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Antibiotics have transformed modern medicine in manifold ways. However, the misuse and over-consumption of antibiotics or antimicrobials have led to the rise in antimicrobial resistance (AMR). Unfortunately, robust tools or techniques for the detection of potential loci responsible for AMR before it happens are lacking. The emergence of resistance even when a strain lacks known AMR genes has puzzled researchers for a long time. Clearly, there is a critical need for the development of novel approaches for uncovering yet unknown resistance elements in pathogens and advancing our understanding of emerging resistance mechanisms. To aid in the development of new tools for deciphering AMR, here we propose a machine learning (ML) based framework that provides ML models trained and tested on (1) genotypic AMR and phenotypic antimicrobial susceptibility testing (AST) data, which can predict novel resistance factors in bacterial strains that lack already implicated resistance genes; and (2) complete gene set and AST phenotypic data, which can predict the most important genetic loci involved in resistance to specific antibiotics in bacterial strains. The validation of resistance loci prioritized by our ML pipeline was performed using homology modeling and in silico molecular docking.

Neisseria gonorrhoeae, the causative agent of gonorrhea, is the second most prevalent sexually transmitted infection that leads to substantial morbidity and economic burden worldwide. Improperly treated or untreated gonorrhea can lead to severe and life-threatening complications, including abortion, infertility, pelvic pain, and maternal death. Neisseria gonorrhoeae has developed resistance to the formally and currently used antibiotics. The Centers for Disease Control and Prevention (CDC) have listed multi-drug resistant N. gonorrhoeae as an urgent threat that promptly requires the development of novel therapeutic agents. Traditional drug discovery and development is a time-consuming and costly process associated with high risks. To address the dire need to replenish the dry pipeline of anti-gonorrhea medications, drug repurposing is a promising approach. In this study, an FDA-approved drug library was screened, and 14 drugs were found to exhibit promising anti-gonococcal activity. Interestingly, three extremely potent and narrow-spectrum novel candidates, itraconazole, isavuconazole, and ravuconazole, are azole antifungals, and their activities were further investigated in vitro. Of the three azoles, ravuconazole displayed the most potent activity against N. gonorrhoeae clinical isolates. The time-kill assay revealed that the three azoles showed bactericidal activity. All three azole drugs showed a low frequency of resistance. Besides, isavuconazole and ravuconazole have a longer post-antibiotic effect than azithromycin. All three azoles cleared the burden of intracellular N. gonorrhoeae completely, which is superior to ceftriaxone. In conclusion, itraconazole, isavuconazole, and ravuconazole merit future investigation for the development of anti-gonorrheal therapeutics. This study provided unexplored avenues and promising opportunities that can be further evaluated to combat N. gonorrhoeae infection. / Master of Science / Neisseria gonorrhoeae, the causative agent of gonorrhea, is the second most prevalent sexually transmitted infection that leads to substantial morbidity and economic burden worldwide. Improperly treated or untreated gonorrhea can lead to severe and life-threatening complications, including abortion, infertility, pelvic pain, and maternal death. Due to the increasing prevalence of drug resistance against the formally and currently used antibiotics, the Centers for Disease Control and Prevention (CDC) have classified multi-drug resistant N. gonorrhoeae as an urgent-threat pathogen. Therefore, the discovery of new anti-gonorrheal therapeutics is an urgent need. Drug repurposing is the process of discovering new therapeutic uses for approved or investigational drugs that go beyond the original medical indication. To address the dire need to replenish the dry pipeline of anti-gonorrheal drugs, repurposing FDA-approved drugs is a promising approach as it significantly reduces the time and expense associated with traditional drug development. By screening an FDA-approved drug library, 14 drugs were found to display promising anti-gonococcal activity. Interestingly, three (itraconazole, isavuconazole, and ravuconazole) out of 14 identified drugs were azole antifungal drugs, and their activities were further investigated in vitro. All three azole drugs showed bactericidal activity, meaning that they killed bacteria, had a low propensity to develop resistance, and completely cleared the burden of intracellular N. gonorrhoeae. Besides, our findings suggested that isavuconazole and ravuconazole possessed exceptional activity in the suppression of bacterial growth following brief antibiotic exposure. In conclusion, the three azole drugs exhibited potent anti-gonococcal activity and merited further investigation. This study provided unexplored avenues and promising opportunities that can be further evaluated to combat multidrug-resistant N. gonorrhoeae. Neisseria gonorrhoeae, the causative agent of gonorrhea, is the second most prevalent sexually transmitted infection that leads to substantial morbidity and economic burden worldwide. Improperly treated or untreated gonorrhea can lead to severe and life-threatening complications, including