Assessment of the knowledge and behavior of backyard and small-scale producers in California regarding disease prevention, biosecurity practices and antibiotics use.

The number and popularity of backyard poultry and livestock farming have rapidly increased in California as well as other states in the United States following consumers' preference for local and organic products in the last few years. This study aimed to investigate current on-farm management and farmers' understanding of Veterinary Feed Directive (VFD) and California Senate Bill (SB) 27 implications for disease prevention, biosecurity procedures, and antimicrobial use in small-scale and backyard farms in California. The survey consisted of 38 questions. The responses of 242 backyard and small-scale livestock owners were investigated in this study. Descriptive statistics summarized survey responses, and multivariable logistic regression evaluated the association of antibiotics purchase and use, and the impact of VFD and SB27 on antibiotic use with demographics and on-farm management. Backyard and small-scale farmers in California mostly raised chickens or small ruminants with small herd sizes kept for personal use. Antibiotics were generally used for individual treatment of a sick animal with the guidance of a veterinarian. VFD and SB27 implementation promoted the judicious use of antibiotics, specifically, by enhancing the relationship between backyard and small-scale farmers with veterinarians and treating fewer animals with antibiotics under veterinary oversight. Therefore, better access to veterinary service in backyard and small-scale farms will improve the farmer's knowledge of good husbandry practices with judicious antimicrobial use in livestock and finally contribute to reducing the risk of antimicrobial resistance in California.

Survey of Management Practices and Farmers' Perceptions of Diseases on Organic Dairy Cattle Farms in California.

In 2019, California accounted for approximately 40% of organic products in the US, and dairy products and milk were the top organic commodity in the state. The objective of this study was to describe organic dairy cattle farmers' management practices and perceptions of diseases in California. A survey inquiring about farm history and demographics, animal diseases, parasite problems, housing and pasture management, and organic education, was mailed to 160 organic dairy farms, of which 36 (22.5%) responded. Among respondents, the majority (83.9%) were located in Northern California; median farm size was 310 cows, and the dominant breed was Holstein (60.0%). Respondents were more likely to report mastitis in cows (45.2%), pinkeye in heifers (31.3%), and digestive problems in calves (47.0%), as issues affecting their stock "often" or "almost always" in the last 12 months. Although most farmers vaccinated their cattle against Bovine Viral Diarrhea (86.1%) and Escherichia coli mastitis (80.6%), they still described that these diseases frequently impacted their animals. Over half of the farmers did not perceive gastrointestinal parasites or biting flies to be a problem and did not observe signs of lice and mites. According to the results, the management of disease in all age classes is a concern; options and efficacies of alternative therapeutic methods, as well as preventive measures for organic dairies need to be further explored.

Identification of high-risk contact areas between feral pigs and outdoor-raised pig operations in California: Implications for disease transmission in the wildlife-livestock interface.

The US is currently experiencing a return to raising domestic pigs outdoors, due to consumer demand for sustainably-raised animal products. A challenge in raising pigs outdoors is the possibility of these animals interacting with feral pigs and an associated risk of pathogen transmission. California has one of the largest and widest geographic distributions of feral pigs. Locations at greatest risk for increased contact between both swine populations are those regions that contain feral pig suitable habitat located near outdoor-raised domestic pigs. The main aim of this study entailed identifying potential high-risk areas of disease transmission between these two swine populations. Aims were achieved by predicting suitable feral pig habitat using Maximum Entropy (MaxEnt); mapping the spatial distribution of outdoor-raised pig operations (OPO); and identifying high-risk regions where there is overlap between feral pig suitable habitat and OPO. A MaxEnt prediction map with estimates of the relative probability of suitable feral pig habitat was built, using hunting tags as presence-only points. Predictor layers were included in variable selection steps for model building. Five variables were identified as important in predicting suitable feral pig habitat in the final model, including the annual maximum green vegetation fraction, elevation, the minimum temperature of the coldest month, precipitation of the wettest month and the coefficient of variation for seasonal precipitation. For the risk map, the final MaxEnt model was overlapped with the location of OPOs to categorize areas at greatest risk for contact between feral swine and domestic pigs raised outdoors and subsequent potential disease transmission. Since raising pigs outdoors is a remerging trend, feral pig numbers are increasing nationwide, and both groups are reservoirs for various pathogens, the contact between these two swine populations has important implications for disease transmission in the wildlife-livestock interface.

