Polyphasic characterization reveals the presence of novel fish-associated Chryseobacterium spp. in the Great Lakes of North America

Genome analysis deciphered Chryseobacterium indicum is a distinct species associated with freshwater pufferfish

A bacterium, strain PS-8T of the genus Chryseobacterium, was isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Strain PS-8T is a Gram-negative, aerobic, non-motile, and rod-shaped bacterium. Colonies appear in yellowish-orange colors. The major cellular fatty acids were C15:0 iso, C17:0 iso 3OH, C15:0 iso 3OH, and C11:0 anteiso. The predominant polar lipids were phosphatidylethanolamine and amino lipids. The genome size is 4.83 Mb. The G + C content was 35.6%. The in silico dDDH homology, ANI, and AAI were below the cutoff value, 70% and 95% to 96%, respectively, suggesting that strain PS-8T represents a defined species. The phylogenetic tree based on core and the non-recombinant genes showed the strain PS-8T clustered with Chryseobacterium gambrini DSM 18014T. Genome-wide analysis decodes several virulence factors of the genus Chryseobacterium, including genes for adherence, biofilm and stability, proliferation, resistance to immune response, and host-defense evasion system. The cladogram of the virulence genes showed a phylogenetic relationship among the Chryseobacterium species. Knowledge of the association of Chryseobacterium with freshwater pufferfish adds a new ecological niche to this bacterium.

Tris(1,3-dichloro-2-propyl) phosphate causes female-biased growth inhibition in zebrafish: Linked with gut microbiota dysbiosis

Tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) is ubiquitous in aquatic environment, but its effect on intestinal health of fish has yet not been investigated. In the present study, the AB strain zebrafish embryos were exposed to environmentally realistic concentrations (0, 30, 300, and 3000 ng·L^-1) of TDCIPP for 90 days, after which the fish growth and physiological activities were evaluated, and the intestinal microbes were analyzed by 16S rRNA gene high-throughput sequencing. Our results manifested that the body length and body weight were significantly reduced in the female zebrafish but not in males. Further analyses revealed that TDCIPP resulted in notable histological injury of intestine, which was accompanied by impairment of epithelial barrier integrity (decreased tight junction protein 2), inflammation responses (increased interleukin 1β), and disruption of neurotransmission (increased serotonin) in female intestine. Male intestines maintained intact intestinal structure, and the remarkably increased activity of glutathione peroxidase (GPx) might protect the male zebrafish from inflammation and intestinal damage. Furthermore, 16S rRNA sequencing analysis showed that TDCIPP significantly altered the microbial communities in the intestine in a gender-specific manner, with a remarkable increase in alpha diversity of the gut microbiome in male zebrafish, which might be another mechanism for male fish to protect their intestines from damage by TDCIPP. Correlation analysis revealed that abnormal abundances of pathogenic bacteria (Chryseobacterium, Enterococcus, and Legionella) might be partially responsible for the impaired epithelial barrier integrity and inhibition in female zebrafish growth. Taken together, our study for the first time demonstrates the high susceptibility of intestinal health and gut microbiota of zebrafish to TDCIPP, especially for female zebrafish, which could be partially responsible for the female-biased growth inhibition.

