Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures

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.

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

“…The samples were subsequently immersed in 100% ethanol (three times for 10 min each) to prevent drying, and then, all the dehydrated samples were placed in a vacuum desiccator to critical point-dry. After coating the specimens with gold-palladium, the samples were observed using cold field emission scanning electron microscope (Hitachi SU8010, Japan; Haddad et al, 2021).…”

Antimicrobial susceptibility testing for Gram positive cocci towards vancomycin using scanning electron microscopy

“…A similar strategy for clinically relevant Gram-negative bacteria against imipenem was investigated by our team, showing morphological changes after one hour of incubation ( Haddad et al., 2021b ). Previously, we also developed an SEM strategy for bacterial identification from blood cultures ( Haddad et al., 2021a ). Merging these studies could make it possible to develop an automated system coupled with artificial intelligence for rapid identification and AST directly from blood cultures, which would mark a milestone in bacteriological diagnosis.…”

A preliminary investigation into bacterial viability using scanning electron microscopy–energy-dispersive X-ray analysis: The case of antibiotics

“…Fluorescence detection by flow cytometry or imaging has also been extensively researched and widely used for the detection and assessment of viable potential foodborne pathogens in various ecosystems ( Diaper and Edwards, 1994 ; Boulos et al, 1999 ; Adams et al, 2003 ; Delgado-Viscogliosi et al, 2005 ; Brauge et al, 2019 ). Recently, scanning electron microscopy (SEM) has been re-evaluated for applications in clinical microbiology ( Cushnie et al, 2016 ; Hannachi et al, 2020 ; Haddad et al, 2021a , b ). In addition to high-resolution images, SEM can provide information on the chemical elements present in a specimen when coupled with energy-dispersive X-ray spectroscopy (EDX).…”