Browsing by Subject "antibiotic resistance"

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    Assessment of Antibiotic Residues, Potential for Antibiotic Resistance, and Exposure Assessment of Virginiamycin use in the Production of Corn Distillers Dried Grains with Solubles
    (2018-08) Walter, Audrey
    The objective of this thesis was to provide information to the U.S. ethanol industry, and global feed, livestock, and poultry industries of the prevalence and concentration of antibiotic residues in DDGS, the potential for selected Lactobacilli sp. to develop resistance to penicillin G and virginiamycin (VM), and the use of thermal degradation kinetics and process modeling to determine the risk of VM residues in animal-derived food products. Survey results suggest that it is unlikely for penicillin and VM residues to be detected in DDGS if ethanol producers are following GRAS approved dosing of these antibiotics, and VM reduces the risk of Lactobacilli sp. from acquiring antibiotic resistance during ethanol production. The exposure assessment showed that concentrations of VM M1 subunit is not greater than maximum residue limit (MRL) in pork and chicken when feeding DDGS at maximum diet inclusion rates and including conservative inputs in the model.
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    Breaking the weakest link: Evolution and ecology of antibiotic tolerance in cross-feeding bacterial communities
    (2019-05) Adamowicz, Elizabeth
    Microbes frequently rely on metabolites excreted by other bacterial species, but little is known about how this cross-feeding influences the effect of antibiotics. We hypothesized that when species rely on each other for essential metabolites, the minimum inhibitory concentration (MIC) for all species will drop to that of the "weakest link"— the species least resistant in monoculture. We tested this hypothesis in an obligate cross-feeding system that was engineered between Escherichia coli, Salmonella enterica, and Methylobacterium extorquens. The effect of tetracycline and ampicillin were tested on both liquid and solid media. In all cases, resistant species were inhibited at significantly lower antibiotic concentrations in the cross-feeding community than in monoculture or a competitive community. However, deviation from the "weakest link" hypothesis was also observed in cross-feeding communities apparently as a result of changes in the timing of growth and cross-protection. Comparable results were also observed in a clinically relevant system involving facultative cross-feeding between Pseudomonas aeruginosa and an anaerobic consortium found in the lungs of cystic fibrosis patients. P. aeruginosa was inhibited by lower concentrations of ampicillin when cross-feeding than when grown in isolation. These results suggest that cross-feeding significantly alters tolerance to antibiotics in a variety of systems.
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    Characterization of Antibiotic Resistant Genes in Two Unique City Sewer Systems
    (2020-12) Keppers, Adelle
    Sewer systems are known as point sources for the release of antibiotic resistance into the environment. Antibiotic resistance genes (ARGs) provide bacteria the ability to fight antibiotics and are viewed as emerging contaminants in environmental waterways. To minimize the spread of ARGs to the environment, this study assessed the prevalence of ARGs in upstream sewer systems that feed into wastewater treatment plants (WWTPs) so that source control strategies can be developed to mitigate the spread of antibiotic resistance. Wastewaters were examined from two unique city sewer systems containing three source types: hospital, residential, and industrial. Twenty-nine ARGs, 3 integron-intergrases, and 4 metal resistance genes were quantified using conventional and microfluidic polymerase chain reactions. Bacterial community compositions were characterized using high-throughput 16S rRNA amplicon sequencing. We found the levels of ARGs and bacterial community compositions to be dependent on the source of wastewater, the city, and the season. The abundance of ARGs in hospital wastewater were relatively constant and associated with clinically relevant antibiotics. ARG abundance in residential wastewater showed seasonal variations with high levels in winter associated with outpatient antibiotics. High levels of integron-integrase genes, a proxy for horizontal gene transfer and anthropogenic impacts, were also observed in residential wastewaters. Based on these findings we suggest satellite treatment of ARGs at hospital and residential sources to reduce their loading to WWTPs and their inevitable release to the environment.