Atypical flavobacteria recovered from diseased fish in the Western United States

Flavobacterial diseases, caused by bacteria in the order Flavobacteriales, are responsible for devastating losses in farmed and wild fish populations worldwide. The genera Flavobacterium (Family Flavobacteriaceae) and Chryseobacterium (Weeksellaceae) encompass the most well-known agents of fish disease in the order, but the full extent of piscine-pathogenic species within these diverse groups is unresolved, and likely underappreciated. To identify emerging agents of flavobacterial disease in US aquaculture, 183 presumptive Flavobacterium and Chryseobacterium isolates were collected from clinically affected fish representing 19 host types, from across six western states. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis using the gyrB gene. Antimicrobial susceptibility profiles were compared between representatives from each major phylogenetic clade. Of the isolates, 52 were identified as Chryseobacterium species and 131 as Flavobacterium. The majority of Chryseobacterium isolates fell into six clades (A-F) consisting of ≥ 5 fish isolates with ≥ 70% bootstrap support, and Flavobacterium into nine (A-I). Phylogenetic clades showed distinct patterns in antimicrobial susceptibility. Two Chryseobacterium clades (F & G), and four Flavobacterium clades (B, G-I) had comparably high minimal inhibitory concentrations (MICs) for 11/18 antimicrobials tested. Multiple clades in both genera exhibited MICs surpassing the established F. psychrophilum breakpoints for oxytetracycline and florfenicol, indicating potential resistance to two of the three antimicrobials approved for use in finfish aquaculture. Further work to investigate the virulence and antigenic diversity of these genetic groups will improve our understanding of flavobacterial disease, with applications for treatment and vaccination strategies.

Integrated Transcriptome and 16S rDNA Analyses Reveal That Transport Stress Induces Oxidative Stress and Immune and Metabolic Disorders in the Intestine of Hybrid Yellow Catfish (Tachysurus fulvidraco♀ × Pseudobagrus vachellii♂)

Live fish are often transported in aquaculture. To explore the effects of transport stress, hybrid yellow catfish (Tachysurus fulvidraco♀ × Pseudobagrus vachellii♂) were subjected to simulated transport treatments (0–16 h) with 96 h of recovery after the 16-h transport treatment, and intestinal biochemical parameters, the transcriptome, and gut microbiota were analyzed. Transportation affected the number of mucus cells and led to oxidative stress in the intestine, which activated immune responses. Changes in lipid metabolism reflected metabolic adaptation to oxidative stress. Toll-like receptor signaling, peroxisome proliferator-activated receptor signaling, and steroid biosynthesis pathways were involved in the transport stress response. Gene expression analyses indicated that transport-induced local immune damage was reversible, whereas disordered metabolism recovered more slowly. A 16S rDNA analysis revealed that transport stress decreased the alpha diversity of the gut microbiota and disrupted its homeostasis. The dominant phyla (Fusobacteria, Bacteroidetes) and genera (Cetobacterium, Barnesiellaceae) were involved in the antioxidant, immune, and metabolic responses of the host to transportation stress. Correlation analyses suggested that gut microbes participate in the transport stress response and the host–microbiota interaction may trigger multiple events in antioxidant, immune, and metabolic pathways. Our results will be useful for optimizing transport processes.

Multifactorial Causes of Chronic Mortality in Juvenile Sturgeon (Huso huso)

This investigation focused on an episode of chronic mortality observed in juvenile Huso huso sturgeons. The examined subjects underwent pathological, microbiological, molecular, and chemical investigations. Grossly severe body shape deformities, epaxial muscle softening, and multifocal ulcerative dermatitis were the main observed findings. The more constant histopathologic findings were moderate to severe rarefaction and disorganization of the lymphohematopoietic lymphoid tissues, myofiber degeneration, atrophy and interstitial edema of skeletal epaxial muscles, and degeneration and atrophy of the gangliar neurons close to the myofibers. Chemical investigations showed a lower selenium concentration in affected animals, suggesting nutritional myopathy. Other manifestations were nephrocalcinosis and splenic vessel wall hyalinosis. Septicemia due to bacteria such as Aeromonas veronii, Shewanella putrefaciens, Citrobacter freundii, Chryseobacterium sp., and pigmented hyphae were found. No major sturgeon viral pathogens were detected by classical methods. Next-generation sequencing (NGS) analysis confirmed the absence of viral pathogens, with the exception of herpesvirus, at the order level; also, the presence of Aeromonas veronii and Shewanella putrefaciens was confirmed at the family level by the metagenomic classification of NGS data. In the absence of a primary yet undetected biological cause, it is supposed that environmental stressors, including nutritional imbalances, may have led to immune system impairment, facilitating the entry of opportunistic bacteria and mycotic hyphae.

