COMPARATIVE STUDY OF STRIPED CATFISH (PANGASIUS HYPOPHTHALMUS) SKIN, NILE TILAPIA (OREOCHROMIS NILOTICUS) SKIN, AND PORCINE SKIN AS A XENOGRAFT MATERIAL FOR BURN WOUND.

Burn injury remains a health problem, specifically in Indonesia. In major burns, xenograft has been proved to be useful as temporary wound coverage. However, some xenografts are not widely available due to cultural, financial and religious backgrounds, or have an unesthetic appearance, such as the scaly appearance of tilapia fish xenograft. Striped catfish (Pangasius hypophthalmus) is a scaleless fish that has abundant type 1 collagen. This study aimed to compare striped catfish skin to commonly used xenograft (Nile tilapia and porcine skin) as xenograft material for burn wound. In this experimental study, nine different skin samples of striped catfish, Nile tilapia and porcine were prepared and histologically examined using hematoxylin-eosin stained samples. Macroscopic and microscopic features of each sample were documented and analysed. The macroscopic skin appearances of striped catfish were hairless and scaleless with black-silver color and moderate thickness. As for microscopic features, the epidermal thickness of striped catfish skin (8.49±1.60 µm) was significantly different to both Nile tilapia (2.18±0.37 µm; p<0.001) and porcine skin (42.22±14.85 µm; p=0.002). The dermal thickness of striped catfish skin (288.46±119.04 µm) was similar to Nile tilapia (210.68±46.62 µm; p=0.783) but differs significantly to porcine skin (1708.44±505.12 µm; p<0.001). The integrity and collagen organization of striped catfish was also similar to tilapia based on semi-quantitative histology scoring system (p>0.05). Striped catfish had potential macroscopic appearance and comparable microscopic features to Nile tilapia; smoother macroscopic appearance, thicker epidermis, and similar dermis thickness. Therefore, we believe it can be potentially used as a xenograft material. Further studies are required to evaluate the effectiveness and feasibility of striped catfish xenograft in burn wound management.

Les brûlures restent un problème de santé publique, en Indonésie comme ailleurs. Les xénogreffes ont montré leur utilité comme couverture temporaire en cas de brûlure étendue. Certaines xénogreffes peuvent n'être pas utilisables pour des raisons financières, culturelles ou religieuses. L'aspect écaillé des xénogreffes de tilapia peut aussi rebuter. Le silure- requin a une peau dépourvue d'écaille, abondante en collagène de type 1. Cette étude expérimentale compare cette xénogreffe à celles de tilapia du Nil et de porc. Neuf biopsies cutanées de silure- requin, tilapia du Nil et de porc ont été examinées macroscopiquement et histologiquement (après coloration hématoxyline- éosine). Macroscopiquement, la peau de silure- requin est glabre, dépourvue d'écaille, argent à noire et d'épaisseur modérée. Microscopiquement, l'épiderme du silure- requin (8,49 +/- 1,6 µm) est plus épais que celui du tilapia du Nil (2,18 +/- 0,37; p<0,001) et moins épaisse que celui du porc (42,22 +/- 14,85; p = 0,002). L'épaisseur du derme du silure- requin est comparable à celle du tilapia du Nil (288,46 +/- 119,04 VS 210,68 +/- 46,62 µm; p = 0,783), nettement plus fin que celui du porc (1 708,44 +/- 505,12 µm; p < 0,001). L'organisation du collagène, évaluée par un score histologique semi- quantitatif, est similaire chez les 2 poissons. Ces aspects macroscopique et microscopique de la peau du silurerequin en font un candidat à la xénogreffe, devant être étudié plus avant.

Optimizing growth and yield of striped catfish (Pangasianodon hypophthalmus) and quinoa (Chenopodium quinoa) in a biosaline integrated aquaculture-agriculture systems.

Soil salinity and freshwater scarcity are among the major global threats to sustainable development owing to their adverse impacts on agricultural productivity especially in arid and semi-arid regions. There is a need to find sustainable alternatives such as salt-tolerant crops and fish to improve people's livelihoods in marginal areas. This study aimed to maximize the growth and yield of striped catfish (Pangasianodon hypophthalmus) and quinoa (Chenopodium quinoa) cultivated under a biosaline integrated aquaculture-agriculture system. The study was laid in a randomized completely block design of three saline effluent treatments under three replicates: 5000 ppm (T1), 10,000 ppm (T2), 15,000 ppm (T3), and control (T0). Agro-morphological and physiological attributes of quinoa were measured. The crop yield in biomass and mineral element composition was also studied. Additionally, fish growth performance parameters such as feed intake and efficiency, growth, and survival rate were also calculated. Our results indicated that irrigating quinoa with saline aquaculture effluents above 10,000 ppm enhanced the plant growth, yield, and nutrient content of seeds. Furthermore, rearing striped catfish in saline water reaching up to 15,000 ppm did not have adverse impacts on the growth and survival of fish. Overall, integrating catfish and quinoa production under a salinity regime of 10,000 ppm could be a potential solution to ensuring alternative food sources in marginal areas.

