MALDI-TOF mass spectrometry: a diagnostic tool for identifying and typing fish pathogenic bacteria

Abstract

Methods used to identify the bacteria responsible for outbreaks of infectious diseases in fish farms still essentially rely on traditional and usually non-discriminatory techniques, such as histology, cytology, phenotypic characteristics and serotyping. Modern molecular methods (e.g., MLST, WGS) tend to replace these classical approaches but are usually employed for retrospective studies within the framework of academic research due to their cost, throughput and the time required. To adapt treatments and take control measures, fish farmers and stakeholders (e.g., aquaculture veterinarians) need an accurate, rapid and, ideally, inexpensive diagnosis of the causative agent. Matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) is a bacterial identification technique widely used in medical microbiology laboratories that is progressively spreading to veterinary diagnostic laboratories. Based on the direct analysis of bacterial cultures, MALDI-TOF MS generates a protein spectrum which is then compared to a set of reference spectra stored in a database. It is a fast, inexpensive technique well-adapted to highthroughput analyses. However, commercial MALDI-TOF MS databases contain only a limited number of bacterial fish pathogens. On the other hand, identification is insufficient to answer questions related to epidemiology, the basis of which is the fine characterization (typing) of bacterial isolates. We have developed a MALDI-TOF MS identification method for species of the genus Tenacibaculum and improved its performance for use as a first-line epidemiological tool for the species T. maritimum, a devastating pathogen of marine fish. This technical notebook includes advice resulting from this experiment and bibliographic research to guide the reader in developing such an approach.