Preventing healthcare-associated infections (HAI) is a national priority. The Centers for Disease Control and Prevention estimates that one of every 25 hospitalized patients contract a HAI while receiving care. In 2009, the annual cost for HAIs in United States’ hospitals was estimated to be $40 billion, and there were 99,000 HAI-associated deaths. In nursing homes (NH), the situation is more dire; among the 4 million NH residents each year, there are 1-2.6 million serious infections and 1 out of every 3 NH residents is colonized with a multi-drug resistant organism. In addition to the frequent infections, over prescription of antibiotics in NH is significant, and frequently inappropriate. NH residents with HAIs are subjected to burdensome treatments and diagnostic procedures, leading to more complications in an already vulnerable population in which quality of life not life prolongation is often the treatment goal. Policy levers are actions designed to realize health objectives that can be taken by either public or private entities, and by individuals or groups. Health policy levers are deployed at all levels including federal, state, regional, and local levels. Vaccinations, such as polio, are one of the great success stories of how policy levers can prevent infections. However, undermined and eroded policy levers can have negative public health consequences, such as seen with the 2018-2019 rash of measles outbreaks. There is much work left to be done improving quality related to infections across all care settings. For this dissertation, I utilized the three-paper format and conducted studies examining the effectiveness of health policy levers used to improve healthcare quality and prevent infections across care settings. These studies were: 1) a systematic review of the published evidence on state mandatory reporting of HAI in hospitals; 2) an environmental scan cataloging state supported initiatives in NH infection prevention, and; 3) a quantitative analysis on the effect of new federal NH regulations on NH quality and patient outcomes. In the systematic review, I found that mandatory reporting was associated with reduced central line associate bloodstream infection rates. The environmental scan demonstrated that wide variation existed between states’ initiatives to support infection prevention in NH. In the quantitative analysis, I found that new federal regulations were significantly associated in improved NH quality in UTI rates and vaccination rates for influenza and pneumonia infections. Based on these results, clinical providers, administrators, policy makers and researchers can use health policy levers to reduce infections and improve quality.

Healthcare-associated infections (HAIs) are among the most common and significant patient safety issues posing great threats to public health. One in every 25 inpatients in the United States experiences a HAI. Because they have continuously been a major reason for increased morbidity and mortality in healthcare facilities, increased attention to understanding the spread of HAIs is an urgently needed. Therefore, the purpose of this dissertation, was to examine the risk factors for two of the most common HAIs (surgical site infection [SSI] and Clostridioides difficile infection [CDI]), using multiple methodological approaches. Chapter 1 provides an overview of HAIs, the risk factors identified from the previous literature, and the necessity of different methodological approaches to identify the risk of HAIs. Chapter 2 is an integrative review synthesizing the findings from seven published studies examining the association between the development of pocket hematoma and the risk of wound infection in individuals with cardiovascular implantable electronic devices. Chapter 3 is a summary of a retrospective cohort study using machine learning techniques—logistic regression, decision tree, and support vector machine approaches—to build predictive models of SSI among individuals with permanent pacemakers, followed by a comparison of the predictive abilities of the three algorithms. Chapter 4 describes a retrospective matched case-control study to examine (1) temporal changes in the incidence of community or hospital-acquired CDI, (2) the risk factors for hospital-acquired CDI including individual-host factors and pharmacological-related factors, and (3) temporal changes in the risk factors for hospital-acquired CDI. Lastly, Chapter 5 summarizes and synthesizes the findings of the studies included in this dissertation, the strengths and limitations of the studies, implications for public health and clinical practice, advanced studies on methodology, and future research. In conclusion, this dissertation adds comprehensive knowledge regarding the associations between risk factors and HAIs by identifying reliable risk factors measured in various ways and applying various methodological approaches.

Health care-associated and hospital-acquired infections are two entities associated with increased morbidity and mortality. They are highly costly and constitute a great burden to the health care system. Vitamin D deficiency (< 20 ng/ml) is prevalent and may be a key contributor to both acute and chronic ill health. Vitamin D deficiency is associated with decreased innate immunity and increased risk for infections. Vitamin D can positively influence a wide variety of microbial infections. Herein we discuss hospital-acquired infections, such as pneumonia, bacteremias, urinary tract and surgical site infections, and the potential role vitamin D may play in ameliorating them. We also discuss how vitamin D might positively influence these infections and help contain health care costs. Pending further studies, we think it is prudent to check vitamin D status at hospital admission and to take immediate steps to address existing insufficient 25-hydroxyvitamin D levels.