Antibiotic resistance profiles of sentinel bacteria isolated from aquaculture in Cambodia.

The misuse of antibiotics and the emergence of antimicrobial resistance (AMR) is a concern in the aquaculture industry because it contributes to global health risks and impacts the environment. This study analyzed the AMR of sentinel bacteria associated with striped catfish (Pangasisanodon hypophthalmus) and giant snakehead (Channa micropeltes), the two main fish species reared in the pond culture in Cambodia. Phenotypic and genotypic characterization of the recovered isolates from fish, water, and sediment samples revealed the presence of bacteria, such as 22 species belonging to families Aeromonadaceae, Enterobacteriaceae, and Pseudomonadaceae. Among 48 isolates, Aeromonas caviae (n = 2), Aeromonas hydrophila (n = 2), Aeromonas ichthiosmia (n = 1), Aeromonas salmonicida (n = 4) were detected. A. salmonicida and A. hydrophilla are known as fish pathogens that occur worldwide in both fresh and marine water aquaculture. Antibiotic susceptibility testing revealed antibiotic resistance patterns of 24 (50 %) isolates among 48 isolates with higher multiple antibiotic resistance index (> 0.2). All the isolates of Enterobacteriaceae were susceptible to ciprofloxacin. Ciprofloxacin is a frontline antibiotic that is not recommended to use in aquaculture. Therefore, its use has to be strictly controlled. This study expands our knowledge of the AMR status in aquaculture farms which is very limited in Cambodia.

Genomic Insights into Edwardsiella ictaluri: Molecular Epidemiology and Antimicrobial Resistance in Striped Catfish (Pangasianodon hypophthalmus) Aquaculture in Vietnam.

Edwardsiella ictaluri is responsible for causing bacillary necrosis (BNP) in striped catfish (Pangasianodon hypophthalmus) in Vietnam. This study offers a comprehensive genomic characterization of E. ictaluri to enhance understanding of the molecular epidemiology, virulence, and antimicrobial resistance. E. ictaluri isolates were collected from diseased striped catfish in the Mekong Delta. The species was confirmed through PCR. Antimicrobial susceptibility testing was conducted using minimum inhibitory concentrations for commonly used antimicrobials. Thirty representative isolates were selected for whole genome sequencing to delineate their genomic profiles and phylogeny. All strains belonged to ST-26 and exhibited genetic relatedness, differing by a maximum of 90 single nucleotide polymorphisms. Most isolates carried multiple antimicrobial resistance genes, with the tet(A) gene present in 63% and floR in 77% of the genomes. The ESBL gene, blaCTX-M-15, was identified in 30% of the genomes. Three plasmid replicon types were identified: IncA, p0111, and IncQ1. The genomes clustered into two clades based on their virulence gene profile, one group with the T3SS genes and one without. The genetic similarity among Vietnamese isolates suggests that disease spread occurs within the Mekong region, underscoring the importance of source tracking, reservoir identification, and implementation of necessary biosecurity measures to mitigate spread of BNP.

Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam.

Aeromonas spp. are commonly found in the aquatic environment and have been responsible for motile Aeromonas septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 Aeromonas isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated Aeromonas species while traditional methods such as aerA PCR and MALDI-TOF were unable identify A. dhakensis. A. dhakensis was found to be more prevalent than A. hydrophila in both diseased catfish and human infections. A. dhakensis sequence type (ST) 656 followed by A. hydrophila ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin ast in A. dhakensis), AMR genes (i.e. presence of imiH carbapenemase in A. dhakensis), and accessory gene content. To uncover potential conserved proteins of Aeromonas spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of Aeromonas in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent A. dhakensis strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing Aeromonas diseases in catfish and humans, and the search for potential vaccine candidates could focus on Aeromonas core genes encoded for membrane and secreted proteins.

Dietary supplementation of cinnamaldehyde positively affects the physiology, feed utilization, growth, and body composition of striped catfish Pangasianodon hypophthalmus.

