Over the past decade, efforts led by the U.S. Department of Health and Human Services (HHS) have reduced healthcare-associated infections in acute care settings nationally. In 2013, HHS identified that the next phase of these healthcare-associated infection reduction initiatives would target long-term care facilities through the publication of a new chapter in the National Action Plan to Prevent Health Care Associated Infections devoted to this setting. Long-term care facilities are nursing facilities that provide “medical, skilled nursing and rehabilitative services on an inpatient basis to individuals who need assistance preforming activities of daily living, such as bathing and dressing”. These facilities are the primary residence for 2.5 million, predominantly elderly Americans and represented $143 billion nationally in healthcare costs as of 2010. Accordingly, it is a national priority to reduce healthcare-associated infections in this setting and protect this vulnerable population. Healthcare-associated infections caused by multidrug-resistant organisms (MDROs) are a particular burden in the long-term care population. These pathogens, usually bacteria, are defined as being resistant to one or more classes of antimicrobial agents. However, MDROs frequently exhibit resistance to nearly all antimicrobial drugs. Clinical infection control guidelines recommend isolation precautions to prevent MDRO transmission, based on evidence collected in acute care settings. However, the limited evidence that is available from studies in long-term care facilities suggests that isolation precautions may not be effective in this setting. Given that the reduction of antibiotic resistant infections is a priority of the HHS, The White House, Healthy People 2020, and the World Health Organization, it is necessary to confirm and support the appropriate use of isolation precautions for MDROs with evidence specific to long-term care facilities. Therefore, this dissertation describes the current evidence for and use of isolation precautions in long-term care facilities for MDROs. Further, it offers the most comprehensive descriptions of both isolation precautions use and predictors of MDRO infection in nursing homes (NHs), a specific type of long-term care residential setting. To assist the reader, Chapter 1 will provide background for these studies including context for current infection control and prevention practices in long-term care facilities, the importance of MDRO infections and the need for new evidence regarding isolation precautions in long-term care. It will also discuss the aims and significance of this dissertation in context of a conceptual framework, gaps in the literature and potential to improve clinical practice. Next, Chapters 2 and 3 of this dissertation systematically review the current evidence regarding effectiveness of isolation precautions against MDROs and the cost of infection prevention and control in this setting, respectively. These chapters outline how publications focused on long-term care are lacking in quality and quantity and offer suggestions for improvement in future research. Chapter 4 qualitatively describes decision-making process regarding use of isolation-based infection prevention techniques in NHs, which depends on four key considerations: perceived risk of transmission, conflict with quality of life goals, resource availability and lack of understanding. Chapter 5 builds on this qualitative analysis by quantitatively examining predictors of isolation precautions use for MDRO infection in a large, national dataset. This analysis confirms that isolation is rarely used and there is variation across NHs’ practice. However, NH staff may be tailoring infection prevention and control practice to the needs of specific residents, as would be expected based on the results of the qualitative analysis. Chapter 6 presents an analysis of MDRO infection predictors among elderly NH residents across the U.S. This study confirms concepts associated with MDRO infection in previous studies (e.g., low functionality) and provides more specificity in operationalization of these concepts than has been previously determined (e.g., needing support with locomotion), which can inform future use of isolation precautions in NHs. Finally, Chapter 7 contains a synthesis and discussion of these findings, as well as recommendations for health policy and future research regarding contact isolation precautions against MDROs in NHs.

Li Lok Yee Mandy. / "June 2004." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (p. 155-165). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

No description available.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2005. / Härtill 5 uppsatser.

Diss. Linköping : Linköpings universitet, 2007.

MSc (Microbiology) / Department of Microbiology

No description available.