abortion, infertility, pelvic pain, and maternal death. Due to the increasing prevalence of drug resistance against the formally and currently used antibiotics, the Centers for Disease Control and Prevention (CDC) have classified multi-drug resistant N. gonorrhoeae as an urgent-threat pathogen. Therefore, the discovery of new anti-gonorrheal therapeutics is an urgent need. Drug repurposing is the process of discovering new therapeutic uses for approved or investigational drugs that go beyond the original medical indication. To address the dire need to replenish the dry pipeline of anti-gonorrheal drugs, repurposing FDA-approved drugs is a promising approach as it significantly reduces the time and expense associated with traditional drug development. By screening an FDA-approved drug library, 14 drugs were found to display promising anti-gonococcal activity. Interestingly, three (itraconazole, isavuconazole, and ravuconazole) out of 14 identified drugs were azole antifungal drugs, and their activities were further investigated in vitro. All three azole drugs showed bactericidal activity, meaning that they killed bacteria, had a low propensity to develop resistance, and completely cleared the burden of intracellular N. gonorrhoeae. Besides, our findings suggested that isavuconazole and ravuconazole possessed exceptional activity in the suppression of bacterial growth following brief antibiotic exposure. In conclusion, the three azole drugs exhibited potent anti-gonococcal activity and merited further investigation. This study provided unexplored avenues and promising opportunities that can be further evaluated to combat multidrug-resistant N. gonorrhoeae.

Antimicrobial resistance (AMR) is a One-Health (human, animal, environment) challenge that requires collaborative, interdisciplinary action. Comparable surveillance data are needed to effectively inform policy interventions aimed at preventing the spread of AMR. Environmental monitoring lags behind that of other One Health sectors and is in need of agreed upon targets and standardized methods. A challenge is that there are numerous microorganisms, antibiotic resistance genes (ARGs), and mobile genetic elements and corresponding methods that have been proposed. In this dissertation, a framework for AMR monitoring of aquatic environments was developed through a combination of literature review and stakeholder input, via surveys and a workshop. Through this process, three targets were selected for standardization: the sulfonamide resistance gene (sul1), the class 1 integron integrase gene (intI1), and cefotaxime-resistant Escherichia coli. Quantitative polymerase chain reaction (qPCR)- and culture-based protocols were developed and pilot tested in two independent laboratories on a set of six water matrices: wastewater, recycled water, and surface water from six different wastewater utilities engaging in water reuse located in five states across the USA. The impact of wastewater treatment and advanced water treatment processes was examined in terms of removal of these targets. Finally, qPCR and culture methods were used to examine the relationship between sul1, intI1, E. coli, and fecal indicators in private household wells across four states in the Southern USA that were identified as susceptible to storm events. The overall findings provide a useful baseline occurrence of the proposed AMR monitoring indicators across a range of water types and protocols that are accessible to water utilities. / Doctor of Philosophy / Life-saving drugs and treatments are failing at an increasing rate because of antimicrobial resistance (AMR). Antimicrobials, such as antibiotics, are a double-edged sword, because they are an effective weapon for killing disease-causing pathogens, but the more they are used the greater the likelihood that microbes that are resistant to them will survive, reproduce, and spread. National action plans for AMR have been created by a majority of countries, emphasizing the importance of antibiotic stewardship and other mitigation strategies. However, numerous data gaps need to be addressed in order to identify strategies that are most likely to be effective and to implement them. Environmental surveillance, including wastewater influent, wastewater effluent, and surface water, could prove an informative means to track AMR trends with time and relate them to human activities and corresponding mitigation efforts. The purpose of this dissertation was to develop a framework for AMR surveillance of aquatic environments and to test it across an array of sample types. We considered an array of possible culture- and DNA-based targets from available scientific literature and engaged experts and stakeholders in narrowing down the list to options that were both informative and feasible. We developed protocols for quantifying an antibiotic resistance gene (sul1), a mobile genetic element that has been implicated in the spread of multi-antibiotic resistance (intI1), and an extended spectrum beta-lactamase (ESBL) producing form of Escherichia coli. We compared the methods between two independent laboratories on untreated wastewater, treated wastewater, recycled water, and surface water collected from six locations across five states. We additionally did a survey of private household well water that was hypothesized to be vulnerable to contamination due to storms and lack of resources for maintenance. The results of this research can help to support environmental monitoring of AMR across the US and globally.

