The abundance and selection of antibiotic resistance genes: A metagenomic study based on wastewater and human gut data.

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dc.contributor.authorHolmström, Michaela
dc.contributor.departmentChalmers tekniska högskola / Institutionen för matematiska vetenskapersv
dc.contributor.examinerKristiansson, Erik
dc.contributor.supervisorJohnning, Anna
dc.contributor.supervisorLund, David
dc.date.accessioned2024-09-10T09:36:58Z
dc.date.available2024-09-10T09:36:58Z
dc.date.issued2024
dc.date.submitted
dc.description.abstractAntibiotic resistance is a global issue, with many consequences for the individual person and society as a whole. Studying potential new genes conferring resistance (latent ARGs) and the flow of resistance genes through environments could be crucial for the prevention and control of ARGs. This project aimed firstly to investigate how antibiotic usage affects new antibiotic resistance genes in the human gut. A metagenomic pipeline including mapping of reads and statistical models using a study of 12 healthy individuals treated with three broad-spectrum antibiotics enabled analysis of ARGs and taxonomy abundances. It was shown that after treatment with the broad-spectrum antibiotics, several latent ARGs were more abundant in the short term, implying the potential selection of these ARGs. The change in ARGs can not be ruled out as being due to the recolonization of fast-growing bacterial species, normally carrying such genes, as also the taxonomy composition was largely affected. This effect was not seen on the last sampling day, after 180 days, in which only one single ARG was found at higher abundance. The short-term effect could, nevertheless, impact the spread of ARGs due to the potential for these ARGs to spread in the disrupted microbiota. Secondly, this project aimed to investigate the flow of ARGs between the human gut and wastewater. For this, a large number of metagenomic samples were used. Similarly to the first part, a metagenomic pipeline was utilized for ARG and taxonomy analysis. Contrary to previous findings, the results implied that ARGs flow from the human gut to the wastewater, while not the other way around. Furthermore, pathogenic presence was highest for ARGs found at high prevalence in both the human gut and wastewater. Interestingly, ARGs present only in wastewater were more prevalent in pathogens compared to ARGs present only in the human gut. This implies that the spread of ARGs to pathogens could be linked to presence in wastewater environments. Moreover, the taxonomy of the human gut and wastewater differed. The results of this project can inform several future research directions, from broadening the data of longitudinal studies to a deeper dive into the flow of ARGs.
dc.identifier.coursecodeMVEX60
dc.identifier.urihttp://hdl.handle.net/20.500.12380/308556
dc.language.isoeng
dc.setspec.uppsokPhysicsChemistryMaths
dc.subjectmetagenomics, antibiotic resistance gene, antibiotic, taxonomy, wastewater, human gut, latent, movement.
dc.titleThe abundance and selection of antibiotic resistance genes: A metagenomic study based on wastewater and human gut data.
dc.type.degreeExamensarbete för masterexamensv
dc.type.degreeMaster's Thesisen
dc.type.uppsokH
local.programmeBiotechnology (MPBIO), MSc
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