The management and outcomes of Staphylococcus aureus Bacteraemia at a South African referral hospital: A prospective observational study

Staphylococcus aureus is a major human pathogen found worldwide, causing a wide variety of clinical infections. This ranges from skin and soft tissue infections to lifethreatening invasive disease, such as S. aureus bacteraemia (SAB). Despite being a common cause of both community-acquired and hospital-acquired infections, limited evidence exists on the management and outcomes of Staphylococcus aureus bacteraemia (SAB) in resource-limited settings. The aim of this study was to describe a cohort of South African patients with SAB, and explore the factors associated with complicated infection and death. A prospective observational study was performed of patients over the age of 13 years admitted to a South African referral hospital with SAB. Data were analysed using Kaplan Meier survival models and linear regression models. One hundred consecutive SAB infection episodes in 98 patients were included. SAB was healthcare-associated in 68.4%, with 57.6% of these linked to drip site infection; 24.0% of all cases were caused by methicillin-resistant S. aureus (MRSA). Ninety-day mortality was 47.0%, with 83.3% of deaths attributable to SAB. Predictors of 90-day mortality were MRSA (odds ratio (OR) 1.28; 95% confidence interval (CI) 1.0 to 15.1) and the presence of co-morbidities (OR 4.1; 95% CI 1.0 to 21.6). The risk of complicated infection was higher with suboptimal antibiotic therapy (OR 8.5; 95% CI 1.8 to 52.4), female sex (OR 3.8; 95% CI 1.1 to 16.3) and community-acquired infection (OR 7.4; 95% CI 2.0 to 33.1). Definitive antibiotic therapy was suboptimal in 22.6% of all cases. Overall, SAB-related mortality was high. A large proportion of SAB episodes may be preventable, and there is a need for improved antibiotic management in this setting. Part A. The study protocol, as submitted for departmental and ethical approval, is presented here. It includes the background, rationale and methodology of the research done for this mini-dissertation. Part B. A structured literature review is presented of articles pertaining to SAB epidemiology and treatment, with the aim to place this research study in context and identify gaps in research. Part C. A journal-ready manuscript according to the requirements of the International Journal of Infectious Diseases. Appendix. All additional documentation necessary as addendums in the presentation of this mini-dissertation

HHS action plan to prevent healthcare-associated infections

"The Department of Health and Human Services (HHS) "Action Plan to Prevent Healthcare-Associated Infections" represents a culmination of several months of research, deliberation, and public comment to identify the key actions needed to achieve and sustain progress in protecting patients from the transmission of serious, and in some cases, deadly infections. In response to the increasing threat of HAIs and national and international concern, the Department has composed a Steering Committee of senior-level representatives from the Offices and Operating Divisions of HHS and conducted a number of in-person meetings and conferences with Federal experts. The Department's Action Plan toward the prevention and elimination of HAIs includes goals toward which the healthcare and public health communities have been moving over the past several years." p 1-2Executive summary -- Introduction -- Prevention: metrics and targets -- Prevention: prioritized recommendations -- Research -- Information systems and technology -- Incentives and oversight -- Outreach and messaging -- Coordination, evaluation, and conclusion -- AppendicesAgency for Healthcare Research and Quality, Office of the Assistant Secretary for Public Affairs, Office of the Assistant Secretary for Planning and Evaluation, Centers for Disease Control and Prevention, Centers for Medicare & Medicaid Services, Food and Drug Administration, National Institutes of Health, Office of the National Coordinator for Health Information Technology, Office of Public Health and Science."06222009."Title from title screen (viewed on March 17, 2011)

Open Data

Open data is freely usable, reusable, or redistributable by anybody, provided there are safeguards in place that protect the data’s integrity and transparency. This book describes how data retrieved from public open data repositories can improve the learning qualities of digital networking, particularly performance and reliability. Chapters address such topics as knowledge extraction, Open Government Data (OGD), public dashboards, intrusion detection, and artificial intelligence in healthcare

The detection of meningococcal disease through identification of antimicrobial peptides using an in silico model creation

