Emerging methodologies for pathogen identification in bloodstream infections: an update

ABSTRACT

Introduction: Bloodstream infections (BSIs) remain a major public health burden worldwide, particularly in high-income countries as they are associated with a significant mortality rate. As early administration of appropriate antimicrobial therapy is a major prognostic factor, there remain unmet needs for shortening BSI diagnosis. Current blood cultures (BC) processing to identify pathogens involved in BSI is not compatible with such delays, although it remains the gold standard.

Areas covered: Herein, we review and discuss emerging or ongoing assessed methodologies dedicated to shorten the identification of microorganisms involved in BSI and published since 2015. A particular focus on the economical and clinical impact of these approaches is provided when hindsight is sufficient. Methods to shorten antibiotic susceptibility testing are also reviewed.

Expert commentary: Post-culture approaches have encountered a huge success as they are reliable, fast and easy to implement in the laboratory. In particular, the MALDI-TOF MS was shown to be a cost-effective method when combined with antimicrobial stewardship policies. However, further research is needed to optimize methods performed on whole blood in particular next-generation sequencing methods, as they represent an opportunity to substantially improve management of high-risk patients.

KEYWORDS:

• Bacteremia
• diagnosis
• MALDI-TOF MS
• PCR
• metagenomics

Declaration of interest

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.

Reviewers disclosure

Peer reviewers on this manuscript have no relevant financial relationships or otherwise to disclose.

Additional information

Funding

This work has benefited from French State support, managed by the ‘Agence Nationale pour la Recherche’ including the ‘Programme d’Investissement d’avenir’ under the reference Méditerranée Infection 10-IAHU-03. This work was also supported by Région Provence Alpes Côte d’Azur and Fonds Européen de Développement Regional – Plateformes de Recherche et d’Innovation Mutualisées Méditerranée Infection (FEDER PRIMI).