Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos

ilustraciones, diagramas, figuras

Autores:
Prada Padilla, Sebastian
Tipo de recurso:
Fecha de publicación:
2023
Institución:
Universidad Nacional de Colombia
Repositorio:
Universidad Nacional de Colombia
Idioma:
spa
OAI Identifier:
oai:repositorio.unal.edu.co:unal/85409
Acceso en línea:
https://repositorio.unal.edu.co/handle/unal/85409
https://repositorio.unal.edu.co/
Palabra clave:
570 - Biología::572 - Bioquímica
Biología Computacional
Farmacorresistencia Microbiana
Computational Biology
Drug Resistance, Microbial
Epidemiológica
Genómica
Infecciones Asociadas a la Atención en Salud (IAAS)
Bioinformática
Epidemiology
Genomics
Healthcare-Associated Infections (HAIs)
Bioinformatics
Rights
openAccess
License
Reconocimiento 4.0 Internacional
id UNACIONAL2_b4710a5e405fc3e67bcaef45ada62a49
oai_identifier_str oai:repositorio.unal.edu.co:unal/85409
network_acronym_str UNACIONAL2
network_name_str Universidad Nacional de Colombia
repository_id_str
dc.title.spa.fl_str_mv Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
dc.title.translated.eng.fl_str_mv Bioinformatic pipeline for epidemiological monitoring of multidrug-resistant bacteria within a hospital based on whole genome and clinical data
title Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
spellingShingle Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
570 - Biología::572 - Bioquímica
Biología Computacional
Farmacorresistencia Microbiana
Computational Biology
Drug Resistance, Microbial
Epidemiológica
Genómica
Infecciones Asociadas a la Atención en Salud (IAAS)
Bioinformática
Epidemiology
Genomics
Healthcare-Associated Infections (HAIs)
Bioinformatics
title_short Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
title_full Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
title_fullStr Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
title_full_unstemmed Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
title_sort Pipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicos
dc.creator.fl_str_mv Prada Padilla, Sebastian
dc.contributor.advisor.none.fl_str_mv Barreto Hernández, Emiliano
dc.contributor.author.none.fl_str_mv Prada Padilla, Sebastian
dc.contributor.researchgroup.spa.fl_str_mv Bioinformática del Instituto de Biotecnología de la Universidad Nacional de Colombia
dc.subject.ddc.spa.fl_str_mv 570 - Biología::572 - Bioquímica
topic 570 - Biología::572 - Bioquímica
Biología Computacional
Farmacorresistencia Microbiana
Computational Biology
Drug Resistance, Microbial
Epidemiológica
Genómica
Infecciones Asociadas a la Atención en Salud (IAAS)
Bioinformática
Epidemiology
Genomics
Healthcare-Associated Infections (HAIs)
Bioinformatics
dc.subject.decs.spa.fl_str_mv Biología Computacional
Farmacorresistencia Microbiana
dc.subject.decs.eng.fl_str_mv Computational Biology
Drug Resistance, Microbial
dc.subject.proposal.spa.fl_str_mv Epidemiológica
Genómica
Infecciones Asociadas a la Atención en Salud (IAAS)
Bioinformática
dc.subject.proposal.eng.fl_str_mv Epidemiology
Genomics
Healthcare-Associated Infections (HAIs)
Bioinformatics
description ilustraciones, diagramas, figuras
publishDate 2023
dc.date.issued.none.fl_str_mv 2023
dc.date.accessioned.none.fl_str_mv 2024-01-23T16:26:56Z
dc.date.available.none.fl_str_mv 2024-01-23T16:26:56Z
dc.type.spa.fl_str_mv Trabajo de grado - Maestría
dc.type.driver.spa.fl_str_mv info:eu-repo/semantics/masterThesis
dc.type.version.spa.fl_str_mv info:eu-repo/semantics/acceptedVersion
dc.type.content.spa.fl_str_mv Text
dc.type.redcol.spa.fl_str_mv http://purl.org/redcol/resource_type/TM
status_str acceptedVersion
dc.identifier.uri.none.fl_str_mv https://repositorio.unal.edu.co/handle/unal/85409
dc.identifier.instname.spa.fl_str_mv Universidad Nacional de Colombia
dc.identifier.reponame.spa.fl_str_mv Repositorio Institucional Universidad Nacional de Colombia
dc.identifier.repourl.spa.fl_str_mv https://repositorio.unal.edu.co/
url https://repositorio.unal.edu.co/handle/unal/85409
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
language spa
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dc.publisher.faculty.spa.fl_str_mv Facultad de Ingeniería
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spelling Reconocimiento 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Barreto Hernández, Emilianob7a2cae2c08b5d6a549e173576c6c82dPrada Padilla, Sebastian9a7d741ed3ba103630222d81b9a31c1fBioinformática del Instituto de Biotecnología de la Universidad Nacional de Colombia2024-01-23T16:26:56Z2024-01-23T16:26:56Z2023https://repositorio.unal.edu.co/handle/unal/85409Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustraciones, diagramas, figurasLa resistencia a los antimicrobianos es una amenaza de salud pública reconocida a nivel mundial y cobra especial atención en entidades hospitalarias, donde se presentas brotes infecciosos problemáticos por la resistencia de las bacterias y las condiciones de salud de los pacientes, por ello, las entidades hospitalarias implementan medidas de seguimiento epidemiológico