The first chapter of this thesis is centered around a simple problem: to do or not to do something. As in life, every decision has an unknown outcome and planning agents try to balance the trade offs of such decision based on some relevant information. After processing the relevant information a decision is reached. In this chapter, the problem is formalized and parameterized in two frameworks: In the first framework discrete decision models known as decision trees are studied, where we design an optimization algorithm to solve the misclassification cost problem in this family of representations; The second framework studies continuously differentiable models (such as logistic regression and Deep Neural Networks) where we propose a two-step optimization procedure of the misclassification cost problem, as well as characterizing the statistical estimation problem relative to the sample size used for training. We illustrate the methodology by developing a computerized scheme to administer (or not) a preventive intervention to patients arriving to the hospital with the objective of minimizing their risk of acquiring a Hospital Acquired Infection (HAI). The second chapter expands on the idea of the first one to a sequential setting. The problem is framed as a Markov Decision Process algorithm using a state aggregation strategy based on Decision Trees. These incremental state aggregations are solved using a Linear Programming (LP) approach to obtain a compact policy that converges to the optimal one asymptotically, as well as showing that the computational complexity of our algorithm depends on the tree structure of the optimal policy rather than the cardinality of the state space. We illustrate the advantages of our approach using the widely known cartpole balancing environment against a Deep Neural Network based approach showing that with a similar computational complexity our algorithm performs better in certain instances of MDP. In the last two chapters we deal with modeling Emergency Medical Service (EMS) optimization such that the demand for medical services is met with the best possible supply allocation in the face of uncertainty of the demand in space and time. In the third chapter we develop a short-term prediction model for call volume at a 911 call center. The rationale of the model is to use the recent call volume to update a historically calibrated model of the call volume that in periods when the call volume distribution drastically changes, can be arbitrarily distant from its expected value. The model is casted as a linear correction of the historical estimation, calculating both the mean and variance of the correction. We justify the formulation using a regime switching doubly stochastic process framework to illustrate the type of distribution changes our model captures. We also propose a staffing model to preemptively staff a call center using our volume prediction as input for the call center demand such that the waiting times of the customers are minimized. This formulation can be casted as a Second Order Cone Program (SOCP) or a Linear Program (LP) with integrality constraints. We illustrate the methodology to predict the call volume during the Covid-19 pandemic to a 911 call center in New York City. In the fourth chapter we modify a well known set covering formulation to perform ambulance scheduling such that the supply of ambulances matches the demand in space and time. We enhance this model using a high resolution simulation model to correct an unknown steady-state service rate of the system (dependent on many exogenous and endogenous factors such as the ambulance dispatch policy and time-varying traffic patterns) as a constraint in the scheduling formulation. We show that this formulation effectively makes the system faster by maximizing the minimum slack between supply and demand during a 24-hour period. We present an algorithm to iteratively solve the scheduling formulation while correcting the implied location and time dependent service rate of the ambulance system using the simulation generated ambulance waiting times of patients in the city. We illustrate our algorithm to schedule municipally managed ambulances in New York City as a case study.

Les infections nosocomiales sont causées par des germes opportunistes souvent résistants aux antibiotiques et persistants sur les surfaces, représentant une source constante de risque d’infection en milieu hospitalier. Dans ce contexte, l’isolement et la caractérisation de bactériophages s’attaquant spécifiquement aux bactéries nosocomiales telles que Staphylococcus aureus résistant (SARM), Enterococcus résistant (ERV), Pseudomonas aeruginosa et Acinetobacter baumanii, pourraient fournir une alternative bactéricide naturelle contre la transmission de ces infections. Des phages isolés des eaux usées, ont été sélectionnés selon leur capacité d’amplification, leur profil génomique et leur potentiel lytique envers différentes souches bactériennes cliniques. Les meilleurs ont été caractérisés en détail pour s’assurer de leur spécificité, sécurité, stabilité et efficacité préalablement à leur utilisation in vivo. Sept phages contre SARM et trois contre Acinetobacter baumanii ont été caractérisés. Quatre phages SARM s’avèrent être de bons candidats potentiels et pourraient être testés en milieu hospitalier comme agents désinfectants dans le but de lutter contre les infections nosocomiales. / Nosocomial infections are directly related to opportunistic germs, which are often resistant to antibiotics and persistent on surfaces, representing a high infectious risk in hospitals. In this context, the isolation and characterization of bacteriophages specifically targeting nosocomial bacteria such as resistant Staphylococcus aureus (MRSA), resistant Enterococcus (VRE), Pseudomonas aeruginosa and Acinetobacter baumanii, could provide a natural bactericidal alternative against the transmission of these infections. Phages, isolated from waste water, were selected according to their capacity of amplification, their genomic profile and lytic potential towards various bacterial clinical strains. The best ones were characterized in detail to primarily ensure their specificity, safety, stability and effectiveness, before studying their in vivo usage. Seven phages against MRSA and three against Acinetobacter baumanii were characterized. Four MRSA phages proved to be good potential candidates and could be tested in hospitals as disinfectant agents with the aim of fighting nosocomial infections.

