Climate Change Shrinks and Fragments Salmon Habitats in a Snow-Dependent Region.

Climate change threatens biodiversity through global alteration of habitats, but efficient conservation responses are often hindered by imprecise downscaling of impacts. Besides thermal effects, warming also drives important ancillary environmental changes, such as when river hydrology evolves in response to climate forcing. Earlier snowmelt runoff and summer flow declines are broadly manifested in snow-dependent regions and relevant to socioeconomically important cold-water fishes. Here, we mechanistically quantify how climate-induced summer flow declines during historical and future periods cause complex local changes in Chinook salmon (Oncorhynchus tshawytscha) habitats for juveniles and spawning adults. Changes consisted of large reductions in useable habitat area and connectivity between the main channel and adjacent off-channel habitats. These reductions decrease the capacity of freshwater habitats to support historical salmon abundances and could pose risks to population persistence in some areas.

Some (Fish Might) Like It Hot: Habitat Quality and Fish Growth from Past to Future Climates.

Current expectation is that projected climate change may have adverse effects on fish habitats and survival. The analysis leading to these concerns is typically done at large scale with limited possibility to quantify the local biological response and compare with previous conditions. Our research investigated the effects of recorded climate conditions on Chinook salmon (Oncorhynchus tshawytscha) spawning and rearing habitats and growth responses to the local climate and compared those conditions to predicted responses to a climate change. The study site was a 7 km long reach of Bear Valley Creek, an important spawning stream for this US Endangered Species Act listed species, in the Pacific Northwest of United States. We used 2D numerical modeling supported by accurate, high-resolution survey data to calculate flow hydraulics at various discharges from base to bankfull flows. For past and future conditions, computed flow hydraulics were combined with habitat suitability indices (SI) to compute spawning and rearing habitat suitability. Information on habitat suitability along with fish density and stream water temperature informed a growth model to quantify the potential fish size, an index of survival rates and fitness. Our results indicate that yearly-averaged rearing habitat quality remains similar to historic, but the timing of high- and low-quality habitat periods shift within the calendar year. Future spawning habitat quality may be significantly reduced during the seasonal period to which Chinook have currently adapted their spawning behavior. The growth model indicates an increase in anticipated size of Chinook salmon for predicted future climate conditions due to water temperature increase. Consequently, future climate conditions may have a substantial negative impact on spawning and limited impact on rearing conditions due to flow reduction and thus quality and extent of available habitat. However, the expected warmer stream water temperatures may benefit rearing, because of increased fish size in these high elevation streams.

Comparison of Antimicrobial Resistance Profiles in Salmonella spp. from Swine Upon Arrival and Postslaughter at the Abattoir.

Antimicrobial resistance (AMR) developed by Salmonella within animals used for food products is a major global issue. Monitoring AMR in animals destined for slaughter is, therefore, critical. Abattoirs may serve as potential candidate checkpoints for monitoring resistance patterns on farms. A complicating factor, however, is the impact of lairage on Salmonella detected in pigs at slaughter. This study sought to compare AMR patterns in Salmonella spp. in swine collected upon arrival (fecal samples) at the abattoir with those at postslaughter (cecal samples) and evaluate the feasibility of using slaughterhouse samples for surveillance of prevailing AMR Salmonella on farms. Eighty-four Salmonella isolates were recovered from a large, midwestern U.S. abattoir between September and November 2013. Isolates were tested for phenotypic AMR to 12 antimicrobials using the broth microdilution assay. Whole-genome sequencing identified the AMR genes harbored by the strains. Significant differences were observed in the isolate phenotypes and genotypes; however, no significant difference was observed in genotypic resistance patterns. Hence, the AMR profiles of Salmonella spp. postslaughter cannot be predicted from preslaughter samples. Further research considering the genetic diversity of isolates and statistical power of the genotypic analysis is warranted to improve the performance of WGS-inferred antimicrobial susceptibility.

