The abundance and selection of antibiotic resistance genes: A metagenomic study based on wastewater and human gut data.
Typ
Examensarbete för masterexamen
Master's Thesis
Master's Thesis
Program
Biotechnology (MPBIO), MSc
Publicerad
2024
Författare
Holmström, Michaela
Modellbyggare
Tidskriftstitel
ISSN
Volymtitel
Utgivare
Sammanfattning
Antibiotic 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.
Beskrivning
Ämne/nyckelord
metagenomics, antibiotic resistance gene, antibiotic, taxonomy, wastewater, human gut, latent, movement.