@article{snyder_hinshaw_welch_2015, title={Diagnostic tools for rapid detection and quantification of Weissella ceti NC36 infections in rainbow trout}, volume={60}, ISSN={["1472-765X"]}, DOI={10.1111/lam.12365}, abstractNote={Abstract Weissellosis of rainbow trout is caused by the Gram-positive bacteria Weissella ceti and has been reported in China, Brazil and the United States. This disease can result in high mortality in market-sized fish and thus can cause significant economic loss. Thus far, phenotypic characterization and 16S rRNA sequencing have been used to confirm a Weissellosis diagnosis. Here, we present the development of PCR-based diagnostic tools for the rapid identification and quantification of W. ceti within bacteriological culture and infected tissues. A duplex PCR, which amplifies both genus- and strain-specific targets, positively identifies isolates as W. ceti NC36. A qPCR assay was also developed to quantify pathogen load from infected tissues, using a W. ceti NC36 unique locus. A proof of concept study was performed to demonstrate that quantification using traditional plate count methods and qPCR were significantly correlated when assessed from infected brain and spleen tissue. These tools were also used to confirm diagnosis of Weissellosis in a commercial rainbow trout farm during an outbreak investigation. These are the first diagnostic tools developed for identification and quantification of W. ceti infection within rainbow trout, contributing to rapid Weissellosis diagnosis, enhanced pathogen surveillance and epidemiological studies. Significance and Impact of the Study Weissellosis is a rapidly emerging infectious disease of farmed rainbow trout caused by Weissella ceti, a Gram-positive lactic-acid bacterium. This disease can cause significant economic loss, and thus, efforts to limit its spread are urgently needed and are dependent on the development of diagnostic tools. The article presents the development of PCR-based diagnostic assays for the rapid identification of W. ceti and for quantification of pathogen load directly from tissues without the need for bacterial amplification or isolation. These tools are critical for rapid confirmation of Weissellosis diagnosis and for studying the epidemiology of this emerging pathogen.}, number={2}, journal={LETTERS IN APPLIED MICROBIOLOGY}, author={Snyder, A. K. and Hinshaw, J. M. and Welch, T. J.}, year={2015}, month={Feb}, pages={103–110} }
 @article{noga_borron_hinshaw_gordon_gordon_seo_2011, title={Identification of histones as endogenous antibiotics in fish and quantification in rainbow trout (Oncorhynchus mykiss) skin and gill}, volume={37}, ISSN={["1573-5168"]}, DOI={10.1007/s10695-010-9422-7}, number={1}, journal={FISH PHYSIOLOGY AND BIOCHEMISTRY}, author={Noga, Edward J. and Borron, Paul J. and Hinshaw, Jeffrey and Gordon, William C. and Gordon, Linda J. and Seo, Jung-Kil}, year={2011}, month={Mar}, pages={135–152} }
 @article{welch_verner-jeffreys_dalsgaard_wiklund_evenhuis_garcia cabrera_hinshaw_drennan_lapatra_2011, title={Independent Emergence of Yersinia ruckeri Biotype 2 in the United States and Europe}, volume={77}, ISSN={["1098-5336"]}, DOI={10.1128/aem.02997-10}, abstractNote={ABSTRACT Biotype 2 (BT2) variants of the bacterium Yersinia ruckeri are an increasing disease problem in U.S. and European aquaculture and have been characterized as serovar 1 isolates that lack both peritrichous flagella and secreted phospholipase activity. The emergence of this biotype has been associated with an increased frequency of enteric redmouth disease (ERM) outbreaks in previously vaccinated salmonid fish. In this study, four independent specific natural mutations that cause the loss of both motility and secreted lipase activity were identified in BT2 strains from the United States, United Kingdom, and mainland Europe. Each of these was a unique mutation in either fliR , flhA , or flhB , all of which are genes predicted to encode essential components of the flagellar secretion apparatus. Our results demonstrate the existence of independent mutations leading to the BT2 phenotype; thus, this phenotype has emerged separately at least four times. In addition, BT2 strains from the United Kingdom were shown to have the same mutant allele found in U.S. BT2 strains, suggesting a common origin of this BT2 lineage. This differentiation of distinct BT2 lineages is of critical importance for the development and validation of alternative vaccines or other treatment strategies intended for the control of BT2 strains.}, number={10}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Welch, Timothy J. and Verner-Jeffreys, David W. and Dalsgaard, Inger and Wiklund, Thomas and Evenhuis, Jason P. and Garcia Cabrera, Jose A. and Hinshaw, Jeffrey M. and Drennan, John D. and LaPatra, Scott E.}, year={2011}, month={May}, pages={3493–3499} }
 @inbook{fornshell_hinshaw_2008, place={Ames, Iowa}, title={Better Management Practices for Flow-Through Aquaculture Systems}, ISBN={9780813818672 9780813820279}, url={http://dx.doi.org/10.1002/9780813818672.ch9}, DOI={10.1002/9780813818672.ch9}, abstractNote={This chapter contains sections titled: Introduction Flow-Through System Hydrology Site Selection Feeds and Feeding Solids Management Solids Disposal Fish Escape Predator Control Mortality Removal and Disposal Facility Operation and Maintenance References}, booktitle={Environmental Best Management Practices for Aquaculture}, publisher={Wiley-Blackwell}, author={Fornshell, Gary and Hinshaw, Jeffrey M.}, editor={Tucker, Craig S. and Hargreaves, John A.Editors}, year={2008}, pages={331–388} }
 @article{engle_pomerleau_fornshell_hinshaw_sloan_thompson_2005, title={The  economic impact of proposed effluent treatment options for production of trout Oncorhynchus mykiss in flow-through systems}, volume={32}, DOI={10.1016/j.nquaeng.2004.07.001}, number={2}, journal={Aquacultural Engineering}, author={Engle, C. R. and Pomerleau, S. and Fornshell, G. and Hinshaw, Jeffrey and Sloan, D. and Thompson, S.}, year={2005}, pages={303–323} }
