Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review.

BACKGROUND: Microbial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges. OBJECTIVES: The aim was to extract managerial, financial and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting. METHODS: This was a systematic review of literature identified through PubMed and Web of Science. English literature studies discussing the applications of microbial WGS without limitation on publication date were eligible. A narrative approach for categorization and synthesis of the sources identified was adopted. RESULTS: A total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programmes or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures). CONCLUSIONS: The decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.

Elevated healthcare utilisation in young adult males with obstructive sleep apnoea.

The aim of the present study was to explore morbidity and healthcare utilisation among young adult males with obstructive sleep apnoea (OSA) compared with middle-aged OSA patients over the 5-yr period preceding diagnosis. A prospective case-control study was performed; 117 young (22-39-yr-old) males with OSA were matched with 117 middle-aged (40-64-yr-old) OSA males for body mass index, apnoea/hypopnoea index, arterial oxygen saturation, arousal and awakening index, and Epworth Sleepiness Scale score. Each OSA patient was matched with controls by age, geographic area and physician. Young adult males with OSA showed no increase in specific comorbidity compared with controls. Middle-aged OSA patients exhibited increased risk of cardiovascular disease. Healthcare utilisation for the 5-yr period was >or=1.9 times higher among young and middle-aged male OSA patients than among controls. Multiple logistic regression analysis revealed that hyperlipidaemia in young adults and a body mass index of >37 kg x m(-2) and cardiovascular disease in middle-aged adults are the only independent determinants of the upper third, most costly, OSA patients. Compared with middle-aged males with obstructive sleep apnoea, in whom increased expenditure was related to cardiovascular disease and body mass index, utilisation was not related to any specific disease in younger cases.