The study evaluated the effects of diverse cinnamaldehyde (CIN) supplementation doses on the physiological attributes, feed utilization, growth, and body composition of striped catfish Pangasianodon hypophthalmus. The study incorporated five doses of CIN supplementation, namely 0, 0.5, 1, 1.5, and 2 g kg-1 feed, with four replicates per group. Commercial extruded isonitrogenous and isoenergetic feeds with crude protein and gross energy levels of 28.46% ± 0.23% and 3858.70 ± 18.06 kcal kg-1, respectively, were used as test feeds. The initial weight of striped catfish was 5.57 ± 0.02 g, and 30 fish were maintained in each cage (2 × 1 × 1 m3) for 60 days. The results illustrated that the incorporation of CIN into the diet increases amylase and lipase levels and the ability of striped catfish to accumulate glucose, as the glucose tolerance test revealed that CIN 1.0 and 1.5 g kg-1 reduced glucose content to its basal level at 3-4 h postinjection and upregulated the insulin receptor, hexokinase, and hormone-sensitive lipase genes. CIN 1.5 g kg-1 also increased plasma total protein and high-density lipoprotein levels and reduced triglyceride and cholesterol levels. CIN 1.0-2.0 g kg-1 increased antioxidant capacity by increasing the levels of superoxide dismutase and glutathione and decreasing malondialdehyde levels. CIN 1.5 g kg-1 was the best treatment for increasing final weight, the specific growth rate, protein retention, and the protein efficiency ratio and for decreasing the feed conversion ratio. CIN additionally increased meat protein and decreased meat and liver lipid content. This study concluded that 1.24 g kg-1 is the optimal CIN dose calculated from the equation Y = - 0.1487x2 + 0.3702x + 5.0724 (R2 = 0.71) to increase growth and feed efficiency in striped catfish by increasing nonprotein catabolism and exerting antioxidant effects.

Comparative genomic analysis of Aeromonas dhakensis and Aeromonas hydrophila from diseased striped catfish fingerlings cultured in Vietnam.

Introduction: Motile Aeromonas septicemia (MAS) is a burden for striped catfish (Pangasius hypophthalmus) farmers in Vietnam. MAS can be caused by several species of Aeromonas but Aeromonas hydrophila is seen as the leading cause of MAS in aquaculture, but recent reports suggest that A. dhakensis is also causing MAS. Methods: Here we investigated the bacterial etiology of MAS and compared the genomic features of A. hydrophila and A. dhakensis. We collected 86 isolates from diseased striped catfish fingerlings over 5 years from eight provinces in Vietnam. Species identification was done using PCR, MALDI-TOF and whole genome sequence (WGS). The MICs of commonly used antimicrobials was established. Thirty presumed A. hydrophila isolates were sequenced for species confirmation and genomic comparison. A phylogenetic analysis was conducted using publicly available sequences and sequences from this study. Results: A total of 25/30 isolates were A. dhakensis sequence type (ST) 656 and 5/30 isolates were A. hydrophila ST 251. Our isolates and all publicly available A. hydrophila isolates from Vietnam belonged to ST 251 and differed with <200 single nucleotide polymorphisms (SNP). Similarly, all A. dhakensis isolates from Vietnam belonged to ST 656 and differed with <100 SNPs. The tet(A) gene was found in 1/5 A. hydrophila and 19/25 A. dhakensis. All A. hydrophila had an MIC ≤2 mg/L while 19/25 A. dhakensis had MIC ≥8 mg/L for oxytetracycline. The floR gene was only found in A. dhakensis (14/25) which showed a MIC ≥8 mg/L for florfenicol. Key virulence genes, i.e., aerA/act, ahh1 and hlyA were present in all genomes, while ast was only present in A. dhakensis. Discussion: This study confirms previous findings where A. dhakensis was the dominating pathogen causing MAS and that the importance of A. hydrophila has likely been overestimated. The differences in antimicrobial susceptibility between the two species could indicate a need for targeted antimicrobial treatment plans. The lipopolysaccharide regions and outer membrane proteins did not significantly differ in their immunogenic potentials, but it remains to be determined with in vivo experiments whether there is a difference in the efficacy of available vaccines against A. hydrophila and A. dhakensis.

Acceleration of gonadal maturity of female striped catfish, Pangasianodon hypophthalmus (Pisces, Pangasiidae) by irradiation to low-power soft-laser.