This thesis examines in detail the nature of postoperative infectious complications in patients who underwent brain tumor surgery. It deals with the incidence of these complications and their severity, depending on various factors and suggests the most appropriate nursing procedures used in the care of a patient in whom these complications occurred. For the structure of the work is divided into two parts - theoretical and empirical. The theoretical part deals with the issues examined in terms of the medical field Neurosurgery (closer diagnoses, conditions, operations and other procedures, and complications to occur after these operations or expected performance), analyzes a nursing practice and patient care on neurosurgical ICU, and finally closely examines infections and nosocomial diseases, including a description of the most common types, their agents, diagnosis and treatment. The second, empirical part focuses on the problems from a practical point of view. With the help of set of case studies it closer which specific complications are most commonly found on the neurosurgical ICU in patients after surgery of brain tumors, what are the most common methods of treatment and nursing procedures which are most used in the care of patients with these complications. In conclusion summarizes the...

O gênero Acinetobacter tem sido implicado em grande variedade de infecções hospitalares, principalmente em Unidades de Terapia Intensiva. O tratamento de infecções por Acinetobacter spp. é geralmente realizado com imipenem embora não haja ensaios clínicos randomizados que embasem esta recomendação. No caso de resistência a esta classe, situação cada vez mais freqüente, as opções mais estudadas são as polimixinas e ampicilinasulbactam. Diante da escassez de dados sobre o assunto, estudos que avaliem o tratamento de infecções por Acinetobacter spp resistente a carbapenem são necessários. Realizou-se um estudo de coorte retrospectivo de pacientes com infecção causada por Acinetobacter spp. resistente a carbapenem, internados no Instituto Central do Hospital das Clínicas (HC-FMUSP) e no Hospital do Servidor Público Estadual (HSPE) no período de 1996 a 2004. Foram considerados como casos os pacientes com diagnóstico de infecção hospitalar baseado em critérios estabelecido pelo Centers for Disease Control and Prevention (CDC) somado ao isolamento de Acinetobacter spp. resistente a carbapenem obtidos de materiais estéreis ou lavado bronco-alveolar.Não foram incluídos casos de infecção do trato urinário. Foi realizada a análise dos prontuários dos pacientes e foram coletadas informações clínico-demográficas, tratamento utilizado, sinais, sintomas e exames auxiliares no diagnóstico da infecção e no decorrer do tratamento. Foram avaliados três desfechos: mortalidade até o final do tratamento, mortalidade até o final da internação e evolução clínica. Oitenta e dois pacientes (30%) receberam polimixina B ou E, oitenta e cinco (31%) foram tratados com ampicilina-sulbactam, 99 (36%) não receberam tratamento específico. As características clínico-demográficas dos grupos foram semelhantes. A mortalidade durante a internação foi de 78% e boa resposta clínica foi observada em 50% dos pacientes tratados. Na análise multivariada de fatores associados à má evolução clínica, início do tratamento após 72 horas do isolamento e piora da função renal durante o tratamento foram estatisticamente significativos. Pontuação de Apache II >= 15, início do tratamento após 72 horas do isolamento; piora da função renal durante o tratamento; presença de choque séptico e uso de polimixina foram variáveis associadas com óbito até o final do tratamento. As variáveis independentemente associadas com óbito durante a internação foram: idade >= 58 