Frontiers of Clinical Bioinformatics Infectious Disease

Details

Title

Frontiers of Clinical Bioinformatics Infectious Disease

Type

Stage Two

Module code

HBI119

Requirement

Optional

Module objective

Infectious disease bioinformatics is a rapidly evolving specialism. The underpinning science base is in a state of flux, driven by changes in both the technology and analytical strategies used to make sense of the data generated, and in the basic scientific understanding of the evolution of pathogens and the process by which they cause disease. The dynamic nature of the field places significant challenges on an infectious disease bioinformatician who must be aware of the current state of the art in their specialist areas and have the knowledge and skills to determine which parts of the current research base might be relevant in order to enhance improvements to outcomes for patients and for population-level public health.

By the end of this module the Clinical Scientist in HSST will be able to perform an analysis of the current state of the research base in the application of bioinformatics to whole-genome sequencing of pathogens and use this knowledge to inform and lead the clinical work undertaken in their current clinical environment. They will be able to interact with others in their organisation to help influence the development of the service to ensure that the work it does is consistent with current best practice and informed by high-quality research. They should also be able to identify areas in which the current research base might need to be developed or expanded to meet the needs of a public health and clinical service and lead that development. The Clinical Scientist in HSST will also be expected to consistently demonstrate the attitudes and behaviours necessary for the role of a CCS.

Knowledge and understanding

By the end of this module the Clinical Scientist in HSST will have systematically acquired and have expert understanding of a substantial body of knowledge that is at the forefront of bioinformatics practice pertaining to infectious disease from the perspective of both patient and population, including:

• The current biological research literature in microbial and viral genomics and bioinformatics.
• How clinical bioinformatics is impacting on the diagnosis, investigation, treatment, management options and public health interventions for infectious disease.
• Analytic methodologies appropriate for determining:
  • identity of infectious disease agent;
  • characteristics of pathogens within a patient or population that may confer antibiotic/antiviral resistance, increased virulence or influence transmissibility;
  • the relationship between isolates/samples from a putative outbreak or large population.
• The current strengths and weaknesses of the theoretical and applied research base in application of whole-genome sequencing technologies (both short and long read) to assembling draft consensus genome sequences from pathogens or determining differences relative to a reference sequence and then inferring information for clinical or public health purposes.
• Recognition that the overall clinical responsibility for patients resides with an accountable medical consultant or General Practitioner.

Technical and clinical skills

By the end of this module the Clinical Scientist in HSST will have a critical understanding of current evidence and its application to the performance and mastery of a range of technical skills and will have the skills to:

Perform an effective literature review

• Carry out an effective search of the current literature in microbial and viral applied genome analyses as it applies to clinical intervention and public health in order to determine current knowledge around new understandings of the biology of pathogens and the new technological and analytical work being done in the area.

Critical appraisal of the current literature

• Take the complex literature identified in the review and determine the key issues and debates in a chosen area.
• Disseminate findings, including scientific data and the path of evidence leading to recommendations for future activity.
• Critically assess competing priorities to choose the best solution so that adaptation to practice can be made in a timely and cost effective manner.

Creation of a strategic view or translation strategy

Either:

• use the critical appraisal to produce a document to inform the strategic direction that a service should be taking. This could take the form of:
  • a forward view to identify areas that should be investigated for future development;
  • benchmarking of the service against the current evidenced best practice in the appropriate area;
  • identification of an area that needs further investigation (and a plan for how that could be achieved).

Or:

• translation work to explore the application of new work to the specific clinical area.

By the end of this module the Clinical Scientist in HSST will be expected to critically reflect and apply in practice a range of clinical and communication skills and will:

• Ensure clinical bioinformatics services are delivered in clean and safe environments that are fit for purpose, based on national best practice.
• Provide advanced infectious disease bioinformatics expertise, advice and interpretation to a multiprofessional team including laboratory scientists, epidemiologists, statisticians, mathematical modellers and clinicians, and be able to communicate key concepts and analyses in layman’s terms to patients/carers and their families.
• Lead high-quality patient-focused infectious disease bioinformatics services that promote excellent patient outcomes at the level of both individual and population.
• Assess the demand and specification for evolving clinical bioinformatics scientific services with patients, clinical colleagues and other relevant stakeholders to inform service development and innovation.
• Evaluate the relevant literature and other scientific sources and work with others to develop a scientific and business case for a service improvement to your area, ensuring a clean, safe and secure environment, fitness for purpose, and a basis in national best practice.
• Support patient involvement and engagement and continually seek to improvethe safety and quality of clinical healthcare science services.
• Collaborate with colleagues across organisational boundaries to develop, promote and participate in a multiprofessional approach to high-quality patient care and management.
• Promote informatics improvements that enable DH officials to gain secure access to information that informs policy and intervention based on both active public health incidents and longer-term surveillance.
• Promote new developments that enable patients tohave improved and safer access to information about their care.
• Educate healthcare professionals in new developments in infectious disease bioinformatics.
• Reflect on the challenges of applying research to practice in relation to these areas of practice and suggest improvements, building on a critique of available evidence.
• Seek creative solutions to problems, working with and encouraging others to find creative solutions to problems through engagement with group creativity approaches and techniques.
• Be positive and confident about developing ideas and putting them into action.
• Actively seek out opportunities for collaborative discussions and research, being open to new developments, attending conferences and keeping up to date with the literature.
• Adopt a forward-looking, progressive approach and be receptive to new ideas, looking out for emerging technologies.
• Promote a sustainable, engrained culture of innovation in an individual, department and/or organisation.
• Ensure clinical and scientist colleagues are kept up to date with novel techniques used within the service.
• Introduce and critically evaluate measures to identify, actively manage andmitigate risk to patients