Effect of sub-inhibitory antibiotic exposure on antimicrobial resistance of river biofilm microbial communities
Date
2023-08-03
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
ORCID
0009-0007-4161-8279
Type
Thesis
Degree Level
Doctoral
Abstract
Biofilms 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.
Description
Keywords
sub-MIC, antibiotics, biofilms, antimicrobial resistance, microbiome, resistome, aquatic environments
Citation
Degree
Doctor of Philosophy (Ph.D.)
Department
Food and Bioproduct Sciences
Program
Applied Microbiology