Risk factors of Shiga toxin-producing Escherichia coli in livestock raised on diversified small-scale farms in California.

The increasing number of diversified small-scale farms (DSSF) that raise outdoor-based livestock in the USA reflects growing consumer demand for sustainably produced food. Diversified farms are small scale and raise a combination of multiple livestock species and numerous produce varieties. This 2015-2016 cross-sectional study aimed to describe the unique characteristics of DSSF in California, estimate the prevalence of Shiga toxin-producing Escherichia coli (STEC) in livestock and evaluate the association between risk factors and the presence of STEC in livestock, using generalised linear mixed models. STEC prevalence was 13.62% (76/558). Significant variables in the mixed-effect logistic regression model included daily maximum temperature (OR 0.95; CI95% 0.91-0.98), livestock sample source (cattle (OR 4.61; CI95% 1.64-12.96) and sheep (OR 5.29; CI95% 1.80-15.51)), multiple species sharing the same barn (OR 6.23; CI95% 1.84-21.15) and livestock having contact with wild areas (OR 3.63; CI95% 1.37-9.62). Identification of STEC serogroups of public health concern (e.g. O157:H7, O26, O103) in this study indicated the need for mitigation strategies to ensure food safety by evaluating risk factors and management practices that contribute to the spread and prevalence of foodborne pathogens in a pre-harvest environment on DSSF.

Role of soil in the regulation of human and plant pathogens: soils' contributions to people.

Soil and soil biodiversity play critical roles in Nature's Contributions to People (NCP) # 10, defined as Nature's ability to regulate direct detrimental effects on humans, and on human-important plants and animals, through the control or regulation of particular organisms considered to be harmful. We provide an overview of pathogens in soil, focusing on human and crop pathogens, and discuss general strategies, and examples, of how soils' extraordinarily diverse microbial communities regulate soil-borne pathogens. We review the ecological principles underpinning the regulation of soil pathogens, as well as relationships between pathogen suppression and soil health. Mechanisms and specific examples are presented of how soil and soil biota are involved in regulating pathogens of humans and plants. We evaluate how specific agricultural management practices can either promote or interfere with soil's ability to regulate pathogens. Finally, we conclude with how integrating soil, plant, animal and human health through a 'One Health' framework could lead to more integrated, efficient and multifunctional strategies for regulating detrimental organisms and processes. This article is part of the theme issue 'The role of soils in delivering Nature's Contributions to People'.

Evaluating the association between climatic factors and sheep condemnations in the United States using cluster analysis and spatio-temporal modeling.

Sheep in the United States are primarily raised and fed on pasture, making them particularly susceptible to the impacts of climatic factors. This study sought to evaluate the association between climate and whole carcass condemnations in the U.S. as a proxy to evaluate overall sheep health across the U.S. USDA FSIS inspection data was evaluated for whole carcass sheep condemnations between 2005-2016. The analysis focused on condemnations attributed to caseous lymphadenitis, the most frequent cause of sheep condemnations during this period. Data was analyzed on the climate division scale - 344 subdivisions of the contiguous United States that divide states into nearly homogenous climatic regions. Using space-time cluster analysis for high rates of condemnations, ten clusters were identified ranging across the United States. All but one of these clusters was confined to single climate division, with lengths ranging from 1 to 72 months. A zero-inflated Poisson regression found significant associations between condemnation counts and precipitation, cooling degree days (an indicator of higher temperatures), year, and division of the United States. The model had a marginal R-squared of 0.54. This study has identified high risk clusters where higher than expected condemnations are concentrated. The confirmation of an association between climatic factors and condemnation numbers suggests that management practices targeted at protecting pasture-raised small ruminants from weather extremes would improve overall animal health and welfare. Mitigation strategies should be considered as we face increasing frequency of extreme weather events and other environmental fluctuations associated with climate change.

