Date of Award
12-22-2023
Degree Name
Doctor of Philosophy (PhD)
Degree Type
Dissertation
Abstract
Our quest as a species to treat and prevent disease has led us to develop medical care that would have been inconceivable even one century ago. However, as we learn to overcome previous roadblocks, new hurdles that we hadn’t even considered continue to present themselves. Once we learned to understand the germ theory of disease, we sought treatments for infectious diseases, which led us to the development of antibiotics. Antibiotics are responsible for saving countless lives and have ushered in the advances in other fields of medicine like cancer treatment and surgery. Now, antibiotic resistance threatens our ability to treat disease once more. Healthcare environments like hospitals have become an epicenter for antibiotic resistance, due to the condensed nature of both antibiotic usage and highly susceptible patients. Combatting healthcare-associated infections (HAIs) is a current challenge in infectious disease treatment, and the incidence of antibiotic resistance only complicates our efforts. In this thesis, I first study two different mechanisms by which antibiotic resistant organisms (AROs) transmit and cause disease in a healthcare setting. Then, I investigate the impacts of a proposed environmental hygiene intervention to reduce the burden of AROs in patient rooms. In Chapter 2, we investigated reservoirs of long-term AROs colonization on hospital surfaces (Sukhum, Newcomer et al. 2022. Communications Medicine). This study included samples from the last three months of an old ward’s operation, two weeks prior to patient and staff move-in in a new ward, and for the new ward’s first year of operation. We collected environmental samples from many surfaces such as sink drains, floors, nurse call buttons, etc, and selectively cultured these samples for AROs. We also collected isolates from patient stool and patient blood stream infections. We found ARO burden to be the highest in sink drains and did not find any increase in sink drain isolates over the year of sampling. Pseudomonas aeruginosa and Stenotrophomonas maltophilia were our most frequently identified organisms, and we utilized whole-genome sequencing methods to track how they colonized sink drains longitudinally throughout the study. Concerningly, we found one strain of P. aeruginosa (of ST1894) that was found before patient and staff move-in, spread to all sinks sampled, and caused 3 patient bloodstream infections across the study. This work highlights how sink drains can function as a reservoir for AROs, and should be a target for future infection prevention interventions. In Chapter 3, we characterized how Clostridioides difficile contaminates hospital surfaces and virulence in current prevalent strains (Newcomer, Fishbein et al. 2023. In submission). From two wards over 6 months, we selectively cultured C. difficile from patient stool and rectal swabs and swabs from surfaces in their rooms. Using genomics analyses, we found some bedrail and keyboard contamination came from a source other than the in-room patient. Despite this, we found no evidence of C. difficile transmission that led to C. difficile infection CDI, suggesting current infection prevention measures focused on CDI patients may be sufficient. However, though hypervirulent strains may be more likely to cause CDI, we found that more total CDI cases were attributable to non-hypervirulent strains. We identified two patients that were C. difficile carriers and were later diagnosed with CDI with the same strain. Thus, we used genomics analyses to further interrogate virulence of clade 1 isolates and identified new associations between C. difficile toxin and binary toxin regulator genes. These data describe how contamination persists in the hospital setting, and how future work must focus on how the accessory genome may contribute to the transition from colonization to CDI. In Chapter 4, I began to investigate the potential of sink hygiene intervention for reducing ARO burden in hospital sink drains (Newcomer, et al. 2023. In submission). We used 10% bleach wipes to wipe sink surfaces, and then pumped a foamed peracid-based disinfect into sink drains to break down bacterial biofilms. This multi-phasic study began with a baseline period of no interventions, followed by two rounds of intervention and baseline. Rooms either received no intervention and just normal cleaning practices, a low-frequency intervention (1x/week), or a high-frequency intervention (5x/week). We collected swabs from sink surfaces and selectively cultured for total growth, gram-negative growth, and unique AROs. This intervention successfully reduced both total microbial and gram-negative bacteria recovered from sink drains when compared to baseline phases. It also significantly reduced the proportion of sink drains yielding P. aeruginosa and S. maltophilia at both intervention frequencies. These results are promising for the potential of this intervention, though future work is necessary to quantify its impact on HAI rates. Finally, in Chapter 5 I utilized whole-genome sequencing to understand the genomic impacts of the intervention described in Chapter 4 (Newcomer et al. 2023. In preparation). I used strain tracking methods to identify closely related strain groups of P. aeruginosa and S. maltophilia, and found the same strains described in Chapter 2 colonizing the same sink drains over 3 years later. The number of unique strains did not significantly decrease during intervention phases, but after intervention there were significantly more new strains of P. aeruginosa isolated from intervention rooms than from control rooms. In contrast, the S. maltophilia strains present largely stayed the same even after intervention phases. Finally, I found no significant increases in the number of antibiotic resistance genes present in P. aeruginosa or S. maltophilia strains during or after interventions. The strains found in intervention rooms also did not appear to acquire mutations more frequently in any specific genes than strains found in control rooms. These findings provide insight into the mechanisms behind long-term colonizing AROs and support the safety of this intervention with respect to antibiotic resistance or mutational adaptations.
Language
English (en)
Chair
Gautam Dantas