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Effect of sub-inhibitory antibiotic exposure on antimicrobial resistance of river biofilm microbial communities

dc.contributor.advisorKorber , Darren R.
dc.contributor.advisorBroadbent , Jordyn
dc.contributor.committeeMemberGhosh, Supratim
dc.contributor.committeeMemberEskiw, Christopher
dc.contributor.committeeMemberHelgason, Bobbi
dc.contributor.committeeMemberTanaka , Takuji
dc.contributor.committeeMemberJackson, Leland
dc.creatorFlores Vargas, Gabriela
dc.creator.orcid0009-0007-4161-8279
dc.date.accessioned2023-08-03T22:12:36Z
dc.date.available2023-08-03T22:12:36Z
dc.date.copyright2023
dc.date.created2023-07
dc.date.issued2023-08-03
dc.date.submittedJuly 2023
dc.date.updated2023-08-03T22:12:36Z
dc.description.abstractBiofilms are ubiquitous throughout aquatic environments and can be influenced by myriad factors including antimicrobial run-off from anthropogenic sources. The South Saskatchewan River is an oligotrophic system that receives discharge from urban wastewater treatment plants (WWTP) and agricultural effluents which can carry antimicrobial residues. Antibiotic concentrations in environmental systems generally occur at low or sub-minimum inhibitory concentrations (sub-MICs). Most of our current understanding of antibiotic resistance comes from clinically relevant monoculture studies. Thus, there is a need for experimental data that explores the response of naturally occurring multispecies microbial communities. This thesis employs a “structure-function” approach by using microscopic and metagenomic methods to characterize the effects of sub-MIC antibiotics in riverine biofilm communities. I aimed to determine whether exposure induced a selective pressure for antibiotic resistance resulting in variations of overall community composition. For this purpose, riverine biofilm communities were developed in a microcosm system under various sub-MIC exposure treatments including constant sub-MIC exposure (1/10, 1/50 and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline), and residual antibiotic concentrations present in WWTP effluent and swine-manure (SM). This research was divided into two microcosm experiments: a pilot experiment and a full-scale experiment. Microscopic methods were used to characterize the structural composition of biofilms, and different metagenomic tools were evaluated and compared seeking to elucidate comprehensive microbiome and resistome profiles in biofilm communities. Results of this thesis research demonstrated shifts in biofilm architecture, microbiome and resistome composition. Biofilm formation and accumulation of extracellular polymeric substances (EPS) were inversely proportional to the concentration of antibiotics. Microbial diversity wasiv reduced after sub-MIC antibiotic exposure, selecting for Pseudomonadota (synonym Proteobacteria) species, particularly at the sub-MIC 1/10 condition. The biofilm resistome consisted of antibiotic resistance genes (ARGs) that conferred resistance to aminoglycosides, tetracyclines, β-lactams, macrolides, phenicols and sulfonamides and trimethoprim. Resistome relative abundance and diversity was consistently higher in biofilms grown under sub-MIC antibiotic exposure. Nonetheless, ARGs and virulence genes were observed across all samples including biofilms grown under non-antibiotic conditions. Correlation between the microbiome and resistome showed that aminoglycoside ARGs were associated with several bacterial genera, and co-occurrence between virulence factors and ARGs was also significant. Functional prediction analysis indicated that abundance of metabolic pathways involved in cell-wall metabolism increased under the presence of sub-MIC antibiotics, thus supporting the notion that low concentrations of antimicrobials exert selective pressure. Overall, results from our whole-community approach demonstrated that the presence of sub-MICs antibiotics increased the abundance of ARGs and resistome-related functions. These responses indicate that riverine biofilm communities promote the prevalence and facilitate the transmission of antimicrobial resistance.
dc.format.mimetypeapplication/pdf
dc.identifier.urihttps://hdl.handle.net/10388/14858
dc.language.isoen
dc.subjectsub-MIC
dc.subjectantibiotics
dc.subjectbiofilms
dc.subjectantimicrobial resistance
dc.subjectmicrobiome
dc.subjectresistome
dc.subjectaquatic environments
dc.titleEffect of sub-inhibitory antibiotic exposure on antimicrobial resistance of river biofilm microbial communities
dc.typeThesis
dc.type.materialtext
thesis.degree.departmentFood and Bioproduct Sciences
thesis.degree.disciplineApplied Microbiology
thesis.degree.grantorUniversity of Saskatchewan
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy (Ph.D.)

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