Complete Genome Sequence of Streptococcus iniae 89353, a Virulent Strain Isolated from Diseased Tilapia in Taiwan

Gong, Hong‐Yi; Wu, Sheng-Han; Chen, Chun‐Yao; Huang, Chang-Wen; Lu, June; Chou, Hsin-Yiu

doi:10.1128/genomea.01524-16

Cited by 11 publications

(6 citation statements)

References 8 publications

(8 reference statements)

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“…One of these ~7 kb discarded contigs encoded an rRNA region (5S, 16S and 23S genes in tandem with an intervening cluster of tRNA genes). Subsequent reassembly and visualization of mapped raw reads indicated that the additional rRNA contig could be placed in three of the five rRNA operon locations to form an ~13 kb putative tandem duplication of 5S, 16S and 23 rRNA genes as seen in the 89 353 genome [ 47 ]. Closer examination of the read pileup for the ~7 kb rRNA contig revealed that the tandem duplication was not well supported by overlapping reads (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, during the preparation of this paper, a PacBio complete genome was published for S. iniae 89 353 (accession: CP017952), which has an identical rRNA arrangement to QMA0248 except that one rRNA locus encodes an ~7 kb tandem duplication (i.e. six loci in total) [47]. Such intraspecies variation in the number of rRNA genes (and tRNA genes) is not uncommon in bacteria (including streptococci) [48,49], and prompted us to investigate further.…”

Section: Genomic Features Of S Iniae Qma0248mentioning

confidence: 99%

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A high-quality reference genome for the fish pathogen Streptococcus iniae

et al. 2022

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Fish mortality caused by Streptococcus iniae is a major economic problem in aquaculture in warm and temperate regions globally. There is also risk of zoonotic infection by S. iniae through handling of contaminated fish. In this study, we present the complete genome sequence of S. iniae strain QMA0248, isolated from farmed barramundi in South Australia. The 2.12 Mb genome of S. iniae QMA0248 carries a 32 kb prophage, a 12 kb genomic island and 92 discrete insertion sequence (IS) elements. These include nine novel IS types that belong mostly to the IS3 family. Comparative and phylogenetic analysis between S. iniae QMA0248 and publicly available complete S. iniae genomes revealed discrepancies that are probably due to misassembly in the genomes of isolates ISET0901 and ISNO. Long-range PCR confirmed five rRNA loci in the PacBio assembly of QMA0248, and, unlike S. iniae 89353, no tandemly repeated rRNA loci in the consensus genome. However, we found sequence read evidence that the tandem rRNA repeat existed within a subpopulation of the original QMA0248 culture. Subsequent nanopore sequencing revealed that the tandem rRNA repeat was the most prevalent genotype, suggesting that there is selective pressure to maintain fewer rRNA copies under uncertain laboratory conditions. Our study not only highlights assembly problems in existing genomes, but provides a high-quality reference genome for S. iniae QMA0248, including manually curated mobile genetic elements, that will assist future S. iniae comparative genomic and evolutionary studies.

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Section: Resultsmentioning

confidence: 99%

Section: Genomic Features Of S Iniae Qma0248mentioning

confidence: 99%

A high-quality reference genome for the fish pathogen Streptococcus iniae

et al. 2022

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“…Zebrafish embryos cultured until they became one-month-old juveniles were used for an RHS toxicity assay. The clinical pathogen methicillin-resistant Staphylococcus aureus (MRSA) was kindly provided by Dr. Huang et al [25], and Streptococcus iniae was kindly provided by Dr. Gong et al [26]. The foodborne pathogens Escherichia coli BCRC11634, Staphylococcus aureus BCRC12991, Salmonella typhimurium BCRC12947, and Listeria monocytogenes BCRC14932; clinical pathogen Pseudomonas aeruginosa BCRC12902; and plant pathogen Burkholderia gladioli BCRC13899 were purchased from the Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, Taiwan.…”