Cross-protection of a live-attenuated Flavobacterium psychrophilum immersion vaccine against novel Flavobacterium spp. and Chryseobacterium spp. strains

For salmonid producers, a common threat is Flavobacterium psychrophilum. Recent advancements in bacterial coldwater disease (BCWD) management include the development of a live-attenuated immersion vaccine that cross-protects against an array of F. psychrophilum strains. Emerging family Flavobacteriaceae cases associated with clinical disease have been increasing, including pathogenic isolates of Flavobacterium spp. and Chryseobacterium spp. The cross-protective ability of a live-attenuated F. psychrophilum vaccine was determined against three virulent Flavobacteriaceae isolates. Juvenile rainbow trout were vaccinated, developed high F. psychrophilum-specific antibody titres and were challenged with Chryseobacterium spp. isolates (S25 and T28), a Flavobacterium sp. (S21) isolate, a mixed combination of S21:S25:T28, and a standard virulent F. psychrophilum CSF259-93 strain. Results demonstrated strong protection in the CSF259-93 vaccinated group (relative per cent survival (RPS)=94.44%) when compared to the relevant CSF259-93 controls (p < .001). Protection was also observed for vaccinated fish challenged with the S21:S25:T28 mix (RPS = 85.18%; p < .001). However, protection was not observed with the S21, S25 or T28 isolates alone. Analysis of whole-cell lysates revealed differences in protein banding by SDS-PAGE, but conserved antigenic regions by Western blot in S25 and T28. Results demonstrate that this live-attenuated vaccine provided protection against mixed flavobacterial infection and suggest further benefits against flavobacteriosis.

Identification of Chryseobacterium spp. isolated from clinically affected fish in California, USA

Chryseobacterium spp. (Family Flavobacteriaceae) are emergent fish pathogens in Europe, Asia and North America. In 2016-2017, 7 bacterial isolates were recovered from posterior kidney or spleen of cultured diseased rainbow trout Oncorhynchus mykiss (n = 1), green sturgeon Acipenser medirostris (n = 1), white sturgeon A. transmontanus (n = 2), blue ram cichlid Mikrogeophagus ramirezi (n = 1), and returning fall Chinook salmon O. tshawytscha (n = 2) from different freshwater systems. Bacterial colonies were visible after 24-48 h incubation at 20°C on agar media. Isolates were Gram-negative, rod-shaped, catalase and oxidase positive. Amplification and partial sequence analysis of the 16S rRNA and gyrB genes allocated the microorganisms to the genus Chryseobacterium sharing 97.2-99.6% similarity to 6 described Chryseobacterium spp. at the 16S rRNA locus, and 87.8-99.1% similarity at gyrB. Phylogenetic analyses in conjunction with percent sequence identity suggest some of the recovered isolates may represent novel Chryseobacterium subspecies or species. The pathogenicity of 5 isolates was evaluated experimentally in rainbow trout (n = 60), brown trout Salmo trutta (n = 60) and white sturgeon (n = 36) in flow-through freshwater at 18°C. Approximately 107 CFU fish-1 was injected in the epaxial musculature of anesthetized animals. Limited mortality was observed and no bacteria were recovered from dead or moribund fish post-challenge. Thirty days post-challenge, survivors were euthanized and multiple tissues were collected and fixed for histological analysis. No consistent histopathological changes were observed in challenged or control fish. While results suggest the recovered Chryseobacterium spp. may be opportunistic pathogens, further research is warranted to better understand the role of these bacteria in fish disease.