 @article{engle_pomerleau_fornshell_hinshaw_sloan_thompson_2005, title={The economic impact of proposed effluent treatment options for production of trout Oncorhynchus mykiss in flow-through systems}, volume={32}, ISSN={0144-8609}, url={http://dx.doi.org/10.1016/j.aquaeng.2004.07.001}, DOI={10.1016/j.aquaeng.2004.07.001}, abstractNote={Abstract The United States Environmental Protection Agency has considered several treatment options for flow-through systems in its Effluent Limitation Guidelines rulemaking effort on aquaculture. However, the economic effects of treating effluents can impose high costs on aquaculture businesses, depending upon the treatment option selected. Survey data from trout farmers in North Carolina and Idaho were used to develop enterprise budgets, a spreadsheet-based risk analysis, and mathematical programming models of medium-sized trout farms in North Carolina (68,182 kg/yr) and Idaho (90,909 kg/yr) and large trout farms in Idaho (1,136,364 kg/yr). These analyses were used to examine the effect of imposing five different effluent treatment options on the net returns of farms raising trout in raceways. Budget analyses showed that the trout farm scenarios considered were generally profitable, although the medium-sized farms exhibited low levels of profitability. All five proposed effluent treatment options resulted in negative net returns for the medium-sized farms in both North Carolina and Idaho. The large farm scenario showed positive net returns after adding costs associated with the affluent treatment options considered, but the risk of generating positive net returns decreased from 82–84% to 10–11%. Thus, financial risk increased considerably when treatment options were imposed. The mixed-integer mathematical programming model demonstrated sensitivities to the level of credit reserves both for operating and investment capital. The effluent treatment options imposed on the models were not economically feasible at the levels of capital available on most trout farms. Subsequent runs of the model used investment capital requirements of treatment options at 50% of the original estimates. The models showed that imposing effluent treatment options forced farms to substitute production units for treatment facilities. This results from a combination of: 1) the additional capital requirements of the treatment options; 2) limited availability of credit reserves; and 3) competing uses for land in trout farming areas that put upward pressure on land prices. Many of the proposed treatment options included substantial investment capital requirements that increased annual fixed costs. Limited availability of investment capital prevented the farm expansion that would be needed to spread the increased fixed costs; hence, the models were forced to remove units from production to meet treatment constraints. Net returns decreased because farms were forced to operate at inefficient levels.}, number={2}, journal={Aquacultural Engineering}, publisher={Elsevier BV}, author={Engle, Carole R. and Pomerleau, Steeve and Fornshell, Gary and Hinshaw, Jeffrey M. and Sloan, Debra and Thompson, Skip}, year={2005}, month={Jan}, pages={303–323} }
 @article{santerre_bush_xu_lewis_davis_grodner_ingram_wei_hinshaw_2001, title={Metal residues in farm-raised channel catfish, rainbow trout, and red swamp crayfish from the southern US}, volume={66}, ISSN={["0022-1147"]}, DOI={10.1111/j.1365-2621.2001.tb11330.x}, abstractNote={ABSTRACT: Farm-raised channel catfish (Ictalurus punctatus), rainbow trout (Oncorhynchus mykiss), and red swamp crayfish (Procambarus clarkii) were collected from production and processing sites across the southern U.S. and analyzed for barium, cadmium, copper, chromium, silver, lead, arsenic, selenium, and mercury. Average metal residues were much lower than recommended safety limits. Residues of barium, copper, and mercury were slightly higher in crayfish than catfish or trout. Selenium was higher in crayfish and trout than catfish, and lead was higher in catfish and trout than crayfish. Residues of mercury in all samples were much lower than the FDA's Action Limit (1 ppm) for mercury in the edible tissue of fish.}, number={2}, journal={JOURNAL OF FOOD SCIENCE}, author={Santerre, CR and Bush, PB and Xu, DH and Lewis, GW and Davis, JT and Grodner, RM and Ingram, R and Wei, CI and Hinshaw, JM}, year={2001}, month={Mar}, pages={270–273} }
 @article{santerre_ingram_lewis_davis_lane_grodner_wei_bush_xu_shelton_et al._2000, title={Organochlorines, organophosphates, and pyrethroids in channel catfish, rainbow trout, and red swamp crayfish from aquaculture facilities}, volume={65}, ISSN={["0022-1147"]}, DOI={10.1111/j.1365-2621.2000.tb15985.x}, abstractNote={Channel catfish (Ictalurus punctatus), rainbow trout (Oncorhynchus mykiss), and red swamp crayfish (Procambarus clarkii) were collected from 8 southern states in the United States and analyzed for 34 organochlorine, organophosphate, and pyrethroid compounds. Approximately 45% of catfish, 72% of trout, and 92% of crayfish contained no detectable residues. Most residues detected were well below action limits for fish. Chlorpyrifos, for which there is no established tolerance, was detected in catfish; however, residues of this pesticide were not detected in samples collected after the 1st year of the study. The data collected during this study further support the safety of aquaculture products.}, number={2}, journal={JOURNAL OF FOOD SCIENCE}, author={Santerre, CR and Ingram, R and Lewis, GW and Davis, JT and Lane, LG and Grodner, RM and Wei, CI and Bush, PB and Xu, DH and Shelton, J and et al.}, year={2000}, month={Mar}, pages={231–235} }