Detection of Cephalosporin and Fluoroquinolone Resistance Genes via Novel Multiplex qPCR in Fecal Salmonella Isolates From Northern Californian Dairy Cattle, 2002-2016.

The objectives of this study were to evaluate the prevalence of extended spectrum ß-lactamase (ESBL) genes, AmpC-type ß-lactamase (ACBL) genes, and plasmid mediated quinolone resistance (PMQR) genes in Salmonella isolated at a Veterinary Medical Teaching Hospital microbiology laboratory, examine trends in presence of these resistance genes, and to explore the correlation between phenotypic resistance and presence of specific genes. The presence of ESBL, ACBL, and PMQR genes were detected using a single, novel multiplex qPCR. Only the genes bla CMY-2 and bla TEM were detected in the 110 Salmonella isolates tested. PMQR genes were not detected in isolates screened. Of 94 third-generation cephalosporin resistant isolates, representing eight serotypes, 48% (n = 45) were positive for bla CMY-2 only and 50% (n = 47) were simultaneously positive for bla CMY-2 and bla TEM. Two third-generation cephalosporin resistant isolates were tested negative for all ß-lactamase genes in our qPCR assay and likely house ESBL genes not screened for by our qPCR assay. A logistic regression model revealed that for serotype Dublin isolates (n = 38) the odds ratio for testing positive for bla TEM when compared to all other serotypes was 51.6 (95% CI: 4.01-664.03, p = 0.0029). For serotype Typhimurium (n = 9) the odds ratio for testing positive for bla TEM when compared to all other serotypes was 43.3 (95% CI: 1.76-1000, p = 0.0216). Overall, our results suggest that the prevalence of resistance to cephalosporins and fluoroquinolones due to ESBLs, ACBLs, and PMQR genes present in bovine nontyphoidal Salmonella enterica isolates has remained relatively constant in the isolates screened over a 14-year period.

Bacterial Response to Oxidative Stress and RNA Oxidation.

Bacteria have to cope with oxidative stress caused by distinct Reactive Oxygen Species (ROS), derived not only from normal aerobic metabolism but also from oxidants present in their environments. The major ROS include superoxide O2 -, hydrogen peroxide H2O2 and radical hydroxide HO•. To protect cells under oxidative stress, bacteria induce the expression of several genes, namely the SoxRS, OxyR and PerR regulons. Cells are able to tolerate a certain number of free radicals, but high levels of ROS result in the oxidation of several biomolecules. Strikingly, RNA is particularly susceptible to this common chemical damage. Oxidation of RNA causes the formation of strand breaks, elimination of bases or insertion of mutagenic lesions in the nucleobases. The most common modification is 8-hydroxyguanosine (8-oxo-G), an oxidized form of guanosine. The structure and function of virtually all RNA species (mRNA, rRNA, tRNA, sRNA) can be affected by RNA oxidation, leading to translational defects with harmful consequences for cell survival. However, bacteria have evolved RNA quality control pathways to eliminate oxidized RNA, involving RNA-binding proteins like the members of the MutT/Nudix family and the ribonuclease PNPase. Here we summarize the current knowledge on the bacterial stress response to RNA oxidation, namely we present the different ROS responsible for this chemical damage and describe the main strategies employed by bacteria to fight oxidative stress and control RNA damage.

Assessment of veterinarians' engagement with backyard poultry and small-scale livestock operations in four western states.

OBJECTIVE: To assess veterinarian engagement with owners of poultry and livestock in urban and peri-urban areas (UPAs) of 4 western states, to evaluate the knowledge and experience of veterinarians in UPAs for treating domestic poultry and livestock, and to identify barriers to the provision of veterinary services to backyard poultry and small-scale livestock operations. SAMPLE: 880 veterinarians in UPAs. PROCEDURES: 2,400 members of the veterinary medical associations of California, Colorado, Oregon, and Washington who worked in metropolitan areas with a population > 5,000 people were randomly selected and invited to participate in a needs assessment survey. Response data were analyzed with univariable logistic regression and multiple correspondence analysis. RESULTS: 880 (37%) invitees completed or partially completed the survey. Most respondents self-reported working in UPAs (686/825 [83%]) and companion animal only (n = 551) or predominant (211) practices. Although most (656/863 [76%]) respondents perceived an increase in backyard poultry and livestock in their practice areas, few were actively treating such animals primarily because of a lack of facilities, interest, or experience. Most respondents believed veterinarians have an important role in ensuring public health and preventing zoonotic disease. CONCLUSIONS AND CLINICAL RELEVANCE: Backyard poultry and livestock are increasing in popularity in UPAs of 4 western states, and veterinarians are needed to provide services to such animals. Further research and continuing education are necessary to encourage practitioners in UPAs to engage with owners of backyard poultry and livestock to ensure the health and welfare of those animals and guard public health. (J Am Vet Med Assoc 2020;257:196-209).