Antiviral drug resistance is a major problem in the treatment of viral infections, including influenza and hepatitis C virus (HCV). Influenza neuraminidase (NA) is a viral sialidase on the surface of the influenza virion and a primary antiviral target in influenza. Two subtypes of NA predominate in humans, N1 and N2, but different patterns of drug resistance have emerged in each subtype. To provide a framework for understanding the structural basis of subtype specific drug resistance mutations in NA, we used molecular dynamics simulations to define dynamic substrate envelopes for NA to determine how different patterns of drug resistance have emerged in N1 and N2 NA. Furthermore, we used the substrate envelope to analyze HCV NS3/4A protease inhibitors in clinical development. In addition, influenza hemagglutinin (HA) is a primary target of neutralizing antibodies against influenza. Novel broadly neutralizing antibodies (BnAbs) against the stem region of HA have been described and inhibit several influenza viral subtypes, but antibody neutralization escape mutations have emerged. We identified potential escape mutations in broadly neutralizing antibody F10 that may impact protein dynamics in HA that are critical for function. We also solved crystal structures of antibody fragments that are important for understanding the structural basis of antibody binding for influenza BnAbs. These studies can inform the design of improved therapeutic strategies against viruses by incorporating an understanding of structural elements that are critical for function, such as substrate processing and protein dynamics, into the development of novel therapeutics that are robust against resistance.

Viral proteases have been shown to be effective targets of anti-viral therapies for human immunodeficiency virus (HIV) and hepatitis C virus (HCV). However, under the pressure of therapy including protease inhibitors, the virus evolves to select drug resistance mutations both in the protease and substrates. In my thesis study, I aimed to understand the mechanisms of how this protease−substrate co-evolution contributes to drug resistance. Currently, there are no approved drugs against dengue virus (DENV); I investigated substrate recognition by DENV protease and designed cyclic peptides as inhibitors targeting the prime site of dengue protease. First, I used X-ray crystallography and subsequent structural analysis to investigate the molecular basis of HIV-1 protease and p1-p6 substrate coevolution. I found that co-evolved p1-p6 substrates rescue the HIV-1 I50V protease’s binding activity by forming more van der Waals contacts and hydrogen bonds, and that co-evolution restores the dynamics at the active site for all three mutant substrates. Next, I used aprotinin as a platform to investigate DENV protease–substrate recognizing pattern, which revealed that the prime side residues significantly modulate substrate affinity to protease and the optimal interactions at each residue position. Based on these results, I designed cyclic peptide inhibitors that target the prime site pocket of DENV protease. Through optimizing the length and sequence, the best inhibitor achieved a 2.9 micromolar Ki value against DENV3 protease. Since dengue protease does not share substrate sequence with human serine proteases, these cyclic peptides can be used as scaffolds for inhibitor design with higher specificity.

Inhibiting BCR-ABL kinase activity with tyrosine kinase inhibitors (TKIs) has been the frontline therapy for CML. Resistance to TKIs frequently occurs, but the mechanisms remain elusive. First, to uncover survival pathways involved in TKI resistance in CML, I conducted a genome-wide RNAi screen in human CML cells to identify genes governing cellular sensitivity to the first generation TKI called IM (Gleevec). I identified genes converging on and activating the MEK/ERK pathway through transcriptional up-regulation of PRKCH. Combining IM with a MEK inhibitor synergistically kills TKI-resistant CML cells and CML stem cells. Next, I performed single cell RNA-seq to compare expression profiles of CML stem cells and hematopoietic stem cells isolated from the same patient. Among the genes that are preferentially expressed in CML stem cells is PIM2, which encodes a pro-survival serine-threonine kinase that phosphorylates and inhibits the pro-apoptotic protein BAD. Inhibiting PIM2 function sensitizes CML stem cells to IM-induced apoptosis and prevents disease relapse in a CML mouse model. Last, I devised a CRISPR-Cas9 based strategy to perform insertional mutagenesis at a defined genomic location in murine hematopoietic Ba/F3 cells. As proof of principle, we showed its capability to perform unbiased, saturated point mutagenesis in a 9 amino acid region of BCR-ABL encompassing the socalled “gatekeeper” residue, an important determinant of TKI binding. We found that the ranking order of mutations from the screen correlated well with their prevalence in IM-resistant CML patients. Overall, my findings reveal novel resistance mechanisms in CML and provide alternative therapeutic strategies.