A MALDI-TOF MS database for fast identification of Vibrio spp. potentially pathogenic to marine mollusks

Abstract

In mollusk aquaculture, a large number of Vibrio species are considered major pathogens. Conventional methods based on DNA amplification and sequencing used to accurately identify Vibrio species are unsuitable for monitoring programs because they are time-consuming and expensive. The aim of this study was, therefore, to develop the MALDI-TOF MS method in order to establish a rapid identification technique for a large panel of Vibrio species. We created the EnviBase containing 120 main spectra projections (MSP) of the Vibrio species that are potentially responsible for mollusk diseases, comprising 25 species: V. aestuarianus, V. cortegadensis, V. tapetis and species belonging to the Coralliilyticus, Harveyi, Mediterranei, and Orientalis clades. Each MSP was constructed by the merger of raw spectra obtained from three different media and generated by three collaborating laboratories to increase the diversity of the conditions and thus obtain a good technique robustness. Perfect discrimination was obtained with all of the MSP created for the Vibrio species and even for very closely related species as V. europaeus and V. bivalvicida. The new EnviBase library was validated through a blind test on 100 Vibrio strains performed by our three collaborators who used the direct transfer and protein extraction methods. The majority of the Vibrio strains were successfully identified with the newly created EnviBase by the three laboratories for both protocol methods. This study documents the first development of a freely accessible database exclusively devoted to Vibrio found in marine environments, taking into account the high diversity of this genus. Key points • Development of a MALDI-TOF MS database to quickly affiliate Vibrio species. • Increase of the reactivity when faced with Vibrio associated with mollusk diseases. • Validation of MALDI-TOF MS as routine diagnostic tool.

PVBase: A MALDI-TOF MS Database for Fast Identification and Characterization of Potentially Pathogenic Vibrio Species From Multiple Regions of China

“…Then we compared the identification results of the two databases, and analyzed the changes in the identification accuracy and accuracy scores of related strains. We also used the Moussa database ( Moussa et al, 2021 ) to identify the blindly tested strains, and related results are presented in Supplementary Table 2 .…”

“…Some Vibrio species have high genome homology, such as V. alginolyticus and V. parahaemolyticus ( Salamone et al, 2019 ) or V. cholerae and V. mimicus ( Wang et al, 2011 ). This makes the characterization, classification, and identification of Vibrio species particularly problematic, especially for the closely related species ( Moussa et al, 2021 ). It is difficult to accurately distinguish among bacterial species using 16S rRNA sequencing ( Johnson et al, 2019 ).…”

“…Previous studies have demonstrated that MALDI-TOF MS is a valuable tool for discriminating among closely related species ( Schaumann et al, 2018 ) and Vibrio spp. are no exception ( Moussa et al, 2021 ). Although scholars have constructed databases related to Vibrio spp.…”

“…Although scholars have constructed databases related to Vibrio spp. and achieved outstanding results, they also pointed out that due to the intra- and inter-species coefficient of variation, a sufficient number of main spectra in the database is crucial for reliable and safe species identification ( Erler et al, 2015 ; Moussa et al, 2021 ).…”

Bacterial species identification using MALDI-TOF mass spectrometry and machine learning techniques: A large-scale benchmarking study

“…Compared to sequencing a bacterial genome, it is a cheaper and faster alternative for situations where a lot of strains need to be analyzed on a daily basis [1] , [2] . Today, MALDI-TOF MS is routinely used in clinical laboratories for the identification of pathogenic strains, but it is also increasingly applied to identify environmental and food-related microbiota [3] , [4] , [5] , [6] , [7] , [8] , [9] , [10] . MALDI-TOF MS generates mass spectra that quantify mostly ribosomal proteins and peptides present in a purified culture.…”