A global rise in humanitarian emergencies, driven by conflict, poses significant health challenges, especially for children under five years old. While the source of such crises and the challenges affected healthcare systems face may be confined to man-made borders, the resulting spread of health problems such as antimicrobial resistant (AMR) infections and diarrheal diseases are not bound geographically. To address concerns in such dynamic environments, healthcare workers utilize simple, fast acting solutions to save as many children as possible. For diarrheal diseases, this entails initially treating with zinc supplements and oral rehydration solutions (ORS), saving antibiotics for the cases that do not respond to this treatment. Determining who needs this care is often assessed through proxy data tracked via routine vaccination records, such as “zero dose communities”. However, both protocols are not without their shortcomings. The goal of this thesis is to examine their risks. We first examine how zinc might impact resistance development in Escherichia coli in vitro. We further demonstrate by computational modeling that slight changes in fitness have disproportionate changes on the rate of resistance onset. After discovering that the use of zinc for diarrhea treatment may be contributing to the AMR crisis, we next focus on ensuring that children suffering from diarrheal diseases can access treatment. We find that using zero dose communities as a means of determining which children could access care, while suitable for other services, is ultimately insufficient for diarrheal diseases in crisis settings such as Democratic Republic of Congo, Afghanistan and Bangladesh. Finally, we look at developing a tool that could be used to better understand access to care patterns for diarrheal disease and show the impacts that conflict, weather and travel infrastructure have on altering access to care in Yemen, which has been in the midst of the world’s worst humanitarian crisis. Overall, this body of work demonstrates how both current treatment practices and access to care assessments for diarrheal diseases have previously overlooked risks which can contribute to poor health outcomes especially for children under five years old living in areas affected by humanitarian crises.

This thesis consists of two chapters, each of which is a unique research project. Chapter 1 is focused on the synthesis and biological evaluation of novel sideromycin antibiotics. Sideromycins are bifunctional “Trojan Horse” molecules that have an iron chelator “siderophore” moiety covalently bound to an antibiotic. Such molecules exploit existing bacterial mechanisms for obtaining iron from their environment. Antibiotics that would typically not pass Gram-negative membranes are allowed access via siderophore transporter proteins. This project utilized a siderophore that has not previously been used in this capacity. The synthesis and biological evaluation of multiple sideromycin conjugates is reported. Chapter 2 describes the chemical synthesis of coumarin natural products using a synthetic process recently developed in the Magolan laboratory that enables the efficient prenylation of phenols. These natural products are molecules of biological interest in various capacities but are rare and difficult to isolate from their plant sources. They have also previously been cumbersome to make via chemical synthesis. The chemistry described herein constitutes an inexpensive and efficient process to produce these compounds that is superior to previously known methods. / Thesis / Master of Science (MSc) / This thesis is divided into two chapters. The first chapter is focused on the development of new sideromycin antibiotics. Sideromycins are “Trojan Horse”-like antibiotics that exploit the mechanisms of Gram-negative bacteria for obtaining iron, an essential nutrient, to enable antibiotic entry. This chapter details the synthesis of molecules that attach functionalities called “siderophores” to antibiotics, enabling them to be “smuggled” into Gram-negative microbes. This project uses a siderophore not previously utilized in sideromycin research. The second chapter is focused on the chemical synthesis of rare natural products that are phenols with prenyl substituents. Many such compounds are plant-derived and have potential for biomedical use. However, difficulty in isolating them makes them prohibitively expensive in the purity and quantity required for research. They are also challenging to make synthetically. This chapter details the application of a recently discovered process in the Magolan laboratory to synthesize coumarin-containing prenylated phenolic natural products.

