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Determinación del microbioma intestinal en pacientes con infección por clostridioides difficile adquirida en unidad de cuidados intensivos y comunidad

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dc.contributorLópez Abán, Julio
dc.contributor.advisorRamírez González, Juan David
dc.contributor.advisorMuñoz Díaz, Claudia Marina
dc.contributor.gruplacGrupo de Investigaciones Microbiológicas UR (GIMUR)
dc.creatorHerrera Ossa, Giovanny Andrés
dc.creator.degreeDoctor en Ciencias Biomédicas y Biológicas
dc.creator.degreeLevelDoctorado
dc.creator.degreetypeFull time
dc.date.accessioned2023-06-22T12:55:13Z
dc.date.available2023-06-22T12:55:13Z
dc.date.created2023-05-15
dc.descriptionClostridioides difficile (CD), es considerada como la principal causa de diarrea asociada al uso de antibióticos, la cual se asocia a una desregulación de la microbiota intestinal del hospedero, que afecta a los diferentes componentes de la microbiota, siendo el bacteriano el más ampliamente estudioado. Sin embargo, otros grupos de organismos, cómo virus y eucariotas, se han descrito como miembros fundamentales dentro del ecosistema intestinal, e incluso se destaca la función de loci clínicamente importantes, especialmente aquellos asociados con resistencia a antibióticos. A pesar de la gran relevancia de los miembros de la microbiota intestinal sobre la homeóstasis de dicho ecosistema, poco se conoce sobre su papel en el ámbito de la ICD, así como la influencia del lugar de adquisición de la diarrea sobre la composición (diversidad y abundancia) del microbioma, en especial en el contexto de las enfermedades inflamatorias intestinales. Por estas razones, este estudio se dirigió a determinar la composición del microbioma intestinal de pacientes con diarrea asociada a la ICD, adquirida en Unidad de Cuidados Intensivos (UCI) y en comunidad, a través de la implementación de técnicas de secuenciación de alto rendimiento. Para esto, se seleccionaron 98 muestras de ADN provenientes de pacientes con diarrea adquirida en comunidad y a nivel intrahospitalario, tanto positivos como negativos para ICD, las cuales fueron sometidas a secuenciación de marcador único ARNr-16S y -18S. Posteriormente, se seleccionaron 48 muestras de este grupo inicial y fueron sometidas a secuenciación metagenómica. Inicialmente, se observaron cambios en la composición de la microbiota asociada a los grupos de pacientes con diarrea adquirida a nivel intrahospitalario (HCFO/+, HCFO/-) caracterizada por la disminución de microorganismos benéficos, sugiriendo la importancia del lugar de adquisición de la infección sobre la modulación del ecosistema intestinal. Así mismo, se observaron interacciones entre los diferentes miembros de la microbiota intestinal. La secuenciación metagenómica permitió evidenciar un grupo de 51 especies diferencialmente abundantes entre los grupos, con una reducción en los genes implicados en el metabolismo del butirato en los grupos de pacientes con diarrea adquirida a nivel intrahospitalario. Finalmente, se observaron microorganismos productores de acetato y butirato característicos para cada uno de los grupos, con diferencias marcadas tanto en sus abundancias como en sus perfiles de resistencia. Se destaca, además, el papel de los microorganismos asociados al metabolismo del butirato sobre el ecosistema intestinal en el ámbito de la ICD. Por su parte, el estudio de la microbiota de las garrapatas se ha convertido en una herramienta de gran utilidad en la vigilancia y control de las enfermedades transmitidas por garrapatas, las cuales se encuentran ampliamente distribuidas en el continente europeo, siendo un problema de salud pública, con especial énfasis en España, donde regiones como Castilla y León han presentado unas tendencias al aumento en las poblaciones de garrapatas así como en los reportes de picaduras. Por lo anterior, empleando el esquema de análisis para secuenciación profunda de marcador único generado en los apartados anteriores se realizó la descripción de 29 ejemplares de 5 especies de garrapatas duras recolectadas en dicha región encontrando diferencias en la composición taxonómica así como en las correlaciones entre los miembros de su microbiota, siendo este el primer estudio piloto realizado en dicho territorio