para el control y prevención de la propagación de dichas infecciones. En los últimos años los investigadores han optado por incluir información genómica a los estudios epidemiológicos obteniendo resultados más precisos que aportan y podrían mejorar el control de estas infecciones en los hospitales. El objetivo de este trabajo fue diseñar e implementar un pipeline que integre datos clínicos y genómicos para el seguimiento de bacterias dentro de un hospital. Primero se hizo un análisis de requerimientos para determinar los métodos y herramientas bioinformáticas necesarias para el seguimiento con ambos tipos de datos, luego, se diseñó e implementó el pipeline basado en el sistema SGIG, una aplicación web para para la identificación, tipificación y seguimiento de la resistencia a antibióticos desarrolla por el grupo de investigación Bioinformática del Instituto de Biotecnología de la Universidad Nacional de Colombia; y por último, se evaluó la implementación del pipeline en el sistema SGIG con un conjunto de datos clínicos y genómicos provenientes de un hospital. Como resultado el SGIG ahora cuenta con el módulo: Reporte de epidemiologia de precisión, el cual genera un árbol de máxima verosimilitud basado en los SNPs del core genome y relaciona el árbol con una línea de tiempo que representa las estancias de los pacientes en los diferentes sitios del hospital. Este análisis permite hacer un seguimiento epidemiológico más preciso dentro del hospital que mejora el control de las infecciones bacterianas. (Texto tomado de la fuente)Antimicrobial resistance is a globally recognized public health threat and receives special attention in hospitals, where infectious outbreaks occur and they are problematic due to the resistance of bacteria and the health conditions of the patients; therefore, hospitals implement epidemiological monitoring measures to control and prevent the spread of these infections. In recent years, researchers have opted to include genomic information to epidemiological studies obtaining more accurate results that provide and could improve the control of these infections in hospitals. The objective of the work is to design and implement a pipeline that integrates clinical and genomic data for the monitoring of bacteria within a hospital, first a requirements analysis was made to determine the methods and bioinformatics tools needed for monitoring with both types of data, then, the pipeline was designed and implemented based on the SGIG system, a web application for the identification, typing and monitoring of antibiotic resistance developed by the Bioinformatica research group of the Instituto de Biotecnología de la Universidad Nacional de Colombia, finally, the implementation of the pipeline in the SGIG system was evaluated with a clinical and genomic dataset from a hospital. As a result, the SGIG now has the module: Precision Epidemiology Report, which generates a maximum likelihood tree based on the SNPs of the core genome and relates the tree to a timeline representing patient stays in the different hospital sites. This analysis allows for more accurate epidemiological monitoring within the hospital that improves bacterial infection controlMaestríaMagíster en BioinformáticaBioinformática funcional y estructuralxiii, 55 páginasapplication/pdfspaUniversidad Nacional de ColombiaBogotá - Ingeniería - Maestría en BioinformáticaFacultad de IngenieríaBogotá, ColombiaUniversidad Nacional de Colombia - Sede Bogotá570 - Biología::572 - BioquímicaBiología ComputacionalFarmacorresistencia MicrobianaComputational BiologyDrug Resistance, MicrobialEpidemiológicaGenómicaInfecciones Asociadas a la Atención en Salud (IAAS)BioinformáticaEpidemiologyGenomicsHealthcare-Associated Infections (HAIs)BioinformaticsPipeline bioinformático para el seguimiento epidemiológico de bacterias multirresistentes dentro de un hospital a partir de genoma completo y datos clínicosBioinformatic pipeline for epidemiological monitoring of multidrug-resistant bacteria within a hospital based on whole genome and clinical dataTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionTexthttp://purl.org/redcol/resource_type/TMColombiaAlcock, B. 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Methods in Ecology and Evolution, 8(1), 28–36. https://doi.org/10.1111/2041-210X.12628BibliotecariosEstudiantesInvestigadoresMaestrosMedios de comunicaciónPadres y familiasPersonal de apoyo escolarPúblico generalResponsables políticosLICENSElicense.txtlicense.txttext/plain; charset=utf-85879https://repositorio.unal.edu.co/bitstream/unal/85409/1/license.txteb34b1cf90b7e1103fc9dfd26be24b4aMD51ORIGINAL1010228638.2023.pdf1010228638.2023.pdfTesis de Maestría en Bioinformáticaapplication/pdf1834088https://repositorio.unal.edu.co/bitstream/unal/85409/2/1010228638.2023.pdfcd690de753095e0453fb82c0a8160d1fMD52unal/85409oai:repositorio.unal.edu.co:unal/854092024-01-23 11:29:55.792Repositorio Institucional Universidad Nacional de Colombiarepositorio_nal@unal.edu.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