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

Type Article
Date 2020-05
Language English
Author(s) Bridel Sébastien1, 2, 3, Bourgeon Frédéric4, Marie Arnaud2, Saulnier Denis5, Pasek Sophie6, Nicolas Pierre7, Bernardet Jean-François1, Duchaud Eric1
Affiliation(s) 1 : Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-En-Josas, France
2 : Labofarm, Finalab, 22603, Loudéac, France
3 : Université de Versailles Saint-Quentin-En-Yvelines, 78180, Montigny-Le-Bretonneux, France
4 : Bio Chêne Vert, Finalab, Rue Blaise Pascal, 35220, Châteaubourg, France
5 : Ifremer, UMR EIO 241, Labex Corail, Centre du Pacifique, BP 49, Taravao, 98719, Tahiti, French Polynesia
6 : Institut de Systématique Evolution, Biodiversité, UMR 7205 Sorbonne Université MNHN CNRS EPHE, Paris, France
7 : Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
Source Veterinary Research (0928-4249) (Springer Science and Business Media LLC), 2020-05 , Vol. 51 , N. 1 , P. 60 (17p.)
DOI 10.1186/s13567-020-00782-0
WOS© Times Cited 6
Abstract

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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Publisher's official version 17 1 MB Open access
Additional file 1. T. maritimum isolates used in this study and their corresponding MALDI-Types. 3 375 KB Open access
Additional file 2. Average Nucleotide Identity (ANI) of pairwise comparison of the T. maritimum isolates. 1 219 KB Open access
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 ... 1 57 KB Open access
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 ... 1 77 KB Open access
Additional file 5. Overview of recombination tracts between two pairs ofT. maritimumisolates. SNPs and recombination tracts between two closely related isolates. 1 943 KB Open access
Additional file 6. Heatmap displaying the diversity of ribosomal protein weights. Lines correspond to strains and columns correspond to ribosomal proteins in ascending order ... 1 86 KB Open access
Additional file 7. Monomorphic biomarker peaks. Screenshots of the 18 conserved peaks produced by 9 ribosomal monomorphic proteins with several degrees of ionization. The ... 2 593 KB Open access
Additional file 8. Quality control andT. maritimumspecies identification. The full dataset is composed of representatives of 24 Tenacibaculum species including 135 isolates ... 1 117 KB Open access
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) 1 636 KB Open access
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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.). Publisher's official version : https://doi.org/10.1186/s13567-020-00782-0 , Open Access version : https://archimer.ifremer.fr/doc/00630/74174/