dc.description.abstractClostridioides difficile (CD) is the main cause of antibiotic-associated diarrhea, associated with dysregulation of the host intestinal microbiota. This dysregulation affects the different components of the microbiota, with the bacterial component being the most widely studied. However, other groups of organisms, such as viruses and eukaryotes, have also been described as fundamental members of the intestinal ecosystem. Additionally, the function of clinically important loci, especially those associated with antibiotic resistance, has been highlighted. Despite the great relevance of the members of the intestinal microbiota in maintaining the homeostasis of the intestinal ecosystem, little is known about their role in the field of CDI. Furthermore, the influence of the acquisition site of diarrhea on the composition (diversity and abundance) of the microbiome, especially in the context of inflammatory bowel diseases, is poorly understood. Therefore, this study aims to determine the intestinal microbiome composition in patients with diarrhea associated with CDI, acquired in the Intensive Care Unit (ICU) and in the community, by implementing high-throughput sequencing techniques. To achieve this, 98 DNA samples from patients with community-acquired and hospital-acquired diarrhea, both positive and negative for CDI, were selected and subjected to 16S rRNA and 18S rRNA single marker sequencing. Subsequently, 48 samples were chosen from this initial pool and subjected to metagenomic sequencing. Initially, we observed changes in the microbiota composition of the groups with hospital-acquired diarrhea (HCFO/+, HCFO/-) characterized by a decrease in beneficial microorganisms, suggesting the importance of the place of acquisition of the infection in the modulation of the intestinal ecosystem. Similarly, we observed interactions between the different members of the intestinal microbiota. The metagenomic sequencing revealed 51 differentially abundant species between the study groups, with a reduction of the genes involved in the butyrate metabolism in the groups of patients with hospital-acquired diarrhea. Finally, we observed distinctive acetate and butyrate-producing microorganisms for each group, with marked differences in their abundances and resistance profiles. The role of microorganisms associated with butyrate metabolism on the intestinal ecosystem in the CDI scenario is also emphasized. On the other hand, the study of tick microbiota has become a useful tool in the surveillance and control of tick-borne diseases, which are widely distributed in the European continent and pose a significant public health problem. This is particularly true in Spain, where regions such as Castilla y León have reported increasing trends in tick populations and bites. Therefore, using the single marker deep sequencing analysis scheme generated in the previous sections, we described the microbiota of 29 specimens of 5 species of hard ticks collected in that region. We found differences in the taxonomic composition as well as in the correlations between the members of their microbiota. This pilot study is the first of its kind carried out in that territory.
dc.description.sponsorshipMinisterio de Ciencia Tecnología e Innovación
dc.description.sponsorshipDirección de Investigación e Innovación Universidad del Rosario
dc.format.extent195 pp
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.48713/10336_39866
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/39866
dc.language.isospa
dc.publisherUniversidad del Rosario
dc.publisher.departmentEscuela de Medicina y Ciencias de la Salud
dc.publisher.programDoctorado en Ciencias Biomédicas y Biológicas
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dc.rights.urihttp://creativecommons.org/publicdomain/zero/1.0/*
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dc.source.instnameinstname:Universidad del Rosario
dc.source.reponamereponame:Repositorio Institucional EdocUR
dc.subjectMicrobiota
dc.subjectMicrobioma
dc.subjectClostridioides difficile
dc.subjectGarrapatas
dc.subject.keywordMicrobiota
dc.subject.keywordMicrobiome
dc.subject.keywordClostridioides difficile
dc.subject.keywordTicks
dc.titleDeterminación del microbioma intestinal en pacientes con infección por clostridioides difficile adquirida en unidad de cuidados intensivos y comunidad
dc.title.TranslatedTitleDetermination of intestinal microbiome in patients with acquired clostridioides difficile infection in the intensive care unit and the community
dc.typedoctoralThesis
dc.type.documentTesis
dc.type.hasVersioninfo:eu-repo/semantics/acceptedVersion
dc.type.spaTesis de doctorado
local.department.reportFacultad de Ciencias Naturales
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Doctorado en Ciencias Biomédicas y Biológicas