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Since penicillin was discovered in 1928, antibiotic usage in human and veterinary medicine and prevalence of antibiotic resistant bacteria (ARB), has been increasing. While antibiotics and antibiotic resistance genes (ARGs) naturally occur in soils, increasing abundances of ARGs correlate with increased antibiotic usage in agricultural settings. When livestock are treated with antibiotics, the antibiotic compounds, ARB, and ARGs can enter soil via manure excreted onto pastures or applied to other fields as fertilizer, thereby spreading antimicrobial resistance (AMR) in the environment. In addition to human health implications, increased AMR has negative impacts on ecosystem services such as carbon and nitrogen cycling. While many studies have researched antibiotic persistence in agricultural systems and their impacts on soil microbial communities, there are still significant knowledge gaps around the long-term effects of antibiotic exposure in soils, how those impacts differ among soils, and how elements of AMR may differentially transport through soil. To address these knowledge gaps, our objectives were to 1) examine the impact of multi-year repeated additions of manure from cattle administered antibiotics on soil microbial communities, 2) determine the interactive effects of soil moisture and type on soil microbial communities exposed to antibiotics and manure, and 3) differentiate between vertical transport of AMR in the form of viable ARB or ARGs in extracellular plasmids. Our results demonstrate that soil bacterial community structures were consistently altered by 3-year additions of manure from cattle administered antibiotics compared to soil amended with antibiotic-free manure. Furthermore, ARG abundances were higher in soils with manure additions compared to soil without manure, although this was true regardless of whether the cattle were administered antibiotics, suggesting that manure and antibiotic impacts on soil microbial communities can persist over multi-year of repeated manure applications. Additionally, in microcosms, effects of manure from cattle administered antibiotics on ARG abundances, microbial community structures, respiration, and nitrogen pools in soil were seen across multiple soil types and moisture contents, suggesting environmental conditions can alter how manure and antibiotics impact microbial community structure and nutrient cycling. Finally, ARB flowed readily through saturated soil, but were also detectable in the top 5 cm of soil columns. However, ARGs on extracellular plasmids did not flow through soil columns and were not detected in soil, indicating that extracellular DNA does not persist or transport through the soil to any meaningful degree. Overall, these results indicate a nuanced approach is required to mitigate the environmental spread of AMR. Soil management strategies for addressing the AMR crisis should consider the broader context of manure management, as high ARG abundances can come from application of manure from antibiotic-free cattle, and soil microbial communities in individual environments may have varied responses to manure antibiotic exposure. Furthermore, the transport of AMR through soil is complex and dynamic, as elements of AMR may transport differently through soil and require separate consideration in modeling and management. Future AMR management practices that consider diverse factors that affect persistence and spread of AMR in the environment can help protect livestock productivity and maintain the efficacy of antibiotics to protect human and animal health. / Doctor of Philosophy / Antibiotics are an important tool used to fight infections in humans, pets, and livestock. As antibiotics are used more frequently, the bacteria they target are more likely to develop resistance to the antibiotics, leading to increasing cases of infections that are harder to treat and higher risk. Antibiotic resistance can persist and spread in multiple forms, including the antibiotic compounds themselves, as antibiotic resistant bacteria (ARB), or as the genetic material that encodes for antibiotic resistance genes (ARGs). In agricultural systems, when livestock are treated with antibiotics they can excrete the antibiotics, along with ARB and ARGs, in the manure, which is then applied to land as fertilizer. In addition to the associated health risks, the spread of antibiotic resistance impacts microscopic bacteria and fungi in the soil, which are important for recycling nutrients for plants and maintaining ecosystem health. The overall goal of this dissertation was to gain a better understanding of how manure from cattle given antibiotics impacts these bacteria and fungi when manure is applied to the soil. The specific objectives were to 1) look impacts after long-term (multiple years) of manure addition, 2) examine how bacteria and fungi might respond differently to antibiotics in soils of different type or with different amounts of water, and 3) determine if ARGs that exist as free genetic material outside of living bacteria can be moved through the soil with flowing water in the same way as living bacteria. Results showed that while the composition of bacterial and fungal communities in the soil vary from year to year, adding manure with and without antibiotics had both caused different and consistent changes on the composition of bacterial communities. There were also higher concentrations of ARGs in soil that had manure added, however antibiotics in the manure did not cause ARGs to increase further, suggesting that even antibiotic-free manure can impact the spread of antibiotic resistance. Experimental work also demonstrated that the soil type and water content of soil can alter how bacteria and fungi respond to antibiotics in manure. The composition of bacterial and fungal communities, their activity rates, and the amount of nitrogen – an important plant nutrient with availability that is strongly affected by microbial activity – all differed with soil type and water content. Thus, while antibiotic resistance antibiotic resistance can cause measurable changes in soil across a range of environmental conditions, it is also likely to persist and spread in different ways in different environments. Finally, when water containing elements of AMR was added to soil, ARB were shown to both move through the soil easily and remain near the top of soil. In contrast, ARGs contained on genetic material outside of living cells did not move through the soil and were broken down within a few days, suggesting that antibiotic resistance likely spreads through living bacteria more than genes outside of cells. Overall, this work highlights the complexity of understanding the role of environmental transmission in the antibiotic resistance crisis and demonstrates the need for nuanced management approaches that take specific environments and conditions into account.