This study was aimed to investigate the effects of red photodiode soft-laser irradiation on gonadal maturity and egg quality of female striped catfish, Pangasianodon hypophthalmus. Four female striped catfish (weighing 700-800 g) at stage I of gonadal maturation (for all treatments) were exposed four times (once a week) to different doses (0.2, 0.4, 0.6, and 0.8 J/cm2) of red photodiode soft-laser in the reproductive acupoint. Doses of 500 IU and 0.5 mL per kg body weight of human chorionic gonadotropin (hCG) and Ovaprim™, respectively were injected intramuscularly at week 4 (positive control), and no treatment (negative control). Finally, gonadal maturation stage (GMS), gonadosomatic index (GSI), hepatosomatic index (HSI), fecundity, and egg diameter were measured at week 5. The results showed that red photodiode soft-laser irradiation of 0.4 J/cm2 dose accelerated GMS IV at early week 3 (100 %) and increases GSI (3.42 %), HSI (1.26 %), fecundity (67,665 eggs/body weight), and egg diameter (1.01 mm) compared to the other treatments. Treatments of 0.2, 0.6, and 0.8 J/cm2 doses, and positive and negative controls only reached GMS III (75 %), III (25 %), I (100 %), II (25 %), and I (100 %), respectively. GSI values were 2.20 %, 1.47 %, 0.93 %, 0.44 %, and 0.42 %, respectively and HSI values were 1.07 %, 0.85 %, 0.7 7%, 0.66 %, and 0.53 %, respectively. Females irradiated with doses of 0.2 and 0.6 J/cm2 had fecundities of 38,822 and 29,530 eggs/body weight, respectively, and egg diameters of 0.88 and 0.29 mm, respectively. These results suggest that a red photodiode soft-laser irradiation accelerates gonadal maturity and improves egg quality in female striped catfish.

Bacteriophage PVN06 protected catfish Pangasianodon hypophthalmus from Edwardsiella ictaluri infection.

Bacillary necrosis of pangasius (BNP) is a disease caused by Edwardsiella ictaluri bacteria in striped catfish Pangasianodon hypophthalmus that results in high mortality rates. To control this disease, bacteriophages have been considered as alternatives to antibiotics. In this study, we applied the lytic bacteriophage PVN06 in striped catfish fingerlings to prevent E. ictaluri infection. In an experimental trial, the phage was administered to fish by feeding phage-coated feed with doses of 7.17±0.09, 8.17±0.09 and 9.17±0.09 log PFU/g feed per day before bacterial infection. Fish were infected by bacteria once with concentrations ranging from 3.01 to 7.01 log CFU/ml tank water. A day after infection, phage treatment resumed at a rate of once per day until the end of the trial. The results of the trial show that bacterial infection caused typical symptoms of BNP in fish with the cumulative fish death rate of 36.7±2.9 to 75.0±5.0%, depending on the bacterial concentration used for infection. Phage treatment with 9.17±0.09 log PFU/g significantly reduced the mortality rate, while treatments with 8.17±0.09 and 7.17±0.09 log PFU/g did not. This phage dose resulted in a 61.7-fold reduction in the toxicity of the bacterial pathogen and the survival rate of 15-23.3% in fish. Our study has demonstrated that the bacteriophage PVN06 protected striped catfish from BNP.

Effect of Citrus aurantium juice as a disinfecting agent on quality and bacterial communities of striped catfish steaks stored at -20 °C.

Sodium hypochlorite is generally used as a disinfectant in washing of freshwater fishes where the safety aspect of health is of concern. Although plant-based essential oils and synthetic chemical agents have been applied, they might contain toxic substances, are expensive and can cause undesirable quality. This research aims to fill the knowledge gap necessary to validate Citrus aurantium juice as a disinfecting agent for preserving striped catfish steaks at -20 °C for 28 days. Fifty (50) ppm sodium hypochlorite was used as a commercial disinfectant (control). The results showed that a negative color characteristic (higher a* and increased b*) was found in the control but not in striped catfish steaks immersed in C. aurantium juice (TM) on days 14 and 28. No significant differences were found in the peroxide value among the treatments on days 14 and 28 (P > 0.05). A lower accumulation of trichloroacetic acid soluble peptides was detected in TM but not in control, while total volatile basic nitrogen of all treatments was up to standard of fish quality during storage. Contrastingly, the total viable count of both treatments increased to >7.0 log CFU/g on day 28 which did not meet the edible limit of standard for freshwater fishes. The spoilage microbial community was observed on days 0 and 28 of storage which showed a decrease in relative abundance of Acinetobacter, Pseudomonas, Brochothrix, Lactococcus, Carnobacterium, Psychrobacter, and Vagococcus as found in TM on day 28, when compared to the control. Thus, these results implied that C. aurantium juice could replace sodium hypochlorite as an alternative disinfecting agent to control the microbiological spoilage and physico-chemical quality of striped catfish steaks.