Philosophiae Doctor - PhDNeisseria meningitidis (the meningococcus), the causative agent of meningococcal disease (MD) was identified in 1887 and despite effective antibiotics and partially effective vaccines, Neisseria meningitidis (N. meningitidis) is the leading cause worldwide of meningitis and rapidly fatal sepsis usually in otherwise healthy individuals. Over 500 000 meningococcal cases occur every year. These numbers have made bacterial meningitis a top ten infectious cause of death worldwide. MD primarily affects children under 5 years of age, although in epidemic outbreaks there is a shift in disease to older children, adolescents and adults. MD is also associated with marked morbidity including limb loss, hearing loss, cognitive dysfunction, visual impairment, educational difficulties, developmental delays, motor nerve deficits, seizure disorders and behavioural problems. Antimicrobial peptides (AMPs) are molecules that provide protection against environmental pathogens, acting against a large number of microorganisms, including bacteria, fungi, yeast and virus. AMPs production is a major component of innate immunity against infection. The chemical properties of AMPs allow them to insert into the anionic cell wall and phospholipid membranes of microorganisms or bind to the bacteria making it easily detectable for diagnostic purposes. AMPs can be exploited for the generation of novel antibiotics, as biomarkers in the diagnosis of inflammatory conditions, for the manipulation of the inflammatory process, wound healing, autoimmunity and in the combat of tumour cells. Due to the severity of meningitis, early detection and identification of the strain of N. meningitidis is vital. Rapid and accurate diagnosis is essential for optimal management of patients and a major problem for MD is its diagnostic difficulties and experts conclude that with an early intervention the patient’ prognosis will be much improved. It is becoming increasingly difficult to confirm the diagnosis of meningococcal infection by conventional methods. Although polymerase chain reaction (PCR) has the potential advantage of providing more rapid confirmation of the presence of the bacterium than culturing, it is still time consuming as well as costly. Introduction of AMPs to bind to N. meningitidis receptors could provide a less costly and time consuming solution to the current diagnostic problems. World Health Organization (WHO) meningococcal meningitis program activities encourage laboratory strengthening to ensure prompt and accurate diagnosis to rapidly confirm the presence of MD. This study aimed to identify a list of putative AMPs showing antibacterial activity to N. meningitidis to be used as ligands against receptors uniquely expressed by the bacterium and for the identified AMPs to be used in a Lateral Flow Device (LFD) for the rapid and accurate diagnosis of MD

