Tissue‐specific differences in detection of <i>Yersinia ruckeri</i> carrier status in rainbow trout (<i>Oncorhynchus mykiss</i>)

Sibinga, N.A.; Marquis, Hélène

doi:10.1111/jfd.13515

Cited by 6 publications

(5 citation statements)

References 27 publications

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“…Y. ruckeri can lead to acute infection and disease during hatchery and sea-transfer stages [ 34 ], causing high mortality rates in salmonids, resulting in significant economic losses in salmonid farming [ 35 ]. Salmonids infected with Y. ruckeri can carry the bacteria as a latent infection for several months, potentially facilitating cryptic spread between facilities that exchange fish [ 36 ]. In this context, rapid and sensitive detection methods for this and other fish pathogens can be crucial for appropriate surveillance in aquaculture.…”

Section: Discussionmentioning

confidence: 99%

Detection of Nucleic Acids of the Fish Pathogen Yersinia ruckeri from Planktonic and Biofilm Samples with a CRISPR/Cas13a-Based Assay

Calderón,

Barros,

Fernández-Navarro

et al. 2024

Microorganisms

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Yersinia ruckeri is the cause of hemorrhagic septicemia, known as enteric redmouth disease, in salmonid fish species. This bacterial pathogen can form biofilms on abiotic surfaces of aquaculture settings or even on the surfaces of the fish themselves, contributing to their persistence in the aquatic environment. Detection methods for this and other fish pathogens can be time-consuming and lack specificity and sensitivity, limiting timely monitoring, the treatment of microbial infections, and effective control of their transmission in aquaculture settings. Rapid and sensitive detection methods for nucleic acids can be crucial for an appropriate surveillance of bacterial pathogens, and the CRISPR/Cas-based assays have emerged as a good alternative since it has been proven to be a useful tool for the rapid, specific, and sensitive detection of viruses and some bacteria. In this study, we explored the capability of the CRISPR/Cas13a system (SHERLOCK) to specifically detect both DNA and RNA (gene transcripts) from planktonic and biofilm samples of the bacterial fish pathogen Y. ruckeri. The assay was designed to detect the gyrA gene and the small noncoding RNAs (sRNAs) MicA and RprA from planktonic cultures and biofilm samples prepared in marine broth. The specific crRNA designed for these gene targets included a 28 nt specific gene sequence, and a scaffold sequence necessary for Cas13-binding. For all the assays, the nucleic acids obtained from samples were previously subjected to isothermal amplification with the recombinase polymerase amplification (RPA) method and the subsequent T7 transcription of the RPA amplicons. Finally, the detection of nucleic acids of Y. ruckeri was by means of a reporter signal released by the Cas13a collateral RNA cleavage triggered upon target recognition, measured by fluorescence- or lateral-flow-based readouts. This CRISPR/Cas13a-based assay was able to specifically detect both DNA and sRNAs from the Y. ruckeri samples, and the sensitivity was comparable to that obtained with qPCR analysis, highlighting the potential applicability of this CRISPR/Cas13a-based assay for fish pathogen surveillance.

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Section: Discussionmentioning

confidence: 99%

Detection of Nucleic Acids of the Fish Pathogen Yersinia ruckeri from Planktonic and Biofilm Samples with a CRISPR/Cas13a-Based Assay

Calderón,

Barros,

Fernández-Navarro

et al. 2024

Microorganisms

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“…As no isolate of K. kristinae has been previously reported in marine fish previously, evaluation of whether this new bacterial isolate could cause infection or death of large yellow croakers was undertaken according to the method for animal regressive infection ( Sibinga and Marquis, 2021 ; Yang et al, 2022 ). First, we streaked the reserved bacterial solution onto a BHI agar plate to obtain a single colony for further cultivation in BHI liquid medium at 37°C for 12 h at 180 rpm; then, we performed an extra inoculation from the obtained bacterial solution, which was at the logarithmic growth phase with an OD600.0 value of 1.874, at a ratio of 1:100 to prepare the bacterial culture.…”

