Thoughts and perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study

Background Effective infectious disease diagnostics (IDD) are vital for informing clinical decision-making regarding the treatment and patient management of disease and infections. Conventional clinical methods rely upon culture-dependent techniques, and there has been little shift in the acceptance and integration of culture-independent sequencing methods into routine clinical IDD. This study explored stakeholders’ experiences within IDD, including those working in clinical settings and those conducting research at the forefront of microbial genomics. We aimed to identify factors driving the development and implementation of metagenome sequencing as a routine diagnostic.

Methods Virtual semi-structured interviews were conducted with purposively selected individuals involved in IDD. The interviews explored the experiences of implementing metagenome sequencing as a diagnostic tool and decisions about which diagnostics are used for identifying bacteria-causing infections. Thematic analysis was used to analyse the data, and an Interpretive Phenomenological approach was used throughout.

Results Ten individuals were interviewed between July 2021 and October 2021, including Clinical scientists, consultants, and professors in academia. Their experience ranged from no knowledge of metagenome sequencing to an expert understanding of the phenomenon. Five themes emerged: Diagnostic Choice, Infrastructure, Open Data Sharing, COVID-19, and Communication. Participants recognised the need for new diagnostics to be implemented to overcome the limitations of current diagnostic approaches but highlighted the barriers to integrating new diagnostics into clinical settings, such as the impact on clinical decision-making, accreditation, and cost. However, participants felt that lessons could be learnt from using metagenomics in COVID-19 and how other diagnostic platforms have been integrated into clinical settings over the last 20 years.

Conclusions The study provided clear evidence to address the knowledge gap in current literature and practice for developing and implementing metagenome sequencing as a potential IDD. The knowledge of new and upcoming genomic diagnostic testing is not equally distributed throughout the UK, impacting the understanding and drive to integrate metagenome sequencing into routine clinical diagnostics. Improvements in access to new diagnostics could improve patient treatment and management and positively impact public health.