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    Data and analyses files for "Evidence for Complex Interplay between Quorum Sensing and Antibiotic Resistance in Pseudomonas aeruginosa"
    (2022-09-26) Sikdar, Rakesh; Elias, Mikael H; mhelias@umn.edu; Elias, Mikael H; Elias Research Lab, Biotechnology Institute, CBS
    This data set contains the experimental data, corresponding analysis files and final and intermediary figure files used in the manuscript titled "Interference in microbial signaling highlights the complex relationship between quorum sensing and antibiotic resistance in Pseudomonas aeruginosa" and is intended to be made publicly available for readers and reviewers. It contains the data files from BioTek HTX/Epoch2 Microplate reader for Pseudomonas aeruginosa growth with lactonases/AHLs in Biolog Phenotype MicroArrays(TM) PM11-PM20 and additional replicate experiments done with Pseudomonas aeruginosa growing in Biolog IF-10A media with antibiotics/antimicrobial compounds and lactonases/AHLs. It also contains qPCR data from Thermo Scientific StepOnePlus(TM) Real Time PCR system for assessment of transcription levels of Pseudomonas aeruginosa folA and folP genes. Additionally, all associated and annotated analysis files generated in Microsoft Excel and GraphPad Prism are included. Analysis data from Caenorhabditis elegans killing assays are also included. All the intermediate and final figures that are used in the manuscript are provided as Microsoft PowerPoint files for easy visualization of the workflow and processing.
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    Effects of deletion mutations in aguA on fitness and survival of Pseudomonas aeruginosa cystic fibrosis isolates
    (2018-08) McCurtain, Jennifer
    Pseudomonas aeruginosa is a pathogen commonly associated with the disease cystic fibrosis (CF) due to the bacterium’s ability to adapt to numerous environments. These adaptations include mutations that benefit the pathogen such as antibiotic resistance and host immune evasion. Five P. aeruginosa isolates from CF sputum were found to have deletion mutations in aguA that encodes the agmatine deiminase for this species. These mutations cause the cationic molecule agmatine to accumulate both within and outside the cell. The purpose of this thesis was to determine the effects of agmatine accumulation on fitness and survival of P. aeruginosa in the context of CF. Compared to the isogenic strains with a native aguA, the mutations led to decreased susceptibility to cationic antibiotics (aminoglycosides and polymyxins). At sub-minimal inhibitory concentrations (MIC) of these antibiotics, growth of the aguA+ strains was delayed and stunted more than the aguA mutants. This growth phenotype at these sub-MICs was also seen when Mg2+ and Ca2+ concentrations in the growth medium were reduced. In an acute pneumonia the aguA mutant recruited fewer neutrophils to the murine lungs relative to the aguA+ strain. When testing the ex vivo bronchial epithelial cell response to LPS, agmatine caused reduced IL-8 production in response to LPS in a dose-dependent manner, with the higher concentration of agmatine (100 μM) eliciting a response similar to the negative control without LPS. Together, these data show that the mutations in aguA that prevent the bacteria from breaking down agmatine may be beneficial to the P. aeruginosa isolates while colonizing the CF airways.
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    Incentivizing Antibiotic Research and Development
    (University of Minnesota, College of Pharmacy, 2015) Scandlen-Finken, Leah; Wertheimer, Albert
    Antibiotic Resistance is an international threat, killing thousands and infecting millions. Although certain populations may be at an increased risk for infections, anyone can find themselves compromised with a multi-drug resistant infection. Treatments are becoming more complicated as the bacteria becomes more elusive. Cures are becoming less certain, and the future antibiotic arsenal is looking thin. Although there are many talented scientists and capable drug development entities, the funding and returns on investment are not sufficient to entice antibiotic research and development. This paper explores the current situation regarding antibiotic resistance and its casualties, as well as the mechanisms being employed to overcome the increase in resistance, and decrease in antibiotic effectiveness. Through analysis of antibiotic research, development, and regulation, this paper adds to the discussion by filling in the current gaps regarding the procurement of sustainable funding via an insurance model framework. By incentivizing the pharmaceutical industry to invest in antibiotic research, and by guaranteeing returns on investment, a global solution to the current antibiotic resistance problem can be contained.
