Genomic characterization of Tenacibaculum maritimum O‐antigen gene cluster and development of a multiplex PCR‐based serotyping scheme

Abstract

Tenacibaculum maritimum is a devastating bacterial pathogen affecting a large variety of marine fish species. It is responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyse bacterial diversity and population structure. Serological heterogeneity has been observed and up to four different serotypes have been described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping and genome‐wide association study, we identified the genomic loci likely involved in the O‐antigen biosynthesis. This finding allowed the development of a robust multiplex PCR‐based serotyping scheme able to detect subgroups within each serotype and therefore performs better than conventional serotyping. This scheme was successfully applied to a large number of isolates from worldwide origin and retrieved from a large variety of fish species. No obvious correlations were observed between the mPCR‐based serotype and the host species or the geographic origin of the isolates. Strikingly, the distribution of mPCR‐based serotypes does not follow the core genome phylogeny. Nevertheless, this simple and cost‐effective mPCR‐based serotyping method could be useful for different applications such as population structure analysis, disease surveillance, vaccine formulation and efficacy follow‐up.

Genomics of Tenacibaculum Species in British Columbia, Canada

“…In this study, 3819.5 ± 2.1 CDS were similar between barcodes 9 and 10 using both 95% and 80% similarity thresholds. The large increase in the number of CDS compared and the amount of core-genes in this study, in contrast to previous work [ 54 , 55 ], could be attributed to factors including, but not limited to: the sample size and selected isolates (i.e., reduced sample size and geographically similar isolates for the same species would provide more similar core-genes); the sequencing platforms; how the genomes were assembled; the tools used to interpret core genes (Panaroo (this study) vs Microscope [ 54 , 55 ]); and potential contamination.…”

“…Few highly similar genes consisting of the core-genome at 95%, but more intermediately similar genes at 80%, indicate substantial genetic diversity across the genus. In contrast to previous studies [ 10 , 54 , 55 ], the different core-genome sizes also likely occurred because the genome sizes vary across the Tenacibaculum species (i.e., 2.7 to 4.2 Mb).…”

“…Future research will focus on using hybrid approaches to sequence and assemble BC Tenacibaculum genomes. A limitation of this study includes the fact that three chromosomes could not be completely assembled, while an unreconciled result of this study includes that the estimated number of nucleotides for barcodes 9 and 10 were ~ 4.2 Mb, which is greater than previously described (i.e., ~ 3.4 Mb) in T. maritimum [ 54 , 55 ]. This limitation and unreconciled result could be due to the quality of the template DNA, the extraction methodology, the sequencing platforms used, the genome assembly criteria, and potential contamination.…”

“…In contrast to previous studies [ 10 , 54 , 55 ], the present study compared the gene content across four Tenacibaculum species, where only 191 and 973 loci comprised the core genome at 95% and 80% gene cluster similarity thresholds, respectively. A small core genome has been recorded in Lactobacillus spp., with 266 core genes [ 100 ].…”

“…In one study, 2116 core-genes accounting for ~75% of the genes in each genome were described in 25 T. maritimum strains [ 54 ]. In another study, 2034 core-genes were identified between 40 T. maritimum strains [ 55 ]. In this study, 3819.5 ± 2.1 CDS were similar between barcodes 9 and 10 using both 95% and 80% similarity thresholds.…”