Dam operations may improve aquatic habitat and offset negative effects of climate change.

Dam operation impacts on stream hydraulics and ecological processes are well documented, but their effect depends on geographical regions and varies spatially and temporally. Many studies have quantified their effects on aquatic ecosystem based mostly on flow hydraulics overlooking stream water temperature and climatic conditions. Here, we used an integrated modeling framework, an ecohydraulics virtual watershed, that links catchment hydrology, hydraulics, stream water temperature and aquatic habitat models to test the hypothesis that reservoir management may help to mitigate some impacts caused by climate change on downstream flows and temperature. To address this hypothesis we applied the model to analyze the impact of reservoir operation (regulated flows) on Bull Trout, a cold water obligate salmonid, habitat, against unregulated flows for dry, average, and wet climatic conditions in the South Fork Boise River (SFBR), Idaho, USA.

Breakthrough seizures after starting vilazodone for depression.

Vilazodone is a new selective serotonin reuptake inhibitor (SSRI) and serotonin 5-HT1a partial agonist that is approved by the United States Food and Drug Administration to treat major depression. SSRI-induced seizures are rare and are more likely to be associated with larger doses and severe symptoms such as those present in serotonin syndrome. Several case reports have implicated SSRIs, buspirone, or the combination of these agents as the cause of seizures, but these reports were confounded with either coingestions or doses that exceeded FDA recommendations. We describe a 22-year-old woman with a history of seizure disorder who had been seizure free for the previous 8 years and experienced two breakthrough seizures shortly after starting vilazodone. Her dose of vilazodone had recently been titrated to 40 mg/day when she experienced the first seizure. She was instructed to taper vilazodone over the next several days, then discontinue the drug, and then follow up with her neurologist. Based on the patient's history, physical examination, and recent dose increase, it was plausible that vilazodone was the cause of the seizures. Use of the Naranjo adverse drug reaction probability scale indicated a possible relationship (score of 4) between her development of seizures and vilazodone therapy. The pharmacodynamics of this particular class of SSRI has both proconvulsive and anticonvulsive mechanisms. This is of particular concern in patients with a history of seizure disorder who are starting antidepressive therapy. In persons with epilepsy who are taking vilazodone and experience breakthrough seizures, practitioners should consider this drug as a potential cause of these seizures. Thus, until future research and experience with vilazodone can provide a definitive answer, clinicians should be cautious when prescribing this medication to treat depression in patients with a history of seizure disorder.

Process mapping the prevalence of Salmonella contamination on pork carcass from slaughter to chilling: a systematic review approach.

A systematic review was conducted to identify and summarize primary research studies that describe the prevalence of Salmonella spp. in pork from slaughter to cooler in the member states of the European Union (EU), Australia, Canada, Hong Kong, Japan, Korea, Mexico, New Zealand, Taiwan, and United States (i.e., a process map). Relevant studies documented Salmonella spp. prevalence at more than one processing point using the same cohort of pigs or the same production line for the post-cooler component. Literature searches retrieved 6811 citations. Sixteen publications, describing 44 studies, evaluated the presence of Salmonella on pork carcasses. The carcass sampling points evaluated were as follows: stun, bleed, kill, scald, dehair, singe, polish, bung removal, evisceration, split, stamp, final wash, immediately after chill, and 18-48 h after chilling. Seventy-eight comparisons of Salmonella spp. prevalence between points along the processing line were reported. The median prevalence of Salmonella spp.-positive carcasses evaluated in the cooler was 0%. The median prevalence of Salmonella spp. after bleeding was 32%. Fifty-nine of the 78 point-to-point comparisons were associated with either no change or a decrease in Salmonella prevalence as the carcass moved closer to the cooler. Nineteen point-to-point changes showed an increase in Salmonella prevalence as the carcass moved toward the cooler; of these, six reported a greater than 10% increase in Salmonella prevalence. The majority of increases were associated with post-evisceration and splitting. These findings suggest that the processing procedures in place generally result in decreased prevalence of Salmonella spp. as the carcasses move toward the cooler.

