Research Project: Integrated Research to Improve On-Farm Animal Health in Salmonid Aquaculture

Location: Cool and Cold Water Aquaculture Research

Publications (Clicking on the reprint icon will take you to the publication reprint.)

Disruption of the Francisella noatunensis orientalis pdpA gene results in virulence attenuation and protection in zebrafish - (Peer Reviewed Journal)
Hansen, J.D., Ray, K., Chen, P., Yun, S., Elliott, D., Conway, C., Calcutt, M., Purcell, M., Welch, T.J., Soto, E. 2021. Disruption of the Francisella noatunensis orientalis pdpA gene results in virulence attenuation and protection in zebrafish. Infection and Immunity. 89(11):220-21. https://doi.org/10.1128/.

In vivo experiments provide evidence that Flavobacterium psychrophilum strains belonging to multilocus sequence typing clonal complex ST191 are virulent to Rainbow Trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)

Recirculation versus Flow-through Rainbow Trout Laboratory Flavobacterium Columnare Challenge - (Peer Reviewed Journal)
Birkett, C., Lipscomb, R.S., Moreland, T.D., Leeds, T.D., Evenhuis, J. 2020. Recirculation versus Flow-through Rainbow Trout Laboratory Flavobacterium Columnare Challenge. Diseases of Aquatic Organisms. 139: 213–221. https://doi.org/10.3354/dao03487.

Characterization of a novel Yersinia ruckeri serotype O1-specific bacteriophage with virulence neutralizing activity - (Peer Reviewed Journal)
Welch, T.J. 2019. Characterization of a novel Yersinia ruckeri serotype O1-specific bacteriophage with virulence neutralizing activity. Journal of Fish Diseases. 43(2):285-293. https://doi.org/10.1111/jfd.13124.

Assessment of genetic variation in the multigene frp locus of Flavobacterium psychrophilum - (Abstract Only)
Wiens, G.D., Osbourn, K.E. 2019. Assessment of genetic variation in the multigene frp locus of Flavobacterium psychrophilum [abstract]. In: American Fishery Society (Fish Health Section) Proceedings. Western Fish Disease Workshop held in Ogden, UT 17 June - 20 June, 2019.

Identification and characterization of putative Aeromonas spp. T3SS effectors - (Peer Reviewed Journal)
Rangel, L.T., Marden, J., Sestubal, J.C., Graf, J., Gogarten, J.P. 2019. Identification and characterization of putative Aeromonas spp. T3SS effectors. PLoS One. 14(6):e0214035. https://doi.org/10.1371/journal.pone.0214035.

Flagellar regulation mediated by the Rcs pathway is required for virulence in the fish pathogen Yersinia ruckeri - (Peer Reviewed Journal)
Jozwick, A., La Patra, S., Graf, J., Welch, T.J. 2019. Flagellar regulation mediated by the Rcs pathway is required for virulence in the fish pathogen Yersinia ruckeri. Fish and Shellfish Immunology. 91:306.314. https://doi.org/10.1016/j.fsi.2019.05.036.

Comparative structural and antigenic characterization of genetically distinct Flavobacterium psychrophilum O-polysaccharides - (Peer Reviewed Journal)
Cisar, J.O., Bush, A., Wiens, G.D. 2019. Comparative structural and antigenic characterization of genetically distinct Flavobacterium psychrophilum O-polysaccharides. Frontiers in Microbiology. 10:1041. https://doi.org/10.3389/fmicb.2019.01041.

Biogeography of the fish pathogen Aeromonas salmonicida inferred by vapA genotyping - (Peer Reviewed Journal)
Gulla, S., Bayliss, S., Björnsdóttir, B., Dalsgaard, I., Haenen, O., Jansson, E., Mccarthy, U., Scholz, F., Vercauteren, M., Verner-Jeffreys, D., Welch, T.J., Wiklund, T., Colquhoun, D.J. 2019. Biogeography of the fish pathogen Aeromonas salmonicida inferred by vapA genotyping. FEMS Microbiology Letters. 366(7). https://doi.org/10.1093/femsle/fnz074.