Section: Fish and Bacterial Strainsmentioning

confidence: 99%

Rice Husk Silica Enhances Innate Immune in Zebrafish (Danio rerio) and Improves Resistance to Aeromonas hydrophila and Streptococcus iniae Infection

et al. 2019

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Rice husk (RH) contains abundant silica such that RH silica (RHS) may be useful for possible industrial exploitation. Here, amorphous silica nanoparticles with multiple pore structures were acquired from RH by simple thermochemical processes. RHS antimicrobial activity and effects on zebrafish innate immunity against pathogen infections were evaluated. A toxicity assay showed that zebrafish exposed to an RHS dose lower than 200 μg/mL did not exhibit damage to zebrafish embryonic development or juvenile survival. RHS showed a wide spectrum of bacteriostatic activity against a variety of pathogens including antibiotic-resistant pathogens, implying its potential application as an antimicrobial agent in diverse industries. Fish exposed to 20 or 200 μg/mL RHS exhibited significantly increased mRNA expression of immune-related genes, including IL-1β, IL-6, IL-15, TNF-α, COX-2a, TLR-4a, lysozyme, and complement C3b. RHS-treated zebrafish exhibited a higher cumulative survival compared to that in control fish after infecting with Aeromonas hydrophila and Streptococcus iniae. The present results showed that a safe RHS dose enhanced innate immunity against infections without toxic effects in healthy fish, suggesting that RHS may be developed as an immunostimulant for improving health status in aquaculture.

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“…Regardless of the PCR supermix used, the newly designed multiplex qPCR assay targeting Fno , S. iniae, and S. agalactiae was found to be repeatable and reproducible, with a linear dynamic range covering at least five orders of magnitude. Based on estimated genome sizes of 1.9 Mb for Fno (Figueiredo et al, ), 2 Mb for S. iniae (Gong et al, ), and 2 Mb for S. agalactiae (Mainardi et al, ), the limit of sensitivity for each assay was approximately 20, 8, and 20 genome equivalents, respectively. Each assay was specific to its respective target, with no evidence of cross‐reactivity from nontarget organisms (Figure ; Table ).…”

Section: Resultsmentioning

confidence: 99%

Application of multiplex quantitative polymerase chain reaction methods to detect common bacterial fish pathogens in Nile tilapia, Oreochromis niloticus, hatcheries in Costa Rica

López-Porras

Elizondo

Chaves

et al. 2018

J World Aquaculture Soc

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Edwardsiella spp., Streptococcus spp., and Francisella noatunensis subsp. orientalis are some of the most important fish pathogens affecting global tilapia, Oreochromis spp., aquaculture. In Costa Rica, the aquaculture industry is dominated by freshwater‐cultured Nile tilapia, Oreochromis niloticus, which are raised in all seven national provinces. At present, little is known regarding the diversity of pathogens present in these facilities, and definitive identification of agents associated with disease outbreaks are rare. To evaluate the prevalence of common bacterial pathogens in these systems, this study used multiplex quantitative polymerase chain reaction (qPCR) assays targeting Edwardsiella, Streptococcus, and Francisella species as a diagnostic and surveillance tool. In 2017, seven different tilapia hatcheries were visited, and 350 fingerlings were subjected to necropsy and molecular diagnostic evaluation. Fish exhibiting gross signs of disease were subjected to histological and microbiological analysis. For the first time, Edwardsiella anguillarum was recovered and molecularly confirmed from diseased tilapia in Costa Rica. In addition, F. noatunensis subsp. orientalis was identified in a region of Costa Rica where it had not been previously reported.

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Complete Genome Sequence of Streptococcus iniae 89353, a Virulent Strain Isolated from Diseased Tilapia in Taiwan

Cited by 11 publications

References 8 publications

A high-quality reference genome for the fish pathogen Streptococcus iniae

A high-quality reference genome for the fish pathogen Streptococcus iniae

Rice Husk Silica Enhances Innate Immune in Zebrafish (Danio rerio) and Improves Resistance to Aeromonas hydrophila and Streptococcus iniae Infection

Application of multiplex quantitative polymerase chain reaction methods to detect common bacterial fish pathogens in Nile tilapia, Oreochromis niloticus, hatcheries in Costa Rica

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