Salmonella enterica in swine production: assessing the association between amplified fragment length polymorphism and epidemiological units of concern.

The aims of this study were to determine the ability of amplified fragment length polymorphism (AFLP) to differentiate Salmonella isolates from different units of swine production and to demonstrate the relatedness of Salmonella between farms and abattoirs by AFLP. Twenty-four farms in the midwestern United States were visited four times from 2006 to 2009. At each farm or abattoir visit, 30 fecal samples or 30 mesenteric lymph nodes were collected, respectively. A total of 220 Salmonella isolates were obtained, serotyped, and genotyped by multilocus sequence typing (MLST) and AFLP. These 220 isolates clustered into 21 serotypes, 18 MLST types, and 14 predominant AFLP clusters based on a genetic similarity threshold level of 60%. To assess genetic differentiation between farms, harvest cohorts, and pigs, analysis of molecular variance was conducted using AFLP data. The results showed 65.62% of overall genetic variation was attributed to variance among pigs, 27.21% to farms, and 7.17% to harvest cohorts. Variance components at the farm (P = 0.003) and pig (P = 0.001) levels were significant, but not at the harvest cohort level (P = 0.079). A second analysis, a permutation test using AFLP data, indicated that on-farm and at-abattoir Salmonella from pigs of the same farms were more related than from different farms. Therefore, among the three subtyping methods, serotyping, MLST, and AFLP, AFLP was the method that was able to differentiate among Salmonella isolates from different farms and link contamination at the abattoir to the farm of origin.

Sub-iliac lymph nodes at slaughter lack ability to predict Salmonella enterica prevalence for swine farms.

The aim of this study was to assess the value of deep systemic sub-iliac lymph nodes collected at slaughter as predictors of Salmonella prevalence in live hogs. An observational study was conducted on 24 farms from September 2006 to February 2009. At least one cohort of market-weight pigs was visited for each farm. Within each cohort, 30 farm fecal samples on farm and 30 sub-iliac lymph nodes from matched pigs at slaughter were collected. Samples were cultured for Salmonella enterica and serotyped by conventional methods. Overall, 3.4% (51 of 1490) of farm feces and 0.06% (1 of 1739) of sub-iliac lymph nodes were Salmonella positive; 71.4% (15 of 21) of farms had at least one positive fecal sample, and 4.2% (1 of 24) had at least one positive sub-iliac lymph node. The median within-farm prevalence of Salmonella in farm fecal samples was 1.7%, ranging from 0% to 38.3%; for sub-iliac lymph nodes the median was 0%, ranging from 0% to 1.1%. The median within-cohort prevalence in farm fecal samples was 0%, ranging from 0% to 43.3%; for sub-iliac lymph nodes the median was 0%, ranging from 0% to 4%. The predominant serotype detected was Derby, followed by Anatum and Typhimurium (Copenhagen). Salmonella Braenderup was recovered from the sub-iliac lymph node. The low detection rate of Salmonella in sub-iliac lymph nodes (0.06%) limits its usefulness as a dependable predictor of Salmonella contamination originating on farm (3.4%).

Split marketing as a risk factor for Salmonella enterica infection in swine.

On-farm reduction of Salmonella carriage prevalence in pigs requires the identification of risk factors to direct interventions development. This study was designed to determine if split marketing of finishing pigs constitutes a risk factor for Salmonella infections, by comparing Salmonella prevalence in the first group of pigs selected for harvest ("first pull") versus the prevalence in the last group of pigs selected for harvest ("close out") from multiple commercial finishing lots. Nine paired samplings were conducted consisting in matched groups of pigs from individual barns as the first pull and the close out with a 4-week interval between groups. From each group, fecal and meat samples were collected, on-farm and at harvest, respectively. Fecal samples were selectively enriched, and analyzed for the presence of Salmonella, whereas meat juice samples were analyzed for the presence of antibodies against Salmonella. In 7/9 (77.8%) of the studied barns, an increase in Salmonella prevalence was observed, based on both bacteriologic and serologic analysis. Overall, there was an increase of 9.2% (p < 0.05) in bacteriologic prevalence, and 31.3% (p < 0.05) in serologic prevalence from first pull to close out groups. This study demonstrates that a significant increase in Salmonella prevalence occurs between the first and the last group of pigs harvested from finishing lots, with close out groups of market pigs posing a higher risk for Salmonella contaminations.

