10.2166/wh.2003.0021.

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Assays for the detection and typing of adenoviruses, enteroviruses and F+ specific coliphages were performed on samples created as part of a national microbial source tracking methods comparison study. The samples were created blind to the researchers, and were inoculated with a variety of types of fecal contamination source (human, sewage, dog, seagull and cow) and mixtures of sources. Viral tracer and pathogen assays demonstrated a general ability to discriminate human from non-human fecal contamination. For example, samples inoculated with sewage were correctly identified as containing human fecal contamination because they contained human adenovirus or human enterovirus. In samples containing fecal material from individual humans, human pathogen analysis yielded negative results probably because the stool samples were taken from healthy individuals. False positive rates for the virus-based methods (0–8%) were among the lowest observed during the methods comparison study. It is suggested that virus-based source tracking methods are useful for identification of sewage contamination, and that these methods may also be useful as an indication of the public health risk associated with viral pathogens. Overall, virus-based source tracking methods are an important approach to include in the microbial source tracking ‘toolbox’.
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Leu, Stephan T., and Stephanie S. Godfrey. "Advances from the nexus of animal behaviour and pathogen transmission: new directions and opportunities using contact networks." Behaviour 155, no. 7-9 (2018): 567–83. http://dx.doi.org/10.1163/1568539x-00003507.

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Abstract Contact network models have enabled significant advances in understanding the influence of behaviour on parasite and pathogen transmission. They are an important tool that links variation in individual behaviour, to epidemiological consequences at the population level. Here, in our introduction to this special issue, we highlight the importance of applying network approaches to disease ecological and epidemiological questions, and how this has provided a much deeper understanding of these research areas. Recent advances in tracking host behaviour (bio-logging: e.g., GPS tracking, barcoding) and tracking pathogens (high-resolution sequencing), as well as methodological advances (multi-layer networks, computational techniques) started producing exciting new insights into disease transmission through contact networks. We discuss some of the exciting directions that the field is taking, some of the challenges, and importantly the opportunities that lie ahead. For instance, we suggest to integrate multiple transmission pathways, multiple pathogens, and in some systems, multiple host species, into the next generation of network models. Corresponding opportunities exist in utilising molecular techniques, such as high-resolution sequencing, to establish causality in network connectivity and disease outcomes. Such novel developments and the continued integration of network tools offers a more complete understanding of pathogen transmission processes, their underlying mechanisms and their evolutionary consequences.
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Zhang, Ying, Der‐Shyang Kao, Bing Gu, Rajdeep Bomjan, Mayank Srivastava, Haojie Lu, Daoguo Zhou, and W. Andy Tao. "Tracking Pathogen Infections by Time‐Resolved Chemical Proteomics." Angewandte Chemie International Edition 59, no. 6 (February 3, 2020): 2235–40. http://dx.doi.org/10.1002/anie.201911078.

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Zhang, Ying, Der‐Shyang Kao, Bing Gu, Rajdeep Bomjan, Mayank Srivastava, Haojie Lu, Daoguo Zhou, and W. Andy Tao. "Tracking Pathogen Infections by Time‐Resolved Chemical Proteomics." Angewandte Chemie 132, no. 6 (January 9, 2020): 2255–60. http://dx.doi.org/10.1002/ange.201911078.

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Sokolova, Ekaterina, Johan Åström, Thomas J. R. Pettersson, Olof Bergstedt, and Malte Hermansson. "Estimation of pathogen concentrations in a drinking water source using hydrodynamic modelling and microbial source tracking." Journal of Water and Health 10, no. 3 (June 6, 2012): 358–70. http://dx.doi.org/10.2166/wh.2012.183.

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The faecal contamination of drinking water sources can lead to waterborne disease outbreaks. To estimate a potential risk for waterborne infections caused by faecal contamination of drinking water sources, knowledge of the pathogen concentrations in raw water is required. We suggest a novel approach to estimate pathogen concentrations in a drinking water source by using microbial source tracking data and fate and transport modelling. First, the pathogen (norovirus, Cryptosporidium, Escherichia coli O157/H7) concentrations in faecal contamination sources around the drinking water source Lake Rådasjön in Sweden were estimated for endemic and epidemic conditions using measured concentrations of faecal indicators (E. coli and Bacteroidales genetic markers). Afterwards, the fate and transport of pathogens within the lake were simulated using a three-dimensional coupled hydrodynamic and microbiological model. This approach provided information on the contribution from different contamination sources to the pathogen concentrations at the water intake of a drinking water treatment plant. This approach addresses the limitations of monitoring and provides data for quantitative microbial risk assessment (QMRA) and risk management in the context of faecal contamination of surface drinking water sources.
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Gulumbe, Bashar Haruna, Abbas Yusuf Bazata, and Musbahu Abdullahi Bagwai. "Campylobacter Species, Microbiological Source Tracking and Risk Assessment of Bacterial pathogens." Borneo Journal of Pharmacy 5, no. 2 (May 31, 2022): 136–52. http://dx.doi.org/10.33084/bjop.v5i2.3363.

