Genetic diversity and population structure of Tenacibaculum maritimum, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing

Tenacibaculum maritimum is responsible for tenacibaculosis, a devastating marine fish disease. This filamentous bacterium displays a very broad host range and a worldwide geographical distribution. We analyzed and compared the genomes of 25 T. maritimum strains, including 22 newly draft-sequenced genomes from isolates selected based on available MLST data, geographical origin and host fish. The genome size (~3.356 Mb in average) of all strains is very similar. The core genome is composed of 2116 protein-coding genes accounting for ~75% of the genes in each genome. These conserved regions harbor a moderate level of nucleotide diversity (~0.0071 bp−1) whose analysis reveals an important contribution of recombination (r/m ≥ 7) in the evolutionary process of this cohesive species that appears subdivided into several subgroups. Association trends between these subgroups and specific geographical origin or ecological niche remains to be clarified. We also evaluated the potential of MALDI-TOF-MS to assess the variability between T. maritimum isolates. Using genome sequence data, several detected mass peaks were assigned to ribosomal proteins. Additionally, variations corresponding to single or multiple amino acid changes in several ribosomal proteins explaining the detected mass shifts were identified. By combining nine polymorphic biomarker ions, we identified combinations referred to as MALDI-Types (MTs). By investigating 131 bacterial isolates retrieved from a variety of isolation sources, we identified twenty MALDI-Types as well as four MALDI-Groups (MGs). We propose this MALDI-TOF-MS Multi Peak Shift Typing scheme as a cheap, fast and an accurate method for screening T. maritimum isolates for large-scale epidemiological surveys.

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Additional file 1. T. maritimum isolates used in this study and their corresponding MALDI-Types.
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Additional file 2. Average Nucleotide Identity (ANI) of pairwise comparison of the T. maritimum isolates.
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Additional file 3. Parsimony based phylogenetic tree. The tree is based on the alignment made by Snippy. It is reconstructed using the parsimony method as implemented in ...
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Additional file 4. Maximum likelihood, Gubbins-based phylogenetic tree. The tree was obtained from the whole genome alignment of 25 T. maritimum strains at the fifth and ...
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Additional file 5. Overview of recombination tracts between two pairs ofT. maritimumisolates. SNPs and recombination tracts between two closely related isolates.
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Additional file 6. Heatmap displaying the diversity of ribosomal protein weights. Lines correspond to strains and columns correspond to ribosomal proteins in ascending order ...
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Additional file 7. Monomorphic biomarker peaks. Screenshots of the 18 conserved peaks produced by 9 ribosomal monomorphic proteins with several degrees of ionization. The ...
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Additional file 8. Quality control andT. maritimumspecies identification. The full dataset is composed of representatives of 24 Tenacibaculum species including 135 isolates ...
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Additional file 9. Amino-acid polymorphism of the 9 retained biomarkers. Protein sequence alignments of the 9 ribosomal proteins selected as polymorphic biomarkers and their corresponding isoform (IF)
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How to cite
Bridel Sébastien, Bourgeon Frédéric, Marie Arnaud, Saulnier Denis, Pasek Sophie, Nicolas Pierre, Bernardet Jean-François, Duchaud Eric (2020). Genetic diversity and population structure of Tenacibaculum maritimum, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing. Veterinary Research. 51 (1). 60 (17p.).,

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