Salmonella and Escherichia coli Prevalence in Meat and Produce Sold at Farmers' Markets in Northern California.

ABSTRACT: As the number of farmers' markets and other direct-to-consumer marketing channels increases, it is crucial to understand the potential risks associated with consuming directly marketed animal products and fresh produce. The overall aim of this project was to assess the prevalence of Salmonella and Escherichia coli in animal products and produce sold at farmers' markets in Northern California and to evaluate the food safety risks associated with consuming meat (e.g., beef, pork, and poultry) and fresh produce purchased from farmers' markets. Animal products and produce were purchased from a total of 44 certified farmers' markets in Northern California. Salmonella was found in 6 (1.8%) of 338 animal products and in 0 (0%) of 128 produce samples; E. coli was found in 40 (31.3%) of 128 fresh produce samples. E. coli concentration in produce ranged from 0 to 2.96, with an overall average of 0.13 log (most probable number + 1)/100 mL. Salmonella isolates were resistant to nalidixic acid and tetracycline. The results from this study highlight the need for further training on mitigation strategies to reduce contamination of animal products and fresh produce by foodborne pathogens.

Improving Biosecurity Procedures to Minimize the Risk of Spreading Pathogenic Infections Agents After Carcass Recycling.

Animal proteins are essential elements of human and animal feed chain and improving the safety of human and animal feed requires understanding and controlling of the transmission of infectious agents in food chain. Many pathogenic infectious agents, such as prion protein is known to damage the central nervous system in the cattle. Bovine spongiform encephalopathy (BSE) results from infection agent (prion), and affects number of species such as cattle, human, and cats. In addition, Salmonella, pathogenic E. coli O157:H7, and Listeria monocytogenes were found in animal by-products used in the human and animal feed production. Increased interest in controlling microbial risks in human and animal feed is evidenced by a large number of publications, which highlights the need for examining the animal disposal method such as rendering process and provides a broader perspective of rendering process. While existing practices help greatly in controlling microbial contamination, this overview study showed that additional biosafety measures are necessary to ensure microbial safety in animal feed.

Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California.

BACKGROUND: In this study cull dairy cows from six California dairy herds were sampled seasonally over the course of a year. The objectives were to determine the prevalence of antimicrobial resistant (AMR) Salmonella spp. shed in cull cow feces, and the factors associated with fecal shedding of AMR and multidrug resistant (MDR) Salmonella. METHODS: Six dairy farms located in the San Joaquin Valley of California were identified and enrolled as a convenience sample. On each dairy, and once during each of the four seasons, 10 cull cows were randomly selected for fecal sampling on the day of their removal from the herd. In addition, study personnel completed a survey based on responses of the herd manager to questions related to the previous 4 month's herd management and the specific cattle sampled. Fecal samples were submitted to the California Animal Health and Food Safety laboratory for Salmonella isolation. Antimicrobial resistance was evaluated using broth microdilution method and a gram-negative assay plate following Clinical Laboratory Standards Institute (CLSI) guidelines and breakpoint references. All statistical models were survey adjusted for number of animals on sampling day. RESULTS: A total of 62 Salmonella were isolated from 60 of the 239 fecal samples collected. For 12% (95% confidence interval (CI) [3-20]) of fecal samples a multidrug resistant Salmonella was isolated. The survey-weighted results for the two most common drug classes for which isolates were resistant were tetracycline (39%; 95% CI [27-51]) and ampicillin (18%; 95% CI [9-27]). An important finding was the identification of cephalosporin as the third most common drug class for which isolates were resistant, with ceftriaxone (10%; 95% CI [2-17]) being the most common drug associated with resistance in that class. At the cow-level, reason for culling, prior treatment with antimicrobial drugs as the reason for culling was associated with higher odds of isolating an AMR Salmonella isolate. At the herd-level, percent of animals monthly culled on the farm as well as number of milking cows in the herd were associated with isolation of antimicrobial resistant Salmonella in cull cows. DISCUSSION: Salmonella isolated from fecal samples from cull cows were resistant to important antimicrobials, such as ceftriaxone. The most common drug classes for which isolates were resistant were tetracyclines and beta-lactams, with ampicillin, ceftriaxone and ceftiofur being the three most common drugs within the latter. Cow and herd level factors were associated with isolating antimicrobial resistant Salmonella that should be further investigated for their potential role in promoting occurrence of AMR Salmonella. Our results also highlight the importance of monitoring dairy cattle sent to slaughter for shedding of Salmonella resistant to medically important antimicrobial drugs.