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Campylobacter species continue to remain critical pathogens of public health interest. They are responsible for approximately 500 million cases of gastroenteritis per year worldwide. Infection occurs through the consumption of contaminated food and water. Microbial risk assessment and source tracking are crucial epidemiological strategies to monitor the outbreak of campylobacteriosis effectively. Various methods have been proposed for microbial source tracking and risk assessment, most of which rely on conventional microbiological techniques such as detecting fecal indicator organisms and other novel microbial source tracking methods, including library-dependent microbial source tracking and library-independent source tracking approaches. However, both the traditional and novel methods have their setbacks. For example, while the conventional techniques are associated with a poor correlation between indicator organism and pathogen presence, on the other hand, it is impractical to interpret qPCR-generated markers to establish the exact human health risks even though it can give information regarding the potential source and relative human risk. Therefore, this article provides up-to-date information on campylobacteriosis, various approaches for source attribution, and risk assessment of bacterial pathogens, including next-generation sequencing approaches such as shotgun metagenomics, which effectively answer the questions of potential pathogens are there and in what quantities.
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Dissertations / Theses on the topic "Pathogen tracking"

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Scheuerman, Phillip R., D. R. Dulaney, M. S. Floresquerra, and Kurt J. Maier. "The Use of Fecal Coliform Source Tracking for Remediation of Pathogen Impaired Surface Waters." Digital Commons @ East Tennessee State University, 2003. https://dc.etsu.edu/etsu-works/2934.

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Clement, Mary. "The use of microbial community fingerprinting as a marker for tracking the source of water application to pathogen and groundwater source tracking /." Morgantown, W. Va. : [West Virginia University Libraries], 2010. http://hdl.handle.net/10450/11132.

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Thesis (M.S.)--West Virginia University, 2010.
Title from document title page. Document formatted into pages; contains ix, 49 p. : ill. (some col.), col. maps. Includes abstract. Includes bibliographical references (p. 47-49).
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Pesapane, Risa Raelene. "Tracking Pathogen Transmission at the Human-Wildlife Interface: Banded Mongoose (Mungos mungo) and Escherichia coli as a Model System in Chobe, Botswana." Thesis, Virginia Tech, 2011. http://hdl.handle.net/10919/76930.

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Anthropozoonotic diseases, defined as infectious diseases caused by pathogens transmitted from humans to wildlife, pose a significant health threat to wildlife populations. Many of these pathogens are also able to move from wildlife reservoirs to humans, termed zoonotic diseases, creating the possibility for bi-directional transmission between humans and wildlife. Recent studies show that a significant proportion of emerging infectious diseases in humans originate in wildlife reservoirs and that the frequency of emergence is increasing, yet the specific transmission pathways still remain speculative in most cases. Human fecal waste is persistent across human-modified landscapes and has been identified as a potential source of disease exposure for wildlife populations living near humans. As part of a long-term study of banded mongoose (Mungos mungo) that live in close association with humans and human fecal waste I used Escherichia coli and banded mongoose (Mungos mungo) for evaluating exchange of fecal waste-borne microorganisms at the human-wildlife interface. Antibiotic resistance was found in 57.5% ° 10.3% (n=87) of mongoose fecal samples and 37.2% ° 5.9% of isolates (n=253). Multidrug resistance was detected in 13.8% ° 4.2% of isolates (n=253). Mongoose and human fecal waste isolates consistently clustered together in phylogenetic analyses and statistical analysis of genetic variation showed no significant differences (p=0.18) between E. coli from human and mongoose populations. These results suggest that human fecal waste contamination is an important mechanism for the transmission of pathogens to both humans and animals, including the spread of antibiotic resistance in the environment, an emerging global health threat.
Master of Science
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Merrick, Natsuko N. "Microbial Source Tracking: Watershed Scale Study of Pathogen Origin, Fate, and Transport in the Upper Sugar Creek Watershed, Northeast Ohio." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1276703299.

