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Piscirickettsiosis, the cause of great losses in Chilean salmonid population, is produced by Piscirickettsia salmonis. The bacterium has developed resistance to treatments over time, including antibiotics and vaccines, due to a variety of evasive strategies, including biofilm formation. The bacterium has genomic islands, clusters of relevant genes that vary between genomes. This work aimed to analyze the relationship between number of pathogenic islands and their virulence genes in complete genomes from different strains of EM and LF genogroups, besides the search for genomic islands with non-virulent factors, like metabolic islands and fitness. Furthermore, we evaluated conservation and variation between strains from different genogroup, considering LF-89 (ATCC) and Psal-001 as reference strains, analyzing genomes through averages by two bioinformatic tools. About 13 pathogenic islands/strain were quantified, with 1 to 47 loci/island with unique behaviors for genogroup. Comparing islands regarding genomes, higher conservation rate was seen in EM genogroup, against oscillating values within LF genogroup strains. Non-virulent factors were also found. Overall, EM genogroup showed greater convergence in island conservation between strains concerning the pathogenic function compared to LF strains. Finally, different transposases were found to support high genomic plasticity and the scarcity of cured genes complicated correct identification.

Introduction: Piscirickettsia salmonis , the causative agent of Piscirickettsiosis, poses a significant threat to the Chilean aquaculture industry, resulting in substantial economic losses annually. The pathogen, first identified as specie in 1992, this pathogen was divided into two genogroups: LF-89 and EM-90, associated with different phenotypic mortality and pathogenicity. Traditional genotyping methods, such as multiplex PCR, are effective but limited by their cost, equipment requirements, and the need for specialized expertise., Methods: This study validates Loop-mediated Isothermal Amplification (LAMP) as a rapid and specific alternative for diagnosing P. salmonis infections. We developed the first qPCR and LAMP assay targeting the species-conserved tonB receptor gene ( ton B-r, WP_016210144.1) for the specific species-level identification of P. salmonis . Additionally, we designed two genotyping LAMP assays to differentiate between the LF-89 and EM-90 genogroups, utilizing the unique coding sequences Nitronate monooxygenase (WP_144420689.1) for LF-89 and Acid phosphatase (WP_016210154.1) for EM-90., Results: The LAMP assays demonstrated sensitivity and specificity comparable to real-time PCR, with additional benefits including rapid results, lower costs, and simplified operation, making them particularly suitable for field use. Specificity was confirmed by testing against other salmonid pathogens, such as Renibacterium salmoninarum, Vibrio ordalii, Flavobacterium psychrophilum, Tenacibaculum maritimum , and Aeromonas salmonicida , with no cross-reactivity observed., Discussion: The visual detection method and precise differentiation between genogroups underscore LAMP's potential as a robust diagnostic tool for aquaculture. This advancement in the specie detection (qPCR and LAMP) and genotyping of P. salmonis represents a significant step forward in disease management within the aquaculture industry. The implementation of LAMP promises enhanced disease surveillance, early detection, and improved management strategies, ultimately benefiting the salmonid aquaculture sector., Competing Interests: JM-S was employed by Mowi Chile S.A. FA and AY were employed by Greenvolution SpA. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Isla, Aguilar, Flores-Martin, Barrientos, Soto-Rauch, Mancilla-Schulz, Almendras, Figueroa and Yañez.)