Retrospective identification of pathogenic mycobacterial species in fish: Mycobacterium pseudoshottsii YM-3, isolated from a yellowtail fish in 1986 in Kochi, Japan.

The complete genome sequence of mycobacterial strain YM-3, isolated from cultured yellowtail in 1986, was determined. The strain was Mycobacterium pseudoshottsii, a closely related subspecies of Mycobacterium marinum, so the strain was isolated earlier than the first report of the subspecies in 2005.

Phenotypic differences between Edwardsiella piscicida and Edwardsiella anguillarum isolates in Japan.

OBJECTIVE: Edwardsiella tarda has been regarded as the causative agent of edwardsiellosis in cultured marine and freshwater fish species in Japan. Our previous study genetically classified an E. tarda-like isolate from diseased Olive Flounder Paralichthys olivaceus as E. piscicida and that from diseased Red Seabream Pagrus major as E. anguillarum. This study aimed to understand the phenotypic differences between E. piscicida and E. anguillarum. METHODS: Fourteen E. piscicida and seven E. anguillarum isolates were used in this study. The colonies of each isolate were grown on brain-heart infusion agar plates and then subjected to DNA extraction. The extracted DNA was amplified using PCR. carbohydrate fermentation of the isolates was examined using API 50 CH test kits. Moreover, the growth of the two species was examined in defined media. Also, free amino acids in Olive Flounder and Red Seabream sera were detected and quantified via high-performance liquid chromatography-mass spectrometry. Statistical differences in the concentrations of free amino acids were analyzed using Welch's t-tests. RESULT: The API 50 CH test revealed that L-arabinose and D-mannitol were fermented by E. anguillarum isolates but not E. piscicida isolates. Furthermore, the growth of E. piscicida and E. anguillarum was reduced in the defined medium without methionine and iron sulfate. The growth of E. piscicida was reduced in the defined medium without phenylalanine, tyrosine, alanine, or nicotinic acid, whereas the growth of E. anguillarum was reduced in the defined medium without serine, cysteine, leucine, threonine, or isoleucine. Tyrosine and alanine were present in higher concentrations in the Olive Flounder serum, whereas threonine and isoleucine were present in higher concentrations in the Red Seabream serum, suggesting favorable growth conditions for E. piscicida and E. anguillarum. CONCLUSION: This study characterizes a minimal defined medium that can be used for developing vaccines against E. piscicida and E. anguillarum.

Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Diseased Ayu (Plecoglossus altivelis altivelis) Caught at Three Sites in the Kagami River in Kochi, Japan.

Flavobacterium psychrophilum is a Gram-negative, psychrophilic bacterium within the family Flavobacteriaceae Here, we report the draft genome sequences of three F. psychrophilum strains isolated from skin ulcers of diseased ayu caught by tomozuri angling at three sites in the Kagami River in Japan.

Draft Genome Sequence of Vibrio harveyi Strain GAN1807, Isolated from Diseased Greater Amberjack (Seriola dumerili) Farmed in Nomi Bay, Japan, in 2018.

Vibrio harveyi is a Gram-negative, bioluminescent bacterium within the family Vibrionaceae Here, we report the draft genome sequence of V. harveyi strain GAN1807, which was isolated from a diseased greater amberjack (Seriola dumerili) with symptoms of V. harveyi-associated vibriosis in Nomi Bay in Japan.

Draft Genome Sequences of Six Flavobacterium psychrophilum Strains Isolated from Dead Juvenile Ayu (Plecoglossus altivelis altivelis) near the Mouth of the Nahari River, Kochi, Japan.

Flavobacterium psychrophilum causes bacterial cold-water disease in ayu inhabiting clear rivers in Japan. In this study, we report the draft genome sequences of six F. psychrophilum strains isolated from the gills and skin of dead juvenile ayu near the mouth of the Nahari River.

Draft Genome Sequences of Two Edwardsiella piscicida Strains, JF1307 and JF1411, Isolated from Diseased Olive Flounder (Paralichthys olivaceus) Cultured in Japan.

Edwardsiella piscicida strains JF1307 and JF1411 were isolated from cultured olive flounder that were diagnosed as being infected with edwardsiellosis. The draft genome sequences of the two isolates comprise 3,882,000 bp and 3,827,424 bp with G+C contents of 59.5% and 59.6%, respectively.

Draft Genome Sequence of Vibrio harveyi Strain GAN1709, Isolated from Diseased Greater Amberjack (Seriola dumerili) Farmed in Japan.

Vibrio harveyi strain GAN1709 was isolated from a diseased greater amberjack farmed in Nomi Bay, Japan. Here, we report the draft genome sequence of this strain, which comprises 6,265,473 bp, with a G+C content of 44.8%.

Draft Genome Sequence of Flavobacteriumpsychrophilum Strain SSADA-1411, Isolated from an Ayu (Plecoglossus altivelis altivelis) Migrating Downriver To Spawn in the Shimanto River, Kochi, Japan.

Here, we report the draft genome sequence and annotation of Flavobacterium psychrophilum strain SSADA-1411. This strain was isolated from the skin ulcer of an ayu (Plecoglossus altivelis altivelis) migrating downriver to spawn in the lower Shimanto River, in western Kochi Prefecture on Shikoku Island in Japan.

Draft Genome Sequence of Flavobacterium psychrophilum Strain KTEN-1510 with Genotype A/G-C, Isolated from an Ayu (Plecoglossus altivelis altivelis) in the Kagami River, Kochi, Japan.

In this paper, we describe the draft genome sequence of Flavobacterium psychrophilum strain KTEN-1510, with genotype A/G-C. This strain was isolated in October 2015 from the gills of an ayu (Plecoglossus altivelis altivelis) in the upper Kagami River in central Kochi Prefecture on Shikoku Island, Japan.

Draft Genome Sequence of Erythromycin- and Oxytetracycline-Sensitive Nocardia seriolae Strain U-1 (NBRC 110359).

In Japan, the emergence of macrolide- and oxytetracycline-resistant strains of Nocardia seriolae has previously been reported. Here, we describe the draft genome sequence of N. seriolae strain U-1, isolated in 2011 from a diseased yellowtail in Kagoshima Prefecture. The draft genome does not have any genes responsible for macrolide and tetracycline resistance.

Draft Genome Sequence of Nocardia seriolae Strain N-2927 (NBRC 110360), Isolated as the Causal Agent of Nocardiosis of Yellowtail (Seriola quinqueradiata) in Kochi Prefecture, Japan.

We report the draft genome sequence of Nocardia seriolae strain N-2927 (NBRC 110360), isolated from cultured yellowtail Seriola quinqueradiata. RAST annotation of the genome revealed 117 genes involved in the virulence, disease, and defense subsystem. Eleven of these genes were predicted as antibiotic resistance genes.

Prevalence and characteristics of Cyprinid herpesvirus 3 (CyHV-3) infection in common carp (Cyprinus carpio L.) inhabiting three rivers in Kochi Prefecture, Japan.

Cyprinid herpesvirus 3 (CyHV-3) causes lethal disease in common and koi carp. Mortality by CyHV-3 disease has not been reported since 2011 in Kochi Prefecture, Japan. Here, we detected and quantified CyHV-3 in common carp inhabiting three rivers in the prefecture to examine if the carp are carriers of CyHV-3 as a source of infection. CyHV-3 DNA was detected in 16.7% (12/72) of brain samples in Kagami River, 3.9% (3/76) of brain and 3.9% (3/76) of gill samples in Monobe River, and 5.1% (4/79) of brain and 1.3% (1/79) of gill samples in Wajiki River. CyHV-3 genotypes identified in the 23 samples were classified as the J genotype A1 that has been found in Japan. The CyHV-3 DNA load did not differ statistically between sampling months, indicating that CyHV-3 has been silent in common carp, unlike Lake Biwa where the annual reactivation occurs in spring. Taken together, our results represented definitive evidence that seasonal changes in water temperature do not affect CyHV-3 activity in carp. Considering that infectious virus was not isolated from CyHV-3 DNA-positive samples, it was suggested that CyHV-3 establishes a latent infection in carp populations inhabiting Kagami River, Monobe River and Wajiki River. Further, the presence of circular or concatameric CyHV-3 DNA was detected in five of 23 CyHV-3 DNA-positive samples. Common carp inhabiting Lake Biwa were reported previously to harbor linear but not circular CyHV-3 DNA. This difference suggested that the CyHV-3 genome may be circularized for long-term maintenance without active viral replication.