Addressing the Burden of Antimicrobial Resistance in Vietnamese Hospitals

Hospital acquired infections (HAIs), especially ventilator associated respiratory infection (VARI) cause significant morbidity and mortality, and disproportionally so in low- and middle-income countries (LMICs), including Vietnam, where infection control in hospitals is often neglected. The management of HAIs in these settings is challenging because of the high proportions of antimicrobial drug resistance and limitations of laboratory diagnostics, financial and human resources in terms of knowledge and skills for antimicrobial stewardship and infection prevention and control. Because resistance is driven by use of antimicrobials, my thesis started with a question on use and cost of antimicrobials in public hospitals in the country followed by a detailed assessment of use and cost of antimicrobials in the management of ventilator associated respiratory infections (VARI). I obtained detailed bids from hospitals and provincial departments of health representing 28.7% (1.68 / 5.85 billion US$) of the total hospital medication budget in Vietnam. Antimicrobials represented 28.6$ 40 million per year. Our studies showed the need for an affordable and scalable intervention in critical care units to reduce the burden of VARI and provide cost savings for national health expenditure. My studies also showed that antimicrobial costs are a major component of the excess cost of VARI management in Vietnam (51.1%) and that a one day reduction in the duration of antimicrobial therapy can save US$ 1.72 million. Therefore, my thesis has focused on interventions to prevent VARI and to shorten antimicrobial therapy. In recognition of human resources constraints in Vietnam, including for microbiology diagnostics and critical care nursing, I have studied automatic technology and equipment, including matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDITOF-MS) for rapid identification of pathogens and continuous automatic cuff pressure control device to prevent VARI. To examine effectiveness of these intervention, I conducted 2 randomised controlled trials to evaluate the clinical effectiveness of matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDITOF-MS) in optimizing antimicrobial therapy and to evaluate the effectiveness of continuous cuff pressure control in preventing VARI. For the latter, pending unblinding and final results I describe the implementation of the trial and report the incidence of hospital acquired bloodstream infection during this trial. A diagnostic randomised controlled trial (RCT) was conducted to evaluate the impact of MALDITOF-MS versus conventional diagnostics in improving antimicrobial use in patients with confirmed infection. Although MALDITOF-MS provided more rapid identification of invasive bacterial and fungal pathogens than conventional microbiology, the proportion of patients on optimal therapy at 24 or 48 hours after growth of specimen did not increase. These findings showed that without human resources and an effective antimicrobial stewardship programme, technology alone cannot provide a solution for antimicrobial overuse in hospitals in LMICs. A randomized controlled clinical trial was conducted to evaluate the effectiveness of continuous cuff pressure control versus daily manual cuff measurement (VARI-prevent). In this study I recruited and followed-up 597 adult patients who were admitted to ICUs and were intubated within 48 hours of admission. The patients were randomised to receive either continuous or manual cuff pressure measurement and control and were followed for occurrence of VARI during ICU stay and up to 90 days after randomisation. The study has completed recruitment and follow-up and final analysis is ongoing. The overall rate of VARI and VAP in eligible patients was 23.7% (140/591) and 17.3% (102/591) respectively. The data from this trial (VARI-prevent) was analysed to estimate the incidence density rate of hospital acquired bloodstream infection (HABSI) in 3 ICUs in Vietnam for the first time. The most common pathogens causing HABSI were Klebsiella pneumoniae followed by Pseudomonas aeruginosa, Acinetobacter baumannii and Coagulase-Negative staphylococci. Polymicrobial culture results were reported in 6.8% (3/44) patients with culture confirmed HABSI. The rate of HABSI and central line associated BSI (CLABSI) were 7.4% (44/591) and 9.3% (31/333), respectively. The incidence density rate of HABSI and CLABSI were 3.76 per 1000 patients-days and 8.43 per 1000 catheter-days, respectively. This suggests that the implementation of infection prevention and control bundle including catheter care is important to reduce the high incidence of HABSI in Vietnam. The findings in my thesis are relevant to healthcare professionals and policy stakeholders. It demonstrates the magnitude of HAI burden and creates awareness of potential beneficial interventions. Results of my trials will be helpful to inform decisions to establish the antimicrobial stewardship programmes and infection prevention and control bundles to improve patients’ outcomes

Identification of biomarkers associated with cervical cancer: a combined in silico and molecular approach

>Magister Scientiae - MScCervical cancer is the leading cause of cancer mortality among black women in South Africa. It is estimated that this disease kills approximately 8 women in South Africa every day. Cervical cancer is caused by the human papillomavirus (HPV) with the most common screening method for cervical cancer being Papanicolaou (Pap) smear, test amongst others. However, less than 20% of South African women go for these tests. There are several reasons why women do not go for these tests but the invasiveness of the test is one of the major causes for the low rate of screening. Lateral flow devices offer medical diagnosis at the point- of-care, allowing for the quick initiation of the appropriate therapeutic response. These tests are more cost-effective for the healthcare delivery industry, and can potentially be used by patients to self-test in the privacy of their homes and allow them to make informed decisions about their health. Therefore, the aim of this study was to use computational methods to identify serum biomarkers for cervical cancer that can be used to develop a point-of-care diagnostic device for cervical cancer. An in silico approach was used to identify genes implicated in the initiation and development of cervical cancer. Several bioinformatics tools were employed to extract a list of genes from publicly available cancer repositories. Multiple gene enrichment analysis tools were employed to analyze the selected candidate genes. Through this pipeline, ~28190 genes were identified from the various databases and were further refined to only 10 genes. The 10 genes were identified as potential cervical cancer biomarkers. A subcellular compartmentalization analysis clustered the proteins encoded by these genes as cell surface, secretory granules and extracellular space/matrix proteins. The selected candidate genes were predicted to be specific for cervical cancer tissue in a cancer tissue specificity meta-analysis study. The expression levels of the candidate genes were compared relative to each other and a graph constructed using gene expression data generated by GeneHub-GEPIS and TiGER databases. Further gene enrichment analysis was performed such as protein-protein interactions, transcription factor analysis, pathway analysis and co-expression analysis, with 9 out of the10 of the candidate genes showing co-expression. A gene expression analysis done on cervical cancer cell lines, other cancer cell lines and normal fibroblast cell line revealed differential expression of the candidate genes. Three candidate genes were significantly expressed in cervical cancer, while the seven remaining genes showed over expression in other cancer types. The study serves as basis for future investigations to diagnosis of cervical cancer, as well as for cancers. Thus, they could also serve as potential drug targets for cancer therapeutics and diagnostics