Genetic improvement of disease resistance through selective breeding: Concepts, considerations and limitations - (Trade Journal)
Leeds, T.D., Wiens, G.D. 2019. Genetic improvement of disease resistance through selective breeding: Concepts, considerations and limitations. Global Aquaculture Advocate. 2019.

Large-scale analysis of Flavobacterium psychrophilum MLST genotypes recovered from North American salmonids indicates both newly identified and recurrent clonal complexes are associated with disease - (Peer Reviewed Journal)
Knupp, C., Wiens, G.D., Faisal, M., Call, D.R., Cain, K.D., Nicolas, P., Van Vliet, D., Yamashita, C., Ferguson, J.A., Meuninck, D., Hsu, H., Baker, B.B., Shen, L., Loch, T.P. 2019. Large-scale analysis of Flavobacterium psychrophilum MLST genotypes recovered from North American salmonids indicates both newly identified and recurrent clonal complexes are associated with disease. Applied and Environmental Microbiology. Mar 6;85(6)e02305-18.

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing - (Peer Reviewed Journal)
Goldstein, S., Beka, L., Graf, J., Klassen, J. 2019. Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing. BMC Bioinformatics. 20(23):1-17. https://doi.org/10.1186/s12864-018-5381-7.

Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Brown, R., Wiens, G.D., Salinas, I. 2018. Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). Fish and Shellfish Immunology. 86:497-506. https://doi.org/10.1016/j.fsi.2018.11.079.

Sequencing and characterization of a novel micro exon gene (Tb-MEG1) in a myxozoan parasite: its utility as a vaccine candidate and as a biomarker of proliferative kidney disease (PKD) in rainbow trout - (Abstract Only)
Farber, M., Tafalla, C., Wiens, G.D., Okamur, B., Hartikainen, H., Wang, T., Holland, J., Secombes, C.J. 2019. Sequencing and characterization of a novel micro exon gene (Tb-MEG1) in a myxozoan parasite: its utility as a vaccine candidate and as a biomarker of proliferative kidney disease (PKD) in rainbow trout. UK & International Veterinary Vaccinology Network Conference. Paper No. D2T37.

Proteome analysis reveals a role of rainbow trout lymphoid organs during the Yersinia ruckeri infection process - (Peer Reviewed Journal)
Kumar, G., Hummel, K., Noebauer, K., Welch, T.J., Razzazi-Fazeli, E., El-Matboul, M. 2019. Proteome analysis reveals a role of rainbow trout lymphoid organs during the Yersinia ruckeri infection process. Scientific Reports. 8:13998. https://doi.org/10.1038/s41598-018-31982-6.

Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads - (Peer Reviewed Journal)
Talagrand-Reboul, E., Latif-Eugenin, F., Beaz-Hidalgo, R., Colston, S., Figueras, M., Graf, J., Jumas-Bilak, E., Lamy, B. 2018. Genome-driven evaluation and redesign of PCR tools for improving the detection of virulence-associated genes in aeromonads. PLoS One. 13(8):e0201428. https://doi.org/10.1371/journal.pone.0201428.

Three generations of selective breeding improved Rainbow trout (Oncorhynchus mykiss) disease resistance against natural challenge with Flavobacterium psychrophilum during early life-stage rearing - (Peer Reviewed Journal)
Wiens, G.D., Palti, Y., Leeds, T.D. 2018. Three generations of selective breeding improved Rainbow trout (Oncorhynchus mykiss) disease resistance against natural challenge with Flavobacterium psychrophilum during early life-stage rearing [abstract]. Aquaculture. 497(2018):414-421.

Microbiome Analyses for Toxicological Studies - (Peer Reviewed Journal)
Benjamino, J., Lidia, B., Graf, J. 2018. Microbiome Analyses for Toxicological Studies. Current Protocols in Molecular Biology. 77(1):e53. https://doi.org/10.1002/cptx.53.