Draft Genome Sequences of Two Genetic Variant Strains of Edwardsiella piscicida, JF1305 and RSB1309, Isolated from Olive Flounder (Paralichythys olivaceus) and Red Sea Bream (Pagrus major) Cultured in Japan, Respectively.

Edwardsiella piscicida is a new species discovered within the group of organisms traditionally classified as Edwardsiella tarda. We present draft genome sequences of two variant strains of E. piscicida, JF1305 and RSB1309. Differences in protein-coding sequence between these isolates are associated with virulence, disease, and defense, suggesting differences in pathogenicity.

PCR array analysis of gene expression profiles in chronic active Epstein-Barr virus infection.

To determine the host cellular gene expression profiles in chronic active Epstein-Barr virus infection (CAEBV), peripheral blood samples were obtained from three patients with CAEBV and investigated using a PCR array analysis that focused on T-cell/B-cell activation. We identified six genes with expression levels that were tenfold higher in CAEBV patients compared with those in healthy controls. These results were verified by quantitative reverse transcription-PCR. We identified four highly upregulated genes, i.e., IL-10, IL-2, IFNGR1, and INHBA. These genes may be involved in inflammatory responses and cell proliferation, and they may contribute to the development and progression of CAEBV.

Draft Genome Sequence of Streptococcus parauberis Strain SK-417, Isolated from Diseased Sebastes ventricosus in Kagoshima, Japan.

Streptococcus parauberis strain SK-417 was isolated from the brain of a diseased Sebastes ventricosus, collected from an aquaculture farm in April 2013 in Kagoshima Prefecture, Japan. The draft genome sequence, obtained with a 454 GS Junior sequencing system, consists of 33 large contigs of >500 bp, totaling 1,958,836 bp, and has a G+C content of 35.4%.

Phylogenetic analysis of Merkel cell polyomavirus based on full-length LT and VP1 gene sequences derived from neoplastic tumours in Japanese patients.

Most Merkel cell polyomavirus (MCPyV) gene sequences have been reported from Western countries and few data are available for the virus sequences from other geographical areas, especially Asia. Thus, we performed phylogenetic analyses based on the nucleotide sequences of the full-length large T-antigen (LT) and viral protein 1 (VP1) genes derived from a variety of cancers in Japanese patients and compared them with sequences from Caucasians. The LT and VP1 gene-based phylogenetic trees identified two main genetic clades. One clade comprised strains isolated from Caucasians, whereas all of the Japanese tumour-derived MCPyV strains belonged to another clade. These findings confirm that most of the MCPyV strains present in Japan form a clade, distinct from Caucasian strains.

Prevalence and viral DNA loads of three novel human polyomaviruses in skin cancers from Japanese patients.

Merkel cell polyomavirus (MCPyV), human polyomaviruses 6 (HPyV6) and 7 (HPyV7) are novel human polyomaviruses. This study investigated their detection rates and DNA loads in various skin cancers from Japanese patients. MCPyV, HPyV6 and HPyV7 were detected in 22.2%, 3.2% and 1.6% of squamous cell carcinomas, 18.0%, 2.0% and 4.0% of basal cell carcinomas, and 19.1%, 4.3% and 4.3% of melanomas, respectively. Quantitative real-time polymerase chain reaction showed that their DNA loads were low. These findings provide the first evidence of the prevalence of HPyV6 and HPyV7 in skin cancers in Asia. Nucleotide differences were found in the large T-sequenced region between Japanese and North American isolates: a nucleotide substitution of A to G for HPyV6; and a nucleotide substitution of T to C and the insertion of a gap for HPyV7. This suggested that two genotypes of HPyV6 and HPyV7 would be present and associated with geographical origin.