New DNA test for various pathogenic bacteria is much faster than current gold-standard system

December 09, 2009

Identification of sepsis-causing bacteria using a new microarray platform* is highly accurate and delivers results an average of 18 hours faster than the current gold-standard system, which uses techniques based on detecting inhibition of growth of bacteria through antibiotics. This is the conclusion of an Article published Online First ( and in an upcoming edition of The Lancet, written by Dr Vanya Gant, University College London Hospitals NHS Foundation Trust, University College London Windeyer Institute, London, UK, and Dr Päivi Tissari, in Helsinki University Central Hospital Laboratory HUSLAB, Helsinki, Finland, and colleagues.

Rapid identification of bacteria commonly causing sepsis could allow species-specific therapy to be started early, leading to improved clinical outcomes. The current gold standard for detection of bacteria from patients with sepsis is blood culture, typically taking 1𔃁 days to become positive. A further 1𔃀 days might be needed for identification of bacteria and their antibiotic sensitivity patterns. To cut this additional 1-2 day period, new diagnostic tests that could identify bacterial species rapidly and accurately are needed. Novel DNA-based microarray platforms now allow rapid detection and species identification of several microbial pathogens. The Prove-it sepsis assay (Mobidiag, Helsinki, Finland) identifies more than 50 species of gram-positive and gram-negative bacteria that cause most cases of sepsis. The assay works through amplification and detection of three genes (gyrB, parE, and mecA) of these bacteria. In this study, the authors compared the sensitivity, specificity, and time to identification of this new molecular platform with the gold standard, conventional culture-based method.

In this observational study, 2107 positive blood-cultures in 3318 blood samples from patients with clinically suspected sepsis were investigated for bacterial species by both conventional culture and the Prove-it sepsis assay in two centres (UK and Finland). The authors found that 1807 of 2107 (86%) positive blood-culture samples included a pathogen covered by the assay. The assay had a clinical sensitivity** of 95% and a specificity*** of 99%, and was 100% for both measures for meticillin-resistant Staphylococcus aureus bacteraemia. The assay was a mean 18 h faster than was the conventional culture-based method, which takes an additional 1𔃀 working days.

The authors say: "The Prove-it sepsis assay yielded a high sensitivity and specificity, and identified bacterial species about 18 h before conventional culture methods did, providing practical and realistic delivery of same-day bacterial identification after blood-culture positivity. Clinical sensitivity and specificity of the assay were 100% for MRSA bacteraemia."

They add: "Our study was not designed to address health-care costs. Although additional costs are associated with this assay, these costs need to be assessed in the context of the effect of early identification on total patient management, which might include savings relating to factors such as targeted investigation, length of stay in hospital, and outcomes for the patient. A study to investigate these factors is being undertaken by some of this study's authors."

The authors are also excited by the potential of use of the kit in developing countries, saying: "Equipment could be modified into a transportable kit run on solar power for use in rural areas of developing countries, and at points of care for broad-range rapid pathogen screening and targeted therapy. Cost will remain an issue but will be inversely related to the number of samples analysed."

They conclude: "We noted that the early knowledge provided by this new diagnostic platform could be easily integrated into everyday laboratory workflow in primary-care and secondary-care settings. Accordingly, we are prospectively investigating the platform's potential contribution to clinical outcomes and management pathways, and its implementation for rapid routine diagnosis of a range of pathogens in both developed and developing countries."

In an accompanying Comment, Dr Shin Lin, Stanford University School of Medicine, Stanford, CA, USA, and Dr Samuel Yang, Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA ask: "Will resolving these scenarios 18 h earlier than usual translate into demonstrable clinical benefit commensurate to the cost of undertaking the additional test?"

They conclude: "Although further study is needed before widespread application, the work by Tissari and co-workers is a major advance. By combining elements of nucleic-acid and standard culture-based methods, the Prove-it sepsis assay represents an approach that encompasses the best of both worlds, bringing molecular methods to the threshold of broad pathogen detection."
Dr Vanya Gant, University College London Hospitals NHS Foundation Trust, University College London Windeyer Institute, London, UK. T) +44 (0) 20 7380 9912 E)

Dr Samuel Yang, Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA. T) +1 (410) 735-6441 E)

For full Article and Comment, see:

Notes to editors:

*microarray platform=a series of microscopic spots of short DNA fragments whose sequences are specific for individual organisms

**Sensitivity: Sensitivity (also called recall rate in some fields) measures the proportion of actual positives which are correctly identified as such (e.g. the percentage of sick people who are identified as having the condition).

***Specificity: Specificity measures the proportion of negatives which are correctly identified (e.g. the percentage of healthy people who are identified as not having the condition).


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