Abstract
Blood culture is currently the most commonly used method for diagnosing sepsis and bloodstream infections. However, the long turn-around-time to achieve microbe identification remains a major concern for clinical microbiology laboratories. Gram staining for preliminary identification remains the gold standard. We developed a new rapid strategy using a tabletop scanning electron microscope (SEM) and compared its performance with Gram staining for the detection of micro-organisms and preliminary identification directly from blood cultures. We first optimised the sample preparation for twelve samples simultaneously, saving time on imaging. In this work, SEM proved its ability to identify bacteria and yeasts in morphotypes up to the genus level in some cases. We blindly tested 1075 blood cultures and compared our results to the Gram staining preliminary identification, with MALDI-TOF/MS as a reference. This method presents major advantages such as a fast microbe identification, within an hour of the blood culture being detected positive, low preparation costs, and data traceability. This SEM identification strategy can be developed into an automated assay from the sample preparation, micrograph acquisition, and identification process. This strategy could revolutionise urgent microbiological diagnosis of infectious diseases.
Highlights
The most common method of diagnosing sepsis remains blood culture [1,2]
We evaluated in parallel scanning electron microscope (SEM) and Gram preliminary identifications on blood cultures that had been detected as positive, with MALDI-TOF/MS colony identification from subcultures as the gold standard reference
Several improvements were made during this work, reducing the SEM sample preparation time to 20 min and using
Summary
The most common method of diagnosing sepsis remains blood culture [1,2]. rapid pathogen identification is a key component in the microbiological diagnosis [3,4].The time-to-results has a significant and direct clinical impact and an impact on the prognosis of patients [5,6]. Insufficient identifications were switched to culture and eventually relied on other high accuracy methods for microbe identification in blood cultures such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF/MS) [14], molecular biology [15,16,17], multiplex PCR assays, specific hybridization assays, or microarrays [18,19,20,21].
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