Epidemiology of carbapenemase-producing organisms (CPO) in Scotland

The emergence and spread of carbapenem-resistant organisms (CRO) is a global public health threat in healthcare settings, resulting in high mortality, prolonged healthcare and increased costs. In the last two decades, many papers aiming to identify individuals at high risk of acquiring CRO have been published. However, the results reported across these studies are inconsistent and there are no studies systematically summarising those findings. Carbapenem resistance is mediated by multiple mechanisms. Carbapenemase production is the most concerning as the encoding genes of carbapenemases are located on mobile genetic elements, facilitating horizontal genetic exchange and therefore promoting the acquisition and spread of resistance genes. Examination of the epidemiology of carbapenemase-producing organisms (CPO) will inform local infection prevention and control strategies. This thesis has two main parts. The aim of the first part is to systematically summarise risk factors for CRO infection and colonisation in healthcare facilities worldwide and identify study characteristics contributing most to the heterogeneity across studies. In the second part I focused on CPO in Scotland to investigate the incidence, microbiological characteristics and outcomes of CPO and determine risk factors associated with CPO among hospitalised patients. In the first part, I conducted a systematic review and meta-analysis to evaluate risk factors associated with infection and/or colonisation of CRO in healthcare facilities. In total, 227 papers published between 1986 and 2016 were identified. Using pooled odds ratio estimates and the likelihood of statistical significance as criteria, prior carriage of multidrug-resistant organisms, prior antibiotics usage (carbapenem or oxazolidinone), prior provision of medical devices (mechanical ventilation or nasogastric tube) and prior healthcare exposure (intensive care unit ICU stay, and longer hospital stay) were most consistently found to be leading risk factors for CRO infection and/or colonisation. Additionally, decubitus ulcer was a specific leading risk factor for CRO infection, and prior antibiotics usage (polymyxin or cefepime) and steroid treatment were specific for hospital acquired CRO infection. However, prior provision of some medical devices (parenteral nutrition or gastrostomy or urinary catheter) were only leading risk factors for CRO colonisation. Study organism, case-control selection, study population, sample size, study setting and specialty (ICU or non-ICU) were the characteristics accounting for most heterogeneity across the published studies examined. In the second part of this thesis, I focused on CPO in Scotland using data extracted from several national datasets. I performed a retrospective analysis on all CPO from clinical and screening cultures in 2003-2016 using generalised linear models and survival analyses, and then conducted a matched casecontrol study to determine risk factors for CPO infection and colonisation among hospitalised patients using conditional logistic regression models. In total, 243 CPO isolates were identified in 214 individuals from 13 of 14 NHS Boards. The overall incidence of CPO cases increased significantly (P<0.001), from 0.02 to 1.38 per 100,000 population. The case fatality rate was 5.6%. Enterobacteriaceae isolates predominated (84.8%) and increased significantly faster than non-fermenters. Community-associated CPO were more likely to be colonisations while healthcare-associated CPO were more likely to be infections. The ‘big 5’ carbapenemases (VIM, NDM, KPC, OXA-48 and IMP) predominated (96.7%). Awareness is required that older patients, with systemic infection or organ failure or presenting non-fermenters are at higher 30-day mortality risk from CPO. Patients with CPO infection had higher hospital mortality and longer hospital stay. A history of prolonged hospitalisation, prolonged ICU or high dependency unit (HDU) stay and being immunocompromised all independently increased the risk of CPO infection, while a history of HDU stay and ‘endocrine, nutritional and metabolic diseases’ were independent risk factors for CPO colonisation. In conclusion, this thesis sheds light on patients at high risk of being infected or colonised by CRO including CPO in healthcare facilities. Pre-emptive management should be prioritised for these patients. The findings also demonstrate the necessity of continuing the existing acute hospital admission screening programme for carbapenemase-producing Enterobacteriaceae in Scotland. Future efforts are required to understand underlying factors accounted for mortality, evolution and transmission of carbapenem resistance in Scotland

