Rapid Identification of Vibrio Species of the Harveyi Clade Using MALDI-TOF MS Profiling With Main Spectral Profile Database Implemented With an In-House Database: Luvibase.

Julia Mougin,Roxane Roquigny,Cédric Le Bris,Maryse Bonnin-Jusserand,Thierry Grard,Christophe Flahaut

doi:10.3389/fmicb.2020.586536

Abstract

Vibrio bacteria, and particularly members of the Harveyi clade, are the causative agents of vibriosis. This disease is responsible for mass mortality events and important economic losses on aquaculture farms. Improvements in surveillance and diagnosis are needed to successfully manage vibriosis outbreaks. 16S rRNA gene sequencing is generally considered to be the gold standard for bacterial identification but the cost and long processing time make it difficult to apply for routine identification. In contrast, MALDI-TOF MS offers rapid diagnosis and is commonly used in veterinary laboratories today. The major limiting factor for using this technique is the low environmental bacterial diversity in the commonly available databases. Here, we demonstrate that the sole use of the commercially available Bruker BioTyper database is not fully adequate for identifying Vibrio bacteria isolated from aquaculture farms. We therefore developed a new in-house database named Luvibase, composed of 23 reference MALDI-TOF mass spectra profiles obtained from Vibrio collection strains, mostly belonging to the Harveyi clade. The comparison of the accuracy of MALDI-TOF MS profiling and 16S rRNA gene sequencing revealed a lack of resolution for 16S rRNA gene sequencing. In contrast, MALDI-TOF MS profiling proved to be a more reliable tool for resolving species-level variations within the Harveyi clade. Finally, combining the Luvibase with the Bruker ver.9.0.0.0 database, led to successful identification of 47 Vibrio isolates obtained from moribund abalone, seabass and oysters. Thus, the use of Luvibase allow for increased confidence in identifying Vibrio species belonging to the Harveyi clade.

Highlights

Bacteria belonging to the Vibrio genus, are highly abundant in aquatic environments (Thompson et al, 2004)
We acquired MALDI-TOF MS profiles for 85 Vibrio bacterial strains, classified into 13 Vibrio species mostly belonging to the Harveyi clade, were acquired
MALDI-TOF MS profiling provided better resolution because this technique is based on the analysis of a large spectrum of peptides/proteins from the whole cell, whereas 16S rRNA gene sequencing is based on a single 1,500 bp gene

Summary

Introduction

Bacteria belonging to the Vibrio genus, are highly abundant in aquatic environments (Thompson et al, 2004). Some of them are well-known enteric human pathogens such as Vibrio parahaemolyticus, V. vulnificus, or even V. cholerae, known as the causative agent of pandemic cholera (Bonnin-Jusserand et al, 2017). Other Vibrio species are pathogenic to aquatic animals such as several species belonging to the Harveyi clade. Associated with a great variety of crustaceans, mollusks, or fishes, these bacteria are problematic in aquaculture, causing vibriosis outbreaks and high economic losses (Austin and Zhang, 2006; Novriadi, 2016; Ina-Salwany et al, 2019). The health risk to aquatic animals and the potential development of zoonosis heighten the need for rapid and reliable identification of Vibrio species belonging to the Harveyi clade (Cantas and Suer, 2014; Destoumieux-Garzón et al, 2018). In case of vibriosis outbreaks, appropriate control measures could be designed and rapidly applied

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