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Sena, Kenton L. "TRACKING A TREE-KILLER: IMPROVING DETECTION AND CHARACTERIZING SPECIES DISTRIBUTION OF PHYTOPHTHORA CINNAMOMI IN APPALACHIAN FORESTS." UKnowledge, 2018. https://uknowledge.uky.edu/pss_etds/102.

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Phytophthora cinnamomi is a soil-borne oomycete pathogen causing root rot in susceptible host species. P. cinnamomi is thought to have originated in Southeast Asia, but has since been introduced to many regions around the world, where it causes dramatic declines in many forest tree species. In the eastern US, the primary susceptible tree species of concern are American chestnut (Castanea dentata), white oak (Quercus alba), and shortleaf pine (Pinus echinata). American chestnut, functionally eliminated in the early 1900s by the rapidly acting chestnut blight (Cryphonectria parasitica), has been the subject of decades-long breeding efforts aimed at improving chestnut resistance to chestnut blight. To improve chestnut restoration success, and restoration of other susceptible species, the distribution patterns of P. cinnamomi on a landscape scale must be better understood. This project was initiated to develop an improved method for detecting P. cinnamomi to permit high-throughput screening of forest soils, and to implement the improved detection approach in characterizing the distribution patterns of P. cinnamomi in developing soils on reclaimed surface mines in eastern Kentucky, as well as mature forest soils within an undisturbed watershed in a reference-quality eastern Kentucky forest. We developed an improved detection method using a molecular DNA-amplification approach (PCR), which demonstrated similar sensitivity to traditional culture-based methods, but required less time and space than traditional methods. We used this detection approach to screen soils from a chronosequence of reclaimed surface mines (reclaimed at different points in time) to evaluate whether reclaimed surface mined sites become favorable for P. cinnamomi colonization over time. Our analysis detected P. cinnamomi at the two older sites (reclaimed in 1997 and 2003), but we did not detect P. cinnamomi at the two newer sites sampled (reclaimed in 2005 and 2007). These results suggest that surface mined sites become favorable for P. cinnamomi colonization over time, and should not be considered permanently “Phytophthora-free.” We also collected ~200 samples from a watershed in UK’s Robinson Forest, from plots representing a gradient of topographic position, slope, and aspect. This survey indicated that P. cinnamomi distribution in forests is complex and can be difficult to predict; however, P. cinnamomi was detected in both drier upslope sites and in moister drainage sites.
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Hennart, Mélanie. "Taxonomie génomique des souches bactériennes et émergence de l'antibiorésistance." Electronic Thesis or Diss., Sorbonne université, 2022. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2022SORUS547.pdf.

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Les maladies infectieuses font partie des préoccupations mondiales en santé publique, en particulier en raison de la résistance aux antimicrobiens chez certaines bactéries pathogènes. L'espèce Klebsiella pneumoniae est identifiée comme l'une des bactéries multirésistantes les plus préoccupantes. Corynebacterium diphtheriae, responsable de la diphtérie, reste largement sensible aux antibiotiques de première intention dont la pénicilline et peut être contrôlée par les vaccins, mais ré-émerge lorsque la couverture vaccinale est insuffisante. Parmi les moyens de contrôle des maladies infectieuses, la détection et l'identification précise de ces agents pathogènes, ainsi que leur suivi épidémiologique, jouent un rôle primordial. La mise en œuvre du séquençage génomique a révolutionné le génotypage bactérien grâce à son haut pouvoir discriminant, qui permet la distinction des agents pathogènes à l'échelle des souches. Le séquençage génomique permet également la détection de variants et de leurs caractéristiques importantes, telles que leur virulence ou leur résistance. Les travaux de recherche de cette thèse s'articulent sur deux axes principaux. Le premier axe apporte des analyses bio-informatiques de la structure populationnelle de la résistance aux antibiotiques chez C. diphtheriae. Une étude d'association génomique (GWAS) a été réalisée pour définir les bases moléculaires de la résistance, ainsi que les associations avec la production de toxine diphtérique et d'autres caractéristiques des souches. Un nouveau gène de résistance à la pénicilline a été découvert sur un élément mobile chez C. diphtheriae. Un outil de génotypage a été développé spécifiquement pour C. diphtheriae, pour laquelle les liens entre génotypes et phénotypes cliniques sont mal connus. Cet outil consolide et facilite la détection et le génotypage des principaux facteurs de virulence et des gènes de résistance, ainsi que l'usage des nomenclatures des souches à partir de génomes assemblés. Il permet également de prédire les biovars et la toxicité des souches. Le second axe est consacré à la taxonomie génomique infra-spécifique. Une nouvelle approche de classification et de nomenclature génomiques est proposée en utilisant comme modèle l'espèce K. pneumoniae. Ces travaux détaillent la conception et l'implémentation d'un système de codes-barres qui combine le regroupement par Single Linkage MultiLevel (MLSL) et les LIN (Life Identification Number) codes, tous deux basés sur le même schéma de typage core-genome MLST (cgMLST). Cette approche taxonomique innovante résulte en une nomenclature infra-spécifique précise et stable, qui est de plus largement déployable chez les autres espèces bactériennes. Une étude de la structure phylogénétique de C. diphtheriae a également été réalisée, avec la mise en œuvre d'un système cgMLST sur la base duquel une taxonomie génomique des souches a été proposée. Sur la base des nouveaux apports et concepts précédemment exposés, plusieurs études de cas ont été réalisées : mise en évidence et caractérisation d'une nouvelle espèce bactérienne (C. rouxii), précédemment confondue avec C. diphtheriae ; et épidémiologie génomique de la diphtérie dans différentes régions du monde, ou à partir de sources cliniques humaines et animales. Ces applications de la taxonomie génomique associée à la détection des gènes de résistance aux antibiotiques illustrent le potentiel des méthodes et des outils développés durant cette thèse afin de contribuer à la recherche et à la surveillance génomique des bactéries pathogènes
Infectious diseases are a global public health concern, particularly due to antimicrobial-resistance in some pathogenic bacteria. Klebsiella pneumoniae is one of the most worrying multiresistant bacteria. Corynebacterium diphtheriae, which causes diphtheria, remains largely susceptible to first-line antibiotics, including penicillin, and can be controlled through vaccination, but re-emerges when vaccination coverage is insufficient. Among the effective infection control measures, the accurate detection and identification of these pathogens, as well as their epidemiological monitoring, play a key role. In the recent years, the implementation of whole-genome sequencing (WGS) has revolutionised bacterial genotyping, by providing discrimination at the strain level. Genomic sequencing also enables the detection of variants and their important characteristics, such as virulence or antimicrobial resistance. The research work of this thesis is structured around two main axes. The first axis provides bioinformatic analyses of the population structure of antimicrobial resistance in C. diphtheriae. A genome-wide association study (GWAS) was performed to determine the genetic basis behind the resistance phenotypes, as well as the associations with diphtheria toxin production and other strain characteristics. A new penicillin resistance gene was discovered on a mobile element in C. diphtheriae. A genotyping tool was developed specifically for C. diphtheriae, for which the links between genotypes and clinical phenotypes are poorly known. This tool consolidates and facilitates the detection and genotyping of the main virulence factors and resistance genes, as well as the use of strain nomenclatures from assembled genomes. It also enables the prediction of biovars and toxicity of strains. The second axis relates to infra-species genomic taxonomy. A new approach of genome-based classification and nomenclature of strains was developed using K. pneumoniae as a model. This work describes the design and implementation of a barcoding system that combines Single Linkage MultiLevel (MLSL) clustering and Life Identification Number (LIN) codes, both based on the same core-genome MLST (cgMLST) typing scheme. This innovative taxonomic approach, widely applicable to other bacterial species, yields precise and stable nomenclatures. A study of the phylogenetic structure of C. diphtheriae was also carried out, with the implementation of a cgMLST scheme on the basis of which a genomic taxonomy of strains was proposed. Based on the contributions and concepts presented above, several case studies were carried out: identification and characterisation of a new species (C. rouxii), previously misidentified as C. diphtheriae; genomic epidemiology of diphtheria in different world regions or clinical sources. These applications of genomic taxonomy in combination with antimicrobial resistance gene detection illustrate the potential of the methods and tools developed during this thesis to support genomic research and surveillance of pathogenic bacteria
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Leach, Mark Daniel. "A discrete, stochastic model and correction method for bacterial source tracking." Online access for everyone, 2007. http://www.dissertations.wsu.edu/Thesis/Spring2007/m_leach_050207.pdf.

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Robinson, Matthew T. "The tracking of pathogens during artificial actoparasite feeding : a focus on Bartonella henselae and Anaplasma phagocytophilum." Thesis, University of Bristol, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501522.

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There has been a surge in the number of emerging zoonotic vector-borne diseases world-wide. Current research on vector-borne diseases is often focused on interactions between mammalian hosts and pathogens. Relatively little is known of the interactions that take place when pathogens are ingested by vector species. The aim of this project is to develop techniques which would allow us to track zoonotic bacteria within the vector and to identify possible interactions. Two models were used in this study: Bartonella henselae and the flea Ctenocephalides felis, and Anaplasma phagocytophilum and the tick Ixodes ricinus.
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Hussein, Khwam Reissan. "Source tracking of faecal indicator bacteria of human pathogens in bathing waters : an evaluation and development." Thesis, University of Plymouth, 2014. http://hdl.handle.net/10026.1/3011.

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Bacterial water pollution is a significant problem because it is associated with reduction in the ‘quality’ of water systems with a potential impact on human health. Faecal indicator bacteria (FIB) are usually used to monitor the quality of water, and to indicate the presence of pathogens in water bodies. However, enumeration alone does not enable identification of the precise origin of these pathogens. This study aimed to monitor the quality of bathing water and associated fresh water in and out of the ‘bathing season’ in the UK, and to evaluate the use of microbial source tracking (MST) such as the host-specific based polymerase chain reaction (PCR) and quantitative PCR (qPCR) to recognize human and other animal sources of faecal pollution. The culture-dependent EU method of estimating FIB in water and sediment samples was performed on beach in the South Sands, Kingsbridge estuary, Devon, UK- a previously ‘problematic’ site. FIB were present at significant levels in the sediments, especially mud, as well as fresh water from the stream and pond flowing onto South Sands beach. However, the quality of bathing water was deemed to be ‘good’ and met with the EU bathing water directive 2006. Using MST it was possible to successfully classify the nature of the source from which the bacteria came. PCR was applied to detect the Bacteroides species 16S rRNA genetic markers from human sewage and animal faeces. All water and sediment samples displayed positive results with a general Bacteroides marker indicating the presence of Bacteroides species. Host-specific PCR showed the human Bacteroides genetic marker only in the sediment of the stream. However, limitations in the ‘types’ of probes available and in the persistence of these markers were identified. Thus, novel dog-specific Bacteroides conventional PCR and qPCR primer sets were developed to amplify a section of the 16S rRNA gene unique to the Bacteroides genetic marker from domestic dog faeces, and these were successfully used to quantify those markers in water samples at a ‘dog permitted’ and ‘dog banned’ beach (Bigbury-on-Sea, Devon, UK). Generic, human and dog Bacteroides PCR primer sets were also used to evaluate the persistence of Bacteroides genetic markers in controlled microcosms of water and sediment at differing salinities (< 0.5 and 34 psu) and temperature (10 and 17 ºC). The rates of decline were found did not differ significantly over 14 and 16 days for the water and sediment microcosms, respectively. Beach sediments which were studied in this project may act as a reservoir for adhesive FIB, and this was confirmed using fluorescence in situ hybridisation (FISH). The similarity in the persistence of these Bacteroides 16S rRNA genetic markers in environmental water and sediment suggests that viable but non-culturable (VBNC) Bacteroides spp. do not persist in the natural environment for long. Therefore, 16S rRNA genetic markers can be of value as additional faecal indicators of bathing water pollution and in source tracking. Thus, in this study MST methods were successfully used and in future applications, dog-specific primer sets can be added to the suite of host-specific Bacteroides genetic markers available to identify the source(s) of problem bacteria found on failing beaches.
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Venkatesan, Lavanya. "Identifying and Tracking the Evolution of Mutations in the SARS-CoV-2 Virus." Thesis, Virginia Tech, 2021. http://hdl.handle.net/10919/103939.

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SARS-CoV-2 is caused by a pathogenic and highly transmissible beta coronavirus leading to severe infections in immuno-compromised individuals. This study first evaluates the primers used in the Reverse Transcription Polymerase Chain Reaction (RT-PCR) to detect SARS-CoV-2 by understanding how mutations might affect the primer efficiency with the SARS-CoV-2 sequences. Mutations on the Spike protein of SARS-CoV-2 are the most important as the spike protein mediates the viral entry into host cells. This study tracks the course of mutations on the spike protein by focusing on the haplogroups of the sequences across the world. A comprehensive database linking three important, currently available databases is curated as part of this study to fill the gaps caused by sequencing errors. Further, this study exploits the data generated by the Illumina and Oxford Nanopore next generation sequencing methods to study the evolution of mutations in a single Septuagenarian patient over an infection period of 102 days using the gene analysis software Geneious Prime.
Master of Science
A novel corona virus named Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken down the entire world by causing Covid-19 pandemic. Initially detected in Wuhan, China, the virus has now made its way to more than 200 countries with a heavy death toll. Understanding the virus through mutation tracking and improving diagnostics and vaccine design have now become the top priority of researchers. Most of these researchers depend on quality viral sequence datasets to identify and track mutations. One aim of this study is to provide a comprehensive dataset linking the GISAID (Global Initiative on Sharing All Influenza Data), NCBI (National Center for Biological Information) and the SRA (Sequence Read Archive) sequences. The dataset can be used for genome analysis and mutation tracking which can provide important insights for vaccine design and in improving diagnostic assays. In addition, this study provides an analysis of viral mutations in in the genomic regions targeted by commonly used primers in the RT-PCR tests for SARS-CoV-2 that may affect the efficiency of detection. This study also uses the haplogroup information of people across the world to track the D614G mutation on the S gene of SARS-CoV-2 as it may be associated with increased transmissibility. To track the course of mutations in SARS-CoV-2, it is important to analyze the sequencing data provided by the Illumina and Oxford Nanopore next generation sequencing methods. We present a case study to investigate the course of SARS-CoV-2 mutations in a single septuagenarian patient over a period of 102days using the Sequence Read Archive (SRA) data generated by two Next Generation Sequencing methods and compare the advantages that one has over the other.
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Books on the topic "Pathogen tracking"

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Tanya, Roberts, Jensen Helen H, Unnevehr Laurian, and United States. Dept. of Agriculture. Economic Research Service., eds. Tracking foodborne pathogens from farm to table: Data needs to evaluate control options : conference proceedings January 9-10, 1995, Washington, D.C. Washington, D.C: U.S. Dept. of Agriculture, ERS, 1995.

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), Wilmington (Del, and Geological Survey (U.S.), eds. Pathogenic bacteria and microbial-source tracking markers in Brandywine Creek Basin, Pennsylvania and Delaware, 2009-10. Reston, Va: U.S. Dept. of the Interior, U.S. Geological Survey, 2011.

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Microbial source tracking: Methods, applications, and case studies. New York: Springer, 2011.

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United States. Dept. of Agriculture, ed. Tracking foodborne pathogens from farm to table: Data needs to evaluate control options : conference proceedings, January 9-10, 1995, Washington, DC. [Washington, DC]: U.S. Dept. of Agriculture, 1995.

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United States. Dept. of Agriculture., ed. Tracking foodborne pathogens from farm to table: Data needs to evaluate control options : conference proceedings, January 9-10, 1995, Washington, DC. [Washington, DC]: U.S. Dept. of Agriculture, 1995.

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United States. Dept. of Agriculture., ed. Tracking foodborne pathogens from farm to table: Data needs to evaluate control options : conference proceedings, January 9-10, 1995, Washington, DC. [Washington, DC]: U.S. Dept. of Agriculture, 1995.

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Tracking Foodborne Pathogens From Farm To Table: Data Needs To Evaluate Control Options. Diane Pub Co, 2004.

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Microbial source tracking. Washington, D.C: ASM Press, 2007.

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Rochelle, Paul A., and Ricardo De Leon. Workshop on Microbial Source Tracking in Water (Werf Report). WERF, 2007.

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Hagedorn, Charles, Anicet R. Blanch, and Valerie J. Harwood. Microbial Source Tracking: Methods, Applications, and Case Studies. Springer, 2014.

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Book chapters on the topic "Pathogen tracking"

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Koczerka, Michaël, Isabelle Lantier, Anne Pinard, Marie Morillon, Justine Deperne, Ohad Gal-Mor, Olivier Grépinet, and Isabelle Virlogeux-Payant. "In Vivo Tracking of Bacterial Colonization in Different Murine Models Using Bioluminescence: The Example of Salmonella." In Methods in Molecular Biology, 235–48. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1971-1_19.

