Emerging commercial molecular tests for the diagnosis of bloodstream infection

Abstract

Bloodstream infection (BSI) by microorganisms can lead to sepsis. This condition has a high mortality rate, which rises significantly with delays in initiation of appropriate antimicrobial treatment. Current culture methods for diagnosing BSI have long turnaround times and poor clinical sensitivity. While clinicians wait for culture diagnosis, patients are treated empirically, which can result in inappropriate treatment, undesirable side effects and contribute to drug resistance development. Molecular diagnostics assays that target pathogen DNA can identify pathogens and resistance markers within hours. Early diagnosis improves antibiotic stewardship and is associated with favorable clinical outcomes. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews recent commercially available molecular methods that use pathogen DNA to diagnose BSI, either by testing positive blood cultures or directly testing patient blood. We critically assess these tests and their application in clinical microbiology. A view of future directions in BSI diagnosis is also provided.

Keywords:

• antibiotic resistance
• blood culture
• blood stream infection
• MALDI-TOF
• molecular diagnostics
• next-generation sequencing
• NGS
• PCR
• PCR/ESI-MS
• sepsis

Financial & competing interests disclosure

S Mwaigwisya and J O’Grady are supported by the Rosetrees Trust and the Norwich Research Park Translational Fund. RAM Assiri is supported by the College of Medicine Research Centre, Deanship of Scientific Research, King Saud University, Riyadh, Saudi Arabia. J O’Grady is a participant in Oxford Nanopore’s MinION access programme (MAP) and has received reagents and consumables for running the MinION device free of charge. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Key issues

• The poor sensitivity and long turnaround time of blood culture, the ‘gold standard’ diagnostic for bloodstream infection/sepsis, results in inappropriate antibiotic prescribing and increased patient morbidity and mortality.

• Rapid and comprehensive molecular diagnostics have the potential to change clinical prescribing and improve clinical outcomes and antibiotic stewardship. However, current methods are limited by the range of pathogens and resistances they can detect.

• Molecular diagnostics can be used on positive blood cultures or directly on patient blood samples. The implementation of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiology laboratories is likely to replace molecular methods for pathogen identification in blood culture. Hence, molecular methods for direct diagnosis in whole blood are likely to be more important in future but current methods lack the comprehensiveness to replace culture.

• NGS-based diagnostic methods have the potential to overcome the shortcomings of PCR-based technologies by offering a comprehensive approach to rapid pathogen and antibiotic resistance marker detection in blood. Rapid pathogen DNA enrichment strategies will be required for this approach to become feasible.

• Blood culture is not sufficiently sensitive to be considered a ‘gold standard’ for the diagnosis of bloodstream infection/sepsis and is unsuitable for determining the performance of new diagnostics methods.