Seroprevalence of Trichinella, Toxoplasma, and Salmonella in antimicrobial-free and conventional swine production systems.

There has been a growing niche-market, outdoor, antimicrobial-free (ABF) swine production system in the last few years prompted by consumers' demand for a more "natural" pork product. The impact of such production systems on reemergence of current and historically significant swine-associated pathogens has not been determined. The objectives of the current study were to determine and compare Salmonella, Toxoplasma, and Trichinella seropositivity in two swine production systems: outdoor ABF and intensive indoor production systems. These three foodborne pathogens represent those with the highest importance for pork consumption. A total of 675 serum samples from three participating states, Wisconsin, North Carolina, and Ohio, were investigated. We found significantly higher seroprevalence of Salmonella and Toxoplasma from ABF herds (54% and 7%, respectively) than conventional (39% and 1%, respectively) (p = 0.001). Two pigs, both from ABF herds, were found to be seropositive for Trichinella. The results from this preliminary study suggest that all three pathogens were more commonly present in pigs that were reared in an ABF, outdoor, niche-market type of environment than the conventional, indoor-reared herds though there were some geographical variation in Salmonella. This warrants a robust epidemiologic study to determine the role of various risk factors in the two production systems that may lead to persistence of bacterial (Salmonella) pathogens and reemergence of parasites (such as Trichinella) of historical significance.

Low prevalence of Listeria monocytogenes in cull sows and pork.

The goal of this study was to determine the prevalence of Listeria monocytogenes in sows slaughtered at a single Midwestern plant on two occasions (trial 1, n = 179 sows; trial 2, n = 160 sows). Fecal samples collected antemortem (trial 1) as well as animal tissues, and carcass swabs collected at the abattoir (trials 1 and 2) were analyzed. Eight isolates of L. monocytogenes were recovered from five samples that represented 0.18% of the total samples (n = 2,775). In trial 1, L. monocytogenes was detected in a tonsil sample (0.6%; 1 positive of 181 tonsils), in a carcass (0.6%; 1 positive of 179 carcasses), which was sampled prior to the organic rinse, and in two chopped meat block samples (1.2%; 2 positive of 165 samples). In trial 2, L. monocytogenes was only detected in a single chopped meat block sample (0.15%; 1 positive of 688 total samples). These data indicate the low prevalence of L. monocytogenes in the cull sow.

Efficacy of vaccination to reduce Salmonella prevalence in live and slaughtered swine: a systematic review of literature from 1979 to 2007.

A systematic review was conducted to evaluate the efficacy of vaccination to reduce Salmonella prevalence in market weight finisher swine. A search of online databases and selected conference proceedings was conducted to identify relevant studies. The review process followed relevance screening, methodological quality assessment, and data extraction. Although multiple outcomes were frequently reported, only outcomes describing culture of Salmonella were extracted. Five clinical trials and 23 challenge studies were considered likely relevant to the review as they described vaccination to reduce Salmonella in swine. Five clinical trials reported vaccination was associated with reduced isolation of Salmonella in market weight pigs, however, information required to assess the internal validity of the study was often not described in the manuscripts. All challenge studies assessed vaccine efficacy in pigs aged <15 weeks reducing the relevance of results to the review which focused on market weight pigs. Only five of the 23 challenge studies reported the majority of information necessary to evaluate the quality of vaccine studies. Given large variability in population type, sample size, type of vaccine, dose and dosing regimens, and type of outcomes observed, pooled data analysis was not possible, and therefore, a qualitative synthesis of the studies was conducted. Available evidence suggests that vaccination is associated with reduced Salmonella prevalence in swine at or near harvest; however, this conclusion is based on studies with design and reporting deficiencies that could potentially indicate biases with the outcome.