Novel single nucleotide polymorphisms of insulin-like growth factor-binding protein 7 (IGFBP7) gene significantly associated with growth traits in striped catfish (Pangasianodon hypophthalmus Sauvage, 1878).

Breeding program to improve economically important growth traits in striped catfish (Pangasianodon hypophthalmus) requires effective molecular markers. This study was conducted to identify single nucleotide polymorphisms (SNPs) of Insulin-like Growth Factor-Binding Protein 7 (IGFBP7) gene which plays multiple roles in regulating growth, energy metabolism and development. The association between SNPs in IGFBP7 gene and growth traits in striped catfish was analyzed in order to uncover the SNPs that have potential to be valuable markers for improving growth traits. Firstly, fragments of IGFBP7 gene from ten fast-growing fish and ten slow-growing fish were sequenced in order to discover SNPs. After filtering the detected SNPs, an intronic SNP (2060A > G) and two non-synonymous SNPs (344 T > C and 4559C > A) causing Leu78Pro and Leu189Met in protein, respectively, were subjected to further validated by individual genotyping in 70 fast-growing fish and 70 slow-growing fish using single base extension method. Our results showed that two SNPs (2060A > G and 4559 C > A (p. Leu189Met)) were significantly associated with the growth in P. hypophthalmus (p < 0.001), thus being candidate SNP markers for the growth traits of this fish. Moreover, linkage disequilibrium and association analysis with growth traits of haplotypes generated from the 3 filtered SNPs (344 T > C, 2060 A > G and 4559 C > A) were examined. These revealed that the non-coding SNP locus (2060A > G) had higher genetic diversity at which the G allele was predominant over the A allele in the fast-growing fish. Furthermore, the results of qPCR showed that expression of IGFBP7 gene with genotype GG (at locus 2060) in fast-growing group was significantly higher than that with genotype AA in slow-growing group (p < 0.05). Our study provides insights into the genetic variants of IGFBP7 gene and useful data source for development molecular marker for growth traits in breeding of the striped catfish.

Evaluation of feed utilization, immune response and disease resistance in striped catfish, Pangasianodon hypophthalmus (Sauvage 1878) fed with a novel Aeromonas hydrophila biofilm vaccine.

Striped catfish, Pangasianodon hypophthalmus was immunized with Biofilm (BF) and Free cell (FC) of Aeromonas hydrophila vaccine at 1010 CFU g-1 for 20 days and monitored for growth parameters, immune responses and disease resistance up to 60 day post vaccination (dpv). Pangasius catfish in the BF vaccinated group had considerably higher growth and feed utilization than the FC vaccinated and unvaccinated groups (p < 0.05). Biofilm vaccinated group showed a significant increase (p < 0.05) in the mean weight gain (46.91 ± 0.59) than the FC (35.94 ± 0.21) and unvaccinated group (34.92 ± 0.35). The vaccinated fishes were challenged with A. hydrophila at 107 CFU/ml. Significant higher relative percentage survival (RPS) was recorded with BF (84.21 ± 1.49%) compared to that with FC (33.33 ± 1.21%). Polyclonal antibody-based ELISA was used to quantify the antibody titre. BF vaccinated group showed significantly higher antibody titer compared to other treatments (p < 0.05). Moreover, higher haematological parameters recorded in the present study were differentially stimulated by the oral administration of A. hydrophila biofilm vaccine. The mean total protein, albumin, and globulin levels of the BF vaccine groups were significantly higher (p < 0.05) than the mean total protein, albumin, and globulin contents of the unvaccinated group. Furthermore, biochemical stress parameters (SGPT, SGOT) in the vaccinated groups showed an incremental trend in the early days of the experimental period. However, the values were significantly lower (p < 0.05) in the biofilm group on 20 dpv onwards indicating improved health condition. Vaccinated BF fishes showed gut associated lymphoid tissues (GALT) within the laminar propria of mid gut. But in FC group fishes showed less aggregation of lymphoid cells. The unvaccinated control fish had no lymphoid cell aggregation in their intestines. The findings of the current research suggested that biofilm vaccine has the capability to be one of the potential oral vaccines in striped catfish against A. hydrophila infection.

High Dietary Histamine Induces Digestive Tract Oxidative Damage in Juvenile Striped Catfish (Pangasianodon hypophthalmus).

