Blood Stream Infections (BSIs) are a massive burden to health services worldwide, present culture based diagnostic methods identify microorganisms phenotypically, based upon physical characteristics such as morphology, growth or not in a specific medium. These methods require up to 4 days for a complete analysis of a clinical sample in order to determine the cause of the infection and define an appropriate antimicrobial chemotherapy. This standard culturing approach is time consuming, complex, costly and diagnostically limited. Yet reliability, reproducibility and broad use of these methods provide a real world 'Gold Standard' in microbiology that molecular techniques have yet to surpass in the clinical setting. A well-defined molecular approach can theoretically overcome the limitations of the culture-based methodology. A molecular technique could be faster, being able to provide a clinically relevant diagnosis at the point-of-care e.g. the patient's bedside and more accurate providing information about the infection based upon primary molecular data within the sample not on a secondary culture from that clinical sample. When translated to the real world these advantages mean that; the patient can be accurately diagnosed upon presentation to a physician allowing the treatment to be delivered without the need for a long hospital stay or a broad-spectrum antibiotic therapy. This reduces costs and evolutionary pressure upon bacteria to develop resistance to antimicrobial chemotherapies. A molecular approach also allows a simplification of the diagnostic process by employing a lab-on-a-chip framework. By integrating the core components of the molecular approach the infrastructural requirements of health care provider such as; well trained staff, expensive laboratory equipment buildings and resources etc could be reduced to a simple hand held device. This thesis details the multidisciplinary work undertaken to thoroughly define the nature of the problem and the requirements of a solution. The research in defining that solution was conducted within three disciplines, bioinformatics, molecular biology and nanotechnology.