The prevalence of antibiotics on farms for therapeutic and prophylactic use in animals can cause negative effects on biomethane production during anaerobic digestion. Previous literature has found decreased biomethane production rates from a variety of antibiotics, but biogas inhibition differs between studies of continuous and batch reactors and the type of antibiotic studied. Cephalosporin drugs are the most common antibiotic class used to treat mastitis in dairy cows and can retain most of their bioactivity after excretion. Ceftiofur is a commonly used cephalosporin drug but no previous study investigating the effect of Ceftiofur on biomethane during continuous anaerobic digestion has been performed. The aim of this study was to examine the effect on biomethane production when manure from cows treated with Ceftiofur was anaerobically digested. Laboratory sized anaerobic digesters (AD) were run at thermophilic (55°C) temperatures and a 10 day hydraulic retention time. Manure from cows treated with Ceftiofur were fed to the antibiotic treatment reactors for 50 days. The reactor performance was measured by i) biomethane production, ii) waste stabilization in terms of solids and chemical oxygen demand, iii) change in mass of Ceftiofur and iv) change in concentration of antibiotic resistant genes, specifically cfx(A), mef(A), and tet(Q). There was statistically significant decrease in cumulative gas production due to the addition of Ceftiofur into the reactors, but no significant difference between treatments in waste stabilization in terms of percent volatile solids (VS) and total chemical oxygen demand (TCOD) reduction. Anaerobic digestion decreased the amount of Ceftiofur in manure, and the amount of Ceftiofur in the reactors reduced over the time of the experiment. Change in antibiotic resistant genes (ARGs) were gene dependent over time. Concentrations of tet(Q) reduced significantly between feed and effluent of both treatments, and cfx(A) reduced significantly for the control treatment but not the Ceftiofur treatment. Concentrations of mef(A) increased over time in both treatments. Overall, the addition of Ceftiofur in continuously operated anaerobic digesters negatively affected biomethane production, a value-added product responsible for on-farm renewable energy. However, anaerobic digestion does decrease the mass of Ceftiofur within manure, thereby reducing the environmental loading from run-off from farms. / Master of Science

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Introduktion: Antibiotikaresistens är idag ett av de största globala hoten mot folkhälsan. Antibiotikaresistens innebär att bakterier blir resistenta mot läkemedlet antibiotika, vilket leder till att sjukdomar som tidigare varit behandlingsbara med antibiotika blir svårbehandlade eller icke behandlingsbara. Detta leder i sin tur till högre dödlighet, längre sjukhusvistelser samt en högre kostnad för vården. Resistensen sker även naturligt men det är tydligt att överanvändning och missbrukning av antibiotikan skyndar på resistensutvecklingen avsevärt. Syfte: Syftet med den här studien är att undersöka människors beteende gällande antibiotikaanvändning utifrån ett antibiotikaresistent perspektiv. Metod: Det här är en empirisk studie som genomförts i form av en enkätundersökning.Studiedesign är en tvärsnittsdesign. Denna design innebär att data samlas in från mer än ettenda fall vid en viss tidpunkt. Studiepopulationen består av män och kvinnor i åldersgruppen18 år och uppåt utan en övre gräns.Resultat: Resultatet visar att respondenterna är medvetna om antibiotikaresistens och 88,7 %svarar att de är medvetna om att det finns antibiotikaresistens, 87,3 % följer läkarens behandlingsrekommendation. Resultatet visar att 18,3 % skulle kunna tänka sig att köpa antibiotika receptfritt på apotek utomlands utan en läkares ordination om de blir sjuka och 25 % av dem har en högskoleutbildning/universitetsutbildning. Slutsats: Generellt sett visar studien på att det finns en medvetenhet om antibiotikaresistens,vilket också visar sig i respondenternas beteende. Respondenternas beteende följer med vadsom bidrar till att resistensutvecklingen minskar i samhället som handlar om att följa läkarensbehandlingsrekommendation samt att inte köpa receptfria antibiotika. Restriktivt användandeav antibiotika bidrar till minskad resistens. / Introduction: Antibiotic resistance is today one of the biggest global threats to public health. Antibiotic resistance means that bacteria become resistant to the drug antibiotics, which leads to diseases that have previously been treatable with antibiotics becoming difficult to treat or not treatable, which in turn leads to a higher mortality, longer hospital stays and a higher cost of care. The resistance also occurs naturally, but it is clear that overuse and misuse of the antibiotic accelerates the development of resistance considerably. Aim: The aim of this study is to investigate human behavior regarding antibiotic use from an antibiotic-resistant perspective. Method: This is an empirical study conducted in the form of a survey. Study design is a cross-sectional design. This design means that data is collected from more than a single case at a given time. Study populations consists of men and women in the age group 18 years and older without an upper limit. Results: The results show that the respondents are aware of antibiotic resistance and 88.7 % answer that they are aware that there is antibiotic resistance. 87.3% follow the doctor's treatment recommendation. The results show that 18.3% could buy antibiotics without a prescription at pharmacies abroad without a doctor's prescription if they become ill and 25 % of them have a university education. Conclusion: In general, the study shows that there is an awareness of antibiotic resistance, which is also reflected in the respondents' behavior. The respondents' behavior follows what contributes to reducing the development of resistance in society, which is about following the doctor's treatment recommendation and not to buy over-the-counter antibiotics. Restrictive use of antibiotics contributes to reduced resistance.

