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Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid
Merianne Mohamad1, Chrysi Sergaki2, Vishal C Patel3
1Roger Williams Institute of Liver Studies, School of Immunology & Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, Foundation for Liver Research and King's College Hospital, London, UK.
Abstract:
Patients with advanced chronic liver disease who have underlying cirrhosis are highly susceptible to bacterial infections, which significantly increase the risk of complications and mortality, compounded by escalating antimicrobial resistance. The current gold standard for infection detection and antimicrobial resistance (AMR) profiling remains dependant on traditional microbiological methods. These conventional approaches are slow, labour-intensive, and often fail to deliver timely and accurate results, delaying critical antimicrobial treatment decisions. Clinical metagenomics (CMg) is emerging as a transformative molecular-based tool in infection diagnostics. By enabling the direct sequencing of pathogens from patient-derived samples, CMg offers rapid and comprehensive identification of pathogens and their resistance profiles. Incorporating this technology into the clinical management of patients with cirrhosis has potential to address diagnostic challenges, reduce reliance on broad-spectrum antibiotics and improve outcomes. To effectively incorporate CMg into infection diagnostics, it will be essential to embed of point-of-care sequencing, standardisation of AMR databases, and accessibility to bioinformatics workflows.
Insights
Patients with chronic liver disease face high infection risks. Clinical metagenomics offers rapid pathogen and antimicrobial resistance (AMR) identification, improving treatment decisions for better patient outcomes.
Area of Science:
- Infectious Diseases
- Genomics
- Hepatology
Background:
- Patients with advanced chronic liver disease and cirrhosis are highly vulnerable to bacterial infections.
- These infections increase mortality and complications, exacerbated by rising antimicrobial resistance (AMR).
- Traditional microbiological methods for infection detection and AMR profiling are slow and labor-intensive, delaying critical treatment.
Purpose of the Study:
- To explore the potential of clinical metagenomics (CMg) as a transformative diagnostic tool for infections in cirrhosis patients.
- To address the limitations of conventional methods in timely pathogen and AMR identification.
- To improve clinical management and patient outcomes by leveraging advanced molecular diagnostics.
Main Methods:
- Direct sequencing of pathogens from patient-derived samples using clinical metagenomics (CMg).
- Comprehensive identification of causative pathogens and their associated AMR profiles.
- Evaluation of CMg's potential to overcome diagnostic delays associated with traditional microbiology.
Main Results:
- Clinical metagenomics enables rapid and comprehensive identification of pathogens and AMR.
- This molecular approach can significantly shorten diagnostic timelines compared to conventional methods.
- CMg holds promise for personalized antimicrobial therapy selection.
Conclusions:
- Clinical metagenomics is a powerful emerging tool for diagnosing infections in patients with cirrhosis.
- Integrating CMg into clinical practice can enhance diagnostic accuracy and speed, improving patient management.
- Further development requires point-of-care sequencing, standardized AMR databases, and accessible bioinformatics workflows for widespread adoption.
