Pseudomonas Aeruginosa AmpR Transcriptional Regulatory Network

In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated using DNA microarrays and RNA-Seq of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion mutant, PAO∆ampR were analyzed. Transcriptome analysis demonstrates that the AmpR regulon is much more extensive than previously thought influencing the differential expression of over 500 genes. In addition to regulating resistance to β-lactam antibiotics via AmpC, AmpR also regulates non-β-lactam antibiotic resistance by modulating the MexEF-OprN efflux pump. Virulence mechanisms including biofilm formation, QS-regulated acute virulence, and diverse physiological processes such as oxidative stress response, heat-shock response and iron uptake are AmpR-regulated. Real-time PCR and phenotypic assays confirmed the transcriptome data. Further, Caenorhabditis elegans model demonstrates that a functional AmpR is required for full pathogenicity of P. aeruginosa. AmpR, a member of the core genome, also regulates genes in the regions of genome plasticity that are acquired by horizontal gene transfer. The extensive AmpR regulon included other transcriptional regulators and sigma factors, accounting for the extensive AmpR regulon. Gene expression studies demonstrate AmpR-dependent expression of the QS master regulator LasR that controls expression of many virulence factors. Using a chromosomally tagged AmpR, ChIP-Seq studies show direct AmpR binding to the lasR promoter. The data demonstrates that AmpR functions as a global regulator in P. aeruginosa and is a positive regulator of acute virulence while negatively regulating chronic infection phenotypes. In summary, my dissertation sheds light on the complex regulatory circuit in P. aeruginosa to provide a better understanding of the bacterial response to antibiotics and how the organism coordinately regulates a myriad of virulence factors.

An Analytical Workflow for Metagenomic Data and its Application to the Study of Chronic Obstructive Pulmonary Disease (COPD)

Metagenomics is the culture-independent study of genetic material obtained directly from environmental samples. It has become a realistic approach to understanding microbial communities thanks to advances in high-throughput DNA sequencing technologies over the past decade. Current research has shown that different sites of the human body house varied bacterial communities. There is a strong correlation between an individual’s microbial community profile at a given site and disease. Metagenomics is being applied more often as a means of comparing microbial profiles in biomedical studies. The analysis of the data collected using metagenomics can be quite challenging and there exist a plethora of tools for interpreting the results. An automatic analytical workflow for metagenomic analyses has been implemented and tested using synthetic datasets of varying quality. It is able to accurately classify bacteria by taxa and correctly estimate the richness and diversity of each set. The workflow was then applied to the study of the airways microbiome in Chronic Obstructive Pulmonary Disease (COPD). COPD is a progressive lung disease resulting in narrowing of the airways and restricted airflow. Despite being the third leading cause of death in the United States, little is known about the differences in the lung microbial community profiles of healthy individuals and COPD patients. Bronchoalveolar lavage (BAL) samples were collected from COPD patients, active or ex-smokers, and never smokers and sequenced by 454 pyrosequencing. A total of 56 individuals were recruited for the study. Substantial colonization of the lungs was found in all subjects and differentially abundant genera in each group were identified. These discoveries are promising and may further our understanding of how the structure of the lung microbiome is modified as COPD progresses. It is also anticipated that the results will eventually lead to improved treatments for COPD.

The effects of advanced practice nurses (APNs) as intensivists in a surgical intensive care unit (SICU) on patient outcomes, healthcare charges, and apn intensivist services in the SICU

Intensive Care Units (ICUs) account for over 10 percent of all US hospital beds, have over 4.4 million patient admissions yearly, approximately 360,000 deaths, and account for close to 30% of acute care hospital costs. The need for critical care services has increased due to an aging population and medical advances that extend life. The result is efforts to improve patient outcomes, optimize financial performance, and implement models of ICU care that enhance quality of care and reduce health care costs. This retrospective chart review study examined the dose effect of APN Intensivists in a surgical intensive care unit (SICU) on differences in patient outcomes, healthcare charges, SICU length of stay, charges for APN intensivist services, and frequency of APNs special initiatives when the SICU was staffed by differing levels of APN Intensivist staffing over four time periods (T1-T4) between 2009 and 2011. The sample consisted of 816 randomly selected (204 per T1-T4) patient chart data. Study findings indicated reported ventilator associated pneumonia (VAP) rates, ventilator days, catheter days and catheter associated urinary tract infection (CAUTI) rates increased at T4 (when there was the lowest number of APN Intensivists), and there was increased pressure ulcer incidence in first two quarters of T4. There was no statistically significant difference in post-surgical glycemic control (M = 142.84, SD = 40.00), t (223) = 1.40, p = .17, and no statistically significant difference in the SICU length of stay among the time-periods (M = 3.27, SD = 3.32), t (202) = 1.02, p = .31. Charges for APN services increased over the 4 time periods from $11,268 at T1 to $51,727 at T4 when a system to capture APN billing was put into place. The number of new APN initiatives declined in T4 as the number of APN Intensivists declined. Study results suggest a dose effect of APN Intensivists on important patient health outcomes and on the number of APNs initiatives to prevent health complications in the SICU. ^

The Effects of Advanced Practice Nurses (APNs) as Intensivists in a Surgical Intensive Care Unit (SICU) on Patient Outcomes, Healthcare Charges, and APN Intensivist Services in the SICU

Intensive Care Units (ICUs) account for over 10 percent of all US hospital beds, have over 4.4 million patient admissions yearly, approximately 360,000 deaths, and account for close to 30% of acute care hospital costs. The need for critical care services has increased due to an aging population and medical advances that extend life. The result is efforts to improve patient outcomes, optimize financial performance, and implement models of ICU care that enhance quality of care and reduce health care costs. This retrospective chart review study examined the dose effect of APN Intensivists in a surgical intensive care unit (SICU) on differences in patient outcomes, healthcare charges, SICU length of stay, charges for APN intensivist services, and frequency of APNs special initiatives when the SICU was staffed by differing levels of APN Intensivist staffing over four time periods (T1-T4) between 2009 and 2011. The sample consisted of 816 randomly selected (204 per T1-T4) patient chart data. Study findings indicated reported ventilator associated pneumonia (VAP) rates, ventilator days, catheter days and catheter associated urinary tract infection (CAUTI) rates increased at T4 (when there was the lowest number of APN Intensivists), and there was increased pressure ulcer incidence in first two quarters of T4. There was no statistically significant difference in post-surgical glycemic control (M = 142.84, SD= 40.00), t (223) = 1.40, p = .17, and no statistically significant difference in the SICU length of stay among the time-periods (M= 3.27, SD = 3.32), t (202) = 1.02, p= .31. Charges for APN services increased over the 4 time periods from $11,268 at T1 to $51,727 at T4 when a system to capture APN billing was put into place. The number of new APN initiatives declined in T4 as the number of APN Intensivists declined. Study results suggest a dose effect of APN Intensivists on important patient health outcomes and on the number of APNs initiatives to prevent health complications in the SICU.