Proteómica cuantitativa e inmunoproteómica dirigidas al estudio de la interacción entre el hospedador y Candida albicans: respuesta mediada por macrófagos y por anticuerpos

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Farmacia, Departamento de Microbiología y Parasitología, leída el 05-11-2019Candida albicans forma parte de la microbiota de individuos sanos. Sin embargo, ante un desequilibrio de la microbiota o inmunosupresión, se puede desarrollar una infección, siendo la candidiasis invasora (IC) un problema clínico relevante. Por esto, el estudio de la interacción hospedador-patógeno es crucial para conocer cómo el sistema inmunitario responde a Candida.Los macrófagos son células inmunes implicadas en el reconocimiento, fagocitosis y destrucción del hongo. Además, se ha descrito la producción de anticuerpos frente a proteínas de C. albicans durante estas infecciones. La proteómica proporciona información de la abundancia de proteínas y de las modificaciones postraduccionales durante la interacción patógeno-hospedador. Así mismo, el análisis de las proteínas secretadas por C. albicans también es importante debido al papel que tienen éstas en la interacción con el hospedador. El estudio de estas proteínas mediante inmunoproteómica resulta útil para el descubrimiento de biomarcadores para el diagnóstico de las IC.Candida albicans can be part of the microbiota of healthy individuals. However, if the balance of the normal microbiota is disrupted or the immune defences are compromised a scenario of infection can arise. Invasive candidiasis (IC) is an important health-care associated fungal infection. Therefore, the study of host –pathogen complex interplay is needed to improve the knowledge on how the immune system responds to Candida.Macrophages are key immune cells involved in recognition, phagocytosis and killing of the fungus. The production of antibodies against several C. albicans proteins has also been described during these infections.Proteomics can be used to understand host-pathogen interactions and give information on the protein abundance and on their post translational modifications. Moreover, C. albicans secreted proteins analysis is crucial due to the role of these proteins in interaction with the host and their study using immunoproteomics is useful for the discovery of biomarkers for the diagnosis of IC...Fac. de FarmaciaTRUEunpu

Doctor of Philosophy

dissertationThe effective diagnosis of infectious diseases, like tuberculosis (TB), through the detection of biomarkers indicative of active infection, continues to challenge the scientific community. Due to the consistently high burden of disease in low-income economies, there has been a renewed interest to transition the capabilities of the diagnostic tests from the research laboratory to point-of-need (PON) applications. To identify the characteristics of these PON tests, the World Health Organization has established the ASSURED ( affordable, sensitive, specific, user-friendly, rapid, equipment-free, and delivered to those in need) guidelines. Using the detection of mannose-capped lipoarabinomannan (ManLAM), a TB biomarker, as a model system, the research presented herein focuses on approaches to meet the challenges faced by modern infectious disease diagnostics with an emphasis on transitioning state-of-the-art surface-enhanced Raman scattering (SERS) immunoassays toward PON applications within the framework of the ASSURED guidelines. First, we build on previous work investigating the underpinnings of an acid treatment method to improve the detection of ManLAM in the serum of infected individuals. This work demonstrates that while acid treatment improves the detection of ManLAM, assay performance is hindered because of the acid-induced degradation of ManLAM and the incomplete decomplexation of endogenous serum proteins. Through the application of an enzymatic sample treatment process, this work also shows that improved ManLAM recoveries lead to improved clinical accuracies. To increase assay performance, we developed, charactered, and validated a novel surface-enhanced resonance Raman scattering (SERRS) immunoassay. This improves the limit of detection (∼10x) and analytical sensitivity (∼39x) for ManLAM measurements compared to an analogous SERS immunoassay. The remainder of the work validates the use of a handheld Raman spectrometer for the detection of phospho-myo-inositol-capped LAM (PILAM), a ManLAM simulant. This work demonstrates the ability to achieve low limits of detection (∼0.2 ng/mL) for PILAM in human serum and document the impact of excitation wavelength and the plasmonic coupling between the labels and planar gold substrates as a basis for further improvements in SERS immunoassays. Taken together, this work begins to establish approaches for improved methodologies to combat the burden of infectious diseases, and to demonstrate the applicability of SERS detection beyond the research laboratory