anos, presença de choque séptico no dia do início do tratamento e pontuação de Apache II >=15. Concluiu-se que para o tratamento de infecções causadas por Acinetobacter spp. resistente a carbapenem, ampicilinasulbactam foi superior a polimixinas considerando mortalidade durante o tratamento. / Acinetobacter spp. is a cause of a number of infections, mainly in the ICU setting. Antimicrobials drugs frequently reported as active against Acinetobacter spp include carbapenems, colistin, ampicillin/sulbactam, amikacin, rifampin and tetracyclines and currently carbapenens are considered the main antimicrobial treatment. Unfortunately, over the past years there has been a worldwide increase in infections caused by carbapenem-resistant Acinetobacter. This poses a therapeutic challenge as few treatment options are avaible. We performed a retrospective review of the case records of patients from 1996 to 2004 who had nosocomial infections caused by carbapenem-resistant Acinetobacter spp. from 2 large teaching hospitals. Diagnosis of infection was based on CDC criteria plus the isolation of Acinetobacter from a usually sterile site or from broncoalvelolar lavage. Urinary tract infections were not included. We collected data on demographic and clinical features, treatment, signs and symptoms from medical records. We evaluate 3 outcomes: mortality until the end of treatment, in-hospital mortality and clinical outcome. Eighty two patients received polymyxins (30%), 85 were treated with ampicilin-sulbactam (31%) and 99 (36%) did not receive any of these antibiotics. The demographic and clinical characteristics of the groups were similar. Multivariate analysis showed that treatment with polymyxins, Apache II score >= 15; septic shock; treatment delay and renal failure were independent predictors of mortality. On multivariate analysis, age >= 58 years, presence of septic shock and Apache II score >=15 were prognosis factors for mortality during hospitalization. Multiple logistic regression analysis revealed that Apache II >=15 and renal failure during treatment were associated with treatment failure. In conclusion, ampicillin-sulbactam was superior to polymyxin considering mortality during treatment.

by Chan Ping Lung. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 108-118). / Abstracts in English and Chinese. / Abstract (in Chinese) --- p.ii / Abstract (in English) --- p.iv / Acknowledgements --- p.vii / Table of Contents --- p.viii / List of Tables --- p.xiii / List of Figures --- p.xiv / List of Appendices --- p.xv / List of Abbreviations --- p.xvi / Chapter Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Epidemiology of catheter associated infections --- p.1 / Chapter 1.1.1 --- Catheter associated infections --- p.1 / Chapter 1.1.2 --- Risk and mortality of CAI --- p.2 / Chapter 1.1.3 --- Etiology of CAI --- p.3 / Chapter 1.1.3.1 --- Venous catheters --- p.4 / Chapter 1.1.3.2 --- Urinary catheters --- p.4 / Chapter 1.2 --- Pathogenesis of CAI --- p.5 / Chapter 1.2.1 --- Central venous catheters (CVC) --- p.6 / Chapter 1.2.2 --- Urinary catheters --- p.7 / Chapter 1.3 --- Adhesion mechanisms --- p.7 / Chapter 1.3.1 --- Definition of adhesion --- p.7 / Chapter 1.3.2 --- Adhesion mechanism --- p.8 / Chapter 1.3.2.1 --- The phase one --- p.8 / Chapter 1.3.2.2 --- The phase two --- p.10 / Chapter 1.4 --- Catheters --- p.10 / Chapter 1.5 --- Biology of Candida albicans --- p.11 / Chapter 1.5.1 --- Taxonomy of Candida albicans --- p.11 / Chapter 1.5.2 --- Morphology --- p.12 / Chapter 1.5.3 --- Genome --- p.13 / Chapter 1.5.4 --- Biology of Candida albicans cell wall --- p.14 / Chapter 1.5.4.1 --- Constituting molecules of Candida albicans cell wall --- p.14 / Chapter 1.5.4.2 --- Organization of Candida