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

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 gol...

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Autores principales: Haddad, Gabriel, Bellali, Sara, Takakura, Tatsuki, Fontanini, Anthony, Ominami, Yusuke, Bou Khalil, Jacques, Raoult, Didier
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227564/
https://www.ncbi.nlm.nih.gov/pubmed/34071713
http://dx.doi.org/10.3390/microorganisms9061170
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author Haddad, Gabriel
Bellali, Sara
Takakura, Tatsuki
Fontanini, Anthony
Ominami, Yusuke
Bou Khalil, Jacques
Raoult, Didier
author_facet Haddad, Gabriel
Bellali, Sara
Takakura, Tatsuki
Fontanini, Anthony
Ominami, Yusuke
Bou Khalil, Jacques
Raoult, Didier
author_sort Haddad, Gabriel
collection PubMed
description 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.
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spelling pubmed-82275642021-06-26 Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures Haddad, Gabriel Bellali, Sara Takakura, Tatsuki Fontanini, Anthony Ominami, Yusuke Bou Khalil, Jacques Raoult, Didier Microorganisms Article 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. MDPI 2021-05-28 /pmc/articles/PMC8227564/ /pubmed/34071713 http://dx.doi.org/10.3390/microorganisms9061170 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Haddad, Gabriel
Bellali, Sara
Takakura, Tatsuki
Fontanini, Anthony
Ominami, Yusuke
Bou Khalil, Jacques
Raoult, Didier
Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures
title Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures
title_full Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures
title_fullStr Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures
title_full_unstemmed Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures
title_short Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures
title_sort scanning electron microscope: a new potential tool to replace gram staining for microbe identification in blood cultures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8227564/
https://www.ncbi.nlm.nih.gov/pubmed/34071713
http://dx.doi.org/10.3390/microorganisms9061170
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