Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae

ilustraciones, gráficas, tablas

Autores:: Talero Osorio, Diego Camilo

Tipo de recurso:

Fecha de publicación:: 2022

Institución:: Universidad Nacional de Colombia

Repositorio:: Universidad Nacional de Colombia

Idioma:: spa

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dc.title.spa.fl_str_mv	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae
dc.title.translated.eng.fl_str_mv	Identification of plasmid-associated contigs obtained from whole genome sequencing of Klebsiella pneumoniae isolates
title	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae
spellingShingle	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae 000 - Ciencias de la computación, información y obras generales::005 - Programación, programas, datos de computación 570 - Biología::576 - Genética y evolución 610 - Medicina y salud::616 - Enfermedades 000 - Ciencias de la computación, información y obras generales::006 - Métodos especiales de computación PipeLine Klebsiella pneumoniae Plásmidos Secuenciación de Nueva Generación Algoritmo de Clasificación
title_short	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae
title_full	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae
title_fullStr	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae
title_full_unstemmed	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae
title_sort	Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae
dc.creator.fl_str_mv	Talero Osorio, Diego Camilo
dc.contributor.advisor.none.fl_str_mv	Barreto Hernández, Emiliano
dc.contributor.author.none.fl_str_mv	Talero Osorio, Diego Camilo
dc.contributor.referee.none.fl_str_mv	Pinzón Velasco, Andrés Mauricio
dc.contributor.researchgroup.spa.fl_str_mv	Centro de Bioinformática del Instituto de Biotecnología (CBIB)
dc.subject.ddc.spa.fl_str_mv	000 - Ciencias de la computación, información y obras generales::005 - Programación, programas, datos de computación 570 - Biología::576 - Genética y evolución 610 - Medicina y salud::616 - Enfermedades 000 - Ciencias de la computación, información y obras generales::006 - Métodos especiales de computación
topic	000 - Ciencias de la computación, información y obras generales::005 - Programación, programas, datos de computación 570 - Biología::576 - Genética y evolución 610 - Medicina y salud::616 - Enfermedades 000 - Ciencias de la computación, información y obras generales::006 - Métodos especiales de computación PipeLine Klebsiella pneumoniae Plásmidos Secuenciación de Nueva Generación Algoritmo de Clasificación
dc.subject.proposal.spa.fl_str_mv	PipeLine Klebsiella pneumoniae Plásmidos Secuenciación de Nueva Generación
dc.subject.proposal.eng.fl_str_mv	Algoritmo de Clasificación
description	ilustraciones, gráficas, tablas
publishDate	2022
dc.date.accessioned.none.fl_str_mv	2022-08-08T19:50:57Z
dc.date.available.none.fl_str_mv	2022-08-08T19:50:57Z
dc.date.issued.none.fl_str_mv	2022-08-08
dc.type.spa.fl_str_mv	Trabajo de grado - Maestría
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dc.identifier.instname.spa.fl_str_mv	Universidad Nacional de Colombia
dc.identifier.reponame.spa.fl_str_mv	Repositorio Institucional Universidad Nacional de Colombia
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url	https://repositorio.unal.edu.co/handle/unal/81811 https://repositorio.unal.edu.co/
identifier_str_mv	Universidad Nacional de Colombia Repositorio Institucional Universidad Nacional de Colombia
dc.language.iso.spa.fl_str_mv	spa
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dc.relation.references.spa.fl_str_mv	Aguilar-Bultet, L., & Falquet, L. (2015). Secuenciación y Ensamble de novo de genomas bacterianos: una alternativa para el estudio de nuevos patógenos. Revista de Salud Animal, 37(2), 125–132. Alimolaei, M., & Golchin, M. (2017). A comparison of methods for extracting plasmids from a difficult to lyse bacterium: Lactobacillus casei. Biologicals, 45, 47–51. https://doi.org/10.1016/j.biologicals.2016.10.001 Antipov, D., Hartwick, N., Shen, M., Raiko, M., Lapidus, A., & Pevzner, P. A. (2016a). PlasmidSPAdes: Assembling plasmids from whole genome sequencing data. Bioinformatics, 32(22), 