albicans cell wall --- p.15 / Chapter 1.6 --- Agglutinin like sequence gene family --- p.16 / Chapter 1.6.1 --- Gene structure of agglutinin like sequence genes --- p.16 / Chapter 1.6.2 --- Sequence similarity --- p.17 / Chapter 1.6.3 --- Sequence variability --- p.18 / Chapter 1.6.4 --- Expression of ALS genes --- p.19 / Chapter 1.6.5 --- The Als proteins --- p.20 / Chapter 1.6.6 --- Functions of Als proteins --- p.21 / Chapter 1.7 --- Adhesion assay --- p.23 / Chapter 1.7.1 --- Adhesion model --- p.24 / Chapter 1.7.2 --- Factors affecting static adhesion model --- p.25 / Chapter 1.7.3 --- Quantitation methods of adherent cells --- p.27 / Chapter 1.7.3.1 --- Sonication --- p.27 / Chapter 1.7.3.2 --- Staining methods --- p.28 / Chapter 1.7.3.3 --- ATP bioluminescence --- p.28 / Chapter 1.8 --- Research model --- p.29 / Chapter Chapter 2 --- Aim of study --- p.31 / Chapter Chapter 3 --- Materials and Methods --- p.32 / Chapter 3.1 --- Preparation of bacteriological reagents --- p.32 / Chapter 3.2 --- Confirmation of identity of Candida albicans and of Saccharomyces cerevisiae --- p.33 / Chapter 3.3 --- Cell culture of fibroblasts --- p.36 / Chapter 3.3.1 --- Preparation of cell culture reagents --- p.36 / Chapter 3.3.2 --- Recovery of freezing fibroblasts --- p.37 / Chapter 3.3.3 --- Establishment of cell line --- p.37 / Chapter 3.4 --- Preliminary study of adherence of Candida albicans to fibroblasts and to catheters --- p.38 / Chapter 3.4.1 --- Adherence to fibroblasts --- p.38 / Chapter 3.4.1.1 --- Preparation of fibroblasts --- p.38 / Chapter 3.4.1.2 --- Preparation of culture of Candida albicans and of Saccharomyces cerevisiae --- p.39 / Chapter 3.4.1.3 --- Adhesion assay --- p.41 / Chapter 3.4.2 --- Adherence to catheters --- p.42 / Chapter 3.4.2.1 --- Preparation of catheters --- p.42 / Chapter 3.4.2.2 --- Adhesion assay --- p.42 / Chapter 3.5 --- "Confirmation of expression of ALS1, ALS5 smaller allele, and ALS6 of Candida albicans in YPD broth" --- p.44 / Chapter 3.5.1 --- RNA extraction of Candida albicans --- p.45 / Chapter 3.5.2 --- "RT-PCR of ALS1, ALS5 smaller allele, and ALS6" --- p.46 / Chapter 3.5.2.1 --- Primers --- p.46 / Chapter 3.5.2.2 --- RT-PCR --- p.47 / Chapter 3.6 --- Establishment of quantitation system of adhesion assay --- p.49 / Chapter 3.6.1 --- Absorbance measurement of Candida albicans stained with safranin --- p.49 / Chapter 3.6.1.1 --- Preparation of Candida albicans culture --- p.49 / Chapter 3.6.1.2 --- Staining of Candida albicans --- p.50 / Chapter 3.6.1.3 --- Viable count of Candida albicans adhered on the 6-well plate --- p.51 / Chapter 3.6.2 --- ATP bioluminescence --- p.52 / Chapter 3.7 --- Effect of inoculum size on adhesion to catheters --- p.53 / Chapter 3.7.1 --- Preparation of adhesion chambers --- p.53 / Chapter 3.7.2 --- Preparation of catheters --- p.54 / Chapter 3.7.3 --- Preparation of Candida albicans culture --- p.54 / Chapter 3.7.4 --- Adhesion assay --- p.55 / Chapter 3.8 --- "Transformation of Saccharomyces cerevisiae with ALS1, ALS5 smaller allele, and ALS6" --- p.57 / Chapter 3.8.1 --- DNA extraction of Candida albicans --- p.58 / Chapter 3.8.2 --- "PCR of ALS1, ALS5 smaller allele, and ALS6" --- p.59 / Chapter 3.8.3 --- Gel extraction --- p.60 / Chapter 3.8.4 --- Restriction digestion of PCR products of ALS genes and cloning plasmids --- p.61 / Chapter 3.8.5 --- "Ligation of ALS1, ALS5 smaller allele, ALS6 with pYES6CT cloning plasmids" --- p.62 / Chapter 3.8.6 --- Transformation of ligated plasmid into Escherichia coli --- p.63 / Chapter 3.8.7 --- Miniprep of plasmids --- p.64 / Chapter 3.8.8 --- DNA sequencing --- p.65 / Chapter 3.8.9 --- Transformation of Saccharomyces cerevisiae --- p.66 / Chapter 3.8.10 --- "Detection of Alsl，Als5, and