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Academic literature on the topic 'Surveillance génomique'
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Journal articles on the topic "Surveillance génomique"
Colijn, Caroline, David JD Earn, Jonathan Dushoff, Nicholas H. Ogden, Michael Li, Natalie Knox, Gary Van Domselaar, Kristyn Franklin, Gordon Jolly, and Sarah P. Otto. "La nécessité d’une surveillance génomique liée du SRAS-CoV-2." Relevé des maladies transmissibles au Canada 48, no. 4 (April 6, 2022): 147–55. http://dx.doi.org/10.14745/ccdr.v48i04a03f.
Full textSEEGERS, H., N. BAREILLE, R. GUATTEO, A. JOLY, A. CHAUVIN, C. CHARTIER, S. NUSINOVICI, et al. "Épidémiologie et leviers pour la maîtrise de la santé des troupeaux bovins laitiers : approche monographique pour sept maladies majeures." INRAE Productions Animales 26, no. 2 (April 17, 2013): 157–76. http://dx.doi.org/10.20870/productions-animales.2013.26.2.3145.
Full textSanchez, A., C. Mayslich, I. Malet, P. A. Grange, M. Janier, J. Saule, P. Martinet, et al. "Surveillance de la résistance génomique aux antibiotiques de Treponema pallidum subs pallidum des cas de syphilis précoce en France." Annales de Dermatologie et de Vénéréologie 147, no. 12 (December 2020): A138. http://dx.doi.org/10.1016/j.annder.2020.09.122.
Full textNeffati, A., M. Safer, W. Klai, A. Hchaichi, S. Dhaouadi, H. Letaief, L. Bouabid, et al. "Surveillance génomique du SARS-CoV-2 - Analyse des données et évaluation de la stratégie de séquençage en Tunisie (janvier 2021-février 2022)." Revue d'Épidémiologie et de Santé Publique 71 (September 2023): 101933. http://dx.doi.org/10.1016/j.respe.2023.101933.
Full textAdepoju, Paul. "Surveillance génomique du COVID-19 en Afrique de l’Ouest." Nature Africa, December 29, 2021. http://dx.doi.org/10.1038/d44148-021-00127-9.
Full text"Surveillance génomique sur le terrain pour repérer les mutations du paludisme." Nature Africa, September 29, 2023. http://dx.doi.org/10.1038/d44148-023-00253-6.
Full textAdepoju, Paul. "La surveillance génomique et épidémiologique pourrait orienter la réponse future au virus." Nature Africa, May 4, 2021. http://dx.doi.org/10.1038/d44148-021-00030-3.
Full text"Priorités nationales canadiennes de surveillance génomique des variants préoccupants existants et émergents de la COVID-19." Relevé des maladies transmissibles au Canada 47, no. 3 (March 31, 2021): 152–54. http://dx.doi.org/10.14745/ccdr.v47i03a03f.
Full textLeclerc, Véronique, Alexandre Tremblay, and Chani Bonventre. "Anthropologie médicale." Anthropen, 2020. http://dx.doi.org/10.17184/eac.anthropen.125.
Full textDissertations / Theses on the topic "Surveillance génomique"
Tran, Dien Alicia. "Génomique épidémiologique de Salmonella." Thesis, Paris, Institut agronomique, vétérinaire et forestier de France, 2018. http://www.theses.fr/2018IAVF0001/document.