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Widespread use of antibiotics in livestock production can result in the dissemination of bacteria carrying antibiotic resistance genes (ARGs) to the broader environment. Within agroecosystems, ARGs can pose a risk to livestock handlers, farmers, and ultimately consumers. The overall goals of this dissertation are to examine the presence of resistance (antibiotic, metal) in agricultural soils and evaluate the most critical potential points of best management control of antibiotic resistance spread along the agricultural production chain. The relative impacts of agricultural practices, manure management, native soil microbiota, and type of crop grown and harvested on the agricultural resistome are multi-dimensional and cannot be captured via a single analytical technique or by focusing on one specific point in the agricultural process. Culture-, molecular "indicator"-, and next-generation sequencing- based methods were employed to characterize antibiotic resistance via taxonomic and functional profiles on the broader manure, soil, and vegetable surface microbial communities through 16S rRNA amplicon sequencing and shotgun metagenomics. Although antibiotic concentrations dissipated in the soil after 28 days after amendment application, antibiotic resistance presence was recoverable throughout the entire 120d growing season in the compost and manure amendments, the amended soil, and on vegetable surfaces. The addition of organic fertilizers increased antibiotic resistance presence compared to background levels. Further, metals and metal resistance were also measured in the amended soils and were found to be at greater levels in the inorganically fertilized soils compared to the manures and compost amended soils. Analysis of the widespread agroecosystem microbial community composition and broader metagenome has characterized varying genera profiles in the soil and on the vegetable surfaces and specific ARG and mobile genetic element (plasmid) co-occurrences. These co-occurrences highlight which ARGs may be most critical for future antibiotic resistance dissemination research. It is imperative to employ multiple methods when measuring agricultural resistance, as one method alone may miss significant patterns and lead to different best management recommendations. Linking the livestock manure, soil, and vegetable surface-associated ARBs, ARGs, resistomes, and microbiomes will help identify critical control points for mitigation of agricultural dissemination of antibiotic resistance to the environment and food production. / Doctor of Philosophy / By 2050, it is estimated that antibiotic resistant infections will be the leading cause of death worldwide. It is important to consider human, animal, and environmental health when researching antibiotic resistance, which is known as a "One Health" approach. In this dissertation work, I focus on the environmental side of antibiotic resistance in our agricultural systems. Agriculture is a known source of antibiotic resistance due to its use of antibiotics in livestock as a treatment for illness, and in some instances, as a growth promoter. Over one growing season, I measured antibiotic resistance in an agricultural setting using many techniques. First, I analyzed the effects of inorganic (chemical) versus organic (manure and compost) fertilization on antibiotic resistance in the soil. I measured antibiotic resistance by growing antibiotic resistant bacteria, quantifying specific antibiotic resistant genes (ARGs) using DNA amplification, and quantifying all the ARGs in the soil using a next-generation sequencing (NGS) technique called shotgun metagenomics. I found that adding manure to the soil increases ARGs compared to background soil levels, and that composting in an effective management strategy in decreasing ARGs in the soil over time. Second, I analyzed the same effects of fertilization on metal resistance in the soil. I was able to use the same NGS dataset to measure metal resistance genes (MRGs). I found that adding inorganic chemical fertilizer increases MRGs in the agricultural soils compared to the organic (manure or compost) fertilizer. Additionally, I studied the microbes that live in the agricultural soils using another kind of NGS data specific for microbial identification. I found that although there were small differences between the microbial populations in the soil when fertilizers were added, they returned to similar composition over the growing season. Lastly, I measured antibiotic resistance and microbes throughout the entire agricultural system. I picked the point of fertilization (manure management), soil, and the lettuce surface to evaluate if antibiotic resistance spreads from the farm to the vegetable that ends up on a consumer's plate. I found that at each point antibiotic resistance is present, but at different levels. Composting reduces ARGs compared to raw manure. Agricultural soils may act as a natural buffer to antibiotic resistance. Lettuce plants grown in compost fertilized soils have less ARGs than lettuce plants grown in manure. There are many agricultural management practices that effectively reduce antibiotic resistance and using all of them plus many measurement methods will ultimately help farmers and consumers reduce antibiotic resistance in our agricultural systems.