Small-scale and backyard livestock owners needs assessment in the western United States.

The number of small-scale and backyard livestock and poultry owners in urban and peri-urban areas has increased greatly over the last 10 years in the U.S. However, these animal owners may live in areas without access to livestock and/or poultry veterinary care. The purpose of this study was to identify potential veterinary service needs of these animal owners in the western US, assess their use of management and husbandry practices with regards to disease prevention, and assess their attitudes about animal health and food safety. A semi-structured survey was made available to small-scale and backyard livestock and poultry owners in Washington State, California, Colorado and Oregon. The survey instrument included questions about types of animals reared, uses of the animals, veterinary services and information-seeking behaviors of owners, attitudes on animal health and food safety, and management practices. Four hundred thirty-five individuals completed at least some portion of the survey. Most described themselves as living in rural areas (76%). Most (86%) owned chickens, 53% owned small ruminants, and 31% owned cattle. Many individuals owned more than one species and most had fewer than 20 animals of a given species. About 74% of respondents utilized their animals' products for their own consumption but 48% sold animal products (primarily through internet sales (35%) or farmers' markets (25%)). Overwhelmingly, respondents gained information about animal health (82%) and animal treatment procedures (71%) from the internet. Respondents reported their veterinarian's practice type as companion animal (26%) or a mixed animal or food animal predominant (66%). Overall, respondents were very satisfied with the level of care (82%), but 43% had not sought animal health care in last 12 months. However, the veterinarian's primary practice type and owner's satisfaction with veterinary care were associated with their location (state), species owned, and urban or peri-urban setting. Livestock species type (cattle, small ruminants and swine), and use (personal or commercial) were associated with implementation of different biosecurity practices. The results of this survey highlight some of the needs of these animal owners for veterinary care and information which are location- and species-specific. Veterinary care for these small-scale and backyard animals is vital to the health and welfare of the animals as well as for identification of zoonoses and assurance of the food safety of animal products.

Persistence of Escherichia coli in the soil of an organic mixed crop-livestock farm that integrates sheep grazing within vegetable fields.

Mixed crop-livestock farms (MCLF) integrate livestock and crops using their animals to graze crop residues and/or cover crops. MCLF are considered sustainable because grazing and the manure deposited by livestock enhance soil fertility and recycles farm nutrients. However, livestock manure may introduce enteric foodborne pathogens to the soil, which could contaminate fresh produce. Organic farmers in the United States follow the USDA National Organic Program (NOP) standards, which require 90 or 120 days between incorporating raw manure into the soil and harvest. Although not specifically addressed in NOP, organic farmers using grazing within production fields may also use this standard. The objectives of this study were to generate preharvest data to assess the die-off of generic Escherichia coli (E. coli) in the soil, after cover crops were grazed by sheep; and assess the genetic relatedness of generic E. coli isolates between soil and sheep faecal samples. We conducted a repeated observational study to evaluate the persistence of generic E. coli, as an indicator of faecal contamination and surrogate for STEC, in the soil of two fields (A and B) on an organic MCLF. Results showed a 3.70 log10 reduction in mean generic E. coli concentration MPN in the soil of field A from the highest of 3.70 log10 MPN/g on 48 day postsheep grazing (DPS) to -0.70 log10 MPN/g on 139 DPS. Field B showed a 3.51 log10 reduction in mean generic E. coli concentration in the soil from the highest mean of 3.51 log10 MPN/g on 14 DPS to the lowest mean -0.35 log10 MPN/g on 112 DPS. STEC prevalence in the sheep flock was 4.17% (1/24). Closely related generic E. coli strains were found between soil and faecal samples. Developing research-based waiting periods between grazing and harvest is important to inform best practices for farmers and food safety regulators.