A 56-day feeding trial investigated the effects of dietary histamine on the antioxidant capacity, gastric and intestinal barrier functions, and growth performance of striped catfish (Pangasianodon hypophthalmus). Seven isonitrogenous (34.0% crude protein) and isolipidic (10.5% crude lipid) diets were formulated with supplemental 0, 15, 30, 60, 120, 240, and 480 mg/kg of histamine, named H0, H15, H30, H60, H120, H240, and H480 group, respectively. Results showed that the weight gain rate, specific growth rate, relative intestinal length in the H240 and H480 groups, and the condition factors in the H480 group were significantly lower than those in the H0 group. Intestinal total antioxidant capacity, peroxidase, catalase, superoxide dismutase, glutathione peroxidase, and glutathione reductase activities in the H480 group were significantly lower than those in the H0 group, whereas intestinal malondialdehyde content exhibited the opposite trend. Intestinal complement 3, complement 4, immunoglobulin M, and Recombinant Mucin 2 in the H480 group were significantly lower than those in the H0 group, in contrast to intestinal lipopolysaccharide content. Intestinal IL-10 gene expression in the H480 group was significantly lower than that in the H0 group, whereas the TNF-α, IL-1, IL-6, and IL-8 gene expression exhibited opposite results. Scanning and transmission electron microscopic observation of the gastrointestinal tract revealed severe damage to the gastric mucosa and intestinal epithelium in the H480 group. The abundance of Treponema in the histamine groups was significantly higher than that in the H0 group. These results indicated that high dietary histamine decreases intestinal immunity and antioxidant capacity, inducing digestive tract oxidative damage and ultimately decreasing the growth of striped catfish.

Genome-Wide Identification, Characterisation and Phylogenetic Analysis of 52 Striped Catfish (Pangasianodon hypophthalmus) ATP-Binding Cassette (ABC) Transporter Genes.

The Pangasianodon hypophthalmus (striped or tra catfish) is a Pangasiidae family member famous for its high unsaturated fatty acid content flesh. This riverine catfish can breathe in the air unlike the channel catfish. One of the most well-known ecotoxicological protein superfamily, the ATP-binding cassette (ABC) transporters, has been characterised in channel catfish through a genome-wide approach. Therefore, it is interesting to unearth these proteins within the striped catfish genome for a comprehensive comparison across all catfishes available. A total of 52 ABC transporters were discovered from the striped catfish genome. The motif analysis has unconcealed various unshared characteristics of some catfishes. The phylogenetic analysis has evidenced its effectiveness in the successful annotations of these transporter proteins. Duplicated genes such as ABCA1, ABCB3, ABCB6, ABCC5, ABCD3, ABCE1, ABCF2 as well as ABCG2 were uncovered within the striped and channel catfish genomes. This entire set of ABC transporters yields precious genomic data for future ecotoxicological, biochemical and physiological research in striped catfish.

A High-Quality Genome Assembly of Striped Catfish (Pangasianodon hypophthalmus) Based on Highly Accurate Long-Read HiFi Sequencing Data.

The HiFi sequencing technology yields highly accurate long-read data with accuracies greater than 99.9% that can be used to improve results for complex applications such as genome assembly. Our study presents a high-quality chromosome-scale genome assembly of striped catfish (Pangasianodon hypophthalmus), a commercially important species cultured mainly in Vietnam, integrating HiFi reads and Hi-C data. A 788.4 Mb genome containing 381 scaffolds with an N50 length of 21.8 Mb has been obtained from HiFi reads. These scaffolds have been further ordered and clustered into 30 chromosome groups, ranging from 1.4 to 57.6 Mb, based on Hi-C data. The present updated assembly has a contig N50 of 14.7 Mb, representing a 245-fold and 4.2-fold improvement over the previous Illumina and Illumina-Nanopore-Hi-C based version, respectively. In addition, the proportion of repeat elements and BUSCO genes identified in our genome is remarkably higher than in the two previously released striped catfish genomes. These results highlight the power of using HiFi reads to assemble the highly repetitive regions and to improve the quality of genome assembly. The updated, high-quality genome assembled in this work will provide a valuable genomic resource for future population genetics, conservation biology and selective breeding studies of striped catfish.

Effects of dietary rambutan (Nephelium lappaceum L.) peel powder on growth performance, immune response and immune-related gene expressions of striped catfish (Pangasianodon hypophthalmus) raised in biofloc system.

