Published October 4, 2023 | Version 1
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Spectra from "Contribution of MALDI-TOF mass spectrometry and Machine Learning including Deep Learning techniques for the detection of virulence factors of Clostridioides difficile strains"

Authors/Creators

  • 1. INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Cimi-Paris, Paris, France, AP-HP (Assistance Publique Hôpitaux de Paris), Département de Bactériologie, Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint-Antoine, Paris, France
  • 2. Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France, Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024, Paris, France
  • 3. AP-HP (Assistance Publique Hôpitaux de Paris), National Reference Laboratory for Clostridioides difficile, Paris, France
  • 4. INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Cimi-Paris, Paris, France, AP-HP (Assistance Publique Hôpitaux de Paris), Hôpital Pitié Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
  • 5. NSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, Sorbonne Université, Cimi-Paris, Paris, France, AP-HP (Assistance Publique Hôpitaux de Paris), Département de Bactériologie, Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Saint-Antoine, Paris, France
  • 6. AP-HP (Assistance Publique Hôpitaux de Paris), National Reference Laboratory for Clostridioides difficile, Paris, France , INSERM 1139, Université Paris Cité, Paris, France

Description

This database includes spectra from 201 C. difficile  (CD) strains :

  • 50 non-toxigenic strains (tcdA- tcdB-) (designated ToxA-B-) belonging to 19 different PR,
  • 151 toxigenic strains harbouring toxins A and B genes (ToxA+B+). Among the 151 ToxA+B+ strains, 46 corresponding to 8 different PR also harboured the binary toxin genes (ToxA+B+CDT+) and 105 (23 different PR) did not (ToxA+B+CDT-).
  • Among the 46 ToxA+B+CDT+ strains, 22 belonged to the Hv strains i.e. PR 027 (n=13), PR 176 (n=5) and PR 181 (n=4) strains (ToxA+B+CDT+Hv) (Table S1). 

Sample preparation. Each isolate stored at −80°C (Microbank; Pro-Lab Diagnostics) was thawed and cultivated on Columbia Blood Agar (CBA, bioMérieux) incubated in anaerobic atmosphere at 37°C for 48 hours. A subculture was performed in the same conditions. A chemical protein extraction was then carried out. Briefly, a single colony was suspended in 200 µl water and vortexed. After adding 900 µl ethanol, samples were vortexed and centrifuged at 13,000 × g for 2 minutes. The supernatant was removed, and the remaining ethanol was evaporated at room temperature. Next, 25 µl of 70% formic acid was added and mixed with the pellet, then 25 µl of acetonitrile was added. After centrifugation at 13,000 × g for 2 minutes, the supernatant was ready for analysis. Eight deposits were performed for each isolate. The dried spots were coated with 1 µl of α-cyano-4-hydroxycinnamic acid (a-HCCA) in 50% acetonitrile-2.5% trifluoroacetic acid and each spot was analysed three times by MALDI-TOF MS.


MALDI-TOF MS acquisition and analysis. Mass spectra were acquired using a Microflex LT instrument (Bruker Daltonics). The standard parameters of the CE-IVD method recommended by the manufacturer were used. This instrument was equipped with an N2 laser (377 nm) using the following parameters: mass range, 2,000 to 20,000 Da; ion source 1, 20 kV; ion source 2, 18.15 kV; lens, 6 kV; pulsed ion extraction, 150 ns; laser frequency, 20 Hz. A manual external calibration standard (Bacterial Test Standard; Bruker Daltonics) was used for calibration. Data acquisition was performed using FlexControl (version 3.0; Bruker Daltonics).


A total of 4659 spectra were produced. 

Fore more details: please contact alexandre.godmer@aphp.fr
 

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Please contact: medecine-drv@sorbonne-universite.fr and alexandre.godmer@aphp.fr for data access.

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