Flagellar regulation is required for virulence in Yersinia ruckeri - (Abstract Only)
Welch, T.J., Jozwick, A. 2018. Flagellar regulation is required for virulence in Yersinia ruckeri [abstract]. International Symposium on Aquatic Animal Health. P156.

Multi-Locus Variable number of tandem repeat Analysis (MLVA) of Yersinia ruckeri 2 confirms the existence of host-specificity, geographic endemism and anthropogenic 3 dissemination of virulent clones - (Peer Reviewed Journal)
Gulla, S., Barnes, A.C., Welch, T.J., Romalde, J.L., Rydere, D., Ormsby, M.J., Carson, J., Lagesen, K., Verner-Jeffreys, D.W., Davies, R.L., Colquhoun, D.J. 2018. Multi-Locus Variable number of tandem repeat Analysis (MLVA) of Yersinia ruckeri 2 confirms the existence of host-specificity, geographic endemism and anthropogenic 3 dissemination of virulent clones. Applied and Environmental Microbiology. doi:10.1128/AEM.00730-18.

Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Shaw, C.H., Gao, G., Wiens, G.D. 2018. Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss). Developmental and Comparative Immunology. 87:193-203. https://doi.org/10.1016/j.dci.2018.06.003.

Rainbow trout genetic resistance to bacterial cold water disease: Contribution of interleukin-1 receptor-like 1 genes - (Abstract Only)
Shaw, C.H., Gao, G., Wiens, G.D. 2018. Rainbow trout genetic resistance to bacterial cold water disease: Contribution of interleukin-1 receptor-like 1 genes [abstract]. Society of Developmental Comparative Immunology. 14:144.

Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that strong long-range LD is a major contributing factor - (Peer Reviewed Journal)
Vallejo, R.L., Silva, R.M., Evenhuis, J., Gao, G., Liu, S., Parsons, J.E., Martin, K.E., Wiens, G.D., Lourenco, D.A., Leeds, T.D., Palti, Y. 2018. Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that strong long-range LD is a major contributing factor. Journal of Animal Breeding and Genetics. 135:263–274. https://doi.org/10.1111/jbg.12335.

Draft genome sequence of the fish pathogen Flavobacterium columnare strain MS-FC-4 - (Peer Reviewed Journal)
Bartelme, R.P., Barbier, P., Lipscomb, R.S., LaPatra, S.E., Evenhuis, J., McBride, M.J. 2018. Draft genome sequence of the fish pathogen Flavobacterium columnare strain MS-FC-4. Genome Announcements. 6(20):e00429-18. https://doi.org/10.1128/genomeA.00429-18.

Genomic diversity and evolution of the fish pathogen Flavobacterium psychrophilum - (Peer Reviewed Journal)
Duchaud, E., Rochat, T., Habib, C., Barbier, P., Loux, V., Guerin, C., Dalsgaard, I., Madsen, L., Nilsen, H., Sundell, K., Wiklund, T., Strepparava, N., Wahli, T., Caburlotto, G., Manfrin, A., Wiens, G.D., Fujiwara-Nagata, E., Avendano-Herrera, R., Bernardet, J., Nicolas, P. 2018. Genomic diversity and evolution of the fish pathogen Flavobacterium psychrophilum. Frontiers in Microbiology. 9(138). https://doi.org/10.3389/fmicb.2018.00138.

Selective breeding for enhance specific disease resistance: Practical considerations and potential applications - (Abstract Only)
Wiens, G.D., Leeds, T.D. 2018. Selective breeding for enhance specific disease resistance: Practical considerations and potential applications [abstract]. Aquaculture America Conference. P-521.

Global proteomic profiling of Yersinia ruckeri strains - (Peer Reviewed Journal)
Kumar, G., Hummel, K., Welch, T.J., Razzazi-Fazeli, E., El-Matbouli, M. 2017. Global proteomic profiling of Yersinia ruckeri strains [online serial]. Veterinary Research. 48:55. https://doi.org/10.1186/s13567-017-0460-3.