Prevalence of exposure to Salmonella spp in finishing swine marketed in Iowa.

OBJECTIVE: To describe the prevalence of antibodies against Salmonella spp in swine marketed in Iowa. ANIMALS: Swine marketed by 1,044 low-volume producers and 45 high-volume producers. PROCEDURE: Samples of diaphragm muscle collected from swine carcasses were tested by an indirect ELISA based on lipopolysaccharides from Salmonella spp, in particular Salmonella serovar Typhimurium. Prevalence of positive results for antibodies against Salmonella spp for carcasses, lots, and swine for each producer was determined. Producer-level seroprevalence was used to classify swine from producers as having negligible, low, moderate, or widespread evidence of previous or historical exposure to Salmonella spp. RESULTS: From low-volume producers, 23,609 of 25,478 (92.7%; 95% confidence interval [CI], 92.4% to 92.9%) samples had negative results, and 1,863 (7.3%; 95% CI, 7.05% to 7.56%) had antibodies against Salmonella spp. Of the 6,299 lots of swine tested, 1,191 (18.9%) contained at least 1 sample with positive results. From high-volume producers, 203 of 2,486 (8.1%; 95% CI, 6.8% to 9.3%) samples had antibodies against Salmonella spp, and 124 of 629 lots had at least 1 sample with positive results for antibodies against Salmonella spp. CONCLUSIONS AND CLINICAL RELEVANCE: Less than 10% of pigs marketed in Iowa are apparently exposed to Salmonella spp. Most swine marketed by low-volume producers had negligible or little evidence of exposure to Salmonella spp, whereas a higher percentage of swine marketed by high-volume producers had positive results when tested to detect antibodies against Salmonella spp.

Culture methods differ on the isolation of Salmonella enterica serotypes from naturally contaminated swine fecal samples.

Four culture methods (A, B, C, and D) were comparatively evaluated for their ability to isolate Salmonella enterica from pooled swine fecal samples (n = 100). None of the methods was able to isolate Salmonella from all positive samples. The relative sensitivity of the culture methods evaluated was 82%, 94%, 95%, and 78% for methods A, B, C, and D, respectively. The comparison of sensitivities showed that methods B and C performed significantly better (P < 0.05) than methods A and D. Although relative sensitivities of methods B and C were equal, from the 89 positive samples concomitantly detected by both, 35 (39.3%) had different serotypes (no match) isolated by each method. On the basis of the results of this study, it was concluded that culture methods differ on the isolation of S. enterica serotypes from naturally contaminated swine fecal samples. Depending on the objective(s) of investigations on the ecology and epidemiology of S. enterica in swine populations, a method or a combination of methods should be considered for more reliable results.

Resting pigs on transport trailers as an intervention strategy to reduce Salmonella enterica prevalence at slaughter.

Recent research has shown that much preharvest Salmonella enterica infection in pigs occurs immediately before slaughter during this rest period in the contaminated abattoir holding pens. The objective of this study was to evaluate a potential intervention strategy to reduce the prevalence of S. enterica-positive pigs at slaughter, which consisted of resting pigs prior to slaughter on their transport vehicle, instead of in the abattoir holding pen. Additionally, the effect of transportation of pigs from farm to the abattoir on S. enterica prevalence was investigated. A total of 120 animals were included in the experiment, divided in four replicates (n = 30 pigs per replicate). Fecal samples were collected from each animal at the farm and at the abattoir, where 15 randomly chosen pigs were unloaded and moved to a holding pen, while the remaining 15 pigs stayed in the transport trailer. After approximately 1.5 h of resting, both groups were slaughtered. Samples collected included distal ileum portion, cecal contents, and ileocecal lymph node. The overall S. enterica prevalence (pigs positive in at least one of the samples collected at slaughter) was higher for pigs held in the abattoir pens (40.7% versus 13.3%, P < 0.05). There was no difference (P > 0.05) for the S. enterica prevalence before and after transportation from farm to abattoir (5.8% versus 0.8%, respectively). This study demonstrates that resting pigs on the transport vehicle has the potential to decrease S. enterica levels entering the abattoir.