Antimicrobial resistance trends in fecal Salmonella isolates from northern California dairy cattle admitted to a veterinary teaching hospital, 2002-2016.

Nontyphoidal Salmonella infections contribute to approximately 1.2 million annual illnesses in the United States. Historical and recent outbreaks have been associated with dairy products, ground beef, and direct contact with cattle. Salmonella antimicrobial resistance (AMR) is a serious concern that can reduce successful treatment of infections, increasing recovery time, medical costs, and mortality rates in humans and animals. This highlights the need to track AMR in Salmonella isolated from cattle to improve treatment plans, manage trends in AMR, and prevent future AMR development. A total of 242 Salmonella isolates were retrieved from 9,162 cattle fecal samples submitted to the University of California, Davis Veterinary Medical Teaching Hospital from 2002 to 2016. These isolates were tested for antimicrobial susceptibility using a standardized broth dilution panel. Multidrug resistance (MDR) to three or more classes of antimicrobials was observed in 50.8% of isolates, and the most common MDR pattern was amoxicillin-ampicillin-cefoxitin-ceftiofur-ceftriaxone-chloramphenicol-streptomycin-tetracycline (23.2%). There were significantly greater odds for antimicrobial resistance to aminoglycosides (OR: 2.03, 95% CI: 1.1-3.7), penicillins (OR: 1.87, 95% CI: 1.007-3.5), and tetracyclines (OR: 1.87, 95% CI: 1.017-3.4) for the 2002-2009 period when compared to the 2010-2016 period. The most prevalent MDR serotypes were Newport (100% MDR, n = 52), Typhimurium (100%, n = 20), and Dublin (71% MDR, n = 46). Risk factors associated with higher odds for isolating MDR Salmonella included isolates from calves when compared to adult cattle (OR: 22.0; 95% C.I.: 3.9-125.7), and isolates obtained from cattle suspect of having salmonellosis versus from the infectious disease control surveillance program (OR:13.7; 95%C.I.: 2.8-66.8). Despite a temporal trend for reduced AMR to most antimicrobial drug classes, a lack of this observed in the 2002-2009 period when compared to the 2010-2016 period for important drug classes such as cephalosporins (OR: 1.6, 95% CI: 0.87-3.1), and a trend for temporal increase in resistant to quinolones drugs (P value 0.004) highlight the relevance of AMR surveillance in cattle with Salmonella infections with the aim of targeting future prophylactic interventions.

Tuberculosis Prevalence Among US Crop-Workers, 2000 to 2012: Trends and Contributing Factors.

OBJECTIVE: We intend to study tuberculosis (TB) in one of the poorest communities in the US, hired agriculture workers, for most recent years (2000 to 2012) including the last recession period. METHODS: Time-chart, simple mean differences, and logistic regressions were used to describe TB-prevalence and risk factors among US crop-workers. Data were drawn from the National Agricultural Workers Survey (NAWS). RESULTS: A high TB-prevalence was found among crop-workers with a dramatically increasing trend in recent years. Hispanic ethnicity, having farmworker family members, the presence of health insurance, and good spoken English were associated with an increased TB-prevalence. CONCLUSION: We found risk factors related to ethnicity and poor access to health care, a strong association between agriculture activity and TB, and an increase of TB-cases due to the 2008 downturn in this underserved population. We urge the health authorities to control this epidemic.