Evolution of three tandem copies of the interleukin-1 receptor-like 1 gene in salmonid fish and their contribution to rainbow trout bacterial cold water disease resistant phenotype - (Abstract Only)
Shaw, C.H., Liu, S., Gao, G., Palti, Y., Wiens, G.D. 2017. Evolution of three tandem copies of the interleukin-1 receptor-like 1 gene in salmonid fish and their contribution to rainbow trout bacterial cold water disease resistant phenotype. Society of Developmental Comparative Immunology. P51.

Delineation of taxonomic species within complex of species: Aeromonas media and related species as a test case - (Peer Reviewed Journal)
Talagrand-Reboul, E., Roger, F., Kimper, J., Colston, S.M., Graf, J., Laftif-Eugenin, F., Figueras, M., Petit, F., Marchadin, H., Jumas-Bilak, E., Lamy, B. 2017. Delineation of taxonomic species within complex of species: Aeromonas media and related species as a test case. Frontiers in Microbiology [serial online]. 8:621. https://doi.org/10.3389/fmicb.2017.00621.

Efficacy testing of 35-year-old commercially-produced ERM bacterin reveals the remarkable stability of this product - (Peer Reviewed Journal)
Welch, T.J., Goodrich, T.D., La Patra, S.E. 2017. Efficacy testing of 35-year-old commercially-produced ERM bacterin reveals the remarkable stability of this product. Journal of Fish Diseases. 00:1–4. doi:10.1111/jfd.12646.

A BCWD-resistant line of rainbow trout exhibits higher abundance of IgT+ B cells and heavy chain tau transcripts compared to a susceptible line following challenge with Flavobacterium psychrophilum - (Peer Reviewed Journal)
Zwollo, P., Hennessey, E., Moore, C., Marancik, D.P., Wiens, G.D., Epp, L. 2017. A BCWD-resistant line of rainbow trout exhibits higher abundance of IgT+ B cells and heavy chain tau transcripts compared to a susceptible line following challenge with Flavobacterium psychrophilum. Developmental and Comparative Immunology. 74:190-199.

Evolution of interleukin-1 receptor-like 1 and its role in rainbow trout (Oncorhynchus mykiss) resistance to Flavobacterium psychrophilum - (Abstract Only)
Shaw, C.H., Palti, Y., Gao, G., Wiens, G.D. 2017. Evolution of interleukin-1 receptor-like 1 and its role in rainbow trout (Oncorhynchus mykiss) resistance to Flavobacterium psychrophilum [abstract]. Immunology. 198(1 Supplement). 201.22.

Draft genome sequence of the fish pathogen Flavobacterium columnare strain CSF-298-10 - (Peer Reviewed Journal)
Evenhuis, J., La Patra, S.E., Graf, J. 2017. Draft genome sequence of the fish pathogen Flavobacterium columnare strain CSF-298-10. Genome Announcements. 5(15):e00173.17. doi:10.1128/genomeA.00173-17.

Detection of the florfenicol resistance gene floR in Chryseobacterium isolates from rainbow trout. Exception to the general rule? - (Peer Reviewed Journal)
Verner-Jeffreys, D., Brazier, T., Perez, R.Y., Ryder, D., Hoare, R., Welch, T.J., Ngao, T., Card, R., Mclaren, N., Ellis, R., Rowe, W., Bartle, K. 2017. Detection of the florfenicol resistance gene floR in Chryseobacterium isolates from rainbow trout. Exception to the general rule? FEMS Microbiology Ecology. 93(4):fix015. doi:10.1093/femsec/fix015.

Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay - (Peer Reviewed Journal)
Kutyrev, I., Cleveland, B.M., Leeds, T.D., Wiens, G.D. 2017. Dataset of proinflammatory cytokine and cytokine receptor gene expression in rainbow trout (Oncorhynchus mykiss) measured using a novel GeXP multiplex, RT-PCR assay. Data in Brief. 11:192-196.

Genomic selection exploits within-family genetic variation for disease resistance in rainbow trout - (Abstract Only)
Evenhuis, J., Leeds, T.D., Palti, Y., Vallejo, R.L., Gao, G., Martin, K., Parsons, J., Wiens, G.D. 2017. Genomic selection exploits within-family genetic variation for disease resistance in rainbow trout [abstract]. Aquaculture America. p. 116.

The flagellar master operon flhDC is a pleiotropic regulator involved in motility and virulence of the fish pathogen Yersinia ruckeri - (Peer Reviewed Journal)
Snyder, A.K., Graf, J., Welch, T.J. 2016. The flagellar master operon flhDC is a pleiotropic regulator involved in motility and virulence of the fish pathogen Yersinia ruckeri. Journal of Applied Microbiology. 122(3):578-588. doi: 10.1111/jam.13374.

Differential expression of long non-coding RNAs in three genetic lines of rainbow trout (Oncorhynchus mykiss) in response to infection with Flavobacterium psychrophilum - (Peer Reviewed Journal)
Paneru, B., Al Tobasei, R., Palti, Y., Wiens, G.D., Salem, M. 2016. Differential expression of long non-coding RNAs in three genetic lines of rainbow trout (Oncorhynchus mykiss) in response to infection with Flavobacterium psychrophilum. Scientific Reports. 6:36032 doi: 10.1038/srep36032.

Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss) - (Peer Reviewed Journal)
Kutyrev, I., Cleveland, B.M., Leeds, T.D., Wiens, G.D. 2016. Proinflammatory cytokine and cytokine receptor gene expression kinetics following challenge with Flavobacterium psychrophilum in resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). Fish and Shellfish Immunology. 58:542-553. doi: 10.1016/j.fsi.2016.09.053.

Shotgun proteomic analysis of Yersinia ruckeri isolates under normal and iron-limited conditions - (Peer Reviewed Journal)
Kumar, G., Hummel, K., Ahrens, M., Menanteau-Ledouble, S., Razzazi-Fazeli, E., Welch, T.J., El-Matbouli, M. 2016. Shotgun proteomic analysis of Yersinia ruckeri isolates under normal and iron-limited conditions. Veterinary Research. 47:100. doi:10.1186/s13567-016-0384-3.

Virulence and molecular variation of Flavobacterium columnare affecting rainbow trout in ID, USA - (Peer Reviewed Journal)
Evenhuis, J., Mohammad, H., Lapatra, S.E., Welch, T.J., Arias, C. 2016. Virulence and molecular variation of Flavobacterium columnare affecting rainbow trout in ID, USA. Aquaculture. 464:106-110. doi: 10.1016/j.aquaculture.2016.06.017.

Draft genome sequence of Lactococcus garvieae str. PAQ102015-99, an outbreak strain isolated from a commercial trout farm in the Northwestern United States - (Peer Reviewed Journal)
Nelson, M., Varney, J., Welch, T.J., Graf, J. 2016. Draft genome sequence of Lactococcus garvieae str. PAQ102015-99, an outbreak strain isolated from a commercial trout farm in the Northwestern United States. Genome Announcements. 4(4):e00781-16. https://doi.org/10.1128/genomeA.00781-16.

Fish Viruses and Bacteria: Pathobiology and Protection - (Book / Chapter)
Welch, T.J., Marancik, D., Good, C. 2017. Weissella ceti. In: Woo, P. T. K., Cipriano, R. C. Fish Viruses and Bacteria: Pathobiology and Protection. Wallingford, Oxfordshire, UK: CABI Publishing. Chapter 24 p.334.