This study aimed to evaluate the effects of rambutan peel powder (RP) on growth, skin mucosal and serum immunities, and immune-related gene expression of striped catfish (Pangasianodon hypophthalmus) reared in a biofloc system. Three hundred fingerlings (17.14 ± 0.12 g fish-1) were randomly selected and assigned to five treatments corresponding to five diets: 0 g kg-1 (control - RP0); 10 g kg-1 (RP10); 20 g kg-1 (RP20); 40 g kg-1 (RP40), and 80 g kg-1 (RP80) for 8 weeks. At weeks 4 and 8 post-feeding, growth, skin mucus, and serum immunity parameters were determined, whereas immune-related gene expressions were performed at the end of the feeding trial. Based on the results, skin mucus lysozyme (SML) and skin mucus peroxidase (SMP) were significantly higher in fish fed the RP diets compared to the control diet (P < 0.05). The highest SML and SMP levels were observed in fish fed RP40 diet, followed by RP20, RP80, RP10, and RP0. Fish-fed RP diets had higher serum lysozyme and serum peroxidase activities, with the highest value found in the RP40 diet (P < 0.05), followed by RP20, RP80, and RP10. Similarly, immune-related gene expressions (IFN2a, IFN2b, and MHCII) in the liver were significantly up-regulated in fish fed RP40. Up-regulation (P < 0.05) of IL-1, IFN2a, IFN2b, and MHCII genes was also observed in fish intestines, with the highest values observed in fish fed RP40 diet, followed by RP10, RP20, RP80, and RP0. Fish-fed diet RP diets also showed enhanced growth and FCR compared to the control, with the highest values observed in fish fed diet RP40. However, no significant differences in survival rates were found among diets. In conclusion, dietary inclusion of RP at 40 g kg-1 resulted in better growth performance, immune response, and immune related gene expressions of striped catfish (Pangasianodon hypophthalmus).

Salinity significantly affects intestinal microbiota and gene expression in striped catfish juveniles.

In the present study, juvenile striped catfish (Pangasianodon hypophthalmus), a freshwater fish species, have been chronically exposed to a salinity gradient from freshwater to 20 psu (practical salinity unit) and were sampled at the beginning (D20) and the end (D34) of exposure. The results revealed that the intestinal microbial profile of striped catfish reared in freshwater conditions were dominated by the phyla Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Alpha diversity measures (observed OTUs (operational taxonomic units), Shannon and Faith's PD (phylogenetic diversity)) showed a decreasing pattern as the salinities increased, except for the phylogenetic diversity at D34, which was showing an opposite trend. Furthermore, the beta diversity between groups was significantly different. Vibrio and Akkermansia genera were affected differentially with increasing salinity, the former being increased while the latter was decreased. The genus Sulfurospirillium was found predominantly in fish submitted to salinity treatments. Regarding the host response, the fish intestine likely contributed to osmoregulation by modifying the expression of osmoregulatory genes such as nka1a, nka1b, slc12a1, slc12a2, cftr, and aqp1, especially in fish exposed to 15 and 20 psu. The expression of heat shock proteins (hsp) hsp60, hsp70, and hsp90 was significantly increased in fish reared in 15 and 20 psu. On the other hand, the expression of pattern recognition receptors (PRRs) were inhibited in fish exposed to 20 psu at D20. In conclusion, the fish intestinal microbiota was significantly disrupted in salinities higher than 10 psu and these effects were proportional to the exposure time. In addition, the modifications of intestinal gene expression related to ion exchange and stressful responses may help the fish to adapt hyperosmotic environment. KEY POINTS: • It is the first study to provide detailed information on the gut microbiota of fish using the amplicon sequencing method. • Salinity environment significantly modified the intestinal microbiota of striped catfish. • Intestinal responses may help the fish adapt to hyperosmotic environment.

Studying the Influence of Copper on the Growth Behavior, Antioxidative Status, and Histology of the Intestine and Liver of Striped Catfish (Pangasianodon hypophthalmus).

Microelements are well recognized as an essential approach in the field of aquaculture nutrition. Thus, this study aimed to evaluate copper (Cu) inclusion (0, 0.5, 1, and 2 mg/kg) on Striped catfish performances. Fish fed the Cu-incorporated diets for 60 days, then their growth behavior, antioxidative capacity, and intestinal and liver histological features were evaluated. The results showed a marked enhancement in Striped catfish's growth behavior fed 1-2 mg/kg of Cu, as shown by the final weight, weight gain, and specific growth rate. The feed and protein efficiency ratios were significantly affected by Cu in a dose-dependent manner. The highest level of Cu was accumulated in the whole body, muscle, liver, and gills of fish fed 2 mg/kg of Cu. The carcass composition of Striped catfish showed higher protein content in groups received 0.5, 1, and 2 mg/kg Cu in a linear and quadratic manner (p=0.001). The ash content was quadratically increased in Striped catfish fed 2 mg/kg Cu (p=0.001). However, no marked effects were observed on the moisture and lipid contents and the somatic indices (p>0.05). The incorporation of Cu showed meaningfully increased superoxide dismutase, catalase, and glutathione peroxidase but decreased malondialdehyde level in Striped catfish. The villous height exhibited visible growth and branching with increased doses of Cu without a significant increase in the goblet cells. No abnormal features were observed in the liver and hepatocytes of fish treated with Cu. It can be concluded that Cu is required at 1-2 mg/kg for better performances of Striped catfish.

Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms.

Assessments of genomic prediction accuracies using artificial intelligent (AI) algorithms (i.e., machine and deep learning methods) are currently not available or very limited in aquaculture species. The principal aim of this study was to examine the predictive performance of these new methods for disease resistance to Edwardsiella ictaluri in a population of striped catfish Pangasianodon hypophthalmus and to make comparisons with four common methods, i.e., pedigree-based best linear unbiased prediction (PBLUP), genomic-based best linear unbiased prediction (GBLUP), single-step GBLUP (ssGBLUP) and a nonlinear Bayesian approach (notably BayesR). Our analyses using machine learning (i.e., ML-KAML) and deep learning (i.e., DL-MLP and DL-CNN) together with the four common methods (PBLUP, GBLUP, ssGBLUP, and BayesR) were conducted for two main disease resistance traits (i.e., survival status coded as 0 and 1 and survival time, i.e., days that the animals were still alive after the challenge test) in a pedigree consisting of 560 individual animals (490 offspring and 70 parents) genotyped for 14,154 single nucleotide polymorphism (SNPs). The results using 6,470 SNPs after quality control showed that machine learning methods outperformed PBLUP, GBLUP, and ssGBLUP, with the increases in the prediction accuracies for both traits by 9.1-15.4%. However, the prediction accuracies obtained from machine learning methods were comparable to those estimated using BayesR. Imputation of missing genotypes using AlphaFamImpute increased the prediction accuracies by 5.3-19.2% in all the methods and data used. On the other hand, there were insignificant decreases (0.3-5.6%) in the prediction accuracies for both survival status and survival time when multivariate models were used in comparison to univariate analyses. Interestingly, the genomic prediction accuracies based on only highly significant SNPs (P < 0.00001, 318-400 SNPs for survival status and 1,362-1,589 SNPs for survival time) were somewhat lower (0.3-15.6%) than those obtained from the whole set of 6,470 SNPs. In most of our analyses, the accuracies of genomic prediction were somewhat higher for survival time than survival status (0/1 data). It is concluded that although there are prospects for the application of genomic selection to increase disease resistance to E. ictaluri in striped catfish breeding programs, further evaluation of these methods should be made in independent families/populations when more data are accumulated in future generations to avoid possible biases in the genetic parameters estimates and prediction accuracies for the disease-resistant traits studied in this population of striped catfish P. hypophthalmus.

Salinity affects growth performance, physiology, immune responses and temperature resistance in striped catfish (Pangasianodon hypophthalmus) during its early life stages.

In this study, striped catfish larvae were gradually exposed to the increase of different salinities, and then they reached the levels of 0, 5, 10, 15, and 20 psu after 10 days, followed by heat shock at 39 °C to determine stress tolerance. After the 10-day experiment, the survival rate of fish exposed to the 20 psu treatment was only 28.6 ± 4%, significantly lower than that of the other treatments. The results showed that the osmolality of the whole-body (WB) homogenate was gradually and significantly increased with salinity elevation, except in fish exposed to freshwater and 5 psu treatments, while there were no significant changes in WB Na+/K+-ATPase activity. Digestive enzymatic activities, i.e., pepsin, α-amylase, alkaline phosphatase, and leucine alanine peptidase (leu-ala) generally increased with salinity, but not aminopeptidase and trypsin. Lysozyme and peroxidase activities increased in fish larvae exposed to 15 and 20 psu. These increases proportionally improved growth performance, with the lowest and the highest final weights observed in fish reared at 0 psu (0.08 ± 0.03 g/larvae) and 20 psu (0.11 ± 0.02 g/larvae), respectively, although the average growth recorded at 20 psu could be biased by the high mortality in this group. Occurrence of skeleton deformities, such as in caudal vertebrae and branchiostegal rays, was significantly higher in fish exposed to the higher osmotic conditions (15.0 ± 1.2% and 10.3 ± 2.1% respectively at 0 psu vs. 31.0 ± 2.9% and 49.0 ± 5.6%, respectively at 15 psu). After the 12.5-h heat shock, survival rates significantly differed between treatments with the highest survival observed in fish submitted to 5 psu (68.9%), followed by those exposed to 0 (27%) and 10 (20%) while all fish died at 15 psu. These findings suggest that the striped catfish larvae could be reared in salinity up to 5 to 10 psu with a higher survival and tolerance to thermal stress when compared to fish maintained in freshwater.