Gamete-associated flavobacteria of the oviparous Chinook salmon (Oncorhynchus tshawytscha) in lakes Michigan and Huron, North America

Flavobacterial diseases, caused by multiple members of the Family Flavobacteriaceae, elicit serious losses in wild and farmed fish around the world. Flavobacteria are known to be transmitted horizontally; however, vertical transmission has been suspected but proven only for one fish-pathogenic flavobacterial species (e.g., Flavobacterium psychrophilum). Herein, we report on the isolation and molecular identification of multiple Flavobacterium and Chryseobacterium taxa from the ovarian fluid and eggs of feral Great Lakes Chinook salmon (Oncorhynchus tshawytscha). Identified egg- and ovarian fluid-associated flavobacteria were either well-known flavobacterial fish pathogens (e.g., F. psychrophilum and F. columnare), most similar to emerging fish-associated flavobacteria (e.g., F. spartansii, F. tructae, F. piscis, C. piscium, C. scophthalmum), or were distinct from all other described Chryseobacterium and Flavobacterium spp., as determined by phylogenetic analyses using neighbor-joining, Bayesian, and Maximum Likelihood methodologies. The gamete-associated flavobacteria fell into three groups (e.g., those that were recovered from the ovarian fluid but not eggs; those that were recovered from the ovarian fluid and eggs; and those that were recovered from eggs but not ovarian fluid), a portion of which were recovered from eggs that were surface disinfected with iodophor at the commonly used dose and duration for egg disinfection. Some gamete-associated flavobacteria were also found in renal, splenic, and neurological tissues. Systemic polymicrobial infections comprised of F. psychrophilum and F. columnare were also detected at nearly an 11% prevalence. This study highlights the potential role that sexual products of female Great Lakes Chinook salmon may play in the transmission of fish-associated flavobacteria.

Flavobacterium psychrophilum Infections in Salmonid Broodstock and Hatchery-Propagated Stocks of the Great Lakes Basin

Bacterial coldwater disease (BCWD), caused by Flavobacterium psychrophilum, threatens wild and propagated salmonids worldwide and leads to substantial economic losses. In addition to being horizontally transmitted, F. psychrophilum can be passed from infected parents to their progeny, furthering the negative impacts of this pathogen. In Michigan, both feral and captive salmonid broodstocks are the gamete sources used in fishery propagation efforts. A 5-year study was initiated to follow the prevalence of systemic F. psychrophilum infections in feral broodstocks of four species (steelhead Oncorhynchus mykiss [potadromous Rainbow Trout]; Coho Salmon O. kisutch; Chinook Salmon O. tshawytscha; and Atlantic Salmon Salmo salar) residing in three Great Lakes watersheds. Additionally, captive broodstocks of four species (Rainbow Trout, Brown Trout Salmo trutta, Lake Trout Salvelinus namaycush, and Brook Trout Salvelinus fontinalis) maintained at two facilities were assessed for the presence of F. psychrophilum. The resultant offspring from each broodstock population were sampled for F. psychrophilum infections multiple times throughout hatchery residency. Using selective flavobacterial culture and PCR confirmation, F. psychrophilum was detected in all broodstocks except the captive Lake Trout and Brook Trout. Logistic regression analysis demonstrated that among the infected feral broodstocks, Chinook Salmon from the Lake Michigan watershed had the highest prevalence of systemic F. psychrophilum infection (mean = 63.2%). Among the captive broodstocks, the Gilchrist Creek strain of Brown Trout had the highest infection prevalence (mean = 5%). Collectively, the captive broodstocks were found to have significantly lower infection prevalence than the feral broodstocks. Despite the high prevalence of systemic F. psychrophilum infections in many broodstock populations, the bacterium was rarely detected in their progeny during hatchery rearing. However, heavy losses associated with clinical BCWD outbreaks did occur. Collectively, our results reinforce that BCWD continues to threaten Great Lakes basin salmonids.

Emerging flavobacterial infections in fish: A review

Flavobacterial diseases in fish are caused by multiple bacterial species within the family Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks around the world. In addition to directly imposing negative economic and ecological effects, flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite nearly 100 years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Europe, South America, Asia, Africa, and North America is also of major concern and has highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish.