ORCID
https://orcid.org/0000-0002-5362-4920
Date of Award
12-14-2023
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
The introduction of antibiotics in the 20th century stands as one of our greatest scientific achievements, profoundly transforming human health and global well-being. Over the past century, antibiotics have ensured that infectious diseases are no longer the most common causes of death worldwide. In further enabling a vast array of invasive medical procedures (e.g., surgeries, organ transplants), antibiotics have effectively added decades to the average human lifespan. In agriculture, antibiotics have been heavily relied upon to meet the nutritional demands of the growing human population. Thus, ever since the introduction of penicillin, antibiotics have been the “miracle drugs” they were promised to be and have made our modern ways of living possible. However, evolution remains the absolute guiding principle of all biology; exerted evolutionary pressure in the form of antibiotics has led to the emergence and enrichment of resistant microorganisms, resulting in a growing number of deaths due to drug-resistant infections. Antibiotic resistance is one of the greatest challenges to global public health, and we are rapidly entering a post-antibiotic world. Unless urgent action is taken, estimates suggest that by the mid-21st century, antimicrobial-resistant infections may yet again become the primary cause of mortality in the world. Accordingly, antibiotic resistance has been the core focus and the unifying theme of my thesis work. This dissertation details my efforts – in close collaborations with others – towards better understanding the spread of resistant microbes (Chapters 2, 3, and 4), as well as combating the growing threat of antimicrobial resistance (Chapter 5). In Chapter 2, I focus on the discovery of genetic determinants of antimicrobial resistance. Specifically, I introduce functional metagenomics, a technique aimed at identification of novel antibiotic resistance genes (ARGs). I subsequently describe our use of functional metagenomics to find genetic elements that confer resistance to irresistin-16 (IR16), a novel antimicrobial agent with a broad spectrum of activity that includes both gram-negative and gram-positive microbes. Notably, IR16 has been described as irresistible, suggestive of the inability of bacteria to develop resistance against the molecule. Contrary to these claims, we find two distinct genes that enable the growth of Escherichia coli in otherwise inhibitory concentrations of IR16. I use these discoveries as an opportunity to comment on the improbability of irresistible antibiotics and to urge caution in assigning irresistibility to novel antimicrobial agents. In Chapter 3, I look at the dissemination of antimicrobial resistance within an agricultural setting. Antimicrobial use in food animals far exceeds in total amounts the antibiotic consumption in humans, and overuse of antibiotics in livestock has been suggested as a key contributor to the rise of antimicrobial resistance. Despite this, the effects of direct exposure to livestock microbes on the human microbiome remained unknown. We addressed this gap in knowledge by conducting longitudinal profiling of the nasal and fecal microbiomes of farmers and their dairy cows. To determine the microbial signatures associated with livestock farming, we extended our investigation to a cohort of age-, sex-, and ZIP code-matched individuals with no occupational exposures to farm animals. We find evidence of acquisition of cow-associated microbes by farmers, with this acquisition being most apparent in the nasal ecosystem. We show that the acquired livestock microbes introduce encoded ARGs into the farmer gut, where the genes subsequently disseminate to new bacterial hosts via mobile genetic elements. In one example, we find a resistance-encoding mobile cassette that is enriched in the cow gut but has disseminated to resident microbes of the farmer gut; notably, this same cassette is also found in clinical bacterial isolates reported elsewhere, directly tying the selection for antimicrobial resistance in farm animals to human health. In Chapter 4, I take a closer look at genetic elements that enable the horizontal dissemination of ARGs. Specifically, I focus on extended-spectrum beta-lactamases (ESBLs) and their increasing prevalence among clinical E. coli isolates. The spread of ESBLs is driven by mobilizable plasmids; however, the roles of individual plasmid lineages in the dissemination of ESBLs remained underexplored. To address this knowledge gap, we sequenced a large set of clinical ESBL-producing E. coli isolates from a tertiary care hospital. We provide further evidence in support of plasmid-mediated spread of ESBLs but demonstrate that ESBL variants differentially rely on plasmids for their dissemination. We further identify key plasmid lineages that are responsible for the dissemination of ESBLs within this clinical setting. Notably, within these lineages, we find genetic elements that may facilitate their transmission and stable maintenance within the clinical E. coli population, providing a mechanistic basis for their success in spreading ARGs. In all, our findings provide valuable insight into plasmid-mediated ESBL spread, adding to our understating of factors underlying the increased prevalence of these genes in nosocomial settings. Addressing the growing threat of antimicrobial resistance necessitates the development of novel anti-infectious strategies. Although such approaches should include the generation of novel antibiotics, emergence of resistance is likely unavoidable, as we discuss in Chapter 2. As such, there is a need for non-antibiotic anti-infectious therapies that can be used in lieu of or in complement with antibiotics. Probiotic microorganisms may provide an avenue for the development of such antibiotic-sparring therapeutics. Specifically, in Chapter 5, I focus on Saccharomyces boulardii, a probiotic yeast with native anti-infectious properties. The therapeutic benefits of S. boulardii could be expanded through tunable expression of functional biologics. We thus designed a transcriptional activation system in S. boulardii for orthogonal expression of exogenous genes. Further, by placing the transcriptional activators under the control of inducible promoters, we achieved reporter expression in response to environmental stimuli. In all, our work sets the stage for future developments of S. boulardii-based engineered therapeutics with precise anti-infective activities. The antibiotic resistance crisis is one of the most consequential public health challenges of our time. This dissertation is an effort to further our understanding of the emergence and spread of resistance, as well as to contribute towards the development of the next generation of anti-infectives. A defining feature of a post-antibiotic world will be the millions of lives lost annually to infections that are no longer amenable to treatment. We stand on the precipice of such a world, and the time to act is now! As we move forward, it is imperative for global well-being that we, as a global community, invest in understanding, tracking, and combating antimicrobial resistance.
Language
English (en)
Chair and Committee
Gautam Dantas
Recommended Citation
Mahmud, Bejan, "Understanding and Combating the Spread of Antibiotic-Resistant Organisms" (2023). Arts & Sciences Electronic Theses and Dissertations. 3205.
https://openscholarship.wustl.edu/art_sci_etds/3205