Pathogen Genomics in Clinical Practice
Routine clinical use of pathogen genomics and metagenomics has great potential to improve diagnosis and management of infection. Standard clinical microbiology methods remain slow and frequently yield no results, leading to empirical use of antibiotics which can be inappropriate and thought to be a driver of the antimicrobial resistance pandemic. As evidence linking microbiomes to health also grows, investigating conditions such as bacterial vaginitis, linked to premature labour, bacterial respiratory infections such as HAP and VAP, as well as gastrointestinal infections would logically benefit from a genomics approach. Dysbiosis and reduced microbial diversity are often key features of these conditions. Use of pathogen sequencing and genomic epidemiology are now recognised as an essential part of public health microbiology and virology surveillance. However, in the complex environments of our health service we have not yet seen a similar transformation in routine diagnostic microbiology.
Barriers to adoption of genomic methods in infection include limited sequencing capacity, high prices, complex logistics, and access to computing and bioinformatics resources. Clinical laboratory accreditation and regulatory measures developed for clinical chemistry services are also perceived as being a poorer fit for genomics in infectious disease diagnostics, and development of ethical frameworks around use of pathogen genomics has barely begun. There are clearly many challenges.
The Journal of Medical Microbiology’s Pathogen Genomics in Clinical Practice collection aims to highlight the benefits of a genomics approach to infectious diseases. The collection is now open for new submissions from all researchers and practitioners working in applied public health and clinical pathogen genomics.
Please indicate upon submission that you would like your paper to be considered for the collection.
Editors: Derek Fairley, Peter Coyle, Kalai Mathee
Status: Open for submissions
Deadline for submissions: 20 December 2024
Image credit: burcu demir