Full textOver a century has passed since the discovery of Salmonella and yet, this pathogen still intrigues researchers. Its ability to withstand many antibiotics is of increasing concern. The monitoring of this pathogen is based on a rapid and discriminatory typing to identify the sources of contaminated food as early as possible. The conventional methods are long, heavy and non-automatable. Understanding the emergence and evolution of Salmonella is the key to eradicate this pathogen, which has remained one of the leading causes of foodborne bacterial diarrhea in the world. During the last decades, spectacular progress has been made in the world of microbiology with the arrival of workbench sequencers, passing from a dozen to hundreds of millions of sequences processed. Facilitated access to numerous genome sequences and dedicated tools are mandatory. Tools currently available are not sufficiently discriminating for the subtype of S. enterica serotype Typhimurium, a predominant serotype of Salmonella. Throughout this study, we showed the interest of whole genome sequencing, a multidisciplinary tool, for the genomic study of Salmonella. (1) After sequencing over 300 S. enterica serotype Typhimurium genomes, we have developed an in silico subtyping tool for this serotype, based on the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) polymorphism. High-throughput microbiological monitoring of salmonellosis has been routinely validated on over 800 genomes. The study of coevolution between the chromosome (SNPs of the core genome) and the two CRISPR regions made it possible to establish a nomenclature defining the different populations of this serotype. (2) Genomic analysis of 280 historical strains of S. enterica serotype Typhimurium showed that plasmids carrying beta-lactamase genes, which confer resistance to ampicillin, were widespread within this serotype in the late 1950s, years before ampicillin was first used for clinical purposes. The presence of penicillin G in the farming environment where these compounds were used as growth promoters, may have led to the selection of the first ampicillin-resistant strains. (3) The phylogenetic study of a genome from the corpse of a young woman who died over 800 years ago, probably due to enteric fever, and 219 historical and recent genomes of the serotypes Paratyphi C, Choleraesuis and Typhisuis have shown, despite the differences in host specificity, that their genomes were very similar over the past 4000 years. Thus, the combination of genotypic and phylogenetic approaches has increased our knowledge of the evolution of this pathogen.Key words: Whole genome sequencing, epidemiological monitoring, CRISPR, SNP, antibiotic resistance, phylogeny, evolution
Henri, Clémentine. "Surveillance of Listeria monocytogenes in food : benchmarking of standard typing tools and implementation of genomic tools." Thesis, Paris Est, 2017. http://www.theses.fr/2017PESC1099.
Full textListeria monocytogenes (L. monocytogenes) is a gram-positive bacterium present in diverse ecological environments and hosts. The microorganism may infect humans and these infections can often be traced back to contaminated foods. The bacterium can sometimes lead to rare but serious infection and in particular a lethal infection known as listeriosis. The bacterium can enter the food chain at all production stages and therefore identification and characterisation of this bacterium are critical steps in the control of potential hazards to the food chain. The current available characterisation methods, which include serotyping, molecular serotyping, PFGE (Pulsed-Field Gel Electrophoresis) and MLST (Multilocus Sequence Type), have provided understanding about the diversity of L. monocytogenes. Further the characterisation methods can facilitate the investigation of outbreaks. During the last few years, (NGS) Next Generation Sequencing and development of computational method for genome wide studies have made it possible to apply WGS (whole genome sequencing) as a typing tool. In this study, we took advantage of the large and the well-characterized collection of L. monocytogenes strains isolated from foods, which is available at Anses. Standard typing tools as well as recent WGS protocols were applied and compared. We observed that L. monocytogenes population could be distinctly separated and structured when analysed by diverse typing tools. Moreover, the investigation displayed consistency among the typing tools. Each cluster of strains, commonly referred to as Sequence Type (ST) or Clonal Complex (CC), shows specific features regarding prevalence, typing results, association to food or the clinical and virulence profile. It opens the possibility for a detailed classification of L. monocytogenes and the possibility to predict the potential pathogenicity of strains based on knowledge of those specific features. By utilising the BlastP program, a virulence associated genes database and the panel of strains housed by Anses, we identified one gene, internalin F (InlF), truncated specifically in ST121. It could therefore explain the observed low frequency of clinical case among strains from ST121.WGS represents a step towards even better identification and management of health risks related to L. Monocytogenes. However, in order to enhance efficiency of foodborne pathogen surveys it would be necessary to implement improvements such as common nomenclature, standard WGS protocols and uniform standards for data sharing
Klotoe, Jésutondin Bernice Mélaine. "Développement de méthodes pour le diagnostic, le contrôle, la surveillance de la tuberculose à bacilles ultra-résistants et des souches épidémiques Beijing." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS379/document.