Als6 protiens expression" --- p.68 / Chapter 3.8.10.1 --- Preparation of cultures in SC synthetic medium --- p.68 / Chapter 3.8.10.2 --- Protein extraction --- p.69 / Chapter 3.8.10.3 --- Dot blot of cell wall lysates --- p.69 / Chapter 3.9 --- Adhesion of transformed Saccharomyces cerevisiae to fibroblasts --- p.71 / Chapter 3.9.1 --- Preparation of fibroblasts and of Saccharomyces cerevisiae cultures --- p.71 / Chapter 3.9.2 --- Adhesion assay --- p.72 / Chapter 3.10 --- "Adhesion of transformed Saccharomyces cerevisiae to FEP, polyurethane, and silicone catheters" --- p.72 / Chapter 3.10.1 --- "Preparation of catheters, adhesion chambers and transformed Saccharomyces cerevisiae cultures" --- p.73 / Chapter 3.10.2 --- Adhesion to catheter fragments --- p.73 / Chapter 3.11 --- Statistical analysis --- p.74 / Chapter Chapter 4 --- Results --- p.75 / Chapter 4.1 --- Confirmation of identity of Candida albicans and of Saccharomyces cerevisiae --- p.75 / Chapter 4.1.1 --- Candida albicans --- p.75 / Chapter 4.1.2 --- Saccharomyces cerevisiae --- p.75 / Chapter 4.2 --- Cell culture of fibroblasts --- p.76 / Chapter 4.3 --- "Preliminary studies of adherence of Candida albicans to fibroblasts and to FEP, polyurethane, and silicone catheters" --- p.76 / Chapter 4.3.1 --- Adherence to fibroblasts --- p.76 / Chapter 4.3.2 --- Adherence to catheters --- p.77 / Chapter 4.4 --- "Confirmation of expression of ALSl, ALS5 smaller allele, and ALS6 of Candida albicans in YPD broth" --- p.78 / Chapter 4.5 --- Establishment of quantitation system of adhesion assay --- p.79 / Chapter 4.5.1 --- Absorbance measurement of Candida albicans stained with safranin --- p.79 / Chapter 4.5.2 --- ATP bioluminescence --- p.79 / Chapter 4.6 --- Effect of inoculum size on adhesion to catheters --- p.80 / Chapter 4.7 --- "Transformation of Saccharomyces cerevisiae with ALS1, ALS5 smaller allele, and ALS6" --- p.81 / Chapter 4.7.1 --- "PCR of ALSl, ALS5 smaller allele, and ALS6" --- p.81 / Chapter 4.7.2 --- Ligation of PCR products with pYES6CT plasmids --- p.82 / Chapter 4.7.3 --- "DNA sequencing results of ALS1, ALS5 smaller allele, and ALS6 ligated plasmids" --- p.83 / Chapter 4.7.4 --- "Detection of Alsl, Als5, and Als6 proteins expression" --- p.84 / Chapter 4.8 --- Adhesion of transformed Saccharomyces cerevisiae to fibroblasts --- p.84 / Chapter 4.9 --- "Adhesion of transformed Saccharomyces cerevisiae to FEP, polyurethane and silicone catheters" --- p.85 / Chapter Chapter 5 --- Discussion --- p.89 / Chapter 5.1 --- Limitations of static adhesion assay model --- p.89 / Chapter 5.2 --- Quantitation System --- p.90 / Chapter 5.2.1 --- Staining method --- p.90 / Chapter 5.2.2 --- ATP bioluminescence assay --- p.91 / Chapter 5.3 --- "Preliminary studies of adherence of Candida albicans to fibroblasts and to FEP, polyurethane, and silicone catheters" --- p.93 / Chapter 5.4 --- Effect of inoculum size on adhesion to catheters --- p.94 / Chapter 5.5 --- Selection of ALS genes --- p.96 / Chapter 5.6 --- Adhesion assay of transformed Saccharomyces cerevisiae to fibroblasts --- p.97 / Chapter 5.7 --- Adhesion assay of transformed Saccharomyces cerevisiae to catheters --- p.99 / Chapter 5.8 --- Alternative research model --- p.101 / Chapter 5.9 --- Implications and future work --- p.102 / Chapter Chapter 6 --- Conclusion --- p.107 / References --- p.108 / Tables --- p.119 / Figures --- p.123 / Appendices --- p.136

