From Genogroups to Control Strategies: A Comprehensive Review of
Piscirickettsia salmonis
and Piscirickettsiosis to Optimize Health Management in Salmonid Aquaculture
This review identifies critical priorities requiring urgent investment: genogroup‐specific bivalent vaccine development, climate‐adaptive biosecurity frameworks, molecular diagnostic standardization for real‐time genogroup surveillance, and integrated control strategies tailored to P. salmonis.
Abstract
Piscirickettsiosis, caused by the facultative intracellular bacterium
Piscirickettsia salmonis
, remains the primary infectious disease economically limiting salmonid aquaculture in Chile, while its incidence has also increased in farmed salmonids in Ireland, Scotland, Australia, and Canada in recent years. This comprehensive review synthesizes 181 peer‐reviewed publications (2014–2026) to integrate transformative advances in
P. salmonis
genomics, pathogenesis, epidemiology, host immunity, and control strategies, updating the foundational 2014 review by Rozas and Enríquez. Comparative genomic studies have consistently resolved LF‐89‐like and EM‐90‐like isolates as two distinct phylogenomic clusters, with marked differences in pan‐genome composition, lineage‐specific proteins, ribosomal operon organization, and Dot/Icm‐associated genomic architecture, supporting genogroup‐level divergence that should not be inferred from any single threshold‐based metric such as Average Nucleotide Identity (ANI) alone. Genogroup‐specific disease phenotypes are also well established. LF‐89 produces chronic granulomatous infections, whereas EM‐90 causes acute hemorrhagic septicemia. Mechanistically,
P. salmonis
evades cell‐mediated immunity by inhibiting phagosome–lysosome fusion and suppressing MHC‐I–mediated antigen presentation, impairing CD8
+
cytotoxic T‐lymphocyte priming and likely explaining the consistently low vaccine efficacy and genogroup‐restricted cross‐protection observed under field conditions. Treatment failures persist despite absent widespread acquired resistance, attributable to intracellular persistence, biofilm formation, and pharmacokinetic–pharmacodynamic mismatches. Despite exponential growth in mechanistic knowledge, a substantial translational gap persists between research findings and operational implementation. This review identifies critical priorities requiring urgent investment: genogroup‐specific bivalent vaccine development, climate‐adaptive biosecurity frameworks, molecular diagnostic standardization for real‐time genogroup surveillance, and integrated control strategies tailored to
P. salmonis
genomic heterogeneity.
Yersinia enterocolitica is a psychrotrophic foodborne bacterium that can proliferate at refrigeration temperatures and is frequently associated with animal-source foods, raising concerns about food safety and public health. However, genomic data on Y. enterocolitica isolates from South Korea are limited, despite the increasing use of whole-genome sequencing (WGS) in bacterial surveillance. Herein, 91 Y. enterocolitica isolates recovered from chicken, pork, beef, and duck samples collected nationwide in 2024 were analyzed using WGS to elucidate their genomic diversity and genomic features. Phylogenomic analysis predicted all isolates as biotype 1A (sub-biotype 1Aa) and revealed substantial genetic diversity, comprising 27 sequence types and 43 core-genome types. Pan-genome analysis identified 11,230 gene clusters, revealing an open pan-genome in which accessory and unique gene clusters were assigned to predicted functional categories associated with metabolism, defense mechanisms, and stress responses. Although the canonical virulence plasmid pYV was absent, conserved chromosomal virulence-associated genes involved in adhesion (yapE), invasion (inv), secretion, and enterotoxicity (ystB) were detected. Antimicrobial resistance genes were predominantly intrinsic, particularly blaA and vat(F), whereas acquired resistance genes were identified sporadically. These findings provide a genomic baseline for biotype 1A Y. enterocolitica isolates recovered from animal-source foods in South Korea. The functional and public health significance of the detected virulence-associated loci requires further phenotypic investigation.
Dabin Kim, Sumin Ryu, Yeeun Kim et al.· Pathogens· 0 citations
This study provides a comprehensive characterization of a highly virulent A. veronii from Nile tilapia and reveals that selective downregulation of B-cell Ig genes is the dominant transcriptional feature of the host head kidney response.