The association between cleaning and disinfection of lairage pens and the prevalence of Salmonella enterica in swine at harvest.

A series of four field trials were conducted to evaluate the ability of a cleaning and disinfection procedure in swine lairage pens to reduce the prevalence of Salmonella enterica in slaughtered pigs. A cleaning and disinfection procedure was applied to lairage pens at a large Midwest abattoir. Each trial consisted of a cleaned (alkaline chloride detergent) and disinfected (H2O2 plus peracetic acid sanitizer) pen (treated) and a control pen, each holding 90 to 95 pigs for 2 to 3 h before slaughter. Ileocecal lymph nodes, cecal contents, and rectal contents were collected from 45 pigs from each study pen at harvest and cultured for S. enterica. In all trials, cleaning and disinfection reduced the prevalence of S. enterica-positive floor swabs in the treated pen (P < 0.05). However, the postharvest prevalence of S. enterica-positive pigs varied between trials. In trial 1, there was no significant difference in the prevalence of S. enterica in pigs between treatment and control groups. In trials 2 and 3, the prevalence of S. enterica was higher in pigs from treated pens versus pigs from control pens (91% versus 40%, P < 0.0001, and 91% versus 24%, P < 0.0001, respectively). In trial 4, the prevalence of S. enterica was lower in pigs from treated pens compared with pigs from control pens (5% versus 42%, P < 0.0001). This study indicates that cleaning and disinfection effectively reduces the amount of culturable S. enterica in lairage pens, but the ability of cleaned and disinfected pens to reduce the prevalence of S. enterica in market-weight pigs remains inconclusive.

Detection of Listeria monocytogenes in pigs and pork.

In this study, we surveyed hogs (n = 300) as well as pork products (ground pork and raw chitterlings) for Listeria monocytogenes. Pig specimens collected before (tonsil swabs) and after slaughter (tonsils, lymph nodes, carcass swabs, and rectal contents) were examined for L. monocytogenes by enrichment with conventional enrichment broths followed by subculturing to selective agar. A multiplex polymerase chain reaction assay targeting the highly conserved 16S rRNA gene of the Listeria species as well as the hlyA gene unique to L. monocytogenes was used to screen aliquots of the enrichment (method I) as well as to confirm presumptive Listeria colonies from Columbia agar with 0.05% glucose supplemented with polymyxin B-acriflavine-lithium chloride-ceftazidime-aesculin-mannitol (PALCAM; method II). Subculturing to PALCAM agar was the more sensitive of the two methods on the basis of the overall detection of Listeria. For hog tissues, method I detected L. monocytogenes (0.87% positive) and no other Listeria spp. in all samples (n = 1,849). In contrast, method II detected significantly more (P < 0.05) L. monocytogenes (2.38%) and Listeria spp. (0.38%) in these tissues. For small intestines (n = 300 raw chitterlings), L. monocytogenes was identified in 8.3% of enrichments with University of Vermont modified Listeria enrichment broth; plating to PALCAM slightly improved recovery (9%). Overall, ground pork samples (n = 340) harbored L. monocytogenes (45% positive) and other Listeria species (1.5% positive), as determined by method I. Subculturing to PALCAM significantly (P < 0.05) improved the detection of L. monocytogenes (50.2%) but not that of other Listeria species (1.7%). L. monocytogenes isolates (n = 243) were assigned to serotype 1 (53.5%), serotype 4 (25%), and serotypes other than 1 and 4 (21.4%).