Full textMDR / XDR (multidrug and extensively resistant to tuberculosis) TB caused by Mycobacterium tuberculosis is still a global public health problem. The study and identification of mutations responsible for resistance are important factors for the control and surveillance of MDR / XDR TB. The expansion of the L2 / Beijing lineage, a family of strains originating from South-East of China (Guangxi) and potentially more virulent, complicates the control of this disease. In this context, we have developed TB-EFI and TB IS-NTF / RINT, two high-speed, multiplexed and high-throughput molecular methods ready to use (developed on the Luminex xMap system). We initiated the development of a molecular method by the selection of relevant molecular markers for the discrimination of Beijing strains by the MLPA technique. TB-EFI is a test that identifies frequent mutations (single nucleotide polymorphisms) in the genes associated with the resistance of Mycobacterium tuberculosis strains to second-line anti-TB drugs including Fluoroquinolone, Injectable, and first-line antituberculosis drug, Ethambutol. TB-EFI may be used in retrospective studies to monitor resistance in a population. The IS-NTF / RINT test is a test specific to Beijing strains that types the IS6110 insertion sequence within the NTF locus (Ancient / Modern) and detects the mutations responsible for the resistance of these strains to Rifampicin and Isoniazid (the two leading primary antibiotics). This test is of paramount importance for the identification and control of epidemic strains, but also for a vision on the evolution of the phenomenon of resistance in time and space. It is not very discriminating among Beijing strains. In view of complete and precise discrimination of the Beijing strains, we have proposed a set of SNPs that will be used for a technique that will be called MLPA-Beijing. In addition, these methods as well as spoligotyping on microbeads allowed us to carry out molecular epidemiological studies of tuberculosis in Kazakhstan, Papua New Guinea, Italy, Mozambique and Peru. The techniques developed in this thesis could contribute significantly to the control of XDR tuberculosis in hot-spot areas, and to the global monitoring of the evolution of Beijing strains especially epidemic MDR strains
Faucher, Benjamin. "Modélisation de la pandémie de COVID-19 pour reconstruire la dissémination du virus et informer la mise en place d’interventions." Electronic Thesis or Diss., Sorbonne université, 2024. http://www.theses.fr/2024SORUS269.
Full textEmerging pathogens pose significant challenges to public health authorities. In the context of the COVID-19 pandemic, the SARS-COV-2 and the variants of concern followed a similar pattern. A new virus emerged in one country, spread globally, and then triggered a rapid surge in cases worldwide. To deal with this situation, it is critical to monitor the epidemic, decipher incomplete and incoherent data, and rapidly design interventions. Mathematical models can help interpret heterogeneous surveillance data and inform the design of interventions. In this thesis, we addressed both aspects. First, we developed a mathematical framework to understand how surveillance and epidemic drivers concur in shaping observations. We retrospectively reconstructed the international spread of the Alpha variant in the Fall of 2020 from sequencing and air travel data. In a second work, we focused on intervention. We proposed an agent-based model to quantify the epidemiological impact of a reactive vaccination strategy targeting workplaces and schools where cases are detected. We tested the effectiveness of this strategy to mitigate a general rise in cases and to limit the spread of a new variant
Leducq, Valentin. "Apport des outils de biologie moléculaire dans l'étude et la surveillance du SARS-CoV-2 au cours de la pandémie de COVID-19." Electronic Thesis or Diss., Sorbonne université, 2023. http://www.theses.fr/2023SORUS203.
