Understanding the intersection between the hospital and patient microbiome

Abstract

The microbiota of the built environment has profound implications especially within healthcare. Identifying the movement of microbes within the hospital environment not only remains central for infection control practices but also has major influences on our understanding and management of hospital acquired infections. Despite this, our awareness of microbial reservoirs and their interaction with patients in hospitals remains poor with research mainly limited to outbreak settings. As we move away from traditional culture-based methods, the ability to investigate some of these questions has increased through utilisation of culture-independent techniques. The overarching aim of this thesis is to understand the complex relationship that exists between microorganisms that colonise a hospital environment and humans occupying the same environment. In this thesis, microbial tracking, and antimicrobial resistance gene (AMR) transmission is explored through utilisation of culture-independent methods specifically by 1) investigating the effects of hospitalisation on inpatient microbiota, 2) examining the characteristics of the hospital microbiome in relation to changes in patient occupancy and space utilisation and 3) evaluating the extent of antimicrobial resistance gene transmission in an open-plan hospital ward. The characteristics of oropharyngeal (OP) microbiota in hospital inpatients without pneumonia is currently unknown. We explored the degree to which the OP microbiology in these patients compared to healthy controls through a cross-sectional study (Chapter 2) which demonstrated a reduction in diversity and abundance of commensal taxa in inpatients, potentially contributing to an increased risk of hospital-acquired pneumonia in these patients. The presence and movement of microbes is largely influenced by human occupancy and space utilisation. A longitudinal study was conducted between two hospital sites exploring the changes within a hospital microbiome during the transition from an established hospital to a brand-new hospital (Chapter 3). In this study, occupancy was found to be a major determinant of bacterial dispersion within the hospital environment. Bacterial load and microbiota composition were unchanged between the old and new facility at similar occupancy levels despite differing building age and architecture. Finally, the extent of AMR gene transmission within an open-plan ward was investigated (Chapter 4). Although preliminary results identified significant relationships between resistance genes and inter-patient distance, the majority of these determinants were found to be associated with the cohorting of patients according to a specific medical condition (tuberculosis) rather than wider inter-patient AMR gene transmission within the ward. This suggests that in lower-middle income countries such as Myanmar, transmission within the hospital is a relatively minor contributor to AMR dispersion and focus of AMR control should be at a population level. Together, the results of this thesis demonstrate the clinical value of culture-independent methods in assessing microbial movement including resistance genes dispersion within the hospital environment and its interaction with the human population. These findings represent an important step towards developing a precision medicine approach to infection control practices based on the microbial characteristics of a healthcare facility