Section: Methodsmentioning

confidence: 99%

A new pathogenic isolate of Kocuria kristinae identified for the first time in the marine fish Larimichthys crocea

et al. 2023

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In recent years, new emerging pathogenic microorganisms have frequently appeared in animals, including marine fish, possibly due to climate change, anthropogenic activities, and even cross-species transmission of pathogenic microorganisms among animals or between animals and humans, which poses a serious issue for preventive medicine. In this study, a bacterium was clearly characterized among 64 isolates from the gills of diseased large yellow croaker Larimichthys crocea that were raised in marine aquaculture. This strain was identified as K. kristinae by biochemical tests with a VITEK 2.0 analysis system and 16S rRNA sequencing and named K. kristinae_LC. The potential genes that might encode virulence-factors were widely screened through sequence analysis of the whole genome of K. kristinae_LC. Many genes involved in the two-component system and drug-resistance were also annotated. In addition, 104 unique genes in K. kristinae_LC were identified by pan genome analysis with the genomes of this strain from five different origins (woodpecker, medical resource, environment, and marine sponge reef) and the analysis results demonstrated that their predicted functions might be associated with adaptation to living conditions such as higher salinity, complex marine biomes, and low temperature. A significant difference in genomic organization was found among the K. kristinae strains that might be related to their hosts living in different environments. The animal regression test for this new bacterial isolate was carried out using L. crocea, and the results showed that this bacterium could cause the death of L. crocea and that the fish mortality was dose-dependent within 5 days post infection, indicating the pathogenicity of K. kristinae_LC to marine fish. Since K. kristinae has been reported as a pathogen for humans and bovines, in our study, we revealed a new isolate of K. kristinae_LC from marine fish for the first time, suggesting the potentiality of cross-species transmission among animals or from marine animals to humans, from which we would gain insight to help in future public prevention strategies for new emerging pathogens.

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“…Extraction of DNA from trout intestines was performed as previously described (Sibinga and Marquis, 2021)…”

Section: Dna Extraction From Fish Intestinesmentioning

confidence: 99%

“…Samples with amplification of the 16S gene in at least two of three replicate qPCR wells were deemed positive for Y. ruckeri. A standard curve generated using genomic DNA from a pure culture of Y. ruckeri was used to estimate bacterial loads as previously described (Sibinga and Marquis, 2021). The limit of quantitation (LOQ) was determined using a published R script (Merkes et al, 2019); the LOQ is the lowest threshold count (Ct) value for which the coefficient of variance -i.e.…”

Section: Qpcr Detection and Quantification Of The Yersinia Ruckeri 16...mentioning

confidence: 99%

Do antimicrobial peptide levels alter performance of insect-based aquaculture feeds – a study using genetic models of insect immune activation

Sibinga

Lee

Buchon

et al. 2023

JIFF

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Insect meals are an increasingly common ingredient in pet food and animal feeds. Some studies have reported increased resistance to disease in animals fed insect-based diets, but the mechanisms of this effect have only rarely been investigated. We hypothesised that antimicrobial peptides (AMPs) naturally present in insects contribute to disease resistance. AMPs are part of the insect immune response, and as such their levels differ dramatically depending on the state of immune activation. In this study, transgenic fruit flies (Drosophila melanogaster) lines were used to generate insect-based feeds with high and low AMP levels. Juvenile rainbow trout (Oncorhynchus mykiss) were fed these insect diets and challenged by immersion with Yersinia ruckeri to assess changes in disease resistance. Survival rates of fish fed the high AMP insect diet were not significantly different from those fed the low AMP insect diet, though there were trends towards higher survival and lower Y. ruckeri load in the intestines of fish fed the high AMP diet. The fish intestinal microbiomes were studied in challenged and mock-challenged fish. In mock-challenged fish, no differences were apparent between the microbiomes of each diet group. In Y. ruckeri challenged fish, however, the intestinal microbial communities differed between fish fed the low and high AMP diets at each time point after infection. Overall, despite its limitations, this study offers a prospective view of how to leverage the genetic tools and experimental approaches present in the Drosophila community for research in commonly farmed insects (e.g. Hermetia illucens and Tenebrio molitor).

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Tissue‐specific differences in detection of Yersinia ruckeri carrier status in rainbow trout (Oncorhynchus mykiss)

Cited by 6 publications

References 27 publications

Detection of Nucleic Acids of the Fish Pathogen Yersinia ruckeri from Planktonic and Biofilm Samples with a CRISPR/Cas13a-Based Assay

Detection of Nucleic Acids of the Fish Pathogen Yersinia ruckeri from Planktonic and Biofilm Samples with a CRISPR/Cas13a-Based Assay

A new pathogenic isolate of Kocuria kristinae identified for the first time in the marine fish Larimichthys crocea

Do antimicrobial peptide levels alter performance of insect-based aquaculture feeds – a study using genetic models of insect immune activation

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