Full textFrom the onset of the COVID-19 pandemic, molecular biology tools for detection and analysis of the SARS-CoV-2 genome were developed and deployed on an unprecedented scale. PCR techniques have been used to diagnose millions of people on a daily basis, while the democratization of next-generation sequencing (NGS) has enabled the rapid generation of hundreds of thousands of viral genomes. These tools have been a major source of information in the study and understanding of the pathophysiology of SARS-CoV-2, but also in the real-time monitoring of the dynamics of the pandemic and the evolution of this virus. We undertook this thesis to evaluate how these molecular biology tools can contribute to the study and surveillance of SARS-CoV-2, in three studies with different objectives. With the PhyloCoV study, we first provided a precise description of the evolution of viral diversity observed during the year 2020 in the Ile-de-France area, thanks to the sequencing of 736 SARS-CoV-2 genomes from patients and healthcare workers of the Pitié-Salpêtrière and Bichat Claude-Bernard University Hospital. This study also allowed us to develop a phylogenetic clustering method allowing the detection of intra-hospital transmission of COVID-19. Then, in the framework of an observational study within the GH Sorbonne Université, we estimated the frequency and mortality associated with nosocomial transmissions of SARS-CoV-2. Between September and November 2020, 209 cases of nosocomial COVID-19 were identified, representing 13.9% of hospitalized patients infected with SARS-CoV-2 and associated with a mortality of 31%. Sequencing of the viral genomes disproved nearly one third of nosocomial transmissions and revealed valuable information about transmission routes within hospital wards. Finally, with the COCOPREV study, we studied the evolution of the SARS-CoV-2 genome during infection in patients treated with monoclonal antibodies, mostly immunocompromised. Several resistance mutations emerge in the SPIKE protein under the three treatments studied. Patients treated with Tixagevimab/Cilgavimab had a 5-fold increased risk of developing mutations at residues R346 and K444. Unlike other mutations found, R346 and K444 substitutions have repeatedly emerged in different variants due to their impact on SARS-CoV-2 fitness. They were finally selected by the currently dominant BQ.1 and XBB variants. In conclusion, we have demonstrated the utility of molecular biology tools in monitoring SARS-CoV-2 transmission in hospitals and the general population, as well as in identifying emerging resistance mutations in patients treated with monoclonal antibodies. These tools will most likely continue to be used in the context of the COVID-19 pandemic but also in monitoring the emergence and spread of other viruses
Lalonde, Christian. "Amélioration des services de génomiques et de surveillance du virus du syndrome reproducteur et respiratoire porcin." Thesis, 2020. http://hdl.handle.net/1866/24260.
Full textPorcine reproductive and respiratory syndrome virus (PRRSV) is an important pathogen, costing over 130 million dollars annually in Canada. Surveillance is done by Sanger sequencing of the ORF5 gene, but we hypothesized that whole genome sequencing (WGS) of PRRSV genome will allow a better epidemiological monitoring of PRRSV compared to ORF5 gene sequencing. To develop an efficient method of PRRSV WGS, 149 PRRSV samples (sera, lungs, pool of tissues and others) collected for surveillance or from sick animals were tested. Viral RNA was concentrated using a poly(A) tailed RNA enrichment method, and sequencing was done on an Illumina platform. WGS was successful in 67.11% of cases. WGS was successful in some tissues and lungs samples with RT-qPCR cycle quantification (Cq) values up to 26.50, and in some sera with Cq value up to 34.13. The developed WGS methodology was 4650 times more sensitive for PRRSV WGS than previously described methods. To quantify the impact of WGS, 88 successful samples for the WGS of PRRSV were used to compare efficiency of WGS and ORF5 sequencing. Two different full-length genomes of PRRSV were found in four of those samples (coinfection rate of 4.55%). Six full-length PRRSV genomes (6.52% of PRRSV strains) were found to cluster differently compared to ORF5 sequencing. WGS of PRRSV also enabled a better classification or characterisation of 9.10% of the PRRSV infected samples compared to ORF5 sequencing. Thus, WGS can be both sensitive and more accurate then ORF5 classification for the characterisation of PRRSV strains.
Books on the topic "Surveillance génomique"
Barcoding Nature: Shifting Cultures of Taxonomy in an Age of Biodiversity Loss. Taylor & Francis Group, 2013.
Find full textEllis, Rebecca J. Bartlett. Barcoding Nature. 2013.
Find full textBarcoding Nature: Shifting Cultures of Taxonomy in an Age of Biodiversity Loss. Routledge, 2013.
Find full textEllis, Rebecca, Claire Waterton, and Brian Wynne. Barcoding Nature: Shifting Cultures of Taxonomy in an Age of Biodiversity Loss. Taylor & Francis Group, 2013.
Find full textBarcoding Nature: Shifting Cultures of Taxonomy in an Age of Biodiversity Loss. Taylor & Francis Group, 2013.
Find full textBarcoding Nature. Taylor & Francis Group, 2013.
Find full textBarcoding Nature. Routledge, 2014.
Find full text