3380–3387. https://doi.org/10.1093/bioinformatics/btw493 Antipov, D., Hartwick, N., Shen, M., Raiko, M., Lapidus, A., & Pevzner, P. A. (2016b). PlasmidSPAdes: Assembling plasmids from whole genome sequencing data. Bioinformatics, 32(22), 3380–3387. https://doi.org/10.1093/bioinformatics/btw493 Antipov, D., Korobeynikov, A., McLean, J. S., & Pevzner, P. A. (2016). HybridSPAdes: An algorithm for hybrid assembly of short and long reads. Bioinformatics, 32(7), 1009–1015. https://doi.org/10.1093/bioinformatics/btv688 Argemi, X., Martin, V., Loux, V., Dahyot, S., Lebeurre, J., Guffroy, A., … Prevost, G. (2017). Whole-Genome Sequencing of Seven Strains of Staphylococcus lugdunensis Allows Identification of Mobile Genetic Elements. Genome Biology and Evolution, 9(5), 1183–1189. https://doi.org/10.1093/gbe/evx077 Benchmarking of de novo assembly tools: SPAdes 3.9 vs Velvet 1.2. (n.d.). Retrieved from https://cge.cbs.dtu.dk/services/cge/ Blair, J. M. A., Webber, M. A., Baylay, A. J., Ogbolu, D. O., & Piddock, L. J. V. (2015). Molecular mechanisms of antibiotic resistance. Nature Reviews Microbiology, 13(1), 42–51. https://doi.org/10.1038/nrmicro3380 Bootsma, H. J., & Schouls, L. M. (2015, March 1). Next-generation sequencing of carbapenem-resistant Gram-negative microorganisms: A key tool for surveillance and infection control. Future Microbiology, 10(3), 299–302. Bousquet, A., Henquet, S., Compain, F., Genel, N., Arlet, G., & Decré, D. (2015). SC. Journal of Microbiological Methods. https://doi.org/10.1016/j.mimet.2015.01.019 Bryson, K., Loux, V., Bossy, R., Nicolas, P., Chaillou, S., Guchte, M. Van De, … Lactique, F. (2006). AGMIAL : implementing an annotation strategy for prokaryote genomes as a distributed system. 34(12), 3533–3545. https://doi.org/10.1093/nar/gkl471 C., L., N., G., S., L., C., G., & G., M. M. (2017). Multi-clasificador para predecir interacción de proteínas usando optimización basada en colonia de hormigas. Revista Cubana de Ciencias Informáticas, 11, 195–210. Retrieved from https://www.redalyc.org/articulo.oa?id=378349711014 Cabrera-Hernández, L., Morales-Hernández, A., & Casas-Cardoso, G. M. (2016). Medidas de diversidad para la construcción de sistemas multi-clasificadores usando algoritmos genéticos. 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PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. Gigascience, 8(6). https://doi.org/10.1093/gigascience/giz066 Founou, R. C., Founou, L. L., & Essack, S. Y. (2018). Extended spectrum beta-lactamase mediated resistance in carriage and clinical gram-negative ESKAPE bacteria: a comparative study between a district and tertiary hospital in South Africa. Antimicrobial Resistance and Infection Control, 7. https://doi.org/10.1186/s13756-018-0423-0 Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: Rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729. https://doi.org/10.1101/gr.210641.116 Kotsianti, S. B., & Kanellopoulos, D. (2007). Combining Bagging, Boosting and Dagging for Classification Problems. 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A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity. Cell, 161(5), 1074–1088. https://doi.org/10.1016/j.cell.2015.04.025 Li, D., Liu, C. M., Luo, R., Sadakane, K., & Lam, T. W. (2015). MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 31(10), 1674–1676. https://doi.org/10.1093/bioinformatics/btv033 Li, X. Z., Plesiat, P., & Nikaido, H. (2015). The Challenge of Efflux-Mediated Antibiotic Resistance in Gram-Negative Bacteria. Clinical Microbiology Reviews, 28(2), 337–418. https://doi.org/10.1128/cmr.00117-14 Liu, Y. Y., Wang, Y., Walsh, T. R., Yi, L. X., Zhang, R., Spencer, J., … Shen, J. Z. (2016). Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infectious Diseases, 16(2), 161–168. https://doi.org/10.1016/s1473-3099(15)00424-7 Lowe, T. 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dc.format.extent.spa.fl_str_mv	xx, 83 páginas
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dc.publisher.spa.fl_str_mv	Universidad Nacional de Colombia
dc.publisher.program.spa.fl_str_mv	Bogotá - Ingeniería - Maestría en Ingeniería - Ingeniería de Sistemas y Computación
