A MALDI-ToF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Bacteria

Overview

Journal Sci Data

Date 2025 Jan 31

PMID 39890826

Authors

Peter Lasch

Wolfgang Beyer

Alejandra Bosch

Rainer Borriss

Michal Drevinek

Susann Dupke

Monika Ehling-Schulz

Xuewen Gao

Roland Grunow

Daniela Jacob

Silke R Klee

Armand Paauw

Jorg Rau

Andy Schneider

Holger C Scholz

Maren Stammler

Le Thi Thanh Tam

Herbert Tomaso

Guido Werner

Joerg Doellinger

Affiliations

Soon will be listed here.

Abstract

Today, MALDI-ToF MS is an established technique to characterize and identify pathogenic bacteria. The technique is increasingly applied by clinical microbiological laboratories that use commercially available complete solutions, including spectra databases covering clinically relevant bacteria. Such databases are validated for clinical, or research applications, but are often less comprehensive concerning highly pathogenic bacteria (HPB). To improve MALDI-ToF MS diagnostics of HPB we initiated a program to develop protocols for reliable and MALDI-compatible microbial inactivation and to acquire mass spectra thereof many years ago. As a result of this project, databases covering HPB, closely related bacteria, and bacteria of clinical relevance have been made publicly available on platforms such as ZENODO. This publication in detail describes the most recent version of this database. The dataset contains a total of 11,055 spectra from altogether 1,601 microbial strains and 264 species and is primarily intended to improve the diagnosis of HPB. We hope that our MALDI-ToF MS data may also be a valuable resource for developing machine learning-based bacterial identification and classification methods.

References

Levasseur M, Hebra T, Elie N, Guerineau V, Touboul D, Eparvier V . Classification of Environmental Strains from Order to Genus Levels Using Lipid and Protein MALDI-ToF Fingerprintings and Chemotaxonomic Network Analysis. Microorganisms. 2022; 10(4). PMC: 9032901. DOI: 10.3390/microorganisms10040831. View

Nozaki Y, Ono D, Yamamoto K, Mimura K, Sasaki M, Horino A . A case of renal abscess and bacteremia caused by Burkholderia pseudomallei that was first unidentifiable by matrix-assisted laser desorption ionization-time of flight mass spectrometry in a Japanese-man. J Infect Chemother. 2021; 27(11):1653-1657. DOI: 10.1016/j.jiac.2021.06.005. View

Thanh Tam L, Jahne J, Luong P, Phuong Thao L, Kim Chung L, Schneider A . Draft Genome Sequences of 59 Endospore-Forming Gram-Positive Bacteria Associated with Crop Plants Grown in Vietnam. Microbiol Resour Announc. 2020; 9(47). PMC: 7679102. DOI: 10.1128/MRA.01154-20. View

Dieckmann R, Hammerl J, Hahmann H, Wicke A, Kleta S, Dabrowski P . Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy. Faraday Discuss. 2016; 187:353-75. DOI: 10.1039/c5fd00165j. View

Lasch P, Nattermann H, Erhard M, Stammler M, Grunow R, Bannert N . MALDI-TOF mass spectrometry compatible inactivation method for highly pathogenic microbial cells and spores. Anal Chem. 2008; 80(6):2026-34. DOI: 10.1021/ac701822j. View

Walewski V, Mechai F, Billard-Pomares T, Juguet W, Jaureguy F, Picard B . MALDI-TOF MS contribution to diagnosis of melioidosis in a nonendemic country in three French travellers. New Microbes New Infect. 2016; 12:31-4. PMC: 4872369. DOI: 10.1016/j.nmni.2016.04.004. View

Doellinger J, Schneider A, Stark T, Ehling-Schulz M, Lasch P . Evaluation of MALDI-ToF Mass Spectrometry for Rapid Detection of Cereulide From Cultures. Front Microbiol. 2020; 11:511674. PMC: 7709880. DOI: 10.3389/fmicb.2020.511674. View

Park J, Kim T, Park H, Kang C . Delay in the diagnosis of Brucella abortus bacteremia in a nonendemic country: a case report. BMC Infect Dis. 2024; 24(1):489. PMC: 11089730. DOI: 10.1186/s12879-024-09377-y. View

Sauer S, Kliem M . Mass spectrometry tools for the classification and identification of bacteria. Nat Rev Microbiol. 2009; 8(1):74-82. DOI: 10.1038/nrmicro2243. View

10.

Contzen M, Hailer M, Rau J . Isolation of Bacillus cytotoxicus from various commercial potato products. Int J Food Microbiol. 2014; 174:19-22. DOI: 10.1016/j.ijfoodmicro.2013.12.024. View

11.

Oberle M, Wohlwend N, Jonas D, Maurer F, Jost G, Tschudin-Sutter S . The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study. PLoS One. 2016; 11(10):e0164260. PMC: 5087883. DOI: 10.1371/journal.pone.0164260. View

11.

Etani T, Mogami T, Yamaguchi S, Takeda T, Sugino T, Shimizu N . Comparison of drug susceptibility between Escherichia coli detected in stool cultures of patients undergoing transrectal prostate needle biopsy and Escherichia coli in hospital-wide urine antibiograms. J Infect Chemother. 2021; 28(2):343-346. DOI: 10.1016/j.jiac.2021.10.022. View

12.

Lasch P, Beyer W, Nattermann H, Stammler M, Siegbrecht E, Grunow R . Identification of Bacillus anthracis by using matrix-assisted laser desorption ionization-time of flight mass spectrometry and artificial neural networks. Appl Environ Microbiol. 2009; 75(22):7229-42. PMC: 2786504. DOI: 10.1128/AEM.00857-09. View

13.

De Waele G, Menschaert G, Vandamme P, Waegeman W . Pre-trained Maldi Transformers improve MALDI-TOF MS-based prediction. Comput Biol Med. 2025; 186:109695. DOI: 10.1016/j.compbiomed.2025.109695. View

14.

Freiwald A, Sauer S . Phylogenetic classification and identification of bacteria by mass spectrometry. Nat Protoc. 2009; 4(5):732-42. DOI: 10.1038/nprot.2009.37. View

15.

Lista F, Reubsaet F, De Santis R, Parchen R, de Jong A, Kieboom J . Reliable identification at the species level of Brucella isolates with MALDI-TOF-MS. BMC Microbiol. 2011; 11:267. PMC: 3314589. DOI: 10.1186/1471-2180-11-267. View

16.

Clark A, Kaleta E, Arora A, Wolk D . Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev. 2013; 26(3):547-603. PMC: 3719498. DOI: 10.1128/CMR.00072-12. View

17.

Howley F, Abukhodair S, de Barra E, OConnell K, McNally C . Misidentification of as species: potential pitfalls in the diagnosis of brucellosis. BMJ Case Rep. 2024; 17(6). DOI: 10.1136/bcr-2024-260072. View

18.

Elhanany E, Barak R, Fisher M, Kobiler D, Altboum Z . Detection of specific Bacillus anthracis spore biomarkers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 2001; 15(22):2110-6. DOI: 10.1002/rcm.491. View

19.

Mortier T, Wieme A, Vandamme P, Waegeman W . Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: A large-scale benchmarking study. Comput Struct Biotechnol J. 2021; 19:6157-6168. PMC: 8649224. DOI: 10.1016/j.csbj.2021.11.004. View