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    Occurences and Temporal Dynamics of Pathogens and Antibiotic Resistance Genes in Different Stormwater Reuse Systems
    (2021-12) Walsky, Tamara
    Stormwater is increasingly considered as an alternative water source for both potable and non-potable uses. However, stormwater has not been widely used as an alternative water source, primarily due to a lack of knowledge about the presence and risks associated with pathogens and antibiotic resistance genes present in raw and treated stormwater and how these populations change with environmental conditions. In my thesis research, five different stormwater reuse systems (SRS) in the Twin Cities metro area were sampled from every three weeks from June to October 2019 to build a comprehensive data set for analysis of temporal dynamics of pathogens and metal and antibiotic resistance genes (MRG/ARG) in raw and treated stormwater samples. As a follow up, two sites were time intensively sampled (i.e., sampled every 20-40 minutes as the SRS ran and water flowed through to irrigate fields) twice in summer 2020, along with tap water and lake water control sites. Microfluidic qPCR, a high-throughput quantification tool provided microbial data for 23 bacterial pathogens, 11 viral pathogens and 48 MRG/ARGs along with physiochemical testing such as turbidity, free and total chlorine, and water temperature to evaluate environmental conditions. Correlations between pathogen and MRG/ARG levels and environmental parameters such as temperature and precipitation assess the impact of precipitation and other environmental variables on pathogen and MRG/ARG concentrations in stormwater both over the season (2019 research) and during an average run where hundreds to thousands of gallons of water may be used (2020 research.) Viral and bacterial pathogens were sporadically detected both years while MRG/ARGs were widely detected. Environmental variables loosely correlated along known patterns with Fecal Indicator Bacteria (FIB) but did not account for any variation and lack of distinguished patterns seen in the data. The system with UV treatment and the system with a ball and bag filter sufficiently eliminated E. coli and limited the concentrations of MRG/ARG/pathogen genes, whereas the chlorinated system did not. SRS without any microbial treatment had no effect on cultured FIB and concentrations of MRG/ARG/pathogen genes. These results will provide previously unknown information crucial to successful expansion of stormwater reuse, especially for uses with greater human exposure.
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    Slowing Antibiotic Resistance by Decreasing Antibiotic Use in Animals
    (Minnesota Journal of Law, Science and Technology, 2014-02-20) Nomura, Jennifer
    Antibiotic resistance in humans is a health concern; it can lead to long, expensive hospital stays and an increased risk of death. Antibiotic use in animals has increased over the years, and it is now commonplace in the United States for farm animals to be fed low doses of antibiotics on a daily basis. Because of the high use of antibiotics in animals, the animals can develop antibiotic-resistant bacteria. The antibiotic-resistant bacteria in farm animals can pass to humans through meat and poultry consumption, and therefore, antibiotic use in animals needs to be more stringently regulated. Currently, the FDA is working with the CDC and the USDA to monitor antibiotic use in animals and the spread of antibiotic resistance in humans. The FDA has decided to employ a wait-and-see approach and continues to perform research, through NARMS, to determine how big of a threat antibiotic use in animals actually is to humans. It seems the FDA is looking for a direct link before it acts. Antibiotic resistance is a major health concern that needs to be prevented. Because antibiotic resistance poses such a large threat to human health, the better solution is to act now before antibiotic resistance spreads even more. The FDA should coordinate its regulation efforts with domestic agencies (the USDA and the CDC) and international groups (the WHO and the EU). Then, the FDA should enact a ban on all antibiotics that are used in human health care. Finally, the FDA can continue to monitor the remaining antibiotics used in animals in order to determine whether these drugs also pose a threat to human health.