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AbstractApplications of bioluminescence for the in vivo study of pathogenic microorganisms are numerous, ranging from the quantification of virulence gene expression to measuring the effect of antimicrobial molecules on the colonization of tissues and organs by the pathogen. Most studies are performed in mice, but recent works demonstrate that this technique is applicable to larger animals like fish, guinea pigs, ferrets, and chickens. Here, we describe the construction and the utilization of a constitutively luminescent strain of Salmonella Typhimurium to monitor in vivo and ex vivo the colonization of mice in the gastroenteritis, typhoid fever, and asymptomatic carriage models of Salmonella infection.
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Moss, Joseph A., and Richard A. Snyder. "Pathogenic Protozoa." In Microbial Source Tracking: Methods, Applications, and Case Studies, 157–88. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-9386-1_7.

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Falkinham, Joseph O. "Detection, Isolation, and Source Tracking of OPPPs." In Opportunistic Premise Plumbing Pathogens, 173–86. New York: Jenny Stanford Publishing, 2023. http://dx.doi.org/10.1201/9781003321002-9.

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Carlson, Brandon A., and Kendra K. Nightingale. "Molecular Subtyping and Tracking of Food-Borne Bacterial Pathogens." In Pathogens and Toxins in Foods, 460–77. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555815936.ch29.

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Kinzelman, Julie, David Kay, and Kathy Pond. "Relating MST Results to Fecal Indicator Bacteria, Pathogens, and Standards." In Microbial Source Tracking: Methods, Applications, and Case Studies, 337–59. New York, NY: Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-9386-1_15.

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Martins, Salonee, Aishwarya Pathare, Purva Salvi, Unnati Bhalerao, Mahalaxmi U. Bhat, Meenakshi Singh, Muneesh Kumar Barman, et al. "Microbial indicators and methods for source tracking faecal contamination of groundwater." In Legacy, Pathogenic and Emerging Contaminants in the Environment, 181–201. London: CRC Press, 2021. http://dx.doi.org/10.1201/9781003157465-10.

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Wong, Sandy M. S., Jeffrey D. Gawronski, David Lapointe, and Brian J. Akerley. "High-Throughput Insertion Tracking by Deep Sequencing for the Analysis of Bacterial Pathogens." In Methods in Molecular Biology, 209–22. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-089-8_15.

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Duffy, Geraldine. "Detecting and Tracking Emerging Pathogenic and Spoilage Bacteria from Farm to Fork." In Safety of Meat and Processed Meat, 447–59. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-89026-5_17.

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Ahmed, Warish, and Valerie Harwood. "Human and animal enteric viral markers for tracking the sources of faecal pollution." In Global Water Pathogen Project, edited by Andreas Farnleitner and Anicet Blanch. Michigan State University, 2017. http://dx.doi.org/10.14321/waterpathogens.8.

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Linke, Rita, P. Stadler, Georg H. Reischer, D. Savio, D. Kollanur, R. Mayer, R. L. Mach, et al. "Using genetic microbial source tracking (MST) markers to identify fecal pollution sources in spring water of a large alpine karst catchment." In Global Water Pathogen Project, edited by Susan Petterson and Gertjan Medema. Michigan State University, 2019. http://dx.doi.org/10.14321/waterpathogens.82.

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Conference papers on the topic "Pathogen tracking"

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Kumar, Aloke, Venu Gorti, and Steve Wereley. "Biological Agent Detection Using Optical Diffusometry Methods." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-13267.

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Biological agent detection has captured the attention of many researchers over the last few years. The present research explores the possibility of directly measuring the diffusion coefficients of sub-micron particles as a means of pathogen detection. At a constant temperature, the diffusion coefficient is simply a function of the drag on the particle. If the particles are functionalized with antibodies against a specific analyte and introduced into a sample containing that analyte, binding of the analyte with the particles will increase the particles' hydrodynamic drag. This results in a decrease in diffusion, which is measured by a particle tracking algorithm. The reduction in diffusion is correlated with the amount of analyte present. Sensitivity to experimental conditions is also explored and it is shown that alternate methods like optical traps provide an even better technique for biological agent detection.
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Fedorka-Cray, Paula J., J. McKean, and G. Beran. "Tracking salmonella on the farm: a farrow to finish study." In Fourth International Symposium on the Epidemiology and Control of Salmonella and Other Food Borne Pathogens in Pork. Iowa State University, Digital Press, 1997. http://dx.doi.org/10.31274/safepork-180809-212.

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