Thesis (MSc (Biomedical Technology))--Cape Peninsula University of Technology, 2017. / Background: It is well established that Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogenic organism that has been frequently identified as the cause of nosocomial and community acquired infections. Furthermore, studies have shown that over the last few decades strains of the genus Klebsiella have systematically developed resistance to numerous antibiotics. Aims and Methods: The primary aim of this study was to investigate the prevalence of K. pneumoniae in nosocomial and community isolates in the Western Cape province of South Africa. Various identification techniques such as the polymerase chain reaction (PCR) using the API 20 E, the VITEK®2 system, primers specific for the 16S-23S rDNA ITS region and the Matrix-assisted laser desorption/ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) were compared for the identification of this pathogen. The VITEK 2 system was used to detect antibiotic resistant profiles of the K. pneumoniae isolates and to identify the extended spectrum beta-lactamase (ESBL) phenotypic among these isolates. The PCR was used to detect Beta-lactam genes viz. CTX-M (blaCTX-M), TEM (blaTEM) and SHV (blaSHV) respectively in both the genome and plasmid DNA of K. pneumoniae using gene specific primers. Results: In total 57 agar plate bacterial cultures or glycerol stock bacterial cultures were obtained during 2011. Of the 57 isolates, the API 20 E test identified 47 (82.5%) of the isolates (n = 57) as K. pneumoniae while 10 isolates (17.5%) were identified as Raoultella species. The VITEK 2 method and PCR identified all 57 isolates as K. pneumoniae (100%). Of the isolates, 82.5% (47/57) were positively identified as Klebsiella species, 14% (8/57) were identified as Klebsiella variicola and 3.5% (2/57) were shown as no reliable identification (NRI) when using the MALDI-TOF MS. Examination of the 57 isolates using primers specific for the CTX-M (blaCTX-M), TEM (blaTEM) and SHV (blaSHV) respectively showed the following: PCR amplicons for the TEM gene were produced successfully for 46 (81%) of the 57 isolates included in this project, while 11 (19%) of the samples did not yield any TEM amplicons; PCR amplicons for the blaSHV gene were obtained successfully for 56 (98%) of the 57 DNA samples, while 1 sample (2%) did not yield any SHV amplicons; and PCR amplicons for the blaCTX-M gene were produced successfully by 89% (n = 51) of the DNA samples included in this project, while 11% (n = 6) did not yield any CTX-M amplicon. Extended-spectrum beta-lactamase phenotypes had been confirmed in 84% (n = 48) K. pneumoniae isolates while nine isolates were found to be non-ESBL. Resistance rates for these 48 isolates were high and showed resistance patterns of: Amoxicillin/Ampicillin, Amoxycillin/Clavulanate, Ceftriaxone/Cefotaxime, Cefuroxime/Cefprozil and Ceftazidime (100%, n = 48); Piperacillin/Tazobactam and Cefoxitin (98%, 47/48); Cefepime (96%, 46/48); Aztreonam (94%; 45/48); Tobramycin (81%, 39/48); Gentamycin and Ciprofloxacin (77%, 37/48); Trimethoprim/Sulfamethoxazole (67%, 32/48); and Tigecycline (25% 12/48). Conclusion: For the analysis by all four methods employed, a total agreement of 68.4% was obtained, indicating the positive identification of K. pneumoniae in 39 of the 57 samples analysed. An average agreement of 28.1% was then obtained for the comparison of results generated for three of the methods utilised, while a 3.5% average agreement was obtained for at least two methods. Furthermore, all four methods agreed that 82.5% of the isolates were Klebsiella species while three methods agreed that 17.5% of the isolates were Klebsiella species. Based on the results obtained in the current study, PCR and VITEK 2 were the methods of choice for the identification of K. pneumoniae. The current study also showed, that ESBL-K. pneumoniae strains are present in the Western Cape province, South Africa; with high resistance profiles to numerous antibiotics including the Cephalosporins.

Abstract not available