Virulence of Flavobacterium columnare genomovars in rainbow trout Oncorhynchus mykiss - (Peer Reviewed Journal)
Evenhuis, J., Lafrentz, B.R. 2016. Virulence of Flavobacterium columnare genomovars in rainbow trout Oncorhynchus mykiss. Diseases of Aquatic Organisms. 120(3):217-224.

Efficacy testing of a 35 year old commercially produced Yersinia ruckeri bacterin for the control of Enteric Redmouth ERM) Disease - (Abstract Only)
Lapatra, S., Welch, T.J. 2016. Efficacy testing of a 35 year old commercially produced Yersinia ruckeri bacterin for the control of Enteric Redmouth ERM) Disease. International Conference on Diseases of Fish and Shellfish. P-O-025.

An outbreak of Plesimonus Shigelloides in Zebrafish - (Abstract Only)
Hansen, J., Woodson, J., Deas, E., Mcpherson, V., Welch, T.J. 2016. An outbreak of Plesimonus Shigelloides in Zebrafish. International Conference on Diseases of Fish and Shellfish. P540.

Genetic diversity of Flavobacterium psychrophilum isolates from three Oncorhynchus spp. in the United States, as revealed by multilocus sequence typing - (Peer Reviewed Journal)
Van Vliet, D., Wiens, G.D., Loch, T.P., Nicolas, P., Faisal, M. 2016. Genetic diversity of Flavobacterium psychrophilum isolates from three Oncorhynchus spp. in the United States, as revealed by multilocus sequence typing. Applied and Environmental Microbiology. 82:3246-3255.

VIRULENCE OF Flavobacterium columnare GENOMOVARS IN RAINBOW TROUT (Oncorhynchus mykiss) - (Abstract Only)
Evenhuis, J., Lafrentz, B.R. 2016. VIRULENCE OF Flavobacterium columnare GENOMOVARS IN RAINBOW TROUT (Oncorhynchus mykiss){abstract}. Aquaculture America Conference. FH2-345.

Yersinia ruckeri lipopolysaccharide is necessary and sufficient for eliciting a protective immune response in rainbow trout (Oncorhynchus mykiss, Walbaum) - (Peer Reviewed Journal)
Welch, T.J., Lapatra, S. 2016. Yersinia ruckeri lipopolysaccharide is necessary and sufficient for eliciting a protective immune response in rainbow trout (Oncorhynchus mykiss, Walbaum). Fish and Shellfish Immunology. 49:420-426. doi:10.1016/j.fsi.2015.12.037

Exposure to pairs of Aeromonas strains enhances virulence in the Caenorhabditis elegans infection model - (Peer Reviewed Journal)
Mosser, T., Talagrand, E., Colston, S.M., Graf, J., Figueras, M., Jumas-Bilak, E., Lamy, B. 2015. Exposure to pairs of Aeromonas strains enhances virulence in the Caenorhabditis elegans infection model. Frontiers in Microbiology. 6:1218. doi: 10.3389/fmicb.2015.01218.

Selective breeding improves rainbow trout resistance against bacterial cold water disease with little evidence for change in tolerance - (Abstract Only)
Wiens, G.D., Marancik, D.P., Leeds, T.D. 2015. Selective breeding improves rainbow trout resistance against bacterial cold water disease with little evidence for change in tolerance. Congress International Society Develop Comparative Immunology. P628-12.

Flagellar regulation in Yersinia ruckeri during infection - (Abstract Only)
Snyder, A.K., Welch, T.J. 2015. Flagellar regulation in Yersinia ruckeri during infection [abstract]. European Association of Fish Pathologists. p. O-102.

Bioinformatic genome comparisons for taxonomic and phylogenic assignments using Aeromonas as a test case - (Peer Reviewed Journal)
Colston, S., Fullmer, M., Beka, L., Lamy, B., Gogarten, J.P., Graf, J. 2014. Bioinformatic genome comparisons for taxonomic and phylogenic assignments using Aeromonas as a test case. mBio. 5(6):e02136-14. DOI:10.1128/mBio.02136-14.