Zulin Fang, Zhengshuang Li, Fuhao Geng et al.· Fish and Shellfish Immunolog...· 0 citations
Aeromonas hydrophila is a major pathogen of Motile Aeromonad Septicemia (MAS) in Nile tilapia, with pathogenesis and immunity poorly understood. In early 2026, a > 70% mortality outbreak occurred at a Nanning tilapia farm. The dominant strain NN0116 was identified as A. hydrophila by 16S rRNA and whole-genome ANI analysis. It exhibited high virulence (LD50 = 5.2 × 103 CFU/fish). Its 5.37 Mb genome encodes 5065 proteins and contains T2SS, T3SS, T6SS, and pore-forming toxins. Virulence and antimicrobial resistance genes co-localized on genomic islands GI2 and GI7. The strain was resistant to 12 antibiotic classes but susceptible to third-generation cephalosporins and fluoroquinolones. Head kidney transcriptomics at 24 h identified 1066 differentially expressed genes, including 61 immunoglobulin (Ig) genes. KEGG enrichment revealed 43 significant pathways; the top ten were driven by 26 Ig genes. Network analysis of the top 20 pathways identified B cell receptor signalling (ko04662) and COVID-19 (ko05171) as central nodes, alongside 10 secondary core pathways, all Ig-driven. Integration of bacterial genomic and host transcriptomic data characterizes hypervirulent A. hydrophila NN0116 and demonstrates that Ig-mediated B cell responses are central to host defence, offering targets for vaccines and therapeutics.
Fuhao Geng, Jifeng Zhang, Zulin Fang et al.· Journal of Fish Diseases· 0 citations
Photobacterium damselae subsp. damselae (Pdd) is a Gram-negative bacillus with zoonotic potential and wide global distribution. Found primarily in marine ecosystems, Pdd has been reported in diverse hosts, including fish, mollusks, crustaceans, marine mammals, sea turtles, birds, and humans. Infection dynamics are influenced by host factors such as environmental stress and pre-existing conditions, while clinical signs are frequently non-specific, making misdiagnosis likely. Its virulence involves iron acquisition systems, a polysaccharide capsule, hemolysins, and other cytotoxic enzymes, some of which are plasmid-encoded and whose expression is influenced by environmental conditions such as water temperature and salinity. This narrative review reports the current knowledge on Pdd’s pathogenic mechanisms, ecological traits, diagnostic approaches, and histopathological features of infections reported in various hosts. It also addresses antimicrobial resistance patterns and alternative prevention and control strategies, available genomic data, and future bioinformatics perspectives. As a conceptual framework, we propose climate change as a dual driver that compromises host defenses and may promote pathogen persistence and virulence, thereby potentially facilitating opportunistic infections and cross-species transmission. By highlighting knowledge gaps, this review aims to inform future surveillance efforts and interdisciplinary research on the ecological and epidemiological dynamics of Pdd in wildlife, livestock, domestic animals, and humans.
Marzia Sapio, Matteo Mellace, X. M. Matanza et al.· Frontiers in Microbiology· 0 citations
Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis, yet the ecological and genomic significance of environmental populations as potential reservoirs remains incompletely characterized. From May to October 2024, 108 water samples were collected monthly at one coastal and two estuarine sites in Haiyan, Zhejiang. Confirmed isolates (n = 39) underwent whole-genome sequencing, MLST/cgMLST, virulence and AMR gene screening, integron characterization with BLASTp (+2.17.0) integrase family typing, and viral-region prediction. Culture-based detection was absent in May and rose to 66.7% in October (Cochran–Armitage trend, p = 0.003), with descriptively higher detection at the coastal site. MLST identified 28 STs including four novel types (Simpson’s diversity = 0.953). All isolates lacked tdh, trh, and T3SS2 but retained T3SS1 and MAM7. One estuarine isolate carried CALIN-associated dfrA31 and qnrVC5. All integrases matched VpaIntIA (95.9–100% identity), not mobile class 1–3 integrases. Viral regions were detected in 38/39 isolates; filamentous phage annotations in 52.6%. Haiyan coastal V. parahaemolyticus shows seasonal and spatial patterns, high diversity, and a mobilome dominated by chromosomal super-integrons, underscoring the need for integrase family typing in environmental surveillance.
A robust single-nucleotide polymorphism (SNP) discovery strategy is designed and applied to existing and novel sequence data sets that represent the global diversity in potato production systems and indicates that potato wart was introduced into Canada from a European source.
Jeremy R. Dettman, Bart T. L. H. van de Vossenberg, Theo A. J. van der Lee et al.· Mycologia· 0 citations