dc.publisher.department.spa.fl_str_mv	Departamento de Ingeniería de Sistemas e Industrial
dc.publisher.faculty.spa.fl_str_mv	Facultad de Ingeniería
dc.publisher.place.spa.fl_str_mv	Bogotá, Colombia
dc.publisher.branch.spa.fl_str_mv	Universidad Nacional de Colombia - Sede Bogotá
institution	Universidad Nacional de Colombia
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spelling	Atribución-NoComercial 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Barreto Hernández, Emilianob7a2cae2c08b5d6a549e173576c6c82dTalero Osorio, Diego Camilo905fff084a30ac2adb99a15891ec625aPinzón Velasco, Andrés MauricioCentro de Bioinformática del Instituto de Biotecnología (CBIB)2022-08-08T19:50:57Z2022-08-08T19:50:57Z2022-08-08https://repositorio.unal.edu.co/handle/unal/81811Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustraciones, gráficas, tablasUno de los problemas frecuentes en salud pública son las Infecciones Asociadas a la Atención en Salud (IAAS), La Organización Mundial de la Salud (WHO) ha publicado una lista de microorganismos de prioridad clínica (WHO, 2017), entre los cuales a nivel crítico están todas las Enterobacterias que presentan resistencia a antibióticos carbapenémicos como Klebsiella pneumoniae que suele contar con múltiples mecanismos de resistencia frente a dichos antibióticos (Schroeder, Brooks, & Brooks, 2017). El desarrollo de tecnologías de secuenciación de nueva generación (NGS) ha permitido el estudio del “comportamiento” y /o “composición” de los genomas de microorganismos de interés clínico; así mismo también se han diseñado y desarrollado algoritmos y flujos de trabajo bioinformáticos para el almacenamiento, anotación y análisis de estos datos, que han facilitado identificar y caracterizar, un gran número de elementos genómicos involucrados en los mecanismos de resistencia. En este trabajo se propone una herramienta de clasificación de contigs pertenecientes a plásmidos, obtenidos por secuenciación de genoma completo (WGS), que implementa varias de las herramientas, que a través de un método experimental iterativo fueron configuradas para obtener un rendimiento maximizado para las cepas de trabajo de K. pneumoniae. (Texto tomado de la fuente)One of the frequent problems in public health is the Infections Associated with Health Care (IAAS). The World Health Organization (WHO) published a list of microorganisms of clinical priority (WHO, 2017), among which at the critical level are all Entero-bacteria with resistance to carbapenems like Klebsiella pneumoniae, which usually has several mechanisms of resistance (González Rocha et al., 2017), frequently associated with the genetic information (Schroeder et al., 2017). The development of New Generation Sequencing technologies (NGS) allows the study of the "behavior" and/or "composition" of the microorganism genomes of clinical interest. Likewise, algorithms and bioinformatics workflows have been designed and developed for the storage, annotation, and analysis of these data, to the point of identifying and characterizing a large number of genomic elements involved in resistance mechanisms. This work shows the implementation of a contig classification pipeline designed to choose which of them are part of a plasmid. It uses contigs obtained by NGS technologies and implements several programs to carry out this task, which, thanks to an iterative experimental method, were configured to obtain a maximized yield for the working strains of K. pneumoniae. (text taken of the source)colcienciasMaestríaMagister en BioinformáticaDiagnóstico molecularEl diseño de la herramienta esta basado en la teoria de Multiclasificador, implementando metodos de inteligencia artificial.xx, 83 páginasapplication/pdfspaUniversidad Nacional de ColombiaBogotá - Ingeniería - Maestría en Ingeniería - Ingeniería de Sistemas y ComputaciónDepartamento de Ingeniería de Sistemas e IndustrialFacultad de IngenieríaBogotá, ColombiaUniversidad Nacional de Colombia - Sede Bogotá000 - Ciencias de la computación, información y obras generales::005 - Programación, programas, datos de computación570 - Biología::576 - Genética y evolución610 - Medicina y salud::616 - Enfermedades000 - Ciencias de la