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    Transcriptional regulation of incompatibility type A/C plasmids
    (2015-05) Lang, Kevin
    Plasmids are extrachromosomal DNA elements that often carry beneficial phenotypes for the bacterial host. Incompatibility type A/C (IncA/C) plasmids are large (~100 ~ 200 kilobases (kb)), conjugative plasmids that are carried by Gram-negative bacteria. IncA/C plasmids often carry numerous genes that confer resistance to antimicrobials and have been isolated from many types of bacteria that pose significant risks in both human and animal medicine. Although IncA/C plasmids have been described in the literature for many years, little is known about their basic biology. For the past decade, many fully sequenced IncA/C variants have been described. There has been a lack of work concerning core functions of these plasmids, such as, replication, conjugative transfer and maintenance. This dissertation focuses on how these plasmids are regulated on a transcriptional level. We used pAR060302, a prototypical IncA/C plasmid, to conduct several experiments investigating exactly what genes are transcribed and how different conditions affect their transcriptional landscape. RNA-Seq was used to understand how antimicrobial exposure can affect the way genes are expressed on IncA/C plasmids. We found that, under the conditions we tested, antimicrobials have little effect on the transcription of genes on pAR060302. However, this initial study was the first to explore genes carried IncA/C plasmids in terms of their expression. Further RNA-Seq experiments were carried out in several different bacterial genera all carrying the same IncA/C plasmid, pAR060302. These experiments attempted to characterize how a broad host-range plasmid, such as IncA/C, might be differentially regulated in different hosts. We found that only subtle changes occur in the expression of plasmid genes. Carriage of IncA/C plasmids was found to have diverse effects on chromosomal gene expression. Genes involved in 2-carbon metabolism in Escherichia coli are up-regulated due to plasmid carriage. Our results suggest that plasmid encoded factors might serve varying levels of importance depending on the host chromosomal background. Experiments were carried out on E. coli carrying plasmids with mutations in a group of predicted transcriptional regulators to determine their function. We identified the positive regulators of conjugative transfer in IncA/C plasmids, acaD and acaC. We also found a repressor of transfer, acr2, which encodes an H-NS-like protein. We further show that acr2 might regulate genes beyond those that are involved in conjugative transfer. This dissertation builds on our understanding on what mechanisms are important for the maintenance of large plasmids in Gram-negative bacteria. Understanding how plasmids might specifically tune host metabolism to improve competitive fitness would impact what evolutionary processes were involved in their emergence. Characterization of regulatory networks that govern core plasmid processes, such as conjugation, might assist in the development of new models of how these plasmids disseminate throughout bacterial populations.
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    Use of Sequencing Technologies to Improve Swine Infectious Disease Management
    (2020-02) Tan, Shaoyuan
    The swine industry is an indispensable part of the food production and agricultural system. However, infectious disease poses great threats to the industry. The current situation is that “old” infectious diseases are not totally under control and “new” pathogens keep emerging. In addition, via food chain and direct or indirect contact, some swine pathogens can infect humans and antimicrobial resistance arising from swine pathogens can also adversely impact public health. The threat of infectious disease to the swine population has been further magnified by globalization which increases the rate and breadth of disease transmission, thus having a more devastating impact. Fortunately, scientific advances have greatly bolstered our ability to develop effective disease control strategies. Sequencing technology has emerged as a powerful solution to deal with the challenging infectious disease situations we are facing today. The advantages of sequencing as a diagnostic tool are numerous. From our research, we confirmed that sequencing has improved the disease diagnostic resolution to the strain level, providing more precise and effective control strategies; it is able to generate additional genomic information for functional prediction of infectious agents, such as antimicrobial resistance profiling; and sequencing can facilitate a prompt response against emerging eventualities due to its ability to rapidly detect pathogens in a sample, including the novel or unexpected ones. Going forward, the more frequent use of sequencing in swine medicine can enhance our ability to predict and control the emergence and transmission of infectious disease within swine populations.