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Decreasing surface water quality in South Africa has become an issue of concern as the population grows, industrial and agricultural activities expand, and environmental pollution increases. Wastewater treatment plants and other anthropogenic activities are liable for releasing raw and inadequately treated effluents into the surface water. Extensive pollution accompanied by the use of disinfectants, pesticides, and other chemical pollutants has been attributed to increased antimicrobial resistance in bacteria such as Escherichia coli in surface water, increasing environmental antibiotic resistance spread. The research aimed to determine water quality and prevalence of antibiotic-resistant bacteria in Naauwpoortspruit River, eMalahleni, Mpumalanga Province. Five sampling sites were selected along the Naauwpoortspruit River and monitoring was done for seven consecutive months. Samples were collected and analysed for physicochemical, microbiological parameters, and susceptibility profile of antibiotic-resistant bacteria using standard methods. Pearson correlation analysis was used to assess the path and strength of the relationship between physicochemical and microbiological parameters in the study area. Results of physicochemical and microbial parameters showed variation throughout the selected study sites. The results revealed a pH range of 4.45 – 7.9 and electrical conductivity levels range of 58.63 - 113.3 mS/m for the different sampling sites during the study period with lower levels detected during the winter period and higher levels in the summer period. Also, water samples showed a high total dissolved solids levels range of 381.1 – 736.45 mg/L and biochemical oxygen demand range of 67.1 – 168 mg/L for the different sampling sites during the study period. The Naauwpoortspruit River had higher levels of ammonia of 33.4 mg/L at Point A during the winter period as compared to 15 mg/L in the summer period. Heavy metals results showed that mercury range of 0.01 – 0.065 mg/L and copper range of 0.001 – 0.0035 mg/L were not compliant with aquatic ecosystem guidelines at all selected sites throughout the study period. The foremost finding of this study was that E. coli were present in all the selected sites at concentrations (>100 cfu/100ml). Elevated concentrations of 5.4 x 103 and 4.2 x 103 cfu/100ml for the total and faecal indicator bacteria were detected from sites downstream to 2.2 x103 and 2.35 x103 cfu/100ml for sites upstream river, in the rainy months. During the dry season, total coliforms, and faecal coliforms concentration of 0.4 x103 to 0.65 x 103 cfu/100ml were detected downstream and 0.25 x 103 and 0.5 x 103 cfu/100ml from upstream, respectively. The physicochemical and microbiological parameters measured at selected sites exceeded acceptable limits and proved unsuitable for applications such as full and intermediate recreational activities, and aquatic ecosystems. The variation in physicochemical parameters results was influenced by both natural processes and human activities such as salinity and Acid Mine Drainage (AMD) within the Naauwpoortspruit River. Using the Kirby-Bauer disc diffusion method, E. coli and faecal coliforms were tested for resistance to antibiotics; ampicillin (10 μg/ml), kanamycin (30 μg), streptomycin (30 μg), chloramphenicol (30 μg), erythromycin (15 μg), ox tetracycline (30 μg), erythromycin (15 μg/ml) and norfloxacin (10 μg). More than 60% of faecal coliform were resistant to at least four of the tested antibiotics and between 60 - 80% of the E. coli isolates were resistant to β lactam. The highest microbial antibiotic resistance (MAR) index value was observed at Site D (0.38 for E. coli) which showed multi-antibiotic resistance. Site D is characterized by wastewater treatment, power generation industries, and agriculture activities. The highest level of MAR observed at Site D indicates the need to control extensive pollution and constantly monitor the changing trends in antimicrobial resistance patterns of these waterborne pathogens. Statistical analysis showed that the development of microbiological parameters loads has a strong correlation with physicochemical parameters due to the association of sampling sites in the river environment. This study shows that the aquatic ecosystem needs constant monitoring to establish their conditions, impacts of pollution activities within the catchment, and input information into sustainable management of the water resources. / Environmental Sciences / M. Sc. (Environmental Science)