computación, información y obras generales::006 - Métodos especiales de computaciónPipeLineKlebsiella pneumoniaePlásmidosSecuenciación de Nueva GeneraciónAlgoritmo de ClasificaciónIdentificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniaeIdentification of plasmid-associated contigs obtained from whole genome sequencing of Klebsiella pneumoniae isolatesTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionTexthttp://purl.org/redcol/resource_type/TMAguilar-Bultet, L., & Falquet, L. (2015). Secuenciación y Ensamble de novo de genomas bacterianos: una alternativa para el estudio de nuevos patógenos. Revista de Salud Animal, 37(2), 125–132.Alimolaei, M., & Golchin, M. (2017). A comparison of methods for extracting plasmids from a difficult to lyse bacterium: Lactobacillus casei. Biologicals, 45, 47–51. https://doi.org/10.1016/j.biologicals.2016.10.001Antipov, D., Hartwick, N., Shen, M., Raiko, M., Lapidus, A., & Pevzner, P. A. (2016a). PlasmidSPAdes: Assembling plasmids from whole genome sequencing data. Bioinformatics, 32(22), 3380–3387. https://doi.org/10.1093/bioinformatics/btw493Antipov, D., Hartwick, N., Shen, M., Raiko, M., Lapidus, A., & Pevzner, P. A. (2016b). PlasmidSPAdes: Assembling plasmids from whole genome sequencing data. Bioinformatics, 32(22), 3380–3387. https://doi.org/10.1093/bioinformatics/btw493Antipov, D., Korobeynikov, A., McLean, J. S., & Pevzner, P. A. (2016). HybridSPAdes: An algorithm for hybrid assembly of short and long reads. Bioinformatics, 32(7), 1009–1015. https://doi.org/10.1093/bioinformatics/btv688Argemi, X., Martin, V., Loux, V., Dahyot, S., Lebeurre, J., Guffroy, A., … Prevost, G. (2017). Whole-Genome Sequencing of Seven Strains of Staphylococcus lugdunensis Allows Identification of Mobile Genetic Elements. Genome Biology and Evolution, 9(5), 1183–1189. https://doi.org/10.1093/gbe/evx077Benchmarking of de novo assembly tools: SPAdes 3.9 vs Velvet 1.2. (n.d.). Retrieved from https://cge.cbs.dtu.dk/services/cge/Blair, J. M. A., Webber, M. A., Baylay, A. J., Ogbolu, D. O., & Piddock, L. J. V. (2015). Molecular mechanisms of antibiotic resistance. Nature Reviews Microbiology, 13(1), 42–51. https://doi.org/10.1038/nrmicro3380Bootsma, H. J., & Schouls, L. M. (2015, March 1). Next-generation sequencing of carbapenem-resistant Gram-negative microorganisms: A key tool for surveillance and infection control. 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Bioinformatics, 26(16), 2051–2052. https://doi.org/10.1093/bioinformatics/btq299“Diagnóstico molecular de resistencia y virulencia, y seguimiento epidemiológico de bacterias Gram negativas multirresistentes causantes de IAAS, basado en secuenciación de genoma completo (WGS) y datos sociodemográficos y clínicoscolcienciasInvestigadoresORIGINAL1019105900.2022.pdf1019105900.2022.pdfTesis de Maestría en Bioinformáticaapplication/pdf2467681https://repositorio.unal.edu.co/bitstream/unal/81811/1/1019105900.2022.pdf92022ac2e85b4ec5d2241e99b26a6574MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-84074https://repositorio.unal.edu.co/bitstream/unal/81811/2/license.txt8153f7789df02f0a4c9e079953658ab2MD52THUMBNAIL1019105900.2022.pdf.jpg1019105900.2022.pdf.jpgGenerated Thumbnailimage/jpeg5323https://repositorio.unal.edu.co/bitstream/unal/81811/3/1019105900.2022.pdf.jpgc4ef82ea017ebc0eb5655b607652aa30MD53unal/81811oai:repositorio.unal.edu.co:unal/818112024-08-07 23:10:17.981Repositorio Institucional Universidad Nacional de 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EVESURBIFBPUiBMQSBTRUNSRVRBUsONQSBHRU5FUkFMLiAqTEEgVEVTSVMgQSBQVUJMSUNBUiBERUJFIFNFUiBMQSBWRVJTScOTTiBGSU5BTCBBUFJPQkFEQS4gCgpBbCBoYWNlciBjbGljIGVuIGVsIHNpZ3VpZW50ZSBib3TDs24sIHVzdGVkIGluZGljYSBxdWUgZXN0w6EgZGUgYWN1ZXJkbyBjb24gZXN0b3MgdMOpcm1pbm9zLiBTaSB0aWVuZSBhbGd1bmEgZHVkYSBzb2JyZSBsYSBsaWNlbmNpYSwgcG9yIGZhdm9yLCBjb250YWN0ZSBjb24gZWwgYWRtaW5pc3RyYWRvciBkZWwgc2lzdGVtYS4KClVOSVZFUlNJREFEIE5BQ0lPTkFMIERFIENPTE9NQklBIC0gw5psdGltYSBtb2RpZmljYWNpw7NuIDE5LzEwLzIwMjEK

Identificación de contigs asociados a plásmidos obtenidos a partir de secuenciación de genoma completo de aislamientos de Klebsiella pneumoniae

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