Phylogenomics of pike cichlids (Cichlidae: Crenicichla): the rapid ecological speciation of an incipient species flock.

The rapid rise of phenotypic and ecological diversity in independent lake-dwelling groups of cichlids is emblematic of the East African Great Lakes. In this study, we show that similar ecologically based diversification has occurred in pike cichlids (Crenicichla) throughout the Uruguay River drainage of South America. We collected genomic data from nearly 500 ultraconserved element (UCEs) loci and >260 000 base pairs across 33 species, to obtain a phylogenetic hypothesis for the major species groups and to evaluate the relationships and genetic structure among five closely related, endemic, co-occurring species (the Uruguay River species flock; URSF). Additionally, we evaluated ecological divergence of the URSF based on body and lower pharyngeal jaw (LPJ) shape and gut contents. Across the genus, we recovered novel relationships among the species groups. We found strong support for the monophyly of the URSF; however, relationships among these species remain problematic, likely because of the rapid and recent evolution of this clade. Clustered co-ancestry analysis recovered most species as well delimited genetic groups. The URSF species exhibit species-specific body and LPJ shapes associated with specialized trophic roles. Collectively, our results suggest that the URSF consists of incipient species that arose via ecological speciation associated with the exploration of novel trophic roles.

Association between thermal environment and Salmonella in fecal samples from dairy cattle in midwestern United States.

The objective of this study was to describe the association between thermal measures in the barn environment (pen temperature and humidity) and fecal shedding of Salmonella in dairy cattle. A repeated cross-sectional study was conducted within a commercial dairy herd located in the midwestern United States. Five pooled fecal samples were collected monthly from each pen for 9 mo and submitted for microbiological culture. Negative binomial regression methods were used to test the association [incidence rate ratio (IRR)] between Salmonella pen status (the count of Salmonella-positive pools) and thermal environmental parameters [average temperature and temperature humidity index (THI)] for 3 time periods (48 h, 72 h, and 1 wk) before fecal sampling. Salmonella was cultured from 10.8% [39/360; 95% confidence interval (CI): 7.8% to 14.5%] of pooled samples. The highest proportion of positive pools occurred in August. The IRR ranged from 1.26 (95% CI: 1.15 to 1.39, THI 1 wk) to 4.5 (95% CI: 2.13 to 9.51, heat exposure 1 wk) across all thermal parameters and lag time periods measured. For example, the incidence rate of Salmonella-positive pools increased by 54% for every 5°C increment in average temperature (IRR = 1.54; 95% CI: 1.29 to 1.85) and 29% for every 5-unit increase in THI (IRR = 1.29; 95% CI: 1.16 to 1.42) during the 72 h before sampling. The incidence rate ratio for pens exposed to higher temperatures (> 25°C) was 4.5 times (95% CI: 2.13 to 9.51) the incidence rate ratio for pens exposed to temperatures < 25°C in the 72 h before sampling. Likewise, the incidence rate ratio for pens exposed to THI > 70 was 4.23 times greater (95% CI: 2.1 to 8.28) than when the THI was < 70 in the 72 h before sampling. An association was found between the thermal environment and Salmonella shedding in dairy cattle. Further research is warranted in order to fully understand the component risks associated with the summer season and increased Salmonella shedding.

L'objectif de cette étude est de décrire l'association entre les mesures thermiques de l'étable (température et humidité des enclos) et l'excrétion fécale de Salmonella chez les bovins laitiers. Une étude transversale répétée a été réalisée dans un troupeau laitier commercial situé dans la région du Midwest des États-Unis. 5 échantillons composites de fèces ont été récoltés de chaque stalle d'une manière mensuelle pendant neuf mois puis soumis pour culture microbiologique. Des méthodes de régression binomiale négative ont été utilisées pour tester l'association (ratio de taux d'incidence, IRR) entre la présence de Salmonella dans les enclos (nombre d'échantillons positifs à Salmonella) et les paramètres environnementaux [température moyenne, index humidité température (THI) pour 3 périodes (48 h, 72 h, 1 semaine)]. Salmonella a été cultivée de 10,8 % (39/360; I.C. 95 % 7,8 %­14,5 %) des échantillons composites. La plus grande proportion d'échantillons positifs ont été collectés durant le mois d'août. Le rapport des taux d'incidence (IRR) a varié de 1,26 (IIR = 1,26; I.C. à 95 % 1,15 à 1,39) à 4,5 (IRR = 4,5; I.C. à 95 % 2,13 à 9,51) pour tous les paramètres thermiques et les des périodes étudiés. Par exemple, l'augmentation d'échantillons Salmonella positifs est de 54 % par incrément de cinq °C de température moyenne (IRR = 1,54; I.C. à 95 % 1,29 à 1,85) et de 29 % pour chaque augmentation de cinq unités de THI (IRR = 1,29; IC à 95 % 1,16 à 1,42) dans les 72 heures avant l'échantillonnage. Le ratio de taux d'incidence pour les enclos exposés à de hautes temperatures (> 25 °C) était 4,5 fois (I.C. à 95 % 2,13 à 9,51) supérieur au ratio de taux d'incidence des enclos exposés à des temperatures < 25 °C. De même, Le ratio de taux d'incidence des enclos exposés à des THI > 70 est de 4,23 (I.C. à 95 % 2,16­8,28) superieur a ceux dont le THI est < 70 dans les 72 heures précédant l'échantionnage. Une association a été trouvée entre les mesures thermiques et l'excrétion de Salmonella chez les bovins laitiers. Plus de recherches sont requises pour comprendre entièrement les risques associés à la saison estivale et à l'excrétion de Salmonella.(Traduit par les autuers).

Colonization and demographic expansion of freshwater fauna across the Hawaiian archipelago.

It is widely accepted that insular terrestrial biodiversity progresses with island age because colonization and diversification proceed over time. Here, we assessed whether this principle extends to oceanic island streams. We examined rangewide mtDNA sequence variation in four stream-dwelling species across the Hawaiian archipelago to characterize the relationship between colonization and demographic expansion, and to determine whether either factor reflects island age. We found that colonization and demographic expansion are not related and that neither corresponds to island age. The snail Neritina granosa exhibited the oldest colonization time (~2.713 mya) and time since demographic expansion (~282 kya), likely reflecting a preference for lotic habitats most prevalent on young islands. Conversely, gobioid fishes (Awaous stamineus, Eleotris sandwicensis and Sicyopterus stimpsoni) colonized the archipelago only ~0.411-0.935 mya, suggesting ecological opportunities for colonization in this group were temporally constrained. These findings indicate that stream communities form across colonization windows, underscoring the importance of ecological opportunities in shaping island freshwater diversity.

Phenotypic and Genotypic Diversity of Salmonella in Finishing Swine.

Salmonella enterica (nontyphoidal) is one of the major causes of foodborne diseases in the United States and worldwide. Molecular typing methods are significant tools used to better understand the transmission and ecology of Salmonella in order to implement pre-harvest control measures. The objectives of this study were to describe the Salmonella genotypes, the distribution of isolate subtypes from different ecological niches (i.e., barn environment, nursery, and individual pigs) and their evolution over time in a longitudinal study conducted in three finishing sites (housing pigs from 10 weeks of age until slaughter at 24-26 weeks of age). Among the 107 Salmonella isolates submitted for pulsed-field gel electrophoresis (PFGE) analysis, there were 25 distinct subtypes. PFGE genotyping results were consistent with the serotype findings. A large number of distinguishable PFGE patterns (i.e., within the same serovar) were observed and different combinations of subtypes were identified within and across sites and cohorts. New subtypes may result of the introduction of new strains, genetic changes, or ongoing transmission of evolved strains within the production system. The same subtypes were detected intermittently during the study period, which suggests the persistence of indistinguishable subtypes in this production system. In addition, this study suggests persistence of the same subtype over several cohorts of pigs and potential residual contamination from the barn. Factors affecting adaptation and transmission of Salmonella within and among ecological systems (e.g., finishing pigs, nursery, and environment) should be further investigated. Understanding genotypic diversity of Salmonella in different ecological niches during pre-harvest may contribute to the development of more targeted and cost effective control programs during nursery and finishing phases.