In the United States, the aquaculture industry has not seen the same levels of growth in production as other countries—made evident by the $17 billion seafood trade deficit estimated in 2020. Nevertheless, aquaculture remains an important industry fully capable of supplementing the domestic seafood supply and reducing the US seafood trade deficit. Infectious diseases is one of several factors that threatens the capability and sustainability of the aquaculture industry, highlighting the importance of effective control strategies for these pathogens. Antimicrobial products are often used to control and eliminate undesirable microbes in effort to prevent or mitigate the impacts of infectious diseases. Some pathogens are capable of adapting to and resisting the antimicrobial effects, escalating the challenges associated with disease management in aquaculture. Antimicrobial resistance (AMR) is now recognised by numerous national and international agencies as a top global health concern and is problematic for US aquaculture. Currently, disease prevention and mitigation strategies utilised by US finfish aquaculture can be broken down into three levels; comprehensive protocols (biosecurity, disease response), good husbandry strategies (stress management, proper diet, optimal environment) and effective antimicrobial products (biocides, therapeutics). This review will discuss how each level contributes differently to the overall protection of fish from pathogens. In the era of AMR, this review will also highlight current and emerging alternative strategies that do not rely on traditional antimicrobial products (e.g., vaccines, dietary supplements, novel antimicrobial, stock selection) for disease prevention and mitigation.

A recently described emergent disease of ornamental fish has been associated with an Erysipelothrix species positive for the surface protective antigen (spa) C gene. Whole genome sequencing was performed on five spaC Erysipelothrix isolates from diseased ornamental fish. In addition, these spaC Erysipelothrix isolates were compared to spaA-, spaB- and other spaC-positive Erysipelothrix species isolated from terrestrial and marine mammals, birds and fish using multi-locus sequence analysis (MLSA). The genomes of fish pathogenic spaC isolates were genetically distinct from Erysipelothrix rhusiopathiae , sharing 86.61–86.94 % average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values of 31.6–32.2 %, but 99.01–99.11 % ANI and 90.8–91.9 % dDDH values with the uncharacterized spaC-positive Erysipelothrix sp. strain 2 isolated from swine. The findings indicate the spaC-positive fish and swine isolates are conspecific and represent a previously unrecognized taxon. While phylogenies inferred from MLSA sequences confirm this conclusion, slight genetic differences between the spaC fish isolates and swine strain 2 were indicated. Bath immersion challenge trials were conducted using tiger barbs (Puntigrus tetrazona) exposed by immersion to 10⁷ c.f.u. ml⁻¹ of three fish pathogenic spaC Erysipelothrix species, and three spaA and two spaB E. rhusiopathiae isolates as a model of infection. Thirty days post-challenge, cumulative mean percentage survival was 37 % for the spaA, 100 % for the spaB and 13 % for the spaC isolates, revealing differences in virulence among the various spa genotypes in fish. Genetic findings and observed differences in virulence demonstrate the fish pathogenic spaC isolates represent a novel species, for which the name Erysipelothrix piscisicarius sp. nov. is proposed. The type strain is E. piscisicarius 15TAL0474^T (=NRRL B-65533^T=ATCC-TSD-175^T=DSM 110099^T).

Piscine lactococcosis is a significant threat to cultured and wild fish populations worldwide. The disease typically presents as a per-acute to acute hemorrhagic septicemia causing high morbidity and mortality, recalcitrant to antimicrobial treatment or management interventions. Historically, the disease was attributed to the gram-positive pathogen Lactococcus garvieae . However, recent work has revealed three distinct lactococcosis-causing bacteria (LCB)— L. garvieae, L. petauri, and L. formosensis— which are phenotypically and genetically similar, leading to widespread misidentification. An update on our understanding of lactococcosis and improved methods for identification are urgently needed. To this end, we used representative isolates from each of the three LCB species to compare currently available and recently developed molecular and phenotypic typing assays, including whole-genome sequencing (WGS), end-point and quantitative PCR (qPCR) assays, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), API 20 Strep and Biolog systems, fatty acid methyl ester analysis (FAME), and Sensititre antimicrobial profiling. Apart from WGS, sequencing of the gyrB gene was the only method capable of consistent and accurate identification to the species and strain level. A qPCR assay based on a putative glycosyltransferase gene was also able to distinguish L. petauri from L. garvieae/formosensis . Biochemical tests and MALDI-TOF MS showed some species-specific patterns in sugar and fatty acid metabolism or protein profiles but should be complemented by additional analyses. The LCB demonstrated overlap in host and geographic range, but there were relevant differences in host specificity, regional prevalence, and antimicrobial susceptibility impacting disease treatment and prevention. IMPORTANCE: Lactococcosis affects a broad range of host species, including fish from cold, temperate, and warm freshwater or marine environments, as well as several terrestrial animals, including humans. As such, lactococcosis is a disease of concern for animal and ecosystem health. The disease is endemic in European and Asian aquaculture but is rapidly encroaching on ecologically and economically important fish populations across the Americas. Piscine lactococcosis is difficult to manage, with issues of vaccine escape, ineffective antimicrobial treatment, and the development of carrier fish or biofilms leading to recurrent outbreaks. Our understanding of the disease is also widely outdated. The accepted etiologic agent of lactococcosis is Lactococcus garvieae . However, historical misidentification has masked contributions from two additional species, L. petauri and L. formosensis , which are indistinguishable from L. garvieae by common diagnostic methods. This work is the first comprehensive characterization of all three agents and provides direct recommendations for species-specific diagnosis and management.

Streptococcus iniae is a re-emerging bacterial pathogen in freshwater and marine aquaculture worldwide. There are no commercial vaccines available for S. iniae in the United States, and autogenous vaccines are restricted to inactivated whole-cell preparations with limited protection against heterogenous strains. Live-attenuated vaccines (LAV) represent an advantageous alternative to these bacterins, as they induce robust cellular and humoral immunity, and may provide longer lasting protection through less stressful routes of administration. We investigated whether accumulation of mutations in S. iniae by serial passage in the presence of rifampin can generate immunogenic LAV conferring protection against challenge with heterologous wild-type (WT) S. iniae strains in Nile tilapia (Oreochromis niloticus). Three lineages of rifampin-resistant S. iniae strains were generated from three genetically distinct parent strains (n = 9) by multiple passages in increments of Rifamycin SV sodium salt. Growth in liquid media, extent of capsulation, antimicrobial susceptibility, survival in Nile tilapia whole blood, and cytotoxicity in an O. mossambicus endothelial cell line were compared between the passaged and WT strains. Nile tilapia challenges were used to assess strain virulence, generation of anti-S. iniae IgM, and the protection conferred by LAV candidates against virulent S. iniae. Rifampin-resistant strains demonstrated changes in growth rate and cytotoxicity in endothelial cells, as well as significant reductions in whole blood survival (p < 0.05). Selected strains also showed attenuated virulence in the Nile tilapia challenge model, and anti-S. iniae IgM generated against these strains demonstrated cross-reactivity against heterologous bacteria. Immunization by intracoelomic injection induced